@article {pmid40621926, year = {2025}, author = {Samson, R and Kumar, S and Dastager, S and Khairnar, K and Dharne, M}, title = {Deciphering the comprehensive microbiome of glacier-fed Ganges and functional aspects: implications for one health.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0172024}, doi = {10.1128/spectrum.01720-24}, pmid = {40621926}, issn = {2165-0497}, abstract = {Glacier-fed rivers are significant ecological components of the river catchments, yet their microbial diversity and the associated antimicrobial potential remain underexplored. The Ganges is a glacier-fed river of immense cultural, religious, and ecological significance that supports over 400 million people downstream, providing essential water for agriculture, industry, and daily use. Despite its importance, the microbial community composition and antimicrobial potential, across its relatively pristine origin, remain largely underexplored. One possible explanation for this could be the lower microbial load in the upstream glacier-fed region, which likely results in a reduced DNA yield, insufficient for whole-metagenome sequencing, in contrast to the more biologically diverse and nutrient-rich lower reaches. In this study, we developed an efficient DNA extraction and amplification method using low-input DNA to sequence the microbiome from sediments of the glacier-fed Ganges River in pre-monsoon and post-monsoon over 2 years. Taxonomic and functional diversity of bacterial and viral (phage) communities were analyzed, together with the seasonal variations in their composition. Significant differences in microbial communities were observed in response to seasonal shifts (P < 0.05). During the dry season, Proteobacteria and Actinobacteria were predominant, while Bacteroidetes and Firmicutes were abundant post-monsoon (P < 0.05). The microbiome harbors potential for the biosynthesis of streptomycin, phenylpropanoid, penicillin, and cephalosporins. Bacteriophages from Podoviridae, Myoviridae, and Siphoviridae showed lytic potential against putrefying and pathogenic bacteria. This first comprehensive study on the glacier-fed Ganges River highlights significant seasonal shifts in microbial diversity. The initial insights into the functional profile of the bacterial and phage diversity offer opportunities to explore various natural compounds and enzymes to tackle antimicrobial resistance under the one-health canopy.IMPORTANCEThis study addresses a knowledge gap by exploring the microbial diversity and antimicrobial potential of the glacier-fed Ganges River across different seasons. The findings reveal various taxa with biosynthetic capabilities for antimicrobial compounds. Additionally, the presence of bacteriophages with lytic potential opens up opportunities for their exploration and application spanning various domains of one health. These findings lay a foundational basis for understanding the unique properties of this riverine ecosystem and offer valuable insights into environmental conservation and the potential to tackle antimicrobial resistance.}, }
@article {pmid40621774, year = {2025}, author = {Albini, A and Trapani, D and Bertolini, F and Noonan, DM and Orecchia, R and Corso, G}, title = {From combination early detection to multicancer testing: shifting cancer care toward proactive prevention and interception.}, journal = {Cancer prevention research (Philadelphia, Pa.)}, volume = {}, number = {}, pages = {}, doi = {10.1158/1940-6207.CAPR-24-0558}, pmid = {40621774}, issn = {1940-6215}, abstract = {Identifying the presence of tumors at a very early stage or deciphering the process underlying their development can enable the interception of pro-malignant mechanisms underpinning cancer emergence, facilitating more effective prevention. Advances in molecular profiling allow the detection of genetic, epigenetic, immune, and microenvironmental alterations associated with cancer risk. Liquid biopsy permits non-invasive analysis of circulating tumor cells, nucleic acids, immune cells, extracellular vesicles, proteins, cytokines, and metabolites, while metagenome analysis facilitates gut microbiota profiling. Multi-cancer early detection (MCED) assays broaden this approach, capturing signals from multiple malignancies using a single blood sample. These technologies go beyond genomics, addressing immune dysregulation and metabolic shifts and may help identify gut microbiota imbalances. Clonal hematopoiesis of indeterminate potential (CHIP) gets increasing recognition of biomarker. Cardiovascular risk scores based on multiple parameters are an inspiring example The analysis of a combination of cancer drivers and enablers should provide a more sensitive and personalized measure of cancer prodromic profiles. Artificial intelligence will further support this transition by integrating molecular, immune, and metabolic data to develop individualized risk profiles. This shift from single-cancer detection to integrated, mechanism-based screening fosters a more proactive prevention model.. This combination early detection empowers cancer interception by using strategies including lifestyle modification, nutritional optimization, drug repurposing, pharmacologic interventions, and targeted chemoprevention. Moving beyond single parameters analysis and organ-specific screening, this multidimensional approach advances early detection and interception as practical clinical goals, facilitating the fundamental aim of positioning prevention at the forefront of oncology.}, }
@article {pmid40621575, year = {2025}, author = {Gupta, S and Bhargava, V and Kaur, J and Lata, P}, title = {Adaptations, diversity, and biotechnological potential of thermophilic microorganisms: exploring culture-dependent and culture-independent approaches in extreme environments.}, journal = {3 Biotech}, volume = {15}, number = {8}, pages = {232}, pmid = {40621575}, issn = {2190-572X}, abstract = {Thermophilic prokaryotes exhibit remarkable adaptations at both physiological and molecular levels, which enables them to survive in elevated-temperature environments (35-113 °C). This review consolidates the current findings on membrane, genomic and proteomic adaptations of thermophiles, including presence of ether-linked lipids, branched-chain fatty, saturated long-chain hydrocarbons, reverse gyrase-mediated DNA supercoiling, and group II chaperonins. Although culture-independent approaches, such as metagenomics and next-generation sequencing (NGS) techniques, have expanded our understanding of thermophilic microbial diversity, which is limited by traditional culture-dependent approaches. However, these findings are largely based on the genomic predictions rather than direct experimental evidence. Therefore, the culture-dependent methods are crucial for isolating and characterizing thermophiles for both genetic and functional studies. India's geothermal spring ecosystems serve as natural laboratories for studying diverse thermophilic communities, offering a valuable resource for both ecological and biotechnological exploration. Enzymes derived from thermophiles, known as thermophiles exhibit remarkable thermal stability and catalytic efficiency at temperatures ranging from 60 to 125 °C, with applications in biofuels, pharmaceuticals, and industrial bioprocessing. Integration of both culture-based and metagenomic approach provide a comprehensive framework for understanding the thermophile biology and reveals their biotechnological potential.}, }
@article {pmid40620900, year = {2025}, author = {Desingu, PA and Arunkumar, S and Nagarajan, K and Saikumar, G}, title = {Metagenomics identification of genetically distinct tick virome in India unveils signs of purifying selection, and APOBEC and ADAR editing.}, journal = {iScience}, volume = {28}, number = {7}, pages = {112873}, pmid = {40620900}, issn = {2589-0042}, abstract = {Recently, several tick-borne zoonotic viruses have been identified through the application of virus metagenomics. However, the tick virome in South Asia and the factors driving the evolution of these viruses remain largely unknown. In this study, we report the complete genomes of the genetically distinct Nairobi sheep disease virus (NSDV), Jingmen tick virus (JMTV), Lihan tick virus (LTV), and Mivirus, along with nearly complete genomes of turnip mosaic virus (TMV) and turnip yellows virus (TYV). We also present partial genomes of Tamdy orthonairovirus, Nayun tick nairoviruses (NTNV), PTV-like viruses, Xinjiang tick-associated virus-1 (XTAV1), Totivirus, Kismayo viruses, Quaranjavirus, and Brown dog tick phlebovirus-2 (BDTPV-2), identified from Indian ticks through virus metagenomics. The diversity was categorized into distinct groups specific to particular host organisms and/or geographical regions. Our findings also indicated that selection pressure for codon usage in these viruses was influenced by purifying selection, which induces transition mutations potentially through apolipoprotein B mRNA editing enzyme, catalytic polypeptide (APOBEC) and adenosine deaminases acting on RNA (ADAR) editing.}, }
@article {pmid40620487, year = {2025}, author = {Luo, W and Zhang, S and Sun, J and Xu, J and Huang, W and Hao, R and Ou, Z and Wen, Z and Wang, D and Xiao, G and Dong, H}, title = {Microbial and clinical disparities in pneumonia: insights from metagenomic next-generation sequencing in patients with community-acquired and severe pneumonia.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1538109}, pmid = {40620487}, issn = {1664-302X}, abstract = {BACKGROUND: Community-acquired pneumonia (CAP) is a major global cause of death, with its varying symptoms and severity complicating diagnosis and treatment. Severe pneumonia (SP), a more critical form of CAP, has higher mortality and often requires intensive care. The identification of clinical markers to differentiate CAP from SP has the potential to improve treatment protocols and patient outcomes. Concurrently, metagenomic next-generation sequencing (mNGS) demonstrates significant promise in pathogen detection and in elucidating microbiome disparities between CAP and SP.<br><br>METHODS: This retrospective study analyzed clinical and pathogen data from 204 patients diagnosed with CAP and 25 patients diagnosed with SP in the Department of Respiratory and Critical Care Medicine at the Zengcheng Branch of Nanfang Hospital, Southern Medical University, spanning the period from September 2022 to June 2023. Clinical characteristics were compared, and bronchoalveolar lavage fluid (BALF) samples underwent mNGS for microbial detection and characterization. Statistical analyses, encompassing Chi-square, Fisher's exact test, Student's t-test, and LEfSe analysis, were employed to compare clinical and microbiological data between the CAP and SP cohorts.<br><br>RESULTS: Patients with SP were significantly older and exhibited higher incidences of sepsis, hypotension, tachycardia, multilobar infiltrates, and consciousness disorders compared to those with CAP. Elevated levels of C-reactive protein (CRP) and procalcitonin (PCT) were more frequently observed in SP patients. mNGS analysis identified diagnostic microbiology profiles between groups. Diverse microbiological profiles (> 5 species) were more common in SP patients (> 30% detection rate). Beta diversity analysis demonstrated significant differences in microbial community composition between CAP and SP groups (p = 0.001), though alpha diversity metrics showed no significant differences. Both LEfSe and ANCOM-BC2 analyses consistently identified Pseudomonas as a potential biomarker for SP and Streptococcus for CAP.<br><br>CONCLUSION: The substantial differences observed in clinical characteristics, pathogen profiles, and microbiomes between patients with CAP and those with SP highlight the imperative need for comprehensive diagnostic methodologies in the management of pneumonia. mNGS has demonstrated substantial utility in informing personalized treatment strategies, with the potential to enhance clinical outcomes. Future research should prioritize elucidating the dynamics of microbial communities and their impact on pneumonia severity, with the objective of refining and optimizing therapeutic strategies.}, }
@article {pmid40619813, year = {2025}, author = {Sabih Ur Rehman, S and Nasar, MI and Mesquita, CS and Al Khodor, S and Notebaart, RA and Ott, S and Mundra, S and Arasardanam, RP and Muhammad, K and Alam, MT}, title = {Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {4}, pages = {}, doi = {10.1093/bib/bbaf323}, pmid = {40619813}, issn = {1477-4054}, support = {G00005310//UAEU-ZU/ ; G00004960//UPAR/ ; G00004540//UPAR/ ; G00004152//UPAR/ ; }, mesh = {Humans ; *Dysbiosis/microbiology ; *Systems Biology/methods ; *Microbiota ; Metagenomics ; Metabolomics ; Proteomics ; }, abstract = {Microbiomes are crucial for human health and well-being, with microbial dysbiosis being linked to various complex diseases. Therefore, understanding the structural and functional changes in the microbiome, along with the underlying mechanisms in disease conditions, is essential. In this review, we outline the structure and function of different human microbiomes and examine how changes in their composition may contribute to diseases. We highlight critical information associated with microbial dysbiosis and explore various therapeutic strategies for restoring a healthy microbiome, including microbiota transplantation, phage therapy, probiotics, prebiotics, dietary interventions, and drug-based approaches. Further, to better understand microbiome dysbiosis, we discuss multi-omics approaches including metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics, alongside computational modeling approaches such as ecological and metabolic network analysis. We outline key challenges associated with multi-omics techniques and emphasize the importance of integrative systems biology approaches that combine multi-omics data with computational modeling. These approaches are crucial for effectively analyzing microbiome data, providing deeper insights into species interactions and microbiome dynamics. Finally, we offer insights into future research directions in the field of microbiome research. This review makes a unique contribution to microbiome research by presenting a holistic framework that integrates multi-omics data with multi-scale modeling to elucidate microbial interactions, microbiome dysbiosis, and their modulation in disease-associated contexts.}, }
@article {pmid40619005, year = {2025}, author = {Hullar, MAJ and Kahsai, O and Curtis, KR and Navarro, SL and Zhang, Y and Randolph, TW and Levy, L and Shojaie, A and Kratz, M and Neuhouser, ML and Lampe, PD and Raftery, D and Lampe, JW}, title = {Metabolic plasticity of the gut microbiome in response to diets differing in glycemic load in a randomized, crossover, controlled feeding study.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajcnut.2025.06.026}, pmid = {40619005}, issn = {1938-3207}, abstract = {BACKGROUND: Dietary patterns characterized by low-glycemic, minimally processed plant foods are associated with lower risk of several chronic diseases.<br><br>OBJECTIVE: Evaluate the effects of a low glycemic load (LGL) versus a high glycemic load (HGL) dietary pattern on stool bacterial community structure and metabolism.<br><br>METHODS: Participants in this crossover-controlled feeding study were healthy men and women (n=69). We identified genera, species, and genes and transcripts of metabolic pathways and bacterial enzymes using 16S rRNA gene, metagenomic and metatranscriptomic sequencing, and bioinformatic analysis.<br><br>RESULTS: Overall community structure measured by alpha and beta diversity were not significantly different across the diets although diet did significantly increase the abundance of 13 out of 161 genera (padj<0.05) and 5 species in the LGL and 7 species in the HGL diet. Gene expression in the hexitol fermentation pathway (&#x3b2;=-1.15, SE=0.24 with 95% CI (-1.63, -0.67); padj=0.002) was significantly higher in the HGL diet, whereas expression in the L-lysine biosynthesis pathway (&#x3b2; =0.20, SE=0.05 with 95% CI (0.09, 0.30); padj=0.03); was enriched in the LGL diet. The beta diversity of expressed carbohydrate-active enzymes (CAZymes) was significantly different between the diets (MiRKAT, p<0.001). CAZymes enriched in the HGL diet reflected dietary additives while CAZymes enriched in the LGL diet reflected diverse phytochemical intake. There was a significant interaction between HOMA IR and the Coenzyme A biosynthesis I pathway involved in bacterial fatty acid biosynthesis (padj=0.035) that was positive in the HGL diet (&#x3b2;=0.20, SE=0.09 with 95% CI (0.02, 0.39)) and negative in the LGL diet (&#x3b2; =-0.23, SE=0.09 with 95% CI (-0.40, -0.06)).<br><br>CONCLUSION: In healthy humans, diet impacts microbial metabolism and enzymatic activity but not the overall diversity of the gut microbiome. This emphasizes the relevance of dietary components in activating expression of specific bacterial genes and their impact on host metabolism. This trial was registered at clinicaltrials.gov as NCT00622661.}, }
@article {pmid40618661, year = {2025}, author = {Gao, Y and Zhang, L and Zhang, Y and Yang, M and Ma, W}, title = {Porous Ca-doped Al2O3 with abundant basic sites for enhanced hydrolysis of fermentative antibiotics.}, journal = {Water research}, volume = {285}, number = {}, pages = {124138}, doi = {10.1016/j.watres.2025.124138}, pmid = {40618661}, issn = {1879-2448}, abstract = {Efficient elimination of antibiotics from wastewater is crucial for the stability of biological treatment systems and the safety of effluent. This study presents a heterogeneous catalytic hydrolysis system using porous calcium-doped alumina (P-Ca-Al), synthesized with ammonium chloride as a green gas template. Characterization reveals that calcium species are highly dispersed in the tetrahedral sites of alumina, forming Ca-O-Al bonds. The coexistence of surface basic sites and Lewis acid sites on P-Ca-Al was confirmed by CO2 temperature-programmed desorption spectrum and pyridine adsorption infrared spectroscopy. These sites are responsible for the highly efficient hydrolysis of Erythromycin-A (Ery-A), achieving an 18-fold increase in efficiency compared to conventional NaOH aqueous solutions, with no degradation observed on solid CaO under identical conditions. The selective hydrolysis of the antibacterial functional groups of Ery-A reduces antimicrobial activity with low energy and reagent consumption. The degradation mechanism is confirmed through solvent kinetic isotope effect (KIE) investigation and identification of hydrolysis intermediates. The macrolide ring and glycosidic bond in Ery-A are hydrolyzed by proton subtraction from surface basic sites, preventing resistance gene formation as confirmed by metagenomic analysis. This work provides a possible way to selectively remove antibiotics from complex industrial wastewater.}, }
@article {pmid40618650, year = {2025}, author = {Wan, X and Li, Q and Li, Z and Shi, L and Pan, Y and Li, M and Liu, Z}, title = {MGE-associated ARGs exhibit higher expression efficiency than chromosomal non-MGE loci and predominantly contribute to resistance expression in pig farm wastewater.}, journal = {Environment international}, volume = {202}, number = {}, pages = {109653}, doi = {10.1016/j.envint.2025.109653}, pmid = {40618650}, issn = {1873-6750}, abstract = {Antibiotic resistance (AMR) in animal agriculture represents a critical One Health challenge, with pig farms serving as major reservoirs for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). While MGEs are known drivers of ARG dissemination, their impact on actual expression of resistance in these complex microbial communities is poorly understood. This study aimed to quantify the contribution of MGE-associated ARGs to overall resistance expression and compare their transcriptional efficiency to chromosomally located ARGs in pig farm wastewater. Utilizing deep metagenomic and metatranscriptomic sequencing on wastewater from five typical Chinese pig farms, we comprehensively elucidated ARG presence, genetic context, host association, and transcriptional activity. We identified a vast dataset comprising 811 ARG types conferring resistance to 27 antibiotic classes, with 71.02 % actively transcribed, indicating significant resistance potential. MGEs were associated with 34.87 % of ARG-like ORFs. Crucially, MGE-associated ARGs were responsible for the majority (62.07 %) of total ARG transcript abundance, exhibiting an expression efficiency nearly 2.5 times higher than ARGs on chromosomal non-MGE loci. Taxonomic analysis revealed that these highly expressed MGE-associated ARGs were primarily hosted by genera known to include opportunistic pathogens, such as Enterococcus, Escherichia, and Klebsiella. Differential coverage binning further uncovered diverse draft genomes simultaneously harboring multiple highly expressed ARGs and MGEs, potentially contributing to the persistence and spread of highly resistant bacterial strains. Our findings underscore that MGEs not only propagate ARGs but critically enhance their expression, providing vital data for effective AMR surveillance and mitigation strategies within the One Health framework.}, }
@article {pmid40618153, year = {2025}, author = {Lin, D and Zhang, X and Wang, D and Liu, T and Li, T and Zhang, Y and Li, L and Huang, Y and Guo, Y and Zhang, R and Chen, X and Feng, T}, title = {UMPlex™: a targeted next-generation sequencing primer design workflow.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {222}, pmid = {40618153}, issn = {1743-422X}, support = {2024A1515030195//Guang Dong Basic and Applied Basic Research Foundation/ ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; Humans ; Workflow ; *Molecular Diagnostic Techniques/methods ; *DNA Primers/genetics ; Sensitivity and Specificity ; Influenza, Human/diagnosis/virology ; }, abstract = {We have developed a tailored next-generation sequencing (tNGS) panel, employing our innovative UMPlex™ primer design workflow, to enhance pathogen identification in clinical diagnostics. Through iterative experimentation and rigorous validation, we refined the primer design by excluding those with insufficient specificity or efficiency. To mitigate amplification challenges arising from pathogenic mutations, we implemented a strategy of using a minimum of two primer pairs per pathogen, ensuring redundancy and robust detection. Validation using clinical samples showcased high specificity and efficacy, with 11 cultured pathogens isolated exclusively. In a study involving 107 positive respiratory samples, tNGS outperformed the TaqMan Array, detecting a higher number of pathogens in patients with influenza-like symptoms of unknown etiology. Additionally, tNGS yielded higher read counts for potentially pathogenic microorganisms and produced results consistent with metagenomic NGS, despite generating a reduced data volume. This approach not only improves detection rates but also offers a flexible tool for both clinical diagnostics and surveillance, particularly in the context of influenza-like illnesses.}, }
@article {pmid40618061, year = {2025}, author = {Liang, H and Yang, Y and Yi, S and Cai, D and Zhou, H and Yin, H and Yuan, C and Zhou, G and Tian, D and Xia, X and Wang, Z and Chen, F}, title = {Metagenomics-based novel Caulimoviridae virus discovery and its development of identification markers in Lilium lancifolium thunb.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {221}, pmid = {40618061}, issn = {1743-422X}, support = {DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; DOQ202402//Wuhan metropolitan area science and technology strong chain project/ ; 2023110201030689//Wuhan science and technology correspondent "industry-university-research" special project/ ; 2023110201030689//Wuhan science and technology correspondent "industry-university-research" special project/ ; 2023110201030689//Wuhan science and technology correspondent "industry-university-research" special project/ ; 2023110201030689//Wuhan science and technology correspondent "industry-university-research" special project/ ; 2023110201030689//Wuhan science and technology correspondent "industry-university-research" special project/ ; XKCX202405-3//Wuhan Academy of Agricultural Sciences innovation system science and technology strong foundation project- -Subject innovation project/ ; XKCX202405-3//Wuhan Academy of Agricultural Sciences innovation system science and technology strong foundation project- -Subject innovation project/ ; XKCX202405-3//Wuhan Academy of Agricultural Sciences innovation system science and technology strong foundation project- -Subject innovation project/ ; XKCX202405-3//Wuhan Academy of Agricultural Sciences innovation system science and technology strong foundation project- -Subject innovation project/ ; XKCX202405-3//Wuhan Academy of Agricultural Sciences innovation system science and technology strong foundation project- -Subject innovation project/ ; }, mesh = {*Lilium/virology ; *Metagenomics/methods ; Genome, Viral ; *Plant Diseases/virology ; Phylogeny ; *Caulimoviridae/genetics/isolation &amp; purification/classification ; Sequence Analysis, DNA ; Genetic Markers ; }, abstract = {Plant viruses cause considerable economic losses in the lily industry due to the emergence of diverse viral mutations and novel pathogens. Effective detection and identification of these viruses are critical for controlling their spread and mitigating infections. In this study, two novel Caulimoviridae viruses, namely Lancifolium Caulimovirus A (LCaA) and Lancifolium Caulimovirus B (LCaB), were identified for the first time in Lilium lancifolium Thunb. (tiger lily) through integrated metagenomic sequencing and Sanger sequencing. The complete genomes of LCaA and LCaB were determined to be 7,542 nt and 7,582 nt in length, respectively. Among the pooled tiger lily samples, seven LCaA isolates exhibited genome sequence identities ranging from 99.59 to 99.73%, while six LCaB isolates showed identities between 98.51% and 98.91%. Leveraging these isolates genomic variations, four sets of diagnostic markers were developed to distinguish the LCa viruses (LCaA and LCaB). Specific marker combinations were employed to identify LCa, LCaA, and LCaB strains. This study reports the discovery of two novel Caulimoviridae species and establishes a robust PCR-based methodology for their detection. The developed markers provide a valuable diagnostic tool for the early detection and management of LCa viruses in lily cultivation systems.}, }
@article {pmid40617811, year = {2025}, author = {Zhu, B and Liang, L and Chen, S and Li, H and Huang, Y and Wang, W and Zhang, H and Zhou, J and Xiong, D and Li, X and Li, J and Ning, Y and Shi, X and Wu, F and Wu, K}, title = {Multi-kingdom microbial changes and their associations with the clinical characteristics in schizophrenia patients.}, journal = {Translational psychiatry}, volume = {15}, number = {1}, pages = {228}, pmid = {40617811}, issn = {2158-3188}, mesh = {Humans ; *Schizophrenia/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Feces/microbiology ; Case-Control Studies ; Metabolic Networks and Pathways ; Fungi ; }, abstract = {Accumulating evidence has highlighted alterations in the gut microbiome in schizophrenia (SZ); however, the role of multi-kingdom microbiota in SZ remains inadequately understood. In this study, we performed metagenomic sequencing of fecal samples from 36 SZ patients and 55 healthy controls (HC) to profile bacterial, fungal, archaeal, and viral communities, along with functional pathways. We also conducted co-occurrence network analysis to explore the relationships among differential microbial species and metabolic pathways separately. Additionally, we assessed the associations of these differential species and functional pathways with clinical characteristics. Our findings revealed significant differences in species between SZ patients and HC, identifying not only 17 bacterial species, but also 8 fungal, 26 archaeal, and 19 viral species. Functional pathway analysis revealed 21 metabolic pathways significantly altered in SZ patients, including an increase in tryptophan metabolism, while biosynthesis of amino acids was decreased. Network analysis further uncovered more complex inter-kingdom interactions in SZ patients, with specific fungal species appearing exclusively in the SZ network. Importantly, significant associations were observed between microbial species and functional pathways with clinical characteristics, including symptom severity, cognitive function, and clinical biochemical marker. For instance, the abundance of Streptococcus vestibularis was positively correlated with homocysteine levels; the ubiquinone and other terpenoid-quinone biosynthesis was positively correlated with both symptom severity and C-reactive protein. Our findings reveal the intricate microbial dysbiosis present in SZ patients, suggesting multi-kingdom microbial interactions play a crucial role in SZ patients, highlighting promising avenues for potential diagnostic and therapeutic applications.}, }
@article {pmid40617568, year = {2025}, author = {Tian, G and Zhang, R and Zhao, M and Ye, Z and Dai, T and Chen, D and Zeng, Y and Yang, Y and Zhou, J and Zhang, B and Guo, X}, title = {Biogeochemical stratification governs microbial hydrocarbon degradation potential in a petrochemical contaminated site.}, journal = {Environmental research}, volume = {285}, number = {Pt 1}, pages = {122286}, doi = {10.1016/j.envres.2025.122286}, pmid = {40617568}, issn = {1096-0953}, abstract = {The success of in situ bioremediation at petrochemical-contaminated sites (defined as those impacted by petrochemical production or accidental release) depends on the structure and functional capacities of indigenous microbial communities, as well as the physicochemical gradients that shape their metabolic potential. While microbial degradation mechanisms are well-documented in homogeneous environments, systematic evaluations of microbial dynamics across environmental compartments (e.g., surface/middle/deep soil vs. groundwater) remain scarce. In this study, we combined chemical profiling with shotgun metagenomic sequencing to characterize layer-specific microbial assemblages and hydrocarbon degradation pathways at a historically contaminated petrochemical site. Total petroleum hydrocarbons (TPHs) were markedly higher in the middle and deep soil layers compared to the surface. In subsurface layers, elevated organic carbon and moisture limited oxygen diffusion, and high concentrations of hydrophobic hydrocarbons imposed toxic stress, together creating a reducing environment that favored anaerobic taxa and pathways such as benzoyl-CoA reductase. In contrast, surface soils, with greater aeration and lower pollutant levels, harbored approximately 50 % greater microbial α-diversity (P < 0.05) and supported more diverse and complex metabolic capabilities. Groundwater showed an 83 % detection frequency of naphthalene, and its high solubility and toxicity selected for specialized degraders. Principal Coordinates Analysis (PCoA) revealed distinct depth-dependent community clustering of microbial communities (P < 0.001), with middle/deep soil microbiomes showing significantly reduced metabolic versatility for xenobiotics (BTEX, PAHs, and derivatives) compared to surface soils and groundwater at the community level. Functional gene annotation identified rate-limiting enzymes in aerobic/anaerobic degradation pathways (dmpK [benzene], badA [ethylbenzene], nahA [naphthalene], and fadA [fatty acid β-oxidation]), and Metagenome-Assembled Genomes (MAGs)-based reconstructions revealed a systemic bias towards anaerobic degradation. These mechanistic insights guide layer-specific in situ bioremediation, integrate environmental gradients with microbial functional potential for targeted treatments, and provide a framework for predicting community succession and functional resilience at petrochemical-contaminated sites.}, }
@article {pmid40617153, year = {2025}, author = {Song, L and Liang, Q and Chen, Y and Wu, L and Zhou, J and Wei, Z and Xie, J and Liu, H and Meng, J}, title = {Clinical characterization and diagnosis of 14 patients with Chlamydia psittaci pneumonia.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {3}, pages = {116985}, doi = {10.1016/j.diagmicrobio.2025.116985}, pmid = {40617153}, issn = {1879-0070}, abstract = {OBJECTIVE: To investigate the clinical features, diagnostic approaches, and therapeutic strategies for Chlamydia psittaci (C. psittaci) pneumonia.<br><br>METHODS: We conducted a retrospective analysis of 14 patients diagnosed with C. psittaci pneumonia between December 2021 and February 2025 at The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China. Diagnosis was confirmed via metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Clinical manifestations, laboratory findings, imaging characteristics, treatment regimens, and outcomes were systematically analyzed.<br><br>RESULTS: The cohort comprised seven males and seven females, aged 46-83 years. A documented history of avian exposure was present in 57.1 % (8/14) of patients. All patients presented with high fever. Lab tests showed increased inflammatory markers (CRP, ESR, d-dimer) in all patients. White blood cell counts were elevated in seven patients and normal in seven others. Neutrophilia occurred in 11 cases and lymphopenia in 13. Elevated procalcitonin (10 cases), LDH (12 cases), creatine kinase (8 cases), and transaminases (ALT: 7 cases; AST: 9 cases) were documented. Electrolyte disturbances included hypokalemia (6 cases), hyponatremia (9 cases), and hypochloremia(13 cases). Eight patients had renal dysfunction (high creatinine/urea), six showed hyperbilirubinemia. Chest imaging revealed varied lung infiltrations: consolidations, ground-glass opacities, nodular shadows, and patchy infiltrates. All cases were confirmed by mNGS and effectively treated with tetracyclines or fluoroquinolones.<br><br>CONCLUSION: C. psittaci pneumonia frequently presents with sepsis-like symptoms and rapid clinical deterioration. Early diagnosis using mNGS is crucial for guiding timely antimicrobial therapy, significantly improving patient outcomes, especially in cases where conventional diagnostics may be limited or delayed.}, }
@article {pmid40616852, year = {2025}, author = {Zhu, X and Gao, X and Zhu, Y and Huang, J and Peng, F and Pang, Q and Yang, F and Xie, L and Hua, Z and Wang, L}, title = {The impact of land use on the composition of dissolved organic matter and its relationship with microbes in a river basin in Northwestern China: Insights into microbial community structure and metabolic function.}, journal = {Journal of environmental management}, volume = {391}, number = {}, pages = {126446}, doi = {10.1016/j.jenvman.2025.126446}, pmid = {40616852}, issn = {1095-8630}, abstract = {Land use variations influence aquatic dissolved organic matter (DOM); however, the responses of relationships between DOM composition and microbial communities/metabolic genes to land use types and landscape indices remain insufficiently explored. This study conducted four field sampling sessions on the Qingshui River, northwestern China, investigated the shifts in DOM-transforming microbes and genes under distinct land use patterns (forest &amp; grassland, urban area, and agricultural land) using metagenomics analysis, elucidated the DOM-microbe interactions in response to land use characteristics from the perspective of both basin and land use types by statistical approaches. At the basin scale, land use primarily influenced DOM quality rather than quantity. Partial least-squares path model demonstrated that landscape indices influenced DOM components predominantly by inhibiting gene abundances associated with metabolic pathways, exerting a more pronounced impact than land use area proportions. Notably, DOM composition, microbial metabolic genes, and their interactions differed significantly across land use types. Urban areas exhibited the highest levels of DOM aromaticity and the largest proportions of autochthonous sources, their fragmented landscape characteristics destabilized the microbial network, resulting in a comprehensive rather than partial suppression of genes involved in DOM transformation pathways (carbohydrate metabolism, energy metabolism, and amino acid metabolism). Compared to other land use scenarios, the downstream agricultural areas emerged as active zones for microbial utilization of DOM, maintained high microbial network stability and gene abundances similar to forest &amp; grassland, highlighting the microbial resilience. These insights advance mechanistic understanding of how land use governs aquatic DOM-microbe interactions in arid and semi-arid watersheds.}, }
@article {pmid40616790, year = {2025}, author = {Wen, Z and Yang, M and Lu, G and Han, M and Song, Y and Sun, Y and Tu, Q and Yin, T and Niu, K and Sun, S and Qi, J and Fazal, A and Yang, Y}, title = {Microbial Alliances: Unveiling the Effects of a Bacterial and Fungal Cross-Kingdom SynCom on Bacterial Dynamics, Rhizosphere Metabolites, and Soybean Resilience in Acidic Soils.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c12416}, pmid = {40616790}, issn = {1520-5118}, abstract = {Acidic soils, covering 40 to 50% of arable land, hinder productivity due to phosphorus limitation and aluminum toxicity. Using a synthetic community (SynCom) approach, we tested a native Rhizobium (Rh) and a non-native Ensifer fredii (Ef) strain, both combined with the mycorrhizal fungus Rhizophagus intraradices (Ri), on soybean growth in acidic soil. The native RhRi SynCom outperformed EfRi, significantly improving soybean growth, yield, and soil health. Metagenomics and metabolomics revealed that RhRi significantly enhanced beneficial microorganisms (AD3, Gemmataceae) and metabolites (putrescine, stearic acid), hence improving nutrient cycling, stress tolerance, and membrane integrity. RhRi also enhanced soil enzyme activity (urease, phosphatases), which resulted in an increase in nitrogen and phosphorus availability and a decrease in rhizosphere toxicity. These alterations enhanced plant resilience, soil structure, and microbial diversity. RhRi activated metabolic pathways (amino acids, lipids, ABC transporters, and secondary metabolites) that are involved in nutrient acquisition and stress response. Conversely, EfRi provided minimal advantages, emphasizing the significance of native microbial compatibility. Our findings show that native SynComs boost crop resilience and production in acidic soils through synergistic microbial interactions and metabolic reprogramming, thereby offering a sustainable agricultural strategy in harsh environments.}, }
@article {pmid40616449, year = {2025}, author = {Alsanea, A and Bounaga, A and Lyamlouli, K and Zeroual, Y and Boulif, R and Zhou, C and Rittmann, B}, title = {Sulfate Reduction in the Hydrogen-Based Membrane Biofilm Reactor Receiving Calcium Reduced Phosphogypsum Water.}, journal = {Biotechnology and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1002/bit.70015}, pmid = {40616449}, issn = {1097-0290}, support = {//This study was supported by the OCP Group's Situation Innovation within the framework of 500 [AS81]./ ; }, abstract = {Phosphogypsum (PG), a byproduct of phosphate mining, contains sulfate that can be leached and converted to elemental sulfur, thus offering a sustainable opportunity to recover sulfur (S) as a step toward a circular economy. Calcium, at ~15 mM in PG leachate, creates inorganic precipitation that interferes with biological sulfate reduction, the first step of S recovery. Here, we evaluated the effectiveness of using cation-exchange to lower the calcium concentration in water-leached PG (PG water) delivered to a H2-based membrane biofilm reactor (H2-MBfR) employed to reduce sulfate to sulfide. A high sulfate flux (1 gS/m[2]-day) and 65% sulfate reduction were achieved despite a high pH (10) resulting from base production during sulfate reduction. However, soluble sulfide was only 20% of the reduced S, possibly due to precipitation of sulfide, iron, and phosphate, and alkalinity analysis revealed possible formation of polysulfides. Shallow metagenomics of the biofilm documented that Desulfomicrobium was the dominant sulfate-reducing bacterium, while Thauera, a mixotroph capable of sulfate reduction and sulfide oxidation, also was an important genus. The metagenomics also revealed the presence of methanogens and acetogens that competed for H2 and CO2. Although calcium removal from PG water improved sulfate reduction and reduced inorganic precipitation in the H2-MBfR, soluble sulfide generation must be improved by supplying sufficient CO2 to moderate pH increase due to sulfate reduction and by controlling the H2-delivery capacity to limit methanogens and acetogens.}, }
@article {pmid40615957, year = {2025}, author = {Durand, K and Ogier, JC and Nam, K}, title = {The evaluation of shotgun sequencing and rpoB metabarcoding for taxonomic profiling of bacterial communities.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {413}, pmid = {40615957}, issn = {1471-2180}, support = {ANR-10-LABX-04-01//Agence Nationale de la Recherche/ ; ANR-10-LABX-001-01//Agence Nationale de la Recherche/ ; ANR-16-IDEX-0006//Agence Nationale de la Recherche,France/ ; Resistome//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Bacteria/genetics/classification ; *DNA-Directed RNA Polymerases/genetics ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; Computational Biology/methods ; Phylogeny ; *Microbiota/genetics ; Metagenomics/methods ; Bacterial Proteins/genetics ; High-Throughput Nucleotide Sequencing/methods ; Shotgun Sequencing ; }, abstract = {BACKGROUND: The importance of microbial community profiling has been increasingly recognized in biological and environmental research. While metabarcoding has been widely used for such analysis by targeting specific DNA sequences as markers, shotgun sequencing has been proposed as an alternative method because the analysis of whole genomes can potentially reduce biases introduced by targeted approaches. However, it is largely unknown whether shotgun sequencing may provide improved precision for qualitative taxonomic identification and quantitative abundance estimation compared with metabarcoding with housekeeping gene markers, such as the rpoB gene. Furthermore, the comparative performance of various bioinformatics pipelines for shotgun data analysis remains uncertain. In this study, we evaluated the performance of rpoB metabarcoding and shotgun sequencing coupled to various bioinformatic pipelines to describe the bacterial diversity of artificially generated mock bacterial communities, which included eukaryote gDNA intentional contamination or whole-genome amplification. For shotgun sequencing, the Assembly-Binning-Method and k-mer-based approaches were evaluated.<br><br>RESULTS: For taxonomic profiling, the Assembly-Binning-Method and rpoB metabarcoding exhibited comparable sensitivity and precision, whereas k-mer approaches produced a notably high number of false negatives. In some cases, the Assembly-Binning-Method improved taxonomic resolution compared with rpoB metabarcoding by identifying taxa at the species level rather than the genus level. Regarding the quantification of microbial composition, the Assembly-Binning-Method consistently showed a higher correlation with expected values &#x200b;&#x200b;and a lower dissimilarity index than rpoB metabarcoding. The use of three sets of reference genomes to calculate depth coverage did not systematically affect the precision of the Assembly-Binning-Method.<br><br>CONCLUSIONS: These results demonstrate that although shotgun sequencing and rpoB metabarcoding have nearly equivalent accuracy in taxonomic profiling, shotgun sequencing has better taxonomic resolution and outperforms rpoB metabarcoding in quantitative estimation of microbial community abundance using the Assembly-Binning approach.}, }
@article {pmid40615853, year = {2025}, author = {Li, S and Xu, Z and Diao, H and Zhou, A and Tu, D and Wang, S and Feng, Y and Feng, X and Lai, Y and Yang, S and Tang, B}, title = {Gut microbiome alterations and hepatic encephalopathy post-TIPS in liver cirrhosis patients.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {745}, pmid = {40615853}, issn = {1479-5876}, mesh = {Humans ; *Hepatic Encephalopathy/microbiology/etiology/blood ; *Liver Cirrhosis/microbiology/surgery/complications ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Portasystemic Shunt, Transjugular Intrahepatic/adverse effects ; Ammonia/blood ; Aged ; }, abstract = {BACKGROUND: The transjugular intrahepatic portosystemic shunt (TIPS), a crucial tool for treating complications related to portal hypertension in patients with liver cirrhosis, is often associated with an increased risk of postoperative complications such as hepatic encephalopathy. Accurate preoperative prediction of the risk of developing hepatic encephalopathy is critical for optimizing the rational clinical application of TIPS.<br><br>METHODS: In this study, stool samples from 67 patients were collected preoperatively and 1&#xa0;month postoperatively and metagenomic sequencing was performed to assess the composition of the gut microbiota. The differential abundances of species and MetaCyc pathways were analyzed using microbiome multivariate associations with linear models. Correlations between variables, including species abundance, the MetaCyc pathway, and clinical characteristics, were assessed using the Pearson correlation test. Prognostic models were developed from metagenomic sequencing cohorts to predict hepatic encephalopathy (HE) and elevated blood ammonia levels.<br><br>RESULTS: We demonstrated that the abundance of Phocaeicola vulgatus increased after TIPS, and the urea cycle decreased. A positive correlation was observed between P.vulgatus and elevated blood ammonia levels (P&#x2009;<&#x2009;0.05). Patients exhibiting increased blood ammonia after TIPS showed significant enrichment of P.vulgatus (LDA&#x2009;>&#x2009;2.5), accompanied by a reduction in the urea cycle (P&#x2009;<&#x2009;0.05) and associated enzymes (P&#x2009;<&#x2009;0.05). Similar microbiota alterations were identified in patients who experienced postoperative hepatic encephalopathy. Furthermore, a comprehensive genetic profile of P.vulgatus was developed, highlighting its ability to increase amino acid metabolism. Many models have shown that the use of gut microbiota characteristics has greater predictive performance.<br><br>CONCLUSION: Multiple machine learning models revealed that P.vulgatus may serve as a significant predictive microbe for hepatic encephalopathy after TIPS, which may be closely related to its ability to metabolize ammonia. These findings establish a microbiome-based framework for postoperative complication risk stratification and personalized preoperative interventions and offer unexplored targets for future research.}, }
@article {pmid40615598, year = {2025}, author = {Shah, M and Sieber, G and Deep, A and Beisser, D and Boenigk, J}, title = {Unravelling the temporal dynamics of community functions in protists induced by treated wastewater exposure using metatranscriptomics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23957}, pmid = {40615598}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; *Transcriptome ; Ecosystem ; Fresh Water/microbiology ; *Eukaryota/genetics ; }, abstract = {The discharge of treated wastewater (TWW) into freshwater ecosystems poses a significant impact on microbial communities, particularly protists, which play a crucial role in nutrient cycling and ecosystem stability. While the ecological effects of TWW on microbial diversity have been studied, understanding the functional responses of protist communities remains limited. This study employs metatranscriptomics to unravel the temporal dynamics of protist community functions in response to TWW exposure. Using mesocosm experiment, water samples were analyzed over a ten-day period to monitor shifts in metabolic pathways and community interactions. Our results indicate that processed metatranscriptomic data, focusing on treatment-significant pathways, is more sensitive than traditional methods, such as meta-barcoding, and non-target screening, in detecting wastewater-induced perturbations. Early exposure to TWW significantly altered expression of pathways associated with signal transduction and environmental interaction, while general metabolic pathways showed resilience. Over time, the protist community showed signs of adaptation with expression levels stabilizing towards the end of the experiment. This study underscores the importance of focussing on functional shifts rather than just taxonomic changes for assessing wastewater impacts on freshwater ecosystems. Our findings advocate for the use of metatranscriptomics as a robust indicator for TWW detection, aiding in development of targeted environmental management strategies.}, }
@article {pmid40615451, year = {2025}, author = {Omar, HS and Hagag, MH and El-Khishin, D and Hashem, M}, title = {Expression of pathogenesis-related proteins in potato brown rot plants confers resistance to filamentous pathogens under field trials.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23927}, pmid = {40615451}, issn = {2045-2322}, mesh = {*Solanum tuberosum/microbiology/genetics ; *Plant Diseases/microbiology/genetics ; *Disease Resistance/genetics ; *Ralstonia solanacearum/pathogenicity ; Soil Microbiology ; Pseudomonas/genetics ; *Plant Proteins/genetics/metabolism ; }, abstract = {The present investigation aims to use innovative metagenomics technologies and denaturing gradient gel electrophoresis (DGGE) to compare the microbial communities of conductive and suppressive soils in connection to brown rot disease in the entire value of Egyptian potato imports. Besides evolution, the bioefficacy of two biocontrol agents, either alone or in consortium, on plant growth promotion and activation of defense responses in potato against the brown rot diseases. The soil status of collecting soil from seven different locations in different governorates was evaluated for tolerance to the artificial inoculation of the pathogen agent of R. solanacearum on potato plants. The DGGE uses 16 srRNA primers that were used to compare two extreme patterns for identifying the microbial population detected in environmental samples. Different bands were extracted from the DGGE gel and sequenced. The sequencing data results revealed that the biocontrol agent factor has a 100% gene bank similarity and belongs to the Pseudomonas species. The Pseudomonas nucleotide sequences isolates were deposited in the Gene Bank under Accession Nos. PP930812, PQ466864, and PQ470140. The findings showed that the soil from the governorates of Kerdasa exhibited a less tolerant treatment, with an estimated disease severity of 78.33%. On the other hand, ElBeheira Kom Hamada soil showed significant tolerance, with an estimated disease severity of 11.67. According to the data of gene expression analysis, both treated plants with the biocontrol agents showed a significant increase in PR-1, PR-2 and PR-Q gene expression, which accelerated the defense response and reduced brown rot disease. The evaluated potato genotype results proved to have the potential for brown rot disease resistance and higher yield production. The findings of this study recommended that biopriming with a microbial consortium enhance potato growth, productivity, and induction of defense responses against S. tuberosum through the induction of systemic resistance via expression of PR pathogenic-related protein network. The present investigation offers significant perspectives that warrant further exploration in subsequent studies to address the traceability requirements of the worldwide economics of disease control for potato plants.}, }
@article {pmid40615445, year = {2025}, author = {Di Gloria, L and Casbarra, L and Lotti, T and Ramazzotti, M}, title = {Testing the limits of short-reads metagenomic classifications programs in wastewater treating microbial communities.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23997}, pmid = {40615445}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Sewage/microbiology ; *Metagenome ; }, abstract = {Biological wastewater treatment processes, such as activated sludge (AS) and aerobic granular sludge (AGS), have proven to be crucial systems for achieving both efficient waste purification and the recovery of valuable resources like poly-hydroxy-alkanoates. Gaining a deeper understanding of the microbial communities underpinning these technologies would enable their optimization, ultimately reducing costs and increasing efficiency. To support this research, we quantitatively compared classification methods differing in read length (raw reads, contigs and MAGs), overall search approach (Kaiju, Kraken2, RiboFrame and kMetaShot), as well as source databases to assess the classification performances at both the genus and species levels using an in silico-generated mock community designed to provide a simplified yet comprehensive representation of the complex microbial ecosystems found in AS and AGS. Particular attention was given to the misclassification of eukaryotes as bacteria and vice versa, as well as the occurrence of false negatives. Notably, Kaiju emerged as the most accurate classifier at both the genus and species levels, followed by RiboFrame and kMetaShot. However, our findings highlight the substantial risk of misclassification across all classifiers and databases, which could significantly hinder the advancement of these technologies by introducing noises and mistakes for key microbial clades.}, }
@article {pmid40614847, year = {2025}, author = {Wang, R and Chen, H and Liu, Y}, title = {Metagenomic insights into the characteristics and co-migration of antibiotic resistome and metal(loid) resistance genes in urban landfill soil and groundwater.}, journal = {Environmental research}, volume = {285}, number = {Pt 1}, pages = {122285}, doi = {10.1016/j.envres.2025.122285}, pmid = {40614847}, issn = {1096-0953}, abstract = {The heavy metals and antibiotic resistance genes (ARGs) in landfills showed a significant correlation; however, the relationship between metal(loid) resistance genes (MRGs) and ARGs in contaminated environments, as well as whether they co-migrate with human pathogenic bacteria (HPB), remains unclear. This study is the first to report the characteristics and co-migration of ARGs and MRGs in the soil and groundwater of aged urban landfill sites. Our findings indicated that quinolone, efflux, and macrolide-lincosamide-streptogramin represented the most abundant ARGs identified. Notably, ARG abundance was higher in groundwater compared to soil, with subtype diversity reflecting a similar trend; however, microbial diversity in soil was greater. Metagenome-assembled genomes data indicated a higher risk of antibiotic-resistant HPB in groundwater. It is imperative to focus on HPB that co-carry ARGs and MRGs alongside mobile genetic elements (MGEs), such as Ralstonia pickettii and Pseudomonas stutzeri. Genes conferring resistance to copper and mercury, as well as MGEs such as qacEdelta and intI1, played a critical role in promoting horizontal gene transfer of antibiotic resistance. MRG may promote ARG migration by affecting the permeability of the cell membrane. Procrustes analysis revealed a strong similarity (87 %) between heavy metals and MRG structures. Variance partitioning analyses demonstrated that both heavy metals and biological factors jointly governed landfill ARGs (96.2 %), exerting a more substantial influence in groundwater than in soil. This study serves as a reference for managing landfill, while emphasizing the importance of addressing the co-migration of MRGs and ARGs in pathogens when controlling the spread of risks.}, }
@article {pmid40614652, year = {2025}, author = {Korotetskiy, I and Kuznetsova, T and Shilov, S and Zubenko, N and Ivanova, L and Korotetskaya, N and Izmailov, T}, title = {Metagenomic data insights into chicken microbiome diversity across various regions of Kazakhstan.}, journal = {Poultry science}, volume = {104}, number = {9}, pages = {105488}, doi = {10.1016/j.psj.2025.105488}, pmid = {40614652}, issn = {1525-3171}, abstract = {Understanding the gut microbiome of poultry is essential for ensuring the health, productivity, and safety of poultry products. This study aimed to assess the regional diversity and composition of chicken microbiota in Kazakhstan using high-throughput metagenomic sequencing. Tracheal and cloacal swabs were collected from chickens on private farms in five geographic locations. Pooled DNA and RNA samples were sequenced using the Ion Torrent PGM platform, and taxonomic classification was performed using Kaiju, with subsequent alpha and beta diversity analyses in R. The results revealed considerable differences in the microbial profiles between regions. Notably, Chlamydia was abundant in the Shymkent samples (>48 %) but was nearly absent elsewhere. In contrast, Pseudomonas was disproportionately dominant in Almaty (32.7 %), suggesting possible dysbiosis. This study provides the first metagenomic characterization of poultry microbiota in Kazakhstan. This highlights region-specific microbial risks and underscores the importance of spatial microbiome monitoring in poultry health management. These findings provide a basis for future strategies aimed at preventing disease outbreaks and controlling zoonotic pathogens in poultry.}, }
@article {pmid40614609, year = {2025}, author = {Ogola, HJO}, title = {Wastewater-driven nutrient enrichment restructures viral community assembly, host interactions, and ecological function along the Nakivubo-Lake Victoria interface in Uganda.}, journal = {The Science of the total environment}, volume = {993}, number = {}, pages = {180002}, doi = {10.1016/j.scitotenv.2025.180002}, pmid = {40614609}, issn = {1879-1026}, abstract = {Gulf ecosystems in freshwater lakes are dynamic interfaces of microbial activity, shaped by complex interactions between natural processes and anthropogenic inputs from surrounding urban catchments. This study investigated viral community composition, functional potential, and virus-host interactions along the Nakivubo catchment-Lake Victoria interface in Murchison Bay, Uganda. Metagenomic profiling of 28 samples across four compartments: wastewater treatment plant (WWTP); a municipal channel; papyrus-dominated wetland; and Lake water, revealed spatially distinct viromes dominated by Uroviricota (45.8-94.8 %), with higher richness observed in Channel and Wetland than in WWTP and Lake samples. Community structure was strongly compartmentalized (PERMANOVA, p < 0.001), with WWTP and Channel viromes distinct from those in less impacted compartments. Human-associated viruses, including crAss-like phages (up to 29.3 %) and Picobirnaviruses (11.4 %), were enriched in WWTP samples, reflecting fecal pollution. Linear discriminant analyses and random forest modeling identified Sinsheimervirus as wetland indicator, while Fukuivirus, Bellamyvirus and Prokaryotic dsDNA virus were characteristic of lake viromes. Viral-bacterial co-occurrence networks were fragmented and less cohesive in WWTP and Channel (average path length = 3.2), but more modular and nested in Wetland (avg. path length = 1.9; modularity = 0.47), reflecting ecological structuring. Among environmental variables, ammonia-N was the strongest correlate of viral beta diversity (Mantel r = 0.67, p < 0.01). Functionally, auxiliary metabolic genes (AMGs) linked to photosynthesis, nitrogen and carbohydrate cycling were enriched in Wetland and Lake, while mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs) were largely confined to WWTP, Channel, and Wetland. These patterns suggest selective viral adaptations to eutrophic, contaminated environments and their attenuation downstream. The findings demonstrate how wastewater-driven nutrient enrichment shapes viral community assembly, host associations, and ecological function along tropical freshwater continua. Viruses emerge as sensitive indicators of anthropogenic impact and offer new perspectives for water quality monitoring and ecosystem health assessment in urban-influenced lake systems.}, }
@article {pmid40614422, year = {2025}, author = {Lee, CE and Messer, LF and Wattiez, R and Matallana-Surget, S}, title = {The invisible threats of sunscreen as a plastic co-pollutant: Impact of a common organic UV filter on biofilm formation and metabolic function in the nascent marine plastisphere.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139103}, doi = {10.1016/j.jhazmat.2025.139103}, pmid = {40614422}, issn = {1873-3336}, abstract = {Plastic debris in marine environments serves as a substrate for microbial colonisation, forming biofilms known as 'plastispheres'. Also accumulated on plastic debris are co-pollutants including UV-protective organic UV-filters from sunscreens, which likely interact with this niche through their lipophilicity. Despite their widespread use and environmental accumulation, the influence of UV-filters on plastisphere composition and function has never been investigated. This study therefore investigates, for the first time, how co-pollution - specifically by an organic UV-filter - impacts the composition and function of marine plastisphere communities. To achieve this, low-density polyethylene (LDPE) was incubated with marine microbial communities for six days to cultivate a nascent plastisphere, which was then exposed to 5 mg/L of EthylHexyl MethoxyCinnamate (EHMC); the most used organic UV-filter in sunscreens, and a prevalent marine pollutant. Metagenomic analyses revealed that EHMC favoured the growth of bacterial generalists Pseudomonas and Psychromonas while reducing pollutant-degrading genera like Marinomonas. Analysis of 3070 proteins revealed a consistent upregulation of proteins used for biofilm maintenance by Pseudomonas with EHMC exposure, including the considerable upregulation of outer membrane porin F (OprF) which regulates exopolymeric substance (EPS) production. Additionally, proteins thought to indicate a shift from aerobic to anaerobic respiration were frequently expressed after exposure to EHMC. This may have selected against the obligate aerobes Marinomonas and Pseudoalteromonas, contributing to the observed shift in community composition. These findings underscore the importance of considering chemical co-pollutants in plastisphere research as we now begin to discover how ecologically significant, and potentially harmful microbial genera are affected by this interaction.}, }
@article {pmid40614349, year = {2025}, author = {Ma, RA and Ding, YH and Zhong, S and Jing, TT and Chen, X and Zhang, SY}, title = {A machine learning approach to predict phyllosphere resistome abundance across urbanization gradients.}, journal = {Environment international}, volume = {202}, number = {}, pages = {109655}, doi = {10.1016/j.envint.2025.109655}, pmid = {40614349}, issn = {1873-6750}, abstract = {Recent studies reported an increased abundance of antibiotic resistance genes (ARGs) in urban greenspaces, yet the predictability of ARG variance along urbanization gradients remains unclear. We sampled paired soil and phyllosphere samples from the same site in wetland parks along urbanization gradients to assess the correlations of soil and phyllosphere ARG abundance with urbanization indices. Our results revealed that the abundance of phyllosphere resistomes correlated better with urbanization gradients than did that of soil resistomes and increased along urbanization gradients. Moreover, the phyllosphere presented more ARG-MGE (mobile gene element) pairs in metagenome-assembled genomes than soil, suggesting greater transmission potential than soil ARGs. Proximity to the built area and microbial diversity were the most important factors that significantly (p < 0.01) drove the variance in phyllosphere ARG abundance. By integrating population density, land use type, landscape metrics, and air quality data into machine learning models, we predicted phyllosphere ARG abundance at a 10-meter resolution. Among the five tested algorithms tested in the machine learning models (ridge regression, K-nearest neighbor, support vector machine, and neural network), the random forest algorithm achieved the highest accuracy with the lowest root mean square error (27.24 vs. 40.79-46.79 for the other models). These results demonstrate a strong association between phyllosphere ARG abundance and urbanization indices and provide predictions of the potential ARG risk along these gradients. The heightened transmission potential in urban greenspaces may facilitate the spread of antibiotic resistance spread to human pathogens, which poses significant public health threats.}, }
@article {pmid40614175, year = {2025}, author = {Khalil, S and Paras, ML and Eichenberger, E and Sohail, MR}, title = {The Next Step: Role of Metagenomic Next Generation Sequencing for Microbial Detection in Culture-negative Cardiovascular infections.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf361}, pmid = {40614175}, issn = {1537-6591}, abstract = {Cardiovascular infections, including those involving native and prosthetic heart valves, implantable cardiac devices, mechanical circulatory assist devices, and vascular grafts, are associated with significant morbidity and mortality risks. Optimal management of these complex infections requires pathogen-directed antimicrobial therapy. However, standard culture-based methods often fail to identify causative organisms due to prior antimicrobial use, infections due to fastidious organisms, or biofilm-associated infections. Emerging evidence suggests that microbial cell-free DNA (mcfDNA) and metagenomic testing can enhance pathogen detection, particularly in culture-negative cases. However, their results require careful clinical interpretation, often necessitating input from infectious diseases specialists. In this review, we examine published evidence regarding metagenomic testing for cardiovascular infections and its impact on patient care. We propose a framework for microbiological adjudication of mcfDNA results, introduce standardized definitions for clinical impact assessment, and provide guidance on integrating mcfDNA testing into diagnostic evaluation of patients with culture-negative cardiovascular infections.}, }
@article {pmid40613917, year = {2025}, author = {Zakerska-Banaszak, O and Ladziak, K and Kruszka, D and Maciejewski, K and Wolko, L and Krela-Kazmierczak, I and Zawada, A and Vibeke Vestergaard, M and Dobrowolska, A and Skrzypczak-Zielinska, M}, title = {New potential biomarkers of ulcerative colitis and disease course - integrated metagenomic and metabolomic analysis among Polish patients.}, journal = {Journal of gastroenterology}, volume = {}, number = {}, pages = {}, pmid = {40613917}, issn = {1435-5922}, support = {2020/04/X/NZ2/02172//Narodowe Centrum Nauki/ ; 2021/02//Institute of Human Genetics, Polish Academy of Sciences, in Poznan, Poland/ ; }, abstract = {BACKGROUND &amp; AIM: The course of ulcerative colitis (UC) involves successive periods of remission and exacerbation but is difficult to predict. Gut dysbiosis in UC has already been intensively investigated. However, are periods of exacerbation and remission associated with specific disturbances in the composition of the intestinal microbiota and its metabolome? Our goal was to answer this question and to identify bacteria and metabolites necessary to maintain the remission.<br><br>METHODS: We enrolled 65 individuals, including 20 UC patients in remission, 15 in exacerbation, and 30 healthy controls. Metagenomic profiling of the gut microbial composition was performed based on 16S rRNA V1-V9 sequencing. Stool and serum metabolic profiles were studied by chromatography combined with mass spectrometry.<br><br>RESULTS: We revealed significant differences in the gut bacterial and metabolic composition between patients in active UC and those in remission, as well as in healthy controls. As associated with UC remission we have identified following bacteria: Akkermansia, Agathobacter, Anaerostipes, Enterorhabdus, Coprostanoligenes, Colinsella, Ruminococcus, Subdoligranulum, Lachnoclostridium, Coriobacteriales, Erysipelotrichaceae, and Family XII, and compounds - 1-hexadecanol, phytanic acid, squalene, adipic acid, cis-gondoic acid, nicotinic acid, tocopherol gamma, ergosterol and lithocholic acid. Whereas, in the serum lithocholic acid, indole and xanthine were found as potential candidates for biomarkers of UC remission.<br><br>CONCLUSION: We have demonstrated that specific bacteria, metabolites, and their correlations could be crucial in the remission of UC among Polish patients. Our results provide valuable insights and a significant source for developing new hypotheses on host-microbiome interactions in diagnosis and course of UC.}, }
@article {pmid40613821, year = {2025}, author = {Saini, N and Ghosh, A and Bhadury, P}, title = {Linking Plastic Degradation Potential and Resistance Gene Abundance in Bacterioplankton Community of the Sundarbans Estuarine Ecosystem.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf067}, pmid = {40613821}, issn = {1574-6968}, abstract = {Harnessing microbial capabilities offers a promising and sustainable approach to address the global challenge of plastic waste. However, the potential of mangrove microbiomes to degrade diverse plastic polymers remains largely unexplored. In this metagenomic-based study, surface water microbiomes were analysed from the Indian Sundarbans, part of the world's largest contiguous mangrove ecosystem, revealing 748.21 hits per billion nucleotides associated with plastic-degrading enzymes (PDEs) targeting 17 different polymer types. Of these, 72.9% corresponded to synthetic polymers and 27.1% to natural polymers. The highest number of hits (223) was associated with polyethylene glycol-degrading enzymes, representing 26.7% of the total PDEs hits. Taxonomic analysis revealed Deltaproteobacteria and Gammaproteobacteria as key degraders of diverse synthetic plastic polymers, with Deltaproteobacteria emerging as a previously unreported group. This suggests that surface sediments may serve as reservoirs for novel plastic-degrading microbes. Co-occurrence network analysis indicated possible emerging co-selection or complex associations between PDEs, antibiotic resistance genes (ARGs), and metal resistance genes (MRGs). Notably, zinc resistance genes and aminoglycoside-related ARGs showed more associations with PDEs. While the presence of PDEs offers a promising avenue for bioremediation, their application may be complicated by the concurrent rise of ARGs and MRGs within PDE-harbouring microbes. Thus, it highlights the need for careful assessment when employing microbes for plastic bioremediation.}, }
@article {pmid40613581, year = {2025}, author = {Dang, T and Lysenko, A and Boroevich, KA and Tsunoda, T}, title = {VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {4}, pages = {}, doi = {10.1093/bib/bbaf300}, pmid = {40613581}, issn = {1477-4054}, support = {JP20H03240//JSPS KAKENHI/ ; JP24K15175//JSPS KAKENHI/ ; JPMJCR2231//JST CREST/ ; }, mesh = {Bayes Theorem ; *Microbiota ; *Neural Networks, Computer ; *Metagenomics/methods ; Humans ; *Computational Biology/methods ; Algorithms ; Multiomics ; }, abstract = {The analysis of high-dimensional microbiome multiomics datasets is crucial for understanding the complex interactions between microbial communities and host physiological states across health and disease conditions. Despite their importance, current methods, such as the microbe-metabolite vectors approach, often face challenges in predicting metabolite abundances from microbial data and identifying keystone species. This arises from the vast dimensionality of metagenomics data, which complicates the inference of significant relationships, particularly the estimation of co-occurrence probabilities between microbes and metabolites. Here we propose the variational Bayesian microbiome multiomics (VBayesMM) approach, which aims to improve the prediction of metabolite abundances from microbial metagenomics data by incorporating a spike-and-slab prior within a Bayesian neural network. This allows VBayesMM to rapidly and precisely identify crucial microbial species, leading to more accurate estimations of co-occurrence probabilities between microbes and metabolites, while also robustly managing the uncertainty inherent in high-dimensional data. Moreover, we have implemented variational inference to address computational bottlenecks, enabling scalable analysis across extensive multiomics datasets. Our large-scale comparative evaluations demonstrate that VBayesMM not only outperforms existing methods in predicting metabolite abundances but also provides a scalable solution for analyzing massive datasets. VBayesMM enhances the interpretability of the Bayesian neural network by identifying a core set of influential microbial species, thus facilitating a deeper understanding of their probabilistic relationships with the host.}, }
@article {pmid40613164, year = {2025}, author = {Zhang, QL and Dong, LL and Zhang, LL and Wu, YJ and Li, M and Bo, J and Wang, LL and Jing, Y and Dou, LP and Liu, DH and Gu, ZY and Gao, CJ}, title = {[Characteristics of Gut Microbiota Changes and Their Relationship with Infectious Complications During Induction Chemotherapy in AML Patients].}, journal = {Zhongguo shi yan xue ye xue za zhi}, volume = {33}, number = {3}, pages = {738-744}, doi = {10.19746/j.cnki.issn.1009-2137.2025.03.017}, pmid = {40613164}, issn = {1009-2137}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Leukemia, Myeloid, Acute/drug therapy/microbiology ; *Induction Chemotherapy ; Feces/microbiology ; Male ; Female ; Middle Aged ; }, abstract = {OBJECTIVE: To investigate the characteristics of gut microbiota changes in patients with acute myeloid leukemia (AML) undergoing induction chemotherapy and to explore the relationship between infectious complications and gut microbiota.<br><br>METHODS: Fecal samples were collected from 37 newly diagnosed AML patients at four time points: before induction chemotherapy, during chemotherapy, during the neutropenic phase, and during the recovery phase. Metagenomic sequencing was used to analyze the dynamic changes in gut microbiota. Correlation analyses were conducted to assess the relationship between changes in gut microbiota and the occurrence of infectious complications.<br><br>RESULTS: During chemotherapy, the gut microbiota &#x3b1;-diversity (Shannon index) of AML patients exhibited significant fluctuations. Specifically, the diversity decreased significantly during induction chemotherapy, further declined during the neutropenic phase (P < 0.05, compared to baseline), and gradually recovered during the recovery phase, though not fully returning to baseline levels.The abundances of beneficial bacteria, such as Firmicutes and Bacteroidetes, gradually decreased during chemotherapy, whereas the abundances of opportunistic pathogens, including Enterococcus, Klebsiella, and Escherichia coli, progressively increased.Analysis of the dynamic changes in gut microbiota of seven patients with bloodstream infections revealed that the bloodstream infection pathogens could be detected in the gut microbiota of the corresponding patients, with their abundance gradually increasing during the course of infection. This finding suggests that bloodstream infections may be associated with opportunistic pathogens originating from the gut microbiota.Compared to non-infected patients, the baseline samples of infected patients showed a significantly lower relative abundance of Bacteroidetes (P < 0.05). Regression analysis indicated that Bacteroidetes abundance is an independent predictive factor for infectious complications (P < 0.05, OR =13.143).<br><br>CONCLUSION: During induction chemotherapy in AML patients, gut microbiota &#x3b1;-diversity fluctuates significantly, and the abundance of opportunistic pathogens increase, which may be associated with bloodstream infections. Patients with lower baseline Bacteroidetes abundance are more prone to infections, and its abundance can serve as an independent predictor of infectious complications.}, }
@article {pmid40613026, year = {2025}, author = {Li, J and Zhou, Y and Zou, N and Chen, M}, title = {A Case of Nocardia cyriacigeorgica Infection and Literature Review.}, journal = {Cureus}, volume = {17}, number = {7}, pages = {e87189}, pmid = {40613026}, issn = {2168-8184}, abstract = {Nocardia bacteria primarily enter the human body through the respiratory tract or open wounds, leading to suppurative infections. These infections are more prevalent in individuals with compromised immune systems and can affect the lungs, resulting in pulmonary nocardiosis. The bacteria may also disseminate via the bloodstream to adjacent tissues or infect various organs. Clinical manifestations, physical signs, and imaging findings of nocardial pneumonia lack specificity. Additionally, Nocardia grows slowly and is often overgrown by faster-growing bacteria in sputum cultures, making it difficult to isolate. As a result, clinical misdiagnosis and missed diagnosis are common. With the growing number of immunocompromised individuals, the incidence of nocardial infections has been increasing. Improving laboratory personnel's awareness of this pathogen and enhancing their technical capabilities are crucial for accurate and timely clinical diagnosis. A 34-year-old female patient was reported to have contracted pneumonia caused by Nocardia cyriacigeorgica. The patient experienced a cough and sputum production without a clear cause 20 days prior. Despite clinical empirical treatment, the cough and sputum persisted, and there was also a high fever accompanied by chills and shivering. Metagenomic next-generation sequencing (mNGS) results of the bronchoalveolar lavage fluid showed that it was caused by Nocardia cyriacigeorgica. After four days of sputum culture, bacterial colonies were observed and subsequently identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) as Nocardia cyriacigeorgica. This patient received a combined treatment of compound sulfamethoxazole/trimethoprim and linezolid. Soon, his condition improved, and he was discharged from the hospital. During the two-month follow-up examination, it was observed that the lesion had been largely absorbed and the affected area had significantly reduced in size. The patient no longer experienced coughing or phlegm production. Following a comprehensive review of the clinical data of this case and relevant literature, we aim to improve the capacity of laboratory personnel in cultivating and identifying this rare bacterial pathogen. Furthermore, this study seeks to emphasize to clinical practitioners that bronchoalveolar lavage fluid should be collected for mNGS when pulmonary Nocardia infection is suspected, which can enhance diagnostic accuracy, facilitate early detection and timely intervention, and ultimately alleviate the burden on patients.}, }
@article {pmid40612788, year = {2025}, author = {Veeranan Arun Giridhari, V and Uma Maheswari, T and Vanniarajan, C and Hariharan, T and Karthikeyan, S}, title = {Probing the metagenome and nutritional composition of idli batter fortified with electrolytic iron for addressing anaemia.}, journal = {Journal of food science and technology}, volume = {62}, number = {8}, pages = {1481-1490}, pmid = {40612788}, issn = {0022-1155}, abstract = {Iron deficiency affects people throughout the world, with preschoolers having the highest frequency followed by women of reproductive age and pregnant mothers. Of the different approaches to reducing iron deficiency, food fortification is a desirable and easily acceptable public health approach. Additionally, food fortification is proven to be economical and offers the benefit of reaching a larger population through current food delivery systems without necessitating significant adjustments to current consumption habits. In light of this, idli, a widely popular and commonly consumed fermented staple breakfast from Southern India, is chosen as a delivery system for addressing iron deficiency. Furthermore, because of its high nutritional content and ease of digestion, idli is eaten by people of all ages. The fortificant's bioavailability will also be successful during idli fermentation. Therefore, following the necessary dietary requirement, the readily accessible form of electrolytic iron is added to the idli batter, and its impact on the microbiological, nutritional, and sensory quality of idli was assessed. A metagenome investigation demonstrated that the fermentation microflora of idli batter was unaffected by electrolytic iron fortification with more probiotic microbiota during fermentation. It has been found that electrolytic iron at 9 mg, or 30% Recommended Dietary Allowance, has superior sensory qualities and bioavailability.}, }
@article {pmid40612471, year = {2025}, author = {Arias, RS and Dobbs, JT and Orner, VA and Conforto, EC and Rago, AM and Cazon, LI and Sobolev, VS and Power, IL and Lamb, MC and Massa, AN}, title = {First metagenome- and metatranscriptome dataset of Thecaphora frezzii teliospores, assembly and annotation of a new bacterial genome.}, journal = {Data in brief}, volume = {61}, number = {}, pages = {111779}, pmid = {40612471}, issn = {2352-3409}, abstract = {These datasets correspond to sequencing of DNA and RNA extracted from surface-disinfected teliospores of the fungus Thecaphora frezzii Carranza and Lindquist, causal agent of smut disease in peanut (Arachis hypogaea L.). The DNA was sequenced using Pacific Biosciences (PacBio) Sequel II and RNA was sequenced in Illumina MiSeq 300 bp paired end (PE). Initial de novo assembly and Basic Local Alignment Search Tool (BLAST) of contigs to the 16S reference sequence database at NCBI had hits on seven bacterial species: Luteibacter pinisoli, Variovorax paradoxus, Rhizobium metallidurans, Caulobacter segnis, Roseateles violae, Novosphingobium rosa, Herbaspirillum seropedicae, and the fungus T. frezzii. High stringency mapping of the RNA sequences to the genomes of these organisms showed that 96% of the reads corresponded to bacteria and only 4% to T. frezzii. De novo assembly of PacBio reads revealed the whole genome of a Luteibacter sp. with 88.56% or lower similarity to those in NCBI database, whereas most RNA sequences (> 10 million reads) mapped to the new Luteibacter sp. genome assembled here. We annotated the new Luteibacter sp. genome, assessed its completeness by BUSCO, and aligned it to its closest relative, Luteibacter aegosomatissinici. We are not aware of any report that describes bacteria colonizing teliospores of T. frezzii. The DNA and RNA sequencing datasets provided here could be used to study the distribution of prokaryotes colonizing T. frezzii teliospores, and to explore the role of the microbiome of T. frezzii teliospores on the outcome of peanut smut disease.}, }
@article {pmid40612390, year = {2025}, author = {Yu, J and Lv, X and Wang, Q and Gao, M and Li, W}, title = {Metagenomic sequencing for identification of nontuberculous mycobacteria and other pathogens in patients with mixed infection of the lung.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1592216}, pmid = {40612390}, issn = {2235-2988}, mesh = {Humans ; *Nontuberculous Mycobacteria/genetics/isolation &amp; purification/classification ; Middle Aged ; Male ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Female ; Retrospective Studies ; *Metagenomics/methods ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Lung/microbiology/pathology ; High-Throughput Nucleotide Sequencing ; *Coinfection/microbiology/diagnosis ; Adult ; Aged, 80 and over ; *Lung Diseases/microbiology/diagnosis ; }, abstract = {BACKGROUND: It can be difficult to distinguish lung disease caused by nontuberculous mycobacteria (NTM), Mycobacterium tuberculosis, and mixed infections (MIs) that include NTM. Metagenomic next generation sequencing (mNGS) is a highly sensitive method that can reliably identify lung pathogens. We retrospectively analyzed the records of patients who had MIs of the lungs that included NTM and received mNGS testing.<br><br>METHODS: The records of 36 patients who were diagnosed with NTM infection of the lungs at the Second Hospital of Jilin University from Nov 2023 to Jun 2024 were analyzed. Initial empirical treatments were ineffective in all patients, leading to the application of mNGS of bronchoalveolar lavage fluid (BALF).<br><br>RESULTS: The average patient age was 62.4 years, 22 patients had one or more underlying chronic disease, and all patients had at least one respiratory symptom (cough, sputum production, fever, or dyspnea). Chest CT examinations showed that patients had different degrees of pneumonia and pleural effusion. Among tested patients, there were elevated levels of erythrocyte sedimentation rate in 81.8% (18/22) and elevated C-reactive protein in 90.5% (19/21). There were variable results from acid-fast staining of bronchoalveolar lavage fluid (BALF; 3/36, 8.3%), and transbronchial lung biopsy (TBLB; 5/14, 35.7%). mNGS identified seven NTM species. Treatment based on the mNGS results led to the resolution of clinical symptoms and absorption of lung lesions in all patients.<br><br>CONCLUSIONS: Most of the 36 patients with MIs of the lungs that included NTM had underlying diseases. The results of traditional tests, including sputum or BALF culture and smear, acute phase markers, and TBLB pathological examination, were problematic. mNGS provides rapid and reliable diagnosis, allowing the rapid implementation of appropriate therapy in patients with MIs of the lungs that include NTM.}, }
@article {pmid40612127, year = {2025}, author = {Madlala, SS and Mchunu, N and Dalasile, M and Pierneef, R and Reddy, P}, title = {Metagenomic evaluation of food hygiene practices in the National School Nutrition Programme in KwaZulu Natal, South Africa.}, journal = {Health SA = SA Gesondheid}, volume = {30}, number = {}, pages = {2814}, pmid = {40612127}, issn = {2071-9736}, abstract = {BACKGROUND: The National School Nutrition Programme (NSNP) provides meals to schools in low-income areas in South Africa, implemented by the Department of Basic Education (DBE) with food safety monitored by Municipal Health Services.<br><br>AIM: To assess compliance of school kitchens with general hygiene requirements (R638 of 2018) and detect food pathogens on food contact surfaces using amplified metagenomics.<br><br>SETTING: The study was conducted in quintile 1 and 2 primary schools in Vryheid, KwaZulu-Natal.<br><br>METHODS: A quantitative cross-sectional study assessed the safety compliance of food preparation and storage areas in 33 primary schools against national legislation standards. Fifteen samples of food contact surfaces were collected from four schools and analysed using Illumina sequencing to identify prevalent bacterial genera.<br><br>RESULTS: None of the schools possessed a Certificate of Acceptability. Significant structural issues include poor pest control, inadequate sanitary facilities, a lack of food safety training and inadequate waste management. Taxonomic analysis revealed several dominant bacterial genera, including Pseudomonas, Stenotrophomonas, Acinetobacter and Pantoea, indicating potential routes for food contamination and subsequent risks for foodborne illnesses.<br><br>CONCLUSION: The study highlighted critical inadequacies in food preparation and storage areas requiring urgent intervention to ensure safe meal preparation. It emphasised the need for improved food safety monitoring and compliance in schools in low-income areas. Next-generation sequencing (NGS) techniques identified a broad spectrum of pathogens, offering a robust method for assessing environmental hygiene.<br><br>CONTRIBUTION: This study provides insights into food safety risks in the NSNP, informing policies and interventions to improve food safety and reduce foodborne illnesses in schools.}, }
@article {pmid40611965, year = {2025}, author = {Ivanova, M and Aarestrup, FM and Otani, S}, title = {Impact of sample multiplexing on detection of bacteria and antimicrobial resistance genes in pig microbiomes using long-read sequencing.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1597804}, pmid = {40611965}, issn = {1664-302X}, abstract = {The effects of sample multiplexing on the detection sensitivity of antimicrobial resistance genes (ARGs) and pathogenic bacteria in metagenomic sequencing remain underexplored in newer sequencing technologies such as Oxford Nanopore Technologies (ONT), despite its critical importance for surveillance applications. Here, we evaluate how different multiplexing levels (four and eight samples per flowcell) on two ONT platforms, GridION and PromethION, influence the detection of ARGs, bacterial taxa and pathogens. While overall resistome and bacterial community profiles remained comparable across multiplexing levels, ARG detection was more comprehensive in the four-plex setting with low-abundance genes. Similarly, pathogen detection was more sensitive in the four-plex, identifying a broader range of low abundant bacterial taxa compared to the eight-plex. However, triplicate sequencing of the same microbiomes revealed that these differences were primarily due to sequencing variability rather than multiplexing itself, as similar inconsistencies were observed across replicates. Given that eight-plex sequencing is more cost-effective while still capturing the overall resistome and bacterial community composition, it may be the preferred option for general surveillance. Lower multiplexing levels may be advantageous for applications requiring enhanced sensitivity, such as detailed pathogen research. These findings highlight the trade-off between multiplexing efficiency, sequencing depth, and cost in metagenomic studies.}, }
@article {pmid40611959, year = {2025}, author = {Qi, S and Qian, J and Li, Y and Li, Y and Li, W and Gao, X}, title = {Effect of acupuncture at Back-Shu points on gut microbiota in insomnia model rats based on metagenomic sequencing technology.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1541958}, pmid = {40611959}, issn = {1664-302X}, abstract = {BACKGROUND: Increasing evidence indicates a bidirectional interaction between the gut microbiota and sleep regulation via the microbiota-gut-brain axis. Acupuncture is widely used to treat insomnia, and its efficacy may be mediated in part by modulation of the gut microbiota and its metabolic pathways.<br><br>METHODS: A rat model of insomnia was established by intraperitoneal injection of para-chlorophenylalanine (PCPA). Rats received acupuncture at Back-Shu points for 2 weeks. Sleep behavior was assessed using the pentobarbital-induced sleep test, and fecal samples were collected for metagenomic sequencing to analyze changes in gut microbial composition and function before and after acupuncture.<br><br>RESULTS: Compared with the model group, acupuncture significantly shortened sleep latency and prolonged sleep duration. Metagenomic analysis revealed that acupuncture partially restored the PCPA-induced decline in &#x3b1;-diversity and markedly altered &#x3b2;-diversity. Functionally, acupuncture enriched beneficial taxa such as Lactobacillus johnsonii and Ligilactobacillus murinus, and promoted pathways involved in tryptophan and glutamate metabolism as well as short-chain fatty acid (SCFA) synthesis. These changes may act by restoring neurotransmitter balance, strengthening gut barrier integrity, and modulating immune responses. Notably, SCFAs can activate G-protein-coupled receptors to suppress overactivation of the hypothalamic-pituitary-adrenal (HPA) axis, counteracting insomnia-related pathophysiology.<br><br>CONCLUSION: Acupuncture at Back-Shu points ameliorates PCPA-induced insomnia-like behavior in rats and beneficially remodels gut microbiota structure and metabolic function. These findings support a key role for the microbiota-gut-brain axis in acupuncture's regulation of sleep and provide a theoretical basis for developing microbiota-targeted adjunctive therapies for insomnia.}, }
@article {pmid40611899, year = {2025}, author = {Pokharel, SK and Shehata, N and Ahearne, A and Knehans, T and Bailey, CB and Boudreau, PD and Stevens, DC}, title = {Establishing Conserved Biosynthetic Gene Clusters of the Phylum Myxococcota.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.06.19.660557}, pmid = {40611899}, issn = {2692-8205}, abstract = {A surge in sequenced myxobacteria catalyzed by advancements in long read genome and metagenome sequencing has provided sufficient data to scrutinize the conserved biosynthetic gene clusters (BGCs) within the phylum Myxococcota. Provided the utility of myxobacteria in environmental nutrient cycles and discovery of novel therapeutic leads, we sought to determine any conserved specialized metabolism in the phylum. Using a pan-genome approach to analyze eleven genera and 195 sequenced genomes including ten newly reported myxobacterial isolate, we observed five conserved BGCs. All five clusters encode for characterized metabolites with established ecological roles for four of the metabolites, and none of the metabolites are known toxins. Validation of our approach was done by analyzing Myxococcota genera without sufficient, sequenced representatives for pan-genome analysis to observe the presence/absence of these five clusters. This approach enabled observation of genus-level conservation of BGCs with varying degrees of confidence due to diversity of sequenced species within each genus. The indigoidine BGC typically found in Streptomyces spp. was notably conserved in Melittangium ; heterologous expression of the core biosynthetic gene bspA in Escherichia coli and subsequent detection of indigoidine confirmed the identity of the indigoidine cluster. Conserved BGCs in myxobacteria reveal maintenance of biosynthetic pathways and cognate metabolites with ecological roles as chemical signals and stress response; these observations suggest competitive specialization of secondary metabolism and toxin production in myxobacteria.}, }
@article {pmid40611207, year = {2025}, author = {Wang, Q and Zhang, M and Meng, M and Luo, Z and Pan, Z and Deng, L and Qin, J and Guo, B and Zhu, D and Zhang, Y and Guo, H and Liang, Y and Su, Z}, title = {Integration bile acid metabolomics and gut microbiome to study the anti-liver fibrosis effects of total alkaloids of Corydalis saxicola Bunting.}, journal = {Chinese medicine}, volume = {20}, number = {1}, pages = {106}, pmid = {40611207}, issn = {1749-8546}, support = {82060763//National Natural Science Foundation of China/ ; GXFCDP-PS-2022//Guangxi First-class Discipline Project for Pharmaceutical Sciences/ ; GXQH202409//Guangxi Youth Qihuang Scholars Training Project/ ; }, abstract = {BACKGROUND: Bile acids and gut microbiota participate in the pathogenesis of liver fibrosis (LF). The total alkaloids of Corydalis saxicola Bunting (TACS) is a traditional Chinese medicine extract that has been used to treat LF, but the underlying mechanisms are not clear. This study performed integrated metabolomics and gut microbiome analysis to study the anti-LF mechanism of TACS using a rat model.<br><br>METHODS: Ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) was used to identify the chemical compounds in TACS. Biochemical and histopathological analysis were performed to determine the efficacy of TACS. Bile acid-targeted metabolomics was used to assess changes in the bile acid (BA) profiles in TACS-treated LF rats. 16S rRNA gene sequencing and metagenomics were used to assess changes in the gut microbiota of the TACS-treated LF rats. Antibiotic cocktail treatment and fecal microbiota transplantation (FMT) were used to determine the relationship between the gut microbiota and the anti-LF effects of TACS. Metagenomics was used to identify significantly enriched gut microbiota after TACS treatment and its correlation with the anti-LF effects was verified by in vivo experiments.<br><br>RESULTS: TACS treatment significantly reduced the levels of serum liver enzymes, fibrosis and pro-inflammatory cytokines in the liver. TACS significantly increased the levels of chenodeoxycholic acid (CDCA) and taurochenodeoxycholic acid&#xa0;(TCDCA) in the cecum and decreased the levels of cholic acid (CA) and deoxycholic acid (DCA) in the liver of the LF rats. TACS significantly increased the abundances of Lactobacillus and Akkermansia in the LF rats. Antibiotic cocktail treatment and FMT have&#xa0;shown that the effect of TACS cure liver fibrosis depends on the gut microbiota. The abundance of Lactobacillus reuteri was significantly increased by TACS. Administration of Lactobacillus reuteri via gavage ameliorated LF.<br><br>CONCLUSIONS: TACS exerted anti-LF effects in rats by modulating bile acid metabolism and gut microbiome.}, }
@article {pmid40610423, year = {2025}, author = {Fuhrmeister, ER and Kim, S and Mairal, SA and McCormack, C and Chieng, B and Swarthout, JM and Paulos, AH and Njenga, SM and Pickering, AJ}, title = {Context-Seq: CRISPR-Cas9 targeted nanopore sequencing for transmission dynamics of antimicrobial resistance.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5898}, pmid = {40610423}, issn = {2041-1723}, support = {OPP1129535//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; UL1TR002544//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 1906957//National Science Foundation (NSF)/ ; }, mesh = {*CRISPR-Cas Systems/genetics ; Animals ; Humans ; *Nanopore Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; Kenya ; Anti-Bacterial Agents/pharmacology ; Dogs ; *Bacteria/genetics/drug effects ; Klebsiella pneumoniae/genetics/drug effects ; Child ; Adult ; Escherichia coli/genetics/drug effects ; Poultry/microbiology ; beta-Lactamases/genetics ; Genome, Bacterial ; Haemophilus influenzae/genetics/drug effects ; }, abstract = {Precisely understanding how and to what extent antimicrobial resistance (AMR) is exchanged between animals and humans is needed to inform control strategies. Metagenomic sequencing has low detection for rare targets such as antibiotic resistance genes, while whole genome sequencing of isolates misses exchange between uncultured bacterial species. We introduce Context-Seq, CRISPR-Cas9 targeted sequencing of ARGs and their genomic context with long-reads. Using Context-Seq, we investigate genetically similar AMR elements containing the ARGs blaCTX-M and blaTEM between adults, children, poultry, and dogs in Nairobi, Kenya. We identify genetically distinct clusters containing blaTEM and blaCTX-M that are shared between animals and humans within and between households. We also uncover potentially pathogenic hosts of ARGs including Escherichia coli, Klebsiella pneumoniae, and Haemophilus influenzae in this study context. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.}, }
@article {pmid40609888, year = {2025}, author = {Maki, T and Takami, H and Pointing, S and Kurosaki, Y and Fukui, H and Bin, C and Kai, K}, title = {Bacterial stress adaptation and antibiotic resistance in dust-transportable bioaerosols originating from the Gobi Desert.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126759}, doi = {10.1016/j.envpol.2025.126759}, pmid = {40609888}, issn = {1873-6424}, abstract = {Airborne microorganisms which dispersed from the Gobi Desert throughout East Asia via long-range dust transports, are believed to maintain their viability against atmospheric stressors that influence ecosystem dynamics and human health during deposition in downwind environments. However, the adaptative mechanisms that facilitate microbial tolerance to environmental stressor, and the persistence of factors such as antibiotic resistance relevant to human health have not been determined. Here, we described the metagenomic and physiological interrogation of airborne bacteria collected from aerosols at an altitude of 500 m using a balloon-mounted sampler and at a parallel site 3 m above the ground in the dust-source region of Gobi Desert. The shotgun metagenomic DNA sequencing which determine was performed for characterizing the taxonomic compositions of airborne bacteria and their potential functions. The communities were dominated by species in the phyla Actinobacteria, Bacillota, Bacteroidota, and Pseudomonadota (Alpha). Metabolic-pathway analysis revealed that Gobi Desert bioaerosols were enriched in functions associated with antibiotic resistance, cell-membrane transporters, and/or environmental adaptation. The antibiotic and osmotic-change resistances were confirmed among viable bacteria isolates showing higher level of resistances in the aerosols collected at 500 m than those of 3 m. These findings suggest that elevated altitudes result in environmental filtering that allows bacterial taxa to survive long-term transport to distant locations during dust events and transfer antibiotic resistance.}, }
@article {pmid40609443, year = {2025}, author = {Lu, B and Wang, P and Hu, J and Qian, J and Liu, F and He, Y and Tang, S and Shen, J and Liu, Y}, title = {PFOS-induced alterations in phosphorus dynamics and soil microbial functions in wetlands.}, journal = {Journal of environmental management}, volume = {391}, number = {}, pages = {126445}, doi = {10.1016/j.jenvman.2025.126445}, pmid = {40609443}, issn = {1095-8630}, abstract = {Perfluorooctanesulfonate (PFOS), a widely persistent pollutant, poses significant ecological risks, yet its impact on critical nutrient cycles, such as phosphorus (P), in wetland ecosystems remains poorly understood. Phosphorus is essential for plant growth and microbial functions, and disruptions in its cycling can have profound effects on ecosystem stability. This study investigates the influence of PFOS on P dynamics and soil microbial functions in the rhizosphere of Phragmites communis. We examined how varying PFOS concentrations affect inorganic and organic P forms and microbial gene expression associated with P transformations. High PFOS concentrations significantly reduced shoot and root P content, corresponding to declines in labile phosphorus (NaHCO3-Pi). Additionally, shifts in microbial community diversity and composition were observed, particularly under high PFOS exposure, where key phosphorus-cycling genes, such as phoD in rhizosphere soils, showed significantly reduced transcriptional levels (as quantified by qRT-PCR), despite increased gene abundance as revealed by metagenomic sequencing. These findings offer new insights into how emerging contaminants like PFOS disrupt phosphorus cycling and microbial functions in wetland ecosystems, with broader implications for ecological risk assessments.}, }
@article {pmid40609272, year = {2025}, author = {Ji, B and Chen, Q and Song, Y and Dong, Z and Ding, J and Wang, G and Liu, G and Gao, P and Zhao, J}, title = {Distributions of pathogenic bacteria, antibiotic resistance genes, and virulence factors in pig farms in China.}, journal = {Ecotoxicology and environmental safety}, volume = {302}, number = {}, pages = {118607}, doi = {10.1016/j.ecoenv.2025.118607}, pmid = {40609272}, issn = {1090-2414}, abstract = {The abundance of antibiotic resistance genes (ARGs) in pig feces can lead to their dissemination in the pig farm environment, posing a serious risk to human health through potential exposure and transmission. However, the extent of microbial contamination in pig farms, including ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and human bacterial pathogens (HBPs), is still largely unknown. In this study, metagenomics was employed to identify the composition and characteristics of microorganism communities, ARGs, VFGs, MGEs and HBPs in pig farm environments from seven different regions of China. The results showed that there were significant differences in the composition of microorganisms and Firmicutes, Bacteroides, Proteobacteriahe Spirochaetes were the dominant phyla in the pig farm environment. The abundance and composition of ARGs, VFGs, MGEs and HBPs varied significantly in pig farm environments in different regions, with the abundance in Fujian being significantly higher than that in other regions. In total, 216 ARGs, 479 VFGs, 143 MGEs and 78 HBPs were identified across all pig feces, soil, and wastewater samples. The most prominent ARGs were those related to tetracycline, aminoglycoside, and MLS resistance. Escherichia coli, Arcobacter cryaerophilus, Corynebacterium xerosis, Aerococcus viridans, and Collinsella aerofaciens were the most commonly found HBPs in the pig farm environment. Procrustes analysis and Mantel test results showed a strong correlation between ARGs and HBPs, VFGs and HBPs, and ARGs and VFGs. ARGs were mainly harbored by E. coli, Klebsiella pneumoniae, and Enterococcus faecalis in the pig farm environments. The random forest model indicated that the presence of MGEs (intI1, IS91, and tnpA) was significantly correlated with the total abundance of resistance genes, which can be utilized as an important indicator for measuring resistance genes. The study establishes a foundational understanding of the prevalence and diversity of ARGs, VFGs, and HBPs in pig farm environments, aiding in the development of effective management strategies to mitigate ecological and public health risks.}, }
@article {pmid40609120, year = {2025}, author = {Jiang, M and Xie, Z and Fan, Q and Tang, G and Pan, N and Zeng, H and Xu, Y and Zhang, C and Luo, M and Li, F}, title = {Epidemiological characteristics of Circovirus Human infection in hospitalized patients in a representative infectious disease hospital in Guangzhou, China, from Feb 2023 to Dec 2024.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {3}, pages = {116962}, doi = {10.1016/j.diagmicrobio.2025.116962}, pmid = {40609120}, issn = {1879-0070}, abstract = {Circovirus Human reported in recent years have drawn attention as potential human pathogens in susceptible patients. However, its epidemiological characteristics are less investigated. We found 3 infected cases in 1330 hospitalized patients with suspected unidentified infections in a designated hospital for treating infectious diseases by retrospectively analyzing their metagenomic sequencing data. All three patients were HIV-positive and immunosuppressed. Liver function tests were normal at admission but showed transient acute injury during antimicrobial therapy, without hepatitis virus coinfection.}, }
@article {pmid40608709, year = {2025}, author = {Jiang, L and Zhou, L and Huang, S and Ao, Z and Han, X}, title = {Venovenous extracorporeal membrane oxygenation in severe community-acquired Acinetobacter baumannii pneumonia.}, journal = {Journal of infection in developing countries}, volume = {19}, number = {6}, pages = {971-976}, doi = {10.3855/jidc.19761}, pmid = {40608709}, issn = {1972-2680}, mesh = {Humans ; Male ; *Extracorporeal Membrane Oxygenation/methods ; Middle Aged ; *Acinetobacter baumannii/isolation &amp; purification ; *Community-Acquired Infections/therapy/microbiology/diagnosis ; *Acinetobacter Infections/therapy/diagnosis/microbiology ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia, Bacterial/therapy/diagnosis/microbiology ; Treatment Outcome ; Respiratory Distress Syndrome/therapy ; Meropenem/therapeutic use ; Tigecycline ; }, abstract = {INTRODUCTION: Globally, Acinetobacter baumannii (A. baumannii) is a significant nosocomial pathogen. Community-acquired pneumonia (CAP) caused by A. baumannii is rare, but often associated with severe outcomes.<br><br>CASE PRESENTATION: A 48-year-old man was admitted to a local hospital, presenting a 14-hour history of acute fever, cough, expectoration, chest pain, and dyspnea. Owing to the development of severe acute respiratory distress syndrome (ARDS) and septic shock, the patient was promptly transferred to our institution for veno-venous extracorporeal membrane oxygenation (VV-ECMO) following intubation and mechanical ventilation. Sputum culture, digital polymerase chain reaction (dPCR) assay of blood, and metagenomic next-generation sequencing (mNGS) assay of bronchoalveolar lavage fluid (BALF) all indicated A. baumannii. The patient responded favorably to treatment with meropenem and tigecycline. The amelioration of his respiratory function allowed for the cessation of ECMO after 7 days; and subsequently, the patient was successfully weaned from ventilatory support.<br><br>CONCLUSIONS: A. baumannii should be considered as a possible causative organism of CAP based on presentation in the tropical or subtropical wet season, a very aggressive clinical course, typical chest imaging features, and the presence of A. baumannii in sputum. ECMO represents an efficacious treatment alternative for severe ARDS and septic shock complications associated with A. baumannii when conventional mechanical ventilation proves inadequate, particularly when initiated early in the clinical course.}, }
@article {pmid40608623, year = {2025}, author = {Nascimento, GMD and Romano, CM and Rozanski, A and de Moura Coletti, T and Urbinatti, PR and Natal, D and Marrelli, MT and de Araújo, AB and Nardi, MS and da Costa, AC and Natal Fernandes, L}, title = {Detection of Furrundu phlebovirus in Aedes scapularis (Diptera: Culicidae) collected in urban parks, in a highly urbanized city.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {67}, number = {}, pages = {e38}, pmid = {40608623}, issn = {1678-9946}, mesh = {Animals ; *Aedes/virology ; Phylogeny ; Brazil ; *Phlebovirus/isolation &amp; purification/genetics/classification ; Female ; *Mosquito Vectors/virology ; Parks, Recreational ; High-Throughput Nucleotide Sequencing ; RNA, Viral/genetics ; }, abstract = {Mosquitoes (Diptera: Culicidae) are arthropods of medical importance because they can carry arboviruses. High-throughput sequencing (HTS) technology and metagenomic approaches conducted in mosquitoes have contributed to the discovery of many insect-specific viruses (ISVs), which have the potential to affect their vector competence. Mosquitoes were collected in urban parks in Sao Paulo city, Brazil and 20 pools with female mosquitoes were subjected to HTS by HiSeq 2500 sequencing system (Illumina). Long viral sequences (1,585-6,701 base pairs) were recovered from two pools of Aedes scapularis. BLASTx analyses revealed they had greater identity with segment L and S of Salarivirus and segment M of Furrundu phlebovirus, which encode, respectively, the RNA-dependent RNA polymerase (RdRd), the nucleocapsid protein, and a polyprotein. Phylogenetic tree of the segment L and S of the Phenuiviridae Family showed our sequences grouped with unverified sequences of Furrundu phlebovirus, an unclassified ISV that belongs to the Hareavirales Order and was first reported in mosquitoes in the Brazilian Pantanal, the largest natural tropical wetland worldwide. We report the second detection of Furrundu phlebovirus in mosquitoes collected in urban parks, showing it could be in mosquitoes from natural places and in green areas in urban cities. We conclude that Furrundu phlebovirus possibly occurs in Aedes scapularis in green areas, in Sao Paulo. Further studies should elucidate the role of this virus in the vector competence of Aedes scapularis and its interaction with different arboviruses.}, }
@article {pmid40608492, year = {2025}, author = {Ozuru, R and Yamagishi, J and Takeuchi, A and Date, Y and Fujii, T and Sugimoto, C and Nakajima, C and Suzuki, Y and Aoki, K and Fujii, J and Matsuba, T}, title = {Unification of Symbiotic Bacteria During Larva-to-Adult Transition in Culicoides circumscriptus (Diptera: Ceratopogonidae).}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf069}, pmid = {40608492}, issn = {1574-6968}, abstract = {Blood-sucking midges such as Leptoconops and Culicoides are of medical importance due to their role in causing skin irritation and potentially transmitting pathogens. Investigating their bacterial communities, including possible endosymbionts, may help clarify ecological adaptations and interactions with hosts. Leptoconops nipponensis Tokunaga (Lnt) and Culicoides circumscriptus (Cc), blood-sucking midges, cause severe itching and inflammation in humans. Cc was collected from a small sample of an outbreak swarm of Lnt in the peninsula area of Yonago City, Tottori Prefecture, Japan. This study compared the bacterial flora of Lnt and Cc, revealing distinct bacterial diversity shifts in these insect species between life stages. We analyzed the bacterial communities of adult and larval females of Cc and Lnt using MiSeq sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Notably, alpha diversity in Cc adults was significantly reduced to 1.5 (n = 43), indicating that Cc adults were dominated by a single bacterial genus, compared to 14.9 in Cc larvae (n = 19). BLAST analysis identified this dominant genus in adult Cc as Rickettsia (Candidatus Tisiphisa), which is known for transovarial transmission in arthropod vectors. In contrast, the bacterial diversity of Lnt showed no significant difference between adults (18.1, n = 32) and larvae (n = 15). These findings suggest that the dominance of Rickettsia in Cc (Candidatus Tisiphisa) adults is linked to their emergence, potentially reflecting differences in reproductive biology and ecological adaptations between these two insect species. Further research is needed to elucidate the functional role of Rickettsia in the life cycle and physiology of Cc.}, }
@article {pmid40607849, year = {2025}, author = {Zhang, H and Zhao, D and Wu, QL and Zeng, J}, title = {Environment selected microbial function rather than taxonomic species in a plateau saline-alkaline wetland.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0220624}, doi = {10.1128/aem.02206-24}, pmid = {40607849}, issn = {1098-5336}, abstract = {UNLABELLED: Comprehending the microbial community in plateau saline-alkaline wetlands, an understudied and vulnerable ecosystem, is vital for predicting ecosystem functions within the context of global climate change. Despite the rapid shrinkage and potential drying up of some of these wetlands, our knowledge of the microbial community in this ecosystem remains fragmented. Here, we utilized metagenomic sequencing to investigate the distribution of methane, nitrogen, and sulfur cycling genes/pathways and formation mechanism of microbial communities across sediment, surface rhizosphere soils (Rsurface), subsurface rhizosphere soils (Rsubsurface), surface bulk soils (Bsurface), and subsurface bulk soils (Bsubsurface) in Cuochuolong Wetland, a typical saline-alkaline wetland located in the Tibetan Plateau. The results showed that sediment exhibited relatively higher functional potentials for methanogenesis but lower potentials for methane oxidation. Denitrification and dissimilatory sulfate reduction potentials increased with decreasing salinity across the five habitats, following the trend: sediment <Rsurface < Rsubsurface <Bsurface < Bsubsurface. The taxonomic compositions of microbial communities varied more dramatically, yet functional genes distributed relatively evenly, indicating functional redundancy. Greater determinacy was observed in functional compositions, whereas taxonomic compositions exhibited more stochasticity. Similar patterns were observed within individual habitats, with the relative importance of deterministic processes increasing as salinity levels increased across the five habitats. Additionally, 188 non-redundant medium- and high-quality metagenome-assembled genomes (MAGs) were reconstructed, with 18 MAGs containing the nod gene, a marker gene of disproportionation of nitric oxide. This study provided a novel perspective on the formation mechanism of microbial community by emphasizing the deterministic selection of extreme environments on microbial function.<br><br>IMPORTANCE: Understanding the formation mechanism of microbial communities is a central goal in ecology. However, our understanding of microbial community remains fragmented in plateau saline-alkaline wetlands, despite their unique status as a vulnerable ecosystem characterized by high altitude, low disturbance, high salinity, sensitivity to global climate change, and localized shrinkage in some areas. Furthermore, previous studies on community formation mechanism have predominantly focused on microbial taxonomic structure, neglecting their functional compositions. Beyond providing a comprehensive understanding of the distribution patterns of methane, nitrogen, and sulfur cycling microbial communities within plateau saline-alkaline wetland, this study offers a novel perspective on formation mechanism of microbial community by emphasizing the deterministic selection of extreme environment on microbial function. This study also expands our comprehension of the diversity of microbes containing the nod gene, which may substantially contribute to global methane and nitrogen budgets.}, }
@article {pmid40607829, year = {2025}, author = {Williams, A and Ravel, J and Armstrong, E and Huibner, S and Rutt, L and Kaul, R and Holm, JB}, title = {Temporal dynamics of the vaginal microbiome and host immune markers before, during, and after metronidazole treatment for bacterial vaginosis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0038025}, doi = {10.1128/msystems.00380-25}, pmid = {40607829}, issn = {2379-5077}, abstract = {This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV-associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify the optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.IMPORTANCEBacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections, among others, is characterized by a dysbiotic vaginal microbiome associated with the predominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at the initiation of treatment, as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during, and after metronidazole treatment.}, }
@article {pmid40607500, year = {2025}, author = {Luo, Y and Cheng, W and Ma, L and Wang, T and Shi, W}, title = {Diagnostic value of nanopore-based metagenomic third-generation sequencing in the diagnosis of Pneumocystis jirovecii infection in patients with lung cancer.}, journal = {Journal of medical microbiology}, volume = {74}, number = {7}, pages = {}, pmid = {40607500}, issn = {1473-5644}, mesh = {Humans ; *Lung Neoplasms/complications/microbiology ; *Pneumonia, Pneumocystis/diagnosis/microbiology/complications ; *Pneumocystis carinii/genetics/isolation &amp; purification ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Prospective Studies ; Sensitivity and Specificity ; Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; *Nanopore Sequencing/methods ; Adult ; Aged, 80 and over ; China ; }, abstract = {Introduction. Pneumocystis jirovecii pneumonia (PJP, formerly known as Pneumocystis carinii pneumonia), an opportunistic fungal infection caused by the fungus P. jirovecii, is a severe pulmonary infection that primarily affects immunocompromised patients, including those with lung cancer. Traditional diagnostic methods for PJP, such as Grocott-Gomori's methenamine silver staining and real-time PCR, have limitations, including low positivity and high missed diagnosis rates.Gap Statement. Despite the critical need for accurate and sensitive diagnostic tools for PJP, especially in immunocompromised populations, existing methods fall short in providing the necessary reliability and efficiency.Aim. This study aims to evaluate the efficacy of nanopore-based metagenomic third-generation sequencing in diagnosing P. jirovecii infection in lung cancer patients, hypothesizing that this approach may offer superior sensitivity and specificity.Methodology. A prospective observational study was conducted on 118 lung cancer patients with suspected pulmonary P. jirovecii infection at the Sixth Hospital of Nantong City, China, from January 2021 to December 2023. The identification of pathogens in bronchoalveolar lavage fluid samples was performed using both metagenomics and traditional tests.Results. Metagenomics showed a significantly higher detection rate of P. jirovecii (33.0%) compared to methenamine silver staining (4.2%) and real-time PCR (30.5%). The sensitivity, specificity and accuracy of metagenomics detection were all 100%, which is markedly superior to traditional methods. Furthermore, metagenomics also identified mixed infections with other pathogens, such as Cytomegalovirus and Epstein-Barr virus.Conclusion. Metagenomics technology demonstrates high sensitivity and specificity in diagnosing P. jirovecii infection, including mixed infections with other pathogens, in lung cancer patients. It provides a clear direction for clinical treatment and is a powerful tool for diagnosing PJP, contributing to improved diagnostic efficiency and accuracy, reducing misdiagnosis and missed diagnosis rates and improving clinical outcomes in these patients.}, }
@article {pmid40607081, year = {2025}, author = {Zhang, Q and Teng, Z and Gong, P}, title = {A case of acute renal dysfunction and multiorgan dysfunction caused by Rickettsia japonica infection.}, journal = {IDCases}, volume = {41}, number = {}, pages = {e02283}, pmid = {40607081}, issn = {2214-2509}, abstract = {This article reports a case of acute renal dysfunction and multi-organ dysfunction syndrome caused by Rickettsia japonica infection. The patient, a 79-year-old male, presented with unexplained fever, fatigue, anorexia, vomiting, and chest tightness, followed by oliguria and a decline in mental status. Laboratory tests revealed significant abnormalities, including elevated white blood cells, thrombocytopenia, hepatic and renal dysfunction, and coagulopathy. Imaging studies showed pulmonary infection and bilateral pleural effusion. Based on the history of tick bite, clinical manifestations, and metagenomic next-generation sequencing (mNGS) results, which detected R. japonica, the patient was diagnosed with Japanese spotted fever (JSF). He received multidisciplinary comprehensive treatment, including mechanical ventilation, continuous renal replacement therapy (CRRT), antimicrobial therapy, blood transfusions, and supportive care. After 15 days of treatment, the patient's fever resolved, inflammatory markers decreased significantly, and organ functions improved gradually, leading to eventual recovery and discharge. This case highlights the importance of early recognition and treatment of R. japonica infection, especially in endemic areas, to prevent rapid deterioration and multi-organ failure.}, }
@article {pmid40606566, year = {2025}, author = {Wang, L and Wang, L and Chen, L}, title = {NetNiche: Microbe-Metabolite Network Reconstruction and Microbial Niche Analysis.}, journal = {Phenomics (Cham, Switzerland)}, volume = {5}, number = {2}, pages = {208-211}, pmid = {40606566}, issn = {2730-5848}, abstract = {UNLABELLED: Metagenomics and metabolomics technologies have been widely used to investigate the microbe-metabolite interactions in vivo. However, the computational methods that accurately infer the microbe-metabolite interactions are lacking. We present a context-aware framework for graph representation learning, NetNiche, which predicts microbe-metabolite and microbe-microbe interactions in an accurate manner, by integrating their abundance data with prior knowledge. We applied NetNiche to datasets on gut and soil microbiome, and demonstrated that NetNiche can outperform the state-of-the-art methods, such as SParse InversE Covariance Estimation for Ecological Association Inference (SPIEC-EASI), Sparse Correlations for Compositional data (SparCC) and microbe-metabolite vectors (mmvec). NetNiche is an effective tool with wide applicability for the multi-omics study of human microbiome.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00168-8.}, }
@article {pmid40606560, year = {2025}, author = {Wang, H and Zhuang, Y and Hua, R and Yao, T and Lin, K and Zhang, Y and Huang, R and Wang, R and Guo, S and Shen, Q and Shao, Y and Wu, W and Fan, L and Feng, Y and Yao, Q and Ye, H and Kong, X and Zhang, Q and Wang, R and Liu, T}, title = {Multi-Omics Exploration of Obesity Biomarkers in Sedentary and Weight Loss Cohorts.}, journal = {Phenomics (Cham, Switzerland)}, volume = {5}, number = {2}, pages = {137-153}, pmid = {40606560}, issn = {2730-5848}, abstract = {UNLABELLED: Sedentary behavior for two years during the coronavirus disease 2019 (COVID-19) pandemic contributes to weight gain. Gut microbiota and blood metabolome are related to body mass index (BMI) and indicate individual metabolic changes. Surgery and exercise are effective weight-loss methods. The precise plasma metabolites and gut microbiota biomarkers involved and the underlying mechanisms are still largely unclear. To address this issue, we analyzed weight gain and weight loss cohorts to identify biomarkers associated with obesity. In the sedentary cohort, 49 subjects were recruited in year 2019. After two years of sedentary behavior during the COVID-19 pandemic, the BMI of 24 subjects significantly increased (Weight gain group), while that of the remnant 25 subjects remained constant (Maintaining weight group). At baseline and two years post baseline, the gut microbiota and blood metabolome, as well as body composition and clinical indicators, were all collected. In weight loss studies, we analyze the plasma metabolome of the two cohorts, including individuals who underwent laparoscopic sleeve gastrectomy (LSG) surgery and exercise intervention. Weight gain through sedentary behavior contributed to the variation of the gut microbiota and plasma metabolites composition. Creatine, phenylalanine and tyrosine exhibited significant positive associations with BMI and fat mass. We further confirmed the association between BMI and plasma metabolites in two weight loss cohorts. By utilizing a linear regression model, we found that 10 metabolites including creatine were correlated with BMI in weight loss individuals. Based on receiver operating characteristic (ROC) curves, creatine exhibited a satisfactory classification performance in regard to predicting weight reduction (AUCLSG = 0.890, AUCS ports = 0.840). Moreover, some gut microbiota, including Bifidobacterium angulatum DSM 20098 = JCM 7096 and Rothia dentocariosa M567I could affect BMI through the mediating factor of creatine.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00165-x.}, }
@article {pmid40606175, year = {2025}, author = {Wang, J and Zhu, Y and Li, D and Zheng, X and Chai, C and Zhang, J and Wu, J and Hu, Q and Zhao, S}, title = {The diversity of viral community in Sogatella furcifera revealed by meta-transcriptomics.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1617239}, pmid = {40606175}, issn = {1664-302X}, abstract = {INTRODUCTION: Metagenomic analyses has significantly advanced our understanding of viral evolution and their functions within organismal biology. In particular, exploring the virome of agricultural pests like the white-backed planthopper (WBPH) is essential for understanding their role as potential virus vectors and developing effective pest management strategies.<br><br>METHODS: To explore viral diversity, we collected white-backed planthoppers (WBPHs) from nine sites spanning four Chinese provinces (Liaoning, Fujian, Guangxi, and Yunnan) and performed metagenomic sequencing.<br><br>RESULTS: Our analysis identified 11 novel viruses belonging to 7 viral families, encompassing positive-sense single-stranded RNA (+ssRNA), negative-sense single-stranded RNA (-ssRNA), and double-stranded RNA (dsRNA) viruses. Remarkably, eight of the southern Chinese sites, excluding one in Liaoning province, contained a previously undiscovered Sobelivirales virus. Using rapid-amplification of cDNA ends (RACE), we determined the complete genome sequence of this novel Sobelivirales virus. Subsequent analyses of its encoded proteins, potential structural domains, and phylogenetic relationships suggested that it may belong to a new genus within the Sobelivirales. Small RNA sequencing confirmed viral replication in WBPH by revealing that virus-derived small interfering RNAs (vsiRNAs) were primarily 21 and 22 nucleotides long.<br><br>DISCUSSION: Our results have important implications for understanding virus carriage in WBPHs, evaluating their role as virus vectors, and informing the development of improved pest management strategies. Furthermore, this study highlights the power of metagenomics in uncovering novel viruses and expanding our knowledge of viral diversity.}, }
@article {pmid40606163, year = {2025}, author = {Komori, E and Kato-Kogoe, N and Imai, Y and Sakaguchi, S and Taniguchi, K and Omori, M and Ohmichi, M and Hamada, W and Nakamura, S and Nakano, T and Lee, SW and Ueno, T}, title = {Gastrectomy-induced alterations in gut microbiota linked to changes in oral and gastric microbiota.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1599503}, pmid = {40606163}, issn = {1664-302X}, abstract = {INTRODUCTION: Gastrectomy serves as a primary treatment for gastric cancer, a leading global malignancy, and affects significant physiological and anatomical changes in the digestive tract. Recent studies highlight the critical role of gastrointestinal microbiota in postoperative health following digestive tract surgeries, including gastrectomy. These alterations possibly impact the gut microbiota and affect patient health by influencing the bacterial environment in the gastrointestinal tract. However, the relationships between the gastrointestinal tract and the oral, gastric, and gut microbiota after gastrectomy are not clear. In this study, we aimed to characterize alterations in the gut microbiota due to gastrectomy and evaluate whether these alterations are associated with the oral and gastric microbiota.<br><br>METHODS: Saliva, gastric fluid, and stool samples were collected from patients diagnosed with primary gastric cancer who underwent gastrectomy at two time points, before and 6 months after gastrectomy. Next, 16S rRNA metagenomic analysis was performed. Diversity and linear discriminant analysis effect size (LEfSe) analyses of each microbiota were conducted before and after gastrectomy to compare alterations in the gut, oral, and gastric microbiota.<br><br>RESULTS: The diversity of gut microbiota increased after gastrectomy compared to that before gastrectomy (Shannon index, p = 0.044), with LEfSe analysis showing increased abundance of Rothia and Lactobacillus in the gut microbiota. Additionally, the proportion of participants with Rothia in their gut microbiota increased, and this genus was present in the oral and gastric microbiota of almost all participants. Furthermore, a significant rise in Lactobacillus was observed in the gut, oral, and gastric microbiota of paired participants.<br><br>DISCUSSION: We characterized gut microbiota alterations caused by gastrectomy and demonstrated their relationship with changes in oral and gastric microbiota, thereby elucidating interactions between the gastrointestinal tract microbiota in response to changes in the gastric environment.}, }
@article {pmid40606158, year = {2025}, author = {Tang, MLY and Lau, SCK}, title = {Varying effects of chlorination on microbial functional repertoire and gene expression in contrasting effluents.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1593147}, pmid = {40606158}, issn = {1664-302X}, abstract = {Effluents produced from different influent sources and sewage treatment processes carry distinct microbial community compositions. These microbiomes exhibit varying degrees of resistance and resilience under chlorination; however, their survival strategies and potential risks to the public health and ecosystem have yet to be fully characterized. In view of this, we subjected microbiomes from two contrasting types of effluents with distinct influent properties (seawater/freshwater-based) and prior treatment processes (primary/secondary) to metagenomics and metatranscriptomics analyses for comparing the alterations in their functional genes and activities under chlorination. The effluents presented highly dissimilar genomic and transcriptomic profiles. The variations in these profiles were significantly correlated to physicochemical factors including salinity, DO, BOD5, TSS, and TN. We recovered novel metagenome-assembled genomes (MAGs) from each type of effluent, revealing that those recovered from the same effluent tended to share similar functional properties which aligned with the physicochemical parameters of the effluent. Notably, the type and extent of alterations in genomic and transcriptomic profiles under chlorination varied greatly between effluents. Most of the genes and transcripts with significant changes in relative abundances were exclusive to their respective effluents. Also, the number of genes and transcripts with significant increase in relative abundances after chlorination were much higher than those with reduction. These enriched genes and transcripts were responsible for a wide range of functions, including energy generation, repair of damaged components and stress responses. Furthermore, the remanent microbiomes in chlorinated effluents still harbored numerous genes related to waterborne diseases and antimicrobial resistance, suggesting the potential risks of discharging these effluents into the environment. This study revealed the diverse effects of chlorination on different types of effluent microbiomes. It suggested that the remanent microbiomes in chlorinated effluents would have great variance in genetic potential and activities, providing insights into the evaluation and regulation of chlorine disinfection in sewage treatment.}, }
@article {pmid40605980, year = {2025}, author = {Xu, Z and Zhang, Y and Wang, D and Xuan, C and Li, Z and Xu, H}, title = {Impact of cytomegalovirus DNAemia detected by next-generation sequencing on short-term prognosis after lung transplantation.}, journal = {Infectious medicine}, volume = {4}, number = {2}, pages = {100185}, pmid = {40605980}, issn = {2772-431X}, abstract = {BACKGROUND: Cytomegalovirus (CMV) is a common opportunistic pathogen following lung transplantation, associated with post-transplant complications and adverse outcomes. This study aims to evaluate the incidence of CMV DNAemia identified through metagenomic next-generation sequencing (mNGS) during the early postoperative phase of lung transplantation and assess its effects on the short-term outcomes for recipients.<br><br>METHODS: We conducted a retrospective analysis of clinical data from 115 patients who received lung transplants at the Affiliated Wuxi People's Hospital of Nanjing Medical University between May 2020 and November 2023. Based on mNGS-detected CMV DNAemia status, patients were stratified into DNAemia group and normal group. Nonparametric tests (Mann-Whitney U/Wilcoxon signed-rank) and mixed-effects models for intergroup comparisons. Kaplan-Meier survival analysis with log-rank testing for overall survival differences. Univariate logistic regression to identify risk factors for ICU mortality and 90-day mortality. Multivariate logistic regression adjusting for confounders. Propensity score matching (1&#x2236;1 optimal nearest neighbor, caliper = 0.25) was implemented to address covariate imbalance, followed by univariate logistic regression analyses in the matched cohort.<br><br>RESULTS: In the early postoperative period following lung transplantation, CMV DNAemia was detected via mNGS with an incidence rate of 15.7%. The CMV DNAemia group demonstrated a significantly lower 90-day overall survival rate compared to the normal group, with the Log-rank test revealing statistically significant survival differences between groups (p < 0.001). Univariate and multivariate logistic regression analyses identified CMV DNAemia as an independent risk factor for ICU all-cause mortality (OR = 5.00, 95% CI: 1.37-18.27, p = 0.015), while with other pathogens infections independently predicted 90-day all-cause mortality (OR = 3.40, 95% CI: 1.10-10.44, p = 0.033). After propensity score matching, baseline characteristics were well-balanced between the CMV DNAemia and normal groups. In the matched cohort, univariate logistic regression further confirmed CMV DNAemia as an independent risk factor for ICU mortality (OR = 7.43, 95% CI: 1.23-45.00, p = 0.029). Mediation analysis demonstrated that co-pathogen infections mediated the relationship between CMV DNAemia and 90-day all-cause mortality, with a proportion mediated of 20.6% (95% CI: 1.7%-138.5%, p < 0.001).<br><br>CONCLUSIONS: mNGS revealed a higher incidence of early CMV DNAemia post-lung transplantation than previously reported. CMV DNAemia significantly correlates with poor prognosis. Despite limitations in sample size and retrospective design, this study provides novel insights into CMV monitoring and management post-transplantation. Future research should determine optimal timing for preemptive antiviral strategies guided by mNGS.}, }
@article {pmid40605848, year = {2025}, author = {Grevskott, DH and Victor, MP and Lima, TE and Radisic, V and Nimje, PS and Marathe, NP}, title = {High-throughput sequencing data of the microbiota and antibiotic resistance genes from biofilms on polystyrene and nylon rope incubated in Bergen harbor.}, journal = {Data in brief}, volume = {61}, number = {}, pages = {111718}, pmid = {40605848}, issn = {2352-3409}, abstract = {Plastics can provide a hydrophobic surface for microorganisms to attach, colonize and form microbial biofilms, referred to as 'plastisphere.' The aim of this study was to determine the microbiota of biofilms on plastic, using field trials in Bergen harbour, Norway using metagenomics. Polystyrene (PS) and nylon ropes (PA) were submerged in sea for four weeks, biofilm communities were collected, and the extracted DNA was subjected to metagenomic sequencing (n=12). The average salinity and temperature during the experiment were 9.02 °C (8.2-10.7) and 28.85 ‰ (26.1 ‰ - 33.1 ‰). We obtained a total of ∼460 Gigabases of sequence data from our samples. Gammaproteobacteria and Alpha proteobacteria were the most prominent on these polymers with β-lactamases as the most abundant resistance gene class. The datasets will be useful for the scientific community working on plastic-associated biofilms.}, }
@article {pmid40605035, year = {2025}, author = {Liu, J and Zhang, Y and Xu, L and Gu, G and Dong, Z}, title = {Parabacteroides johnsonii inhibits the onset and progression of colorectal cancer by modulating the gut microbiota.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {734}, pmid = {40605035}, issn = {1479-5876}, support = {School Science [2022] No.7//Clinical Program of Air Force Medical University/ ; 22BJQN004//Fourth Military Medical University/ ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is the third most prevalent malignant tumor and the second leading cause of cancer-related deaths globally. The genus Parabacteroides is an important component of the gut microbiota. P. distasonis and P. goldsteinii are reported probiotics, and their roles in CRC have been investigated in related studies. However, the association between P. johnsonii and CRC remains unknown.<br><br>METHODS: P. johnsonii (10&#x2013;42) and Lactococcus formosensis (22&#x2013;2) were isolated from healthy human feces. 29 mice that demonstrated normal feeding and activity were randomly assigned to four groups: normal control (NC group), CRC model (IC group), P. johnsonii (PJ group), and L. formosensis (LO group). Colonic tumor tissues from the IC, PJ, and LO groups and normal colon tissues from the NC group were then collected for HE staining and immunohistochemical staining. Fecal samples from mice during the hyperproliferative and adenoma phases were collected for Metagenomic sequencing and metabolite analysis.<br><br>RESULTS: P. johnsonii intervention reduced the number and slowed the growth of colonic tumors, improved tumor histological scores, and decreased microenvironmental inflammation levels. P. johnsonii improved the composition of intestinal flora in mice with colon cancer, increased gut microbial species diversity, and maintained gut microbiota stability. Furthermore, P. johnsonii intervention increased the abundance of Bifidobacterium pseudolongum and Lactobacillus, which play a role in ameliorating AOM/DSS-induced gut microbiota dysbiosis. P. johnsonii intervention affected the metabolic pathways, including amino sugar degradation and galactose metabolism, sphingolipid synthesis, amino acid synthesis, and polyphenol synthesis pathways, with the tryptophan metabolism pathway as the primary pathway being affected.<br><br>CONCLUSION: Our study profiled the P. johnsonii administration reduces the number of tumors and lower tumor staging in AOM/DSS-induced colon cancer mice by modulating gut microbiota and its metabolites at early stages.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-06675-0.}, }
@article {pmid40585104, year = {2025}, author = {Madi, N and Sayeed, MA and Cato, ET and Creasy-Marrazzo, A and Islam, K and Khabir, MIU and Bhuiyan, MTR and Begum, Y and Freeman, E and Vustepalli, A and Brinkley, L and Kamat, M and Bailey, LS and Basso, KB and Qadri, F and Khan, AI and Shapiro, BJ and Nelson, EJ}, title = {Ranked placement of phage predation as a determinant of dehydration severity among cholera patients in Bangladesh.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {40585104}, abstract = {Phage predation is inversely associated with severe cholera yet its importance as a determinant of dehydration severity is unknown relative to other factors. Here we used machine learning to assess and rank potential host, microbial, and environmental factors as determinants of severe dehydration among a cohort of cholera patients enrolled at hospital admission across Bangladesh. We found the phage to pathogen ratio ranked among the top classifying features, placing just behind patient age and admission location. We advocate that phage predation is a key factor to include in the characterization of cholera for scientific, clinical and epidemiological applications.}, }
@article {pmid40605092, year = {2025}, author = {Han, Y and Deng, Z and Peng, Y and Peng, J and Cao, L and Xu, Y and Yang, Y and Zhou, H and Zhang, C and Zhang, D and Wang, M and Zhang, C and Greening, C and Dong, X}, title = {Evidence of microbial reductive dehalogenation in deep-sea cold seeps and its implications for biogeochemical cycles.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {156}, pmid = {40605092}, issn = {2049-2618}, support = {42406109//National Natural Science Foundation of China/ ; 42406131//National Natural Science Foundation of China/ ; 42376084//National Natural Science Foundation of China/ ; 42276150//National Natural Science Foundation of China/ ; 92351304//National Natural Science Foundation of China/ ; 20250131//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; 2022025//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; 2023M734096//China Postdoctoral Science Foundation/ ; 2024M762799//China Postdoctoral Science Foundation/ ; GZC20241467//Postdoctoral Fellowship Program of CPSF/ ; 2023B0303000015//Guangdong Major Project of Basic and Applied Basic Research/ ; 2023J06042//Natural Science Foundation of Fujian Province/ ; }, mesh = {*Geologic Sediments/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification/enzymology ; Phylogeny ; *Halogenation ; *Archaea/genetics/classification/metabolism/isolation &amp; purification/enzymology ; *Seawater/microbiology ; Metagenomics/methods ; Bacterial Proteins/genetics/metabolism ; Metagenome ; Oxidation-Reduction ; }, abstract = {BACKGROUND: Reductive dehalogenation is crucial for halogen cycling and environmental remediation, yet its ecological role is not completely understood, especially in deep-sea environments. To address this gap, we investigated the diversity and expression of genes encoding reductive dehalogenase catalytic subunits (RdhAs), and ecophysiology of potential organohalide reducers in deep-sea cold seeps, which are environments rich in halogenated compounds.<br><br>RESULTS: Through genome-resolved metagenomic analysis of 165 global cold seep sediment samples, 4 types of RdhA-like sequences were identified based on their features and phylogenetic relationships: prototypical respiratory, transmembrane respiratory, cytosolic, and a novel clade. Cold seeps were found to harbor a higher abundance of these rdhA-like genes compared to other marine sediments, highlighting their potential as microbial reductive dehalogenation hotspots. These rdhA-like genes are encoded by a wide range of microorganisms across 4 archaeal and 36 bacterial phyla, significantly expanding the known diversity of organohalide reducers. Halogen geochemistry, laboratory incubations, metatranscriptomic data, and metabolomic profiling confirmed the presence of organohalides at concentrations of up to 18&#xa0;mg/g in these sediments and suggested the potential for microbial reductive dehalogenation. Our findings suggest that organohalide reducers in cold seep sediments may participate in diverse biogeochemical processes, as inferred from the presence of genes related to carbon, hydrogen, nitrogen, sulfur, and trace element cycling. Additionally, RdhA-like proteins from cold seeps have diverse N-terminal structures across different gene groups.<br><br>CONCLUSIONS: These findings collectively suggest that reductive dehalogenation is an important process in deep-sea environments, mediated by a diverse array of microbes and novel enzymes. The discovery of diverse and abundant rdhA-like genes, along with their genomic context and potential metabolic linkages, highlights the role of cold seeps as reservoirs of microbial diversity with possible implications for environmental remediation. Video Abstract.}, }
@article {pmid40605027, year = {2025}, author = {Yun, CS and Kim, JK and Kwon, H and Kim, Y and Her, M and Moon, JS}, title = {Conventional diagnosis and metagenomic analysis of a novel co-infection case involving Escherichia coli and immunosuppressive conditions with petechial hepatitis of broilers in South Korea: a case report.}, journal = {BMC veterinary research}, volume = {21}, number = {1}, pages = {432}, pmid = {40605027}, issn = {1746-6148}, support = {N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; N-1543084-2025-29-01//Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs of the Republic of Korea/ ; }, mesh = {Animals ; *Chickens ; *Poultry Diseases/diagnosis/microbiology/virology ; *Escherichia coli Infections/veterinary/diagnosis/microbiology/complications ; *Coinfection/veterinary/diagnosis/microbiology ; Metagenomics ; Escherichia coli/isolation &amp; purification/genetics ; Republic of Korea ; *Hepatitis, Animal/diagnosis/microbiology/virology ; *Purpura/veterinary/diagnosis/microbiology ; Liver/pathology/microbiology ; }, abstract = {BACKGROUND: The conventional diagnosis in poultry disease enhances accuracy by combining clinical and necropsy observation with various molecular biological analysis. However, if the causative agents of a disease are not isolated and detected, accurate diagnosis and future disease management become challenging. The purpose of the present study aimed to diagnose and identify the causes of disease in broilers with novel petechial hepatitis by applying metagenomic analysis.<br><br>CASE PRESENTATION: Through the necropsy, tracheal and pericardial congestion, and severe petechia and perihepatitis in the livers were observed. Histopathological examination revealed infiltration of lymphocytes and bacterial colonies in various organs, as well as severe sinusoidal congestion, hemorrhages and hepatocyte necrosis in the livers. E. coli was isolated and identified in the liver samples. Although FAdV, CkChpV, CAstV, IBV and IBDV were detected, no viral agents were detected in the livers. Metagenomic analysis of the livers showed a predominance of bacterial composition, followed by fungal and viral agents, with E. coli being the most abundant. Analysis of virulence factors in E. coli revealed the presence of those associated with APEC, as well as other IPEC and ExPEC pathotypes.<br><br>CONCLUSION: The present study identified a novel petechial hepatitis in broilers, associated with co-infections of antigenic variant IBDV, multiple pathotypes of E. coli, and possibly various causative. The application of metagenomic analysis proved valuable in identifying diverse potential pathogens when conventional methods were limited. These findings highlight the utility of metagenomic approaches as a complementary diagnostic tool and support their continued use in advancing poultry disease management.}, }
@article {pmid40604425, year = {2025}, author = {Wang, C and Song, W and Li, C and Cao, Y and Li, X and Zhao, J and Yang, F and Yu, H and Liang, Q and Yang, KQ and Liu, JN and Fang, H}, title = {Metagenomic analysis reveals Bacillus cereus OTU8977 as a potential probiotic in promoting walnut growth.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {839}, pmid = {40604425}, issn = {1471-2229}, support = {2024LZGC025//Improved Variety Program of Shandong Province of China/ ; }, mesh = {*Bacillus cereus/genetics/physiology ; *Juglans/growth &amp; development/microbiology ; Rhizosphere ; Metagenomics ; Soil Microbiology ; *Probiotics ; Plant Roots/microbiology/growth &amp; development ; }, abstract = {BACKGROUND: Rhizosphere microorganisms can improve soil quality, promote plant growth, and enhance plant health. Despite the isolation of numerous plant growth-promoting rhizobacteria (PGPR) strains, research on how PGPR enhances walnut growth remains limited.<br><br>RESULTS: In this study, the metagenomic sequencing of the rhizosphere soil in 8 major walnut-producing areas in China was conducted to identify 150 shared core amplicon sequence variants. Then, we isolated a strain of Bacillus cereus OTU8977 from the walnut rhizosphere soil and evaluated its potential plant growth-promoting functions. B. cereus OTU8977 can optimize the walnut rhizosphere microecology and promote its growth through its considerable potential in nitrogen fixation, phosphorus solubilization, and potassium dissolution. Transcriptomic analysis of walnut roots revealed that B. cereus OTU8977 promotes the growth of walnuts by enhancing phenylpropanoid biosynthesis and carbohydrate metabolic processes.<br><br>CONCLUSIONS: This study identified a strain of Bacillus cereus with multiple plant growth-promoting functions, which significantly enhanced walnut growth. Moreover, the study further elucidated the mechanisms underlying its growth-promoting effects, providing a theoretical foundation for the development of walnut-specific microbial fertilizers.}, }
@article {pmid40604389, year = {2025}, author = {Yang, J and Wang, L and Liang, Q and Wang, Y and Yang, X and Wu, X and Pei, X}, title = {Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {406}, pmid = {40604389}, issn = {1471-2180}, support = {TB2024045//Special Funding for Postdoctoral Research Projects in Sichuan Province/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; }, }
@article {pmid40604345, year = {2025}, author = {Kang, JW and Khatib, LA and Heston, MB and Dilmore, AH and Labus, JS and Deming, Y and Schimmel, L and Blach, C and McDonald, D and Gonzalez, A and Bryant, M and Ulland, TK and Johnson, SC and Asthana, S and Carlsson, CM and Chin, NA and Blennow, K and Zetterberg, H and Rey, FE and ,  and Kaddurah-Daouk, R and Knight, R and Bendlin, BB}, title = {Gut microbiome compositional and functional features associate with Alzheimer's disease pathology.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {21}, number = {7}, pages = {e70417}, doi = {10.1002/alz.70417}, pmid = {40604345}, issn = {1552-5279}, support = {U01AG061359/AG/NIA NIH HHS/United States ; U19AG063744/AG/NIA NIH HHS/United States ; R01AG070973/AG/NIA NIH HHS/United States ; R01AG083883/AG/NIA NIH HHS/United States ; #S10 OD026929/GF/NIH HHS/United States ; //Vilas Early-Career Investigator Award/ ; #2023-00356//Swedish Research Council/ ; #2022-01018//Swedish Research Council/ ; #2019-02397//Swedish Research Council/ ; #101053962//European Union's Horizon Europe research and innovation programme/ ; #ALFGBG-71320//Swedish State Support for Clinical Research/ ; #201809-2016862//Alzheimer Drug Discovery Foundation (ADDF)/ ; #ADSF-21-831376-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-21-831381-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-21-831377-C//AD Strategic Fund and the Alzheimer's Association/ ; #ADSF-24-1284328-C//AD Strategic Fund and the Alzheimer's Association/ ; #22HLT07//European Partnership on Metrology co-financed from the European Union's Horizon Europe Research and Innovation Programme and by the Participating States/ ; //Bluefield Project/ ; //Cure Alzheimer's Fund/ ; //Olav Thon Foundation/ ; //Erling-Persson Family Foundation/ ; #FO2022-0270//Familjen R&#xf6;nstr&#xf6;ms Stiftelse, Stiftelsen f&#xf6;r Gamla Tj&#xe4;narinnor, Hj&#xe4;rnfonden, Sweden/ ; #860197//European Union's Horizon 2020 research and innovation programme under the Marie Sk&#x142;odowska-Curie/ ; JPND2021-00694//European Union Joint Programme-Neurodegenerative Disease Research/ ; UKDRI-1003//NIH and Care Research University College London Hospitals Biomedical Research Centre and the UK Dementia Research Institute at UCL/ ; }, mesh = {Humans ; *Alzheimer Disease/microbiology/pathology/cerebrospinal fluid ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Aged ; Biomarkers/cerebrospinal fluid ; Feces/microbiology ; Metagenomics ; Amyloid beta-Peptides/cerebrospinal fluid ; Aged, 80 and over ; }, abstract = {BACKGROUND: The gut microbiome is a potentially modifiable risk factor for Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited.<br><br>METHODS: Shallow-shotgun metagenomics was used to analyze the fecal microbiome of participants in the Wisconsin Microbiome in Alzheimer's Risk Study, leveraging clinical data and cerebrospinal fluid (CSF) biomarkers. Differential abundance and ordinary least squares regression analyses were performed to find differentially abundant gut microbiome features and their associations with CSF biomarkers of AD and related pathologies.<br><br>RESULTS: Gut microbiome composition and function differed between individuals with and without AD dementia. The compositional difference was replicated in an independent cohort. Differentially abundant gut microbiome features were associated with CSF biomarkers of AD and related pathologies.<br><br>DISCUSSION: These findings enhance our understanding of alterations in gut microbial composition and function in AD, and suggest that gut microbes and their pathways are linked to AD pathology.<br><br>HIGHLIGHTS: Gut microbiome composition and function differ between people with Alzheimer's disease (AD) dementia and cognitively unimpaired (CU) individuals. Co-occurring gut microbes show differential abundance across AD-related groups (AD vs CU, amyloid status+ vs amyloid status-, and apolipoprotein E (APOE) &#x3b5;4 status+ vs APOE &#x3b5;4 status-). Gut microbiome composition also differs between people with AD dementia and CU individuals in a larger validation cohort. Differentially abundant gut microbiome composition and function between AD and CU groups are correlated with cerebrospinal fluid biomarkers for AD and related pathologies.}, }
@article {pmid40604305, year = {2025}, author = {Li, Y and Shi, Z and Zhang, X and Ren, H and Ji, H and Yang, F and Fu, Z and Kong, X and Cheng, X and Li, J and Wu, K and Zhong, Y and Zhong, H and Ji, L}, title = {Metagenomic analysis revealing links between age, gut microbiota and bone loss in Chinese adults.}, journal = {npj metabolic health and disease..}, volume = {3}, number = {1}, pages = {18}, pmid = {40604305}, issn = {2948-2828}, support = {7222238//Beijing Natural Science Founding/ ; }, abstract = {Accumulating evidence has linked gut microbiota to bone health. However, investigations into the impacts of aging, gut microbiota, and their interactions in the development of osteoporosis remain inconclusive. We employed quantitative computed tomography to measure lumbar bone mass density (BMD) and analyzed shotgun metagenomic data in 684 Chinese adults. Our analyses revealed significant positive associations between BMD and abundances of multiple Lachnospiraceae species, including Lachnospira eligens, Blautia wexlerae, and Roseburia hominis, as well as pathways involved in L-arginine biosynthesis and butyrate production-independent of age, diet habits, and lifestyles. Moreover, we demonstrated that individuals with enterotype Bacteroides exhibited a more pronounced age-related decline in BMD compared to those with enterotype Prevotella, a pattern we validated in an independent cohort. Our findings offer valuable insights into BMD-related gut microbial features and interactions between aging, gut microbiota, and bone loss, opening potential avenues for microbiota-based prevention and treatment strategies for osteoporosis.}, }
@article {pmid40604156, year = {2025}, author = {Kim, H and Nelson, P and Nzabarushimana, E and Shen, J and Jensen, J and Bhosle, A and Li, C and Lee, N and Everett, C and Berdy, B and Frongillo, G and Livny, J and Hu, FB and Simon, TG and McIver, L and Franzosa, EA and Chan, AT and Hayete, B and Thompson, KN and Huttenhower, C and Nguyen, LH}, title = {Multi-omic analysis reveals transkingdom gut dysbiosis in metabolic dysfunction-associated steatotic liver disease.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, pmid = {40604156}, issn = {2522-5812}, support = {K23DK125838//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; T32CA009001//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R35CA253185//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R24DK110499//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's &amp; Colitis Foundation)/ ; Research Professorship//American Cancer Society (American Cancer Society, Inc.)/ ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common condition linked to obesity and the metabolic syndrome, yet its transkingdom connections have been under-investigated. We performed high-resolution multi-omic profiling-including stool metagenomes, metatranscriptomes and metabolomes-in 211 MASLD cases and 502 controls from a cohort of female nurses. Here we show that MASLD is associated with shifts in 66 gut bacterial species, including widespread enrichment of oral-typical microbes, and transkingdom dysbiosis involving not only bacterial but also viral taxa. Streptococcus spp. are more abundant in non-lean versus lean MASLD, the latter being a paradoxical subtype of a disease typically associated with increased adiposity. These microbial changes correspond with shifts in transcripts and metabolites, including increases in polyamines and acylcarnitines and reductions in secondary bile acids. We highlight gut viral perturbations in MASLD, showing that expansions of bacteriophage targeting oral-typical bacteria correspond to expansions of their bacterial hosts in the gut. We provide a comprehensive resource for understanding MASLD and highlight transkingdom multi-omic microbial shifts as potential contributors to its aetiopathogenesis.}, }
@article {pmid40604089, year = {2025}, author = {Das, B and Desai, M and Bhagora, NJ and Koringa, P and Pathan, M and Thakor, JC and Savaliya, FP and Adil, S and Hati, S}, title = {Influence of fermented whey protein fractions on the growth performance, haematological traits, serum biochemistry, faecal and caeca microbiota of broiler chickens.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23678}, pmid = {40604089}, issn = {2045-2322}, mesh = {Animals ; *Chickens/growth &amp; development/microbiology/blood ; *Whey Proteins/pharmacology/metabolism ; *Feces/microbiology ; Fermentation ; Animal Feed ; *Gastrointestinal Microbiome/drug effects ; Dietary Supplements ; *Cecum/microbiology ; Male ; Limosilactobacillus fermentum/metabolism ; Female ; }, abstract = {Nowadays researchers and consumers are concerned about antibiotic resistance in poultry products causing antibiotic-resistant pathogens. Here, we investigated the effects of fermented whey peptides (FWP) with Limosilactobacillus fermentum (M4) as a nutraceutical supplement on growth performance, blood parameters, relative organs, and metagenomic analysis of broiler chickens, aiming to develop substitute for antibiotics in poultry feeds. An active culture of Lactobacillus fermentum (M4, GenBank Accession Number: MF951096) was inoculated into sterilized cheese whey at a rate of 2% (v/v) (10[7] CFU/ml) and incubated at 37 °C for 48 h. Ninety-six one-day-old mixed-sex commercial broiler chicks were randomly assigned in a Completely Randomized Design (CRD) experiment with four treatments, each having four replicates of six broiler chickens (6 × 4 × 4). One millilitre of liquid FWP fractions (> 10 kDa, < 10 kDa, and < 3 kDa) was freshly prepared and administered daily to the respective groups along with the basal diet from the 8th to the 15th day. Our current study revealed that supplementation with FWPs to broiler diets had no significant (p < 0.05) impact on body weight and FCR but numerically FCR value was high in control group. Blood cholesterol was significantly reduced in FWP fed groups. FWP had no significant impact on various blood parameters but influenced leukocytes and platelets. Metagenomic analysis showed no significant differences in microbial proportions. Histological analysis revealed no organ toxicity. The current findings suggest that broiler diets can substitute FWP for antibiotics to improve the growth performance and birds' health, without posing any biohazards. Furthermore, FWPs provide a variety of health benefits, potentially improving the health of humans who consume broiler meat or eggs.}, }
@article {pmid40604039, year = {2025}, author = {Meng, K and Bao, Y and Chen, G and Qu, J and Liang, S and An, S and Chen, Y and Liu, X and Fu, X}, title = {Metagenomics and transcriptomics analysis of aspartame's impact on gut microbiota and glioblastoma progression in a mouse model.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23298}, pmid = {40604039}, issn = {2045-2322}, support = {GNK2023ZX06//Guangxi Academy of Agricultural Science and Technology Development Project/ ; GK-AA22117015-3//the Guangxi Major Science and Technology Program/ ; GNK2021YT117//Guangxi Academy of Agricultural Sciences Basic Research Project/ ; 2019E016//Guangdong 3D Orthopedics Biomimetic Translational Medicine Engineering Technology Research Center/ ; }, mesh = {Animals ; *Aspartame/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Glioblastoma/pathology/genetics/microbiology ; Mice ; Disease Models, Animal ; *Metagenomics/methods ; Disease Progression ; Gene Expression Profiling ; *Transcriptome/drug effects ; *Brain Neoplasms/pathology/genetics/microbiology ; Humans ; Gene Expression Regulation, Neoplastic/drug effects ; Male ; Sweetening Agents/pharmacology ; }, abstract = {Aspartame, a widely used artificial sweetener, has been extensively studied for its potential health effects. Emerging evidence suggests that aspartame intake may directly impact the composition and function of the intestinal microbiota, which could subsequently influence the risk, progression, and treatment of glioblastoma multiforme (GBM) within the tumor microenvironment. However, it remains unclear whether aspartame intake affects intestinal flora, gene expression, and epigenetic regulation during tumor progression. To address these gaps in knowledge, we conducted a comprehensive metagenomics and transcriptomics analysis of aspartame's impact on gut microbiota and glioblastoma progression in a mouse model. Using a well-established mouse model and a rigorous metagenomics and transcriptomics approach, our results demonstrated that although the aspartame diet did not significantly affect tumor growth, it induced changes in the composition of the gut microbiota, particularly a decrease in the relative abundance of the Rikenellaceae family. Additionally, key N6-methyladenosine (m[6]A)-regulated genes, such as cyclin-dependent kinase inhibitor 1A (CDKN1A), MYC (myelocytomatosis) oncogene, and transforming growth factor-β (TGFB1), were significantly upregulated in GBM tumors exposed to aspartame. Notably, the expression of TGFB1 (transforming growth factor-β) suggested a critical role in the progression of GBM mediated by aspartame-induced m[6]A modifications. Our integrative analysis offered novel perspectives on the intricate interplay between dietary aspartame intake, gut microbiota, and tumor biology.}, }
@article {pmid40603748, year = {2025}, author = {Zhou, W and Kang, L and Qiao, S and Duan, H and Yin, C and Liu, C and Liao, Z and Tang, M and Zhang, R and Li, L and Shi, L and Du, M and Wang, Y and Yue, W and Xiao, Y and Di, L and Zhang, X and Pang, Y and Li, M and Ren, L and Wang, J and Chen, Z and Huang, Y}, title = {A fuzzy sequencer for rapid DNA fragment counting and genotyping.}, journal = {Nature biomedical engineering}, volume = {}, number = {}, pages = {}, pmid = {40603748}, issn = {2157-846X}, support = {T2225005//National Natural Science Foundation of China (National Science Foundation of China)/ ; Z201100005320016//Beijing Municipal Science and Technology Commission/ ; Z211100003321006//Beijing Municipal Science and Technology Commission/ ; Z221100007022003//Beijing Municipal Science and Technology Commission/ ; }, abstract = {High-throughput sequencing technologies generate a vast number of DNA sequence reads simultaneously, which are subsequently analysed using the information contained within these fragmented reads. The assessment of sequencing technology relies on information efficiency, which measures the amount of information entropy produced per sequencing reaction cycle. Here we propose a fuzzy sequencing strategy that exhibits information efficiency more than twice that of currently prevailing cyclic reversible terminator sequencing methods. To validate our approach, we develop a fully functional and high-throughput fuzzy sequencer. This sequencer implements an efficient fluorogenic sequencing-by-synthesis chemistry and we test it across various application scenarios, including copy-number variation detection, non-invasive prenatal testing, transcriptome profiling, mutation genotyping and metagenomic profiling. Our findings demonstrate that the fuzzy sequencing strategy outperforms existing methods in terms of information efficiency and delivers accurate resequencing results with faster turnaround times.}, }
@article {pmid40603380, year = {2025}, author = {Wang, R and Wang, J and Wang, L and Cai, Y and Wang, Y and Luo, H and Chen, B and Chen, J and Fang, J and Song, Z}, title = {A novel eco-friendly Acinetobacter strain A1-4-2 for bioremediation of aquatic pollutants.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23207}, pmid = {40603380}, issn = {2045-2322}, support = {2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; 2022YFE0203900//National Key Research and Development Program of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; No. 92251303//National Natural Science Foundation of China/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; STCSM 20050501700//Science, Technology Commission of Shanghai Municipality/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; 2023ZKZD53//Shanghai Municipal Education Commission/ ; }, mesh = {*Acinetobacter/metabolism/genetics/isolation &amp; purification/classification ; *Biodegradation, Environmental ; Animals ; *Water Pollutants, Chemical/metabolism ; Zebrafish ; Phylogeny ; Metagenomics ; }, abstract = {The increasing accumulation of hydrocarbons and aromatic compounds in aquatic ecosystems, stemming from anthropogenic activities, poses severe ecological challenges, including disrupting biodiversity and threatening human health through the food chain. This study presents Acinetobacter strain A1-4-2, isolated from a hairy crab farming base, which could represent a novel Acinetobacter species. The metagenomic analysis of approximately 12,000 publicly available datasets revealed that this novel Acinetobacter species is widely distributed across various environments, particularly in those with high organic matter content, such as sludge, feces, and wastewater. Strain A1-4-2 exhibited exceptional metabolic capabilities, effectively degrading a diverse range of substrates, including amino acids, organic acids, oils, n-alkanes, lignin, and aromatic monomers. Genomic analysis, coupled with biological experiments, revealed that strain A1-4-2 exhibited resistance to a very limited kind of antibiotics. Moreover, the strain's biosafety, affirmed through zebrafish toxicity assays, underscores its suitability for environmental release. Additionally, the feasibility of genetic manipulation of strain A1-4-2 gives it the potential to become a chassis cell, enabling it to degrade organic pollutants more efficiently through genetic engineering. Our findings elucidate the strain's genomic and metabolic attributes, offering insights into its biodegradation potentials and developing effective strategies for ecological restoration in face of pollution.}, }
@article {pmid40603374, year = {2025}, author = {Guta, M and Van Eenooghe, B and Bacha, K and Cools, P}, title = {Bacterial community profile of three Ethiopian hot springs based on 16S rRNA gene nanopore sequencing.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23491}, pmid = {40603374}, issn = {2045-2322}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Hot Springs/microbiology ; Ethiopia ; *Bacteria/genetics/classification/isolation &amp; purification ; Phylogeny ; *Nanopore Sequencing/methods ; Biodiversity ; }, abstract = {Ethiopia harbors a number of hot springs not yet well explored or studied using a metagenomic approach to reveal their bacterial diversity. Understanding the bacterial diversity of these ecosystems is valuable for uncovering their ecological roles and potential for biotechnological applications. The aim of this study was, therefore, to perform the first full-length 16S rRNA gene nanopore sequencing on the three Ethiopian hot springs, namely Shalla, Woliso and Wondo Genet. The bacterial community composition of the three hot springs, whose temperatures ranged from 45 to 96 °C, was effectively assessed using the ONT MinION sequencer. It was found that Shalla hot spring had the highest species richness and accounted for 323 species, followed by 116 species from Woliso and 54 species from Wondo Genet hot springs. Pseudomonadota and Bacillota were the most dominant phyla recovered from the three hot springs, whereas Acinetobacter and Paracoccus were the most abundant bacterial genera. The most abundant species were Alkalihalobacterium elongatum from Shalla hot spring, and Acinetobacter junii and Acinetobacter johnsonii from Wondo Genet hot spring. Our study provided the first insight into the bacterial diversity of three Ethiopian hot springs and may serve as a basis for further functional analysis of these hot springs.}, }
@article {pmid40603287, year = {2025}, author = {Samarra, A and Alcañiz, AJ and Martínez-Costa, C and Marina, A and Comas, I and Segata, N and Quijada, NM and Collado, MC}, title = {Breastfeeding and early Bifidobacterium-driven microbial colonization shape the infant gut resistome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {6099}, pmid = {40603287}, issn = {2041-1723}, support = {MAMI-639226 project//EC | EU Framework Programme for Research and Innovation H2020 | H2020 European Institute of Innovation and Technology (H2020 The European Institute of Innovation and Technology)/ ; PROMETEO2020/12//Generalitat Valenciana (Regional Government of Valencia)/ ; CIPROM2023/030//Generalitat Valenciana (Regional Government of Valencia)/ ; }, mesh = {Humans ; *Breast Feeding ; *Bifidobacterium/physiology/genetics ; *Gastrointestinal Microbiome/genetics/drug effects ; Infant ; Female ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Cesarean Section ; Metagenome ; Adult ; Male ; Milk, Human/microbiology ; Feces/microbiology ; }, abstract = {The assembly of the gut resistome in early life is key to infant health. Specific perinatal factors such as cesarean section (C-section), antibiotic exposure and lack of breastfeeding practices are detrimental to proper microbial development and increase the antimicrobial resistance genes (ARGs). Using 265 gut longitudinal metagenomes from 66 mother-infant pairs, we investigated how perinatal factors influence the acquisition and dynamics of ARGs during the first year of life. Our findings reveal that Bifidobacterium plays a crucial role in modulating the infant resistome, with its high relative abundance being associated with a lower ARG load. Exclusive breastfeeding during the first month of life accelerates the reduction of ARGs and ensures a lower resistome burden at six months. Moreover, early breastfeeding cessation correlates with a higher ARG load, underscoring its long-term influence on microbial resilience. Importantly, we identify exclusive breastfeeding as a key strategy to mitigate the impact of C-section delivery on the infant gut resistome, counteracting the early-life antibiotic exposure associated with this procedure and the resulting resistance acquisition. By promoting a microbiome enriched in Bifidobacterium, breastfeeding may help suppress ARG-carrying taxa, reducing the risk of resistance dissemination. Our findings underscore the importance of breastfeeding as a natural intervention to shape the infant microbiome and resistome. Supporting breastfeeding through public health policies could help limit the spread of antimicrobial resistance in early life.}, }
@article {pmid40602621, year = {2025}, author = {Zhang, Z and Yuan, G and Turgun, X and Turgun, Z and Hou, L and Ye, M and Wang, Y and Xu, X}, title = {Biogeographic Patterns and Ecological Roles of Microorganisms in Sediments Along an Estuarine Salinity Gradient.}, journal = {Environmental microbiology reports}, volume = {17}, number = {4}, pages = {e70139}, doi = {10.1111/1758-2229.70139}, pmid = {40602621}, issn = {1758-2229}, support = {2023A1515110368//Guangdong Basic and Applied Basic Research Foundation/ ; XJNUZBS2423//Doctoral Research Foundation of Xinjiang Normal University/ ; 42361144846 and 42461006//National Natural Science Foundation of China/ ; //Tianchi Talents (Xinjiang) Plan Project (Young Doctor)/ ; }, mesh = {*Geologic Sediments/microbiology/chemistry ; *Salinity ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Estuaries ; China ; Biodiversity ; Microbiota ; Ecosystem ; Metagenome ; Phylogeny ; }, abstract = {The distribution patterns and driving mechanisms of microbial biogeographic patterns are fundamental questions in microbiology. This study analysed and compared the bacterial biogeographic patterns in the coastal environment, focusing on the Yangtze Estuary and its adjacent coastal zone. The purpose is to explore the driving mechanisms under spatial distribution, the community assembly processes and potential functions. Our results revealed that the sediment bacterial community structure exhibited a distinct geographical pattern and was significantly influenced by environmental factors. The microbial community displayed a non-random co-occurrence pattern, and the biogeographic patterns were shaped not only by environmental constraints (deterministic processes) but also by stochastic processes resulting from dispersal limitation. The metagenome sequencing analysis revealed a pronounced salinity gradient in the nitrogen-cycling function of the bacterial community. This functional difference appears to be driven by microbial diversity changes from the estuarine region to the ocean, highlighting the key role of microbial ecological characteristics. The findings of this study contribute to a deeper understanding of microbial ecology in estuarine environments, emphasizing the complex interplay between environmental factors and microbial community dynamics in shaping the function of estuarine sediment bacterial communities.}, }
@article {pmid40602565, year = {2025}, author = {Rajeswari, G and Kumar, V and Jacob, S}, title = {Advanced lignocellulose bioprocessing for Aloe vera leaf rind through novel termite gut microbiome consortia for acetone butanol ethanol (ABE) production: Metagenomics insights and process economic analysis.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {145691}, doi = {10.1016/j.ijbiomac.2025.145691}, pmid = {40602565}, issn = {1879-0003}, abstract = {Consolidated bioprocessing (CBP) of lignocellulosic biomass (LCB) using microbes simplifies the process, eliminates enzyme cost and reduces the overall processing expenses. In this regard, termite gut, a potent reservoir of microbial symbionts produces various lignocellulolytic enzymes which acts synergistically to degrade LCB. However, the effectiveness of adapting the microbes with LCB for improved lignocellulolytic enzyme secretion and substrate degradation has been overlooked. Hence, in this study adaptive laboratory (ALE) of termite gut isolates was performed with various substrates such as saw dust (SD) and Aloe vera leaf rind (AVLR) under different conditions. Among the consortia, enriched termite consortium (ETC-3) showed the highest degradation of lignin (51.86 ± 2.03 %, w/w), hemicellulose (29.27 ± 1.29 %, w/w) and cellulose (41.97 ± 2.99 %, w/w) with maximum specific enzyme activities. High throughput sequencing revealed the significant enrichment of Proteobacteria (88.95 %) and Ascomycota (99.94 %) groups in ETC-3. Further, the efficiency of ETC-3 in consolidated pretreatment and bioprocessing (CPBP) and CBP of AVLR towards acetone, butanol and ethanol (ABE) production was studied. Compared to the CPBP, CBP resulted in 1.6-fold higher glucose yield which subsequently enhanced the butanol yield (7.97 ± 0.40 g/L). Finally, cost benefit analysis ensured the economic feasibility of process strategies for AVLR valorization.}, }
@article {pmid40602513, year = {2025}, author = {Zhang, Z and Wang, X and Yang, L and Cui, Y and Zhang, Z}, title = {Soil redox-adaptive anode potentials enhance microbial electroactivity through targeted enrichment of exoelectrogenic consortia in paddy soil.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122265}, doi = {10.1016/j.envres.2025.122265}, pmid = {40602513}, issn = {1096-0953}, abstract = {Exoelectrogenic bacteria (EEB) act as critical drivers in terrestrial and aquatic ecosystems, mediating pivotal biogeochemical processes. However, their low abundance in natural environments poses significant challenges for accurate identification and enrichment. Bioelectrochemical systems (BESs) have emerged as a promising tool for enriching EEB from environmental samples, yet the influence of applied potentials on shaping specific EEB populations remains poorly understood. Here, we developed an effective strategy to selectively enrich targeted exoelectrogenic consortia by adapting anode potentials to the redox conditions of paddy soil. Notably, in BESs inoculated with flooded soil, an applied potential of -0.28 V (simulating the redox conditions dominated by iron oxide-hydroxide reduction) preferentially enriched Geobacter-dominated EEB consortia. Metagenomic functional analysis indicated these EEB were primarily engaged in iron respiration. In contrast, drained soil-inoculated BESs required a higher potential (0.33 V, mimicking nitrate-reducing conditions) for optimal enrichment, resulting in Aeromonas as the predominant genus. The enriched community in this scenario exhibited chemoheterotrophic metabolism and nitrate reduction capabilities. The enrichment dynamics underscore how applied potentials modulate both taxonomic composition and functional specialization of EEB along soil redox gradients, with implications for targeted manipulation of microbial communities for environmental biotechnology applications.}, }
@article {pmid40602191, year = {2025}, author = {de Sant'Anna, FM and Chakrawarti, A and Haley, BJ and Barlow, J}, title = {The resistome of pasteurized and raw milk cheeses from the state of Vermont.}, journal = {International journal of food microbiology}, volume = {441}, number = {}, pages = {111333}, doi = {10.1016/j.ijfoodmicro.2025.111333}, pmid = {40602191}, issn = {1879-3460}, abstract = {This study investigates the resistome dynamics in cheese production, focusing on both raw milk and pasteurized varieties comparing a standard and lytic method of DNA extraction. Metagenomic analysis revealed the presence of single nucleotide polymorphism (SNP) confirmed antimicrobial resistance genes (ARGs) in core and rind samples of cheeses at different stages of ripening. No statistical significance was found between the extraction methods for antimicrobial resistance gene (ARG) classes. In pasteurized cheese, the resistome was influenced by the initial microbial composition and ripening period, with limited ARGs detected due to pasteurization. Nonetheless, detection of class B β-lactamase and Fosfomycin B resistance genes was observed in the pasteurized cheese core, possibly harbored by Bacillus cereus. Raw milk cheese exhibited a distinct resistome profile, with fluctuations in macrolide and oxazolidinone resistance genes associated with changes in microbial populations during ripening. Notably, the likely presence of multi-drug resistance genes in Lactococcus lactis highlights the importance of understanding resistance mechanisms in starter cultures. The study emphasizes the need for antimicrobial stewardship and hygiene practices in dairy production to mitigate the spread of resistance genes. Despite sequencing biases, this research contributes valuable insights into the cheese resistome, advocating for future studies to employ enhanced sequencing methods for comprehensive analysis and to develop practical strategies for resistance management in dairy products.}, }
@article {pmid40602179, year = {2025}, author = {Tang, X and Zheng, W and Chen, L and Liu, H and Li, M and Chen, M and Yang, Y}, title = {Enhanced neonicotinoid removal in constructed wetlands using Fungus-Fe/Mn biochar.}, journal = {Journal of environmental management}, volume = {390}, number = {}, pages = {126430}, doi = {10.1016/j.jenvman.2025.126430}, pmid = {40602179}, issn = {1095-8630}, abstract = {The environmental persistence and toxicity of neonicotinoids, such as imidacloprid (IMI) and thiamethoxam (THX), pose substantial threats to aquatic ecosystems. This study evaluated the performance of constructed wetlands (CWs) amended with a novel Fungus-Fe/Mn biochar substrate (synthesized by immobilizing the white-rot fungus Phanerochaete chrysosporium onto Fe/Mn-modified biochar) for enhanced removal of IMI and THX from simulated agricultural wastewater. CWs integrated with Fungus-Fe/Mn biochar demonstrated significantly improved removal efficiencies of 73.3 % for IMI and 66.7 % for THX, surpassing those of Fe/Mn biochar alone (66.4 % IMI, 58.1 % THX) and control systems (55.1 % IMI, 37.3 % THX). Mechanistic analysis indicated that removal was facilitated by both substrate adsorption (32.3-37.5 %) and microbial degradation (32.4-35.1 %), with enhanced production of degradation metabolites in the amended systems. Metagenomic analysis revealed increased microbial diversity and the enrichment of biodegradation and pesticide degradation genes, including key genes such as p450 and mnp. Additionally, potential microbial hosts for these genes, such as Rhodococcus and Pseudomonas, were identified. Redox-active Fe[3+]/Fe[2+] and Mn[4+]/Mn[2+] species additionally promoted electron transfer and rhizosphere iron plaque formation, improving pollutant sequestration and on-situ degradation. These findings highlight the potential of fungus-biochar synergism to overcome the limitations of conventional substrates, offering a scalable and sustainable approach for pesticide remediation in CWs.}, }
@article {pmid40601836, year = {2025}, author = {Tarek, S and ElMaghloob, Y and Smith, H and Smith, TJ and ElRakaiby, MT and Habib, MH}, title = {A Scavenger Hunt for a DyP-Peroxidase from a Metagenome: Curated Peroxidase Database-Assisted Primer Design and Protein Structure Elucidation.}, journal = {ACS chemical biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acschembio.5c00323}, pmid = {40601836}, issn = {1554-8937}, abstract = {Dye-decolorizing peroxidase (DyP)-type peroxidases are heme-containing enzymes that play a role in lignin synthesis and degradation and dye decolorization. Despite numerous studies about this class of enzymes, the enzyme remains under-explored. We used 1000 DyP sequences retrieved from the NCBI database to forge a phylogenetic tree. Nodes in the tree, where sequences displayed a degree of conservation, were used to design degenerate primers to locate DyP-peroxidase sequences from the DNA extract of a tannery wastewater sample. After PCR amplification and visualization using agarose electrophoresis, a band at the expected size of a DyP peroxidase (500-700 bp) was seen. TA cloning followed by blue-white colony selection validated our finding after amplicon sequencing of the PCR product to confirm the presence of an Acinetobacter species DyP-peroxidase. Our metagenomic DyP displayed 99% similarity to the DyP-peroxidase sequence found in the Acinetobacter baumannii ATCC 19606 strain. As a result, and due to the minute differences between our found DyP and the ATCC 19606 strain DyP, we expressed the latter cloned in a pET28b(+) vector and purified it from culture medium using Escherichia coli SoluBl21 as a host strain. A crude oxidation assay using 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) deemed the enzyme active as shown by the formation of a green color. The crystal structure of the enzyme was solved at 2.6 Å resolution (PDB ID 9OBR) using X-ray crystallography and presented as a hexamer in solution.}, }
@article {pmid40601719, year = {2025}, author = {Wanjiru, T and Bulimo, W and Langat, S and Kinyua, J and Odemba, N and Yalwala, S and Oullo, D and Ochieng, R and Ngere, F and Kerich, G and Ambale, J and Achieng, E and Abuom, D and Egbo, T and Johnson, J and Ojwang, E and Eads, J and Garges, E and Eyase, F}, title = {Vertical transmission of Dengue virus type-3 and metagenomic virome profiles of Aedes aegypti mosquitoes collected in Kisumu, Kenya.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0315492}, doi = {10.1371/journal.pone.0315492}, pmid = {40601719}, issn = {1932-6203}, mesh = {Animals ; *Aedes/virology ; Kenya ; *Dengue Virus/genetics/isolation &amp; purification/classification ; *Virome/genetics ; *Mosquito Vectors/virology ; *Infectious Disease Transmission, Vertical ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Dengue/transmission/virology ; Metagenome ; Female ; }, abstract = {Aedes aegypti is the main vector of several arboviruses including chikungunya, dengue, yellow fever and Zika. Beyond arboviruses, Aedes aegypti harbours insect-specific viruses (ISVs), which can modulate mosquito's ability to transmit diseases by interfering with viral processes and triggering immune responses. Both arboviruses and ISVs can be transmitted vertically, where viruses are passed from parent to offspring. The lack of systematic molecular and entomological surveillance, has left the diversity of viruses in local Aedes aegypti populations largely unexplored. This study aimed to characterize the viromes of Aedes aegypti mosquitoes from Kisumu, Kenya, focusing on viral diversity. Immature larvae and pupae were collected from Jua Kali area in Kisumu, reared into adults, and subjected to viral isolation by cell culture and metagenomic next-generation sequencing. RNA extraction, library preparation, and Illumina MiSeq sequencing were performed on CPE positive pools and metagenomic superpools. Initial data analysis was conducted using the CZ-ID platform, with quality control applied using PrinseqLite v0.20.4 to filter low-quality reads and remove adapters. De novo sequence assembly was performed with MEGAHIT v1.2.9, followed by BLAST analysis. Phylogenetic relationships were analyzed using the Maximum Likelihood method. A total of 2,142 female Aedes aegypti, grouped into 86 pools and 4 superpools, were analyzed using cell culture and metagenomic next-generation sequencing respectively. Dengue virus type-3 was detected in one of the 86 pool. Additionally, a variety of ISVs were identified, including Iflaviruses related to Tesano Aedes Iflavirus (TeAV), Armigeres Iflavirus, and Negeviruses related to Rabai Virus. An unclassified virus closely related to Korle-Bu Aedes virus was also detected. Our study provides insights into the viral diversity within Aedes aegypti mosquitoes in Kisumu and evidence of natural vertical transmission, specifically transovarial transmission of dengue virus type-3. Ongoing research is imperative to unravel vertical transmission mechanisms and subtleties governing ISV-arbovirus interactions across diverse environmental settings.}, }
@article {pmid40601568, year = {2025}, author = {Manavalan, S and Pradeep, D and Dharmalingam, D and Semalaiyappan, J and Sivarasan, T and Venkatesan, S and Thirumal, S and Kuttiatt, VS}, title = {Comparative analysis of skin microbiome of patients with filarial lymphedema and healthy individuals.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0325380}, pmid = {40601568}, issn = {1932-6203}, mesh = {Humans ; *Microbiota/genetics ; Male ; *Skin/microbiology ; *Elephantiasis, Filarial/microbiology ; Adult ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; *Lymphedema/microbiology ; Pilot Projects ; Skin Microbiome ; }, abstract = {BACKGROUND: Lymphatic filariasis, a vector borne parasitic disease is a public health problem in the tropical region. Recurrent skin and soft tissue infections termed adenolymphangitis (ADL) is a major complication of filarial lymphedema. Understanding the changes in skin microbiome associated with this disease may provide novel insights on ADL attacks and lymphedema progression. This study investigates the changes in skin microbial flora in patients affected with filarial lymphedema.<br><br>METHODS: We employed 16S rRNA gene amplicon-based metagenomic technique to profile the skin microbiome of patients with filarial lymphedema in comparison with healthy volunteers.<br><br>RESULTS: There were notable differences in the bacterial flora between patients and healthy controls. Actinobacteria were under-represented in the patient group. Staphylococcus dominated both the groups, 63% in patients and 44% in controls. Samples from a few patients showed the presence of certain rare bacteria like Eremococcus and Facklamia.<br><br>CONCLUSION: This pilot study applying advanced molecular tools provides insight on the changes in skin microflora associated with filarial lymphedema for the first time. Further studies are necessary for a better understanding of the role of the altered skin microbiome in frequent episodes of adenolymphangitis in patients with filarial lymphedema.}, }
@article {pmid40601244, year = {2025}, author = {Posthumus, AM and Knobbe, TJ and Kremer, D and Gomes-Neto, AW and Dielwart, IJC and Jonker, J and Doorenbos, CSE and Eisenga, MF and van Londen, M and Douwes, RM and Nieuwenhuis, LM and Annema, C and de Boer, MT and de Borst, MH and Damman, K and Pol, RA and Gan, CT and Verschuuren, EAM and Blokzijl, H and de Meijer, VE and Bakker, SJL and , }, title = {TransplantLines, a biobank and cohort study of solid organ transplant recipients and donors.}, journal = {European journal of epidemiology}, volume = {}, number = {}, pages = {}, pmid = {40601244}, issn = {1573-7284}, support = {TransplantLines Biobank//Astellas Pharma, Netherlands/ ; Cohort study//Astellas Pharma, Netherlands/ ; PA-SP/PRJ-2020-9136//Chiesi Pharmaceuticals BV/ ; project code: 14939//DSM, Animal Nutrition and Health/ ; project code: PPP-2019-032//Ministerie van Economische Zaken en Klimaat/ ; PPP-2022-015//Ministerie van Economische Zaken en Klimaat/ ; }, abstract = {The TransplantLines Biobank and Cohort Study (NCT03272841) is an ongoing prospective study conducted at the University Medical Centre Groningen, The Netherlands. TransplantLines aims to identify risk factors and biomarkers associated with health problems following solid organ transplantation and donation. Additionally, the study seeks to develop new interventions to reduce symptom burden and improve long-term outcomes, including health-related quality of life, cardiovascular complications, graft failure, and mortality. It includes recipients of (combined) heart, liver, lung, kidney, pancreas, and small bowel transplants, as well as living liver and kidney donors, and deceased (multi-)organ donors. The biobank contains a wide range of biomaterials including whole blood, serum, EDTA-plasma, buffy coat, 24-h urine samples, faeces, hair, nails, and tissues. Data collection includes physical and cognitive assessments, extensive laboratory analysis, metagenomic sequencing, and questionnaires. TransplantLines, initiated in 2015, consists of 5143 participants as of October 2024, among 2312 (45%) females. The mean age was 50 (± 16) years at transplantation, 55 (± 11) years at living donation and 56 (± 15) years at deceased donation. Both cross-sectional and longitudinal biomaterials and data are included. For recipients, longitudinal biomaterials and data were collected at: pre-transplantation, at transplantation, and at 3, 6, 12, 24, and 60 months post-transplantation. For living donors, data were collected at pre-donation, donation, 3 months post-donation, and/or 5 or 10 years post-donation.}, }
@article {pmid40600930, year = {2025}, author = {Gómez-Gómez, A and Aterido, A and Li, T and Guillén, Y and Martínez, S and Julià, A and Marsal, S and Andreu, JL}, title = {Understanding the molecular basis of Sjögren's disease using omic technologies.}, journal = {Rheumatology (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/rheumatology/keaf360}, pmid = {40600930}, issn = {1462-0332}, abstract = {Primary Sjögren's Disease (SjD) is a chronic autoimmune disease (AD) that primarily affects the exocrine glands, particularly lacrimal and salivary glands, presenting extra glandular manifestations in a significant number of patients. Although it is a prevalent and globally widespread disease, its pathogenesis has not been fully elucidated. Recently, high-throughput omics technologies are providing unprecedented insights into the molecular landscape of various ADs, including SjD. These technical advances are prepared to decipher new aspects of its pathogenesis and to eventually enable the development of more effective treatment strategies. This review explores recent developments in genetics, transcriptomics, epigenomics, proteomics, and metagenomics in SjD, highlighting the potential of integrating multiple omics datasets to identify better drug targets and useful biomarkers for precision medicine.}, }
@article {pmid40600714, year = {2025}, author = {Li, Y and Sun, C and Zhu, J and Geng, M and Li, M and Zhao, X-M and Chen, W-H}, title = {Biases and complementarity in gut viromes obtained from bulk and virus-like particle-enriched metagenomic sequencing.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0001325}, doi = {10.1128/spectrum.00013-25}, pmid = {40600714}, issn = {2165-0497}, abstract = {UNLABELLED: Due to varying sequencing strategies, current gut virome findings show significant variability. Specifically, bulk- and virus-like particle (VLP)-enriched metagenomic sequencing (termed bulk and VLP, respectively) present unique advantages and limitations, affecting viral genome discovery, taxonomic annotation, and community structure analysis. A comprehensive comparison of these strategies is crucial for thoroughly understanding the gut virome. This study comprehensively compared gut viromes identified from paired bulk and VLP data from 151 adult and 141 infant fecal samples. The VLP method showed superior performance to bulk in viral genome discovery in both data sets by recovering longer and more complete viral genomes, with higher sensitivity for low-abundant ones, resulting in a higher taxonomic annotation rate. However, we observed no correlations in the viral community structure (i.e., Shannon diversities) between bulk- and VLP-derived viromes, implying biases introduced during VLP enrichment. Such biases could be caused by the bacterial host features, such as the structural differences in cell walls and the prevalence and abundance of the viruses. Viruses that are of low prevalence, low abundance, or have Gram-positive bacteria as their hosts were enriched in VLP-derived viromes, in both the adult and infant data sets. Significant complementarity was observed between bulk and VLP viromes, with only about a quarter (26.7% in infants; 29.3% in adults) of VLP-viral genomes overlapping with bulk viruses. Together, our study identifies causal factors underlying the biases of bulk and VLP strategies in human gut virome studies and advocates the use of both strategies to enhance a comprehensive understanding of gut viromes.<br><br>IMPORTANCE: The two mainstream gut phageome profiling strategies, namely bulk and virus-like particle (VLP), generated significantly overlapped results and have their own merits and drawbacks. Particularly, VLP exhibits higher efficiency in obtaining more, longer, and more complete viral genomes. However, VLP sequencing has the potential to alter the natural structure of viral communities, often resulting in the identification of viruses with lower prevalence and those specifically associated with Gram-positive bacterial hosts. While bulk metagenome features a more stable and diverse community, which can well reveal the interactions between viruses and bacteria. Nevertheless, bulk sequencing can suffer from lower coverage, leading to fragmented sequences and potentially missing some viral species. Therefore, it is essential to recognize that these methods are complementary rather than competitive in the comprehensive characterization of the gut phageome.}, }
@article {pmid40600712, year = {2025}, author = {Comeault, AA and Orta, AH and Fidler, DB and Nunn, T and Ellison, AR and Anspach, TA and Matute, DR}, title = {Phylogenetic and functional diversity among Drosophila-associated metagenome-assembled genomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0002725}, doi = {10.1128/msystems.00027-25}, pmid = {40600712}, issn = {2379-5077}, abstract = {Host-associated microbial communities can mediate interactions between their hosts and biotic and abiotic environments. While much work has been done to document how microbiomes vary across species and environments, much less is known about the functional consequences of this variation. Here, we test for functional variation among drosophilid-associated bacteria by conducting Oxford Nanopore long-read sequencing and generating metagenome-assembled genomes (MAGs) from communities associated with six species of drosophilid flies collected from "anthropogenic" environments in North America, Europe, and Africa. Using phylogenetic analyses, we find that drosophilid flies harbor a diverse microbiome that includes core members closely related to the genera Gilliamella, Orbus, Entomomonas, Dysgonomonas, and others. Comparisons with publicly available bacterial genomes show that many of these genera are associated with phylogenetically diverse insect gut microbiomes. Using functional annotations and predicted secondary metabolite biosynthetic gene clusters, we show that MAGs belonging to different bacterial orders and genera vary in gene content and predicted functions, including metabolic capacity and how they respond to environmental stressors. Our results provide evidence that wild drosophilid flies harbor phylogenetically and functionally diverse microbial communities. These findings highlight a need to quantify the abundance and function of insect-associated bacteria from the genera Gilliamella, Orbus, Entomomonas, and others on the performance of their insect hosts across diverse environments.IMPORTANCEWhile much attention has been given to catalogue the taxonomic diversity intrinsic to host-associated microbiomes, much less is known about the functional consequences of this variation, especially in wild, non-model host species. In this study, we use long-read sequencing to generate and analyze 103 high-quality metagenome-assembled genomes from host-associated bacterial communities from six species of wild fruit fly (Drosophila). We find that the genomes of drosophilid-associated bacteria possess diverse metabolic pathways and biosynthetic gene clusters that are predicted to generate metabolites involved in nutrition and disease resistance, among other functions. Using functional gene predictions, we show that different bacterial lineages that comprise the insect microbiome differ in predicted functional capacities. Our findings highlight the functional variation intrinsic to microbial communities of wild insects and provide a step towards disentangling the ecological and evolutionary processes driving host-microbe symbioses.}, }
@article {pmid40600350, year = {2025}, author = {Dike, CR and Duan, Q and Ahmed, F and Denson, LA and Haslam, D and Minar, P and Ollberding, NJ and Papachristou, GI and Setchell, KDR and Thompson, T and Vitale, DS and Zhao, X and Abu-El-Haija, M}, title = {Acute pancreatitis gut dysbiosis persists at 1-year follow-up and is associated with clinical outcomes.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpn3.70135}, pmid = {40600350}, issn = {1536-4801}, support = {K23DK118190 (MAH)/DK/NIDDK NIH HHS/United States ; R03 DK131156 (MAH)/DK/NIDDK NIH HHS/United States ; P30DK078392/GF/NIH HHS/United States ; //Digestive Diseases Research Core Center in Cincinnati (LAD) and The Helmsley Charitable Trust (LAD, PM)/ ; }, abstract = {OBJECTIVES: Pediatric acute pancreatitis (AP) is associated with gut dysbiosis. We aimed to determine if dysbiosis persisted during follow-up and whether it is associated with clinical outcomes.<br><br>METHODS: Prospective enrollment of participants <21 years with first AP. Stool samples were obtained at baseline (n&#x2009;=&#x2009;41), 3 months (n&#x2009;=&#x2009;19), and 12 months (n&#x2009;=&#x2009;12) and in healthy controls (HC; n&#x2009;=&#x2009;34). Evaluation for diabetes (DM) or prediabetes (pre-DM) was performed. At 12-month follow-up gastrointestinal (GI) symptom surveys were completed and AP recurrence-acute recurrent pancreatitis (ARP) recorded. Shotgun metagenomic sequencing was performed on extracted microbial DNA.<br><br>RESULTS: Microbial alpha diversity was lower for AP versus HC at all three time points (p&#x2009;<&#x2009;0.008). Bray-Curtis ordinations showed the AP cohort did not cluster by time point, highlighting similarity in microbial composition over time. Within 12-month follow-up: 7/44 participants developed pre-DM/DM, 7/42 developed ARP, 16 had zero or one while 15 had multiple GI symptoms. Distinct clustering of samples was observed in the baseline samples of the group that developed ARP (p&#x2009;=&#x2009;0.023) and in follow-up samples with multiple GI symptoms, p&#x2009;<&#x2009;0.05. Relative abundance of most species was lower in AP samples when compared to HC at all time points with enrichment in Ruminococcus gnavus and Clostridium innocuum (AQ) (False Discovery Rate p&#x2009;<&#x2009;0.05). Several pathways involved in protein biosynthesis were depleted in the AP cohort at all time points.<br><br>CONCLUSIONS: Gut dysbiosis persisted following AP in children at 3 and 12 months follow-up compared to HC. Microbiome signatures differed in the ARP cohort and those with multiple GI symptoms.}, }
@article {pmid40600142, year = {2025}, author = {Xia, Y and Lu, L and Wang, L and Qiu, Y and Liu, X and Ge, W}, title = {Multi-omics analyses reveal altered gut microbial thiamine production in obesity.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1516393}, pmid = {40600142}, issn = {1664-302X}, abstract = {OBJECTIVE: Accumulating evidence highlights the important role of B vitamins in maintaining the balance of gut microbial ecology and metabolism, however, few studies have focused on changes in B vitamins homeostasis in the gut and their associations with disease. This study aims to investigate the potential interplay between B vitamins, gut microbiota, and obesity.<br><br>METHODS: We conducted an integrated analysis of fecal shotgun metagenomics, fecal metabolome concerning B vitamins and short chain fatty acids (SCFAs), and obese phenotypes in a cohort of 63 participants, including 31 healthy controls and 32 individuals with obesity.<br><br>RESULTS: Metabolomic analysis identified significantly lower levels of fecal thiamine in individuals with obesity (P Wilcoxon < 0.001). Fecal thiamine levels exhibited a positive correlation with HDL-C and a negative correlation with BMI, DBP, fasting serum insulin, HOMA-IR, triglycerides, and propionic acid. Binary logistics regression suggested that fecal thiamine deficiency may be a potential contributor to the onset of obesity (Odds ratio: 0.295). Metagenomic analysis indicated that the microbial composition in individuals with obesity was characterized by a predominance of potential opportunistic pathogens, a loss of complexity, and a decrease in thiamine-producing bacteria. Integrated analysis indicated that thiamine deficiency was positively associated with the depletion of thiamine auxotrophic bacteria in the obese microbiome. Functional analysis revealed that KOs content for enzymes involved in the microbial production of thiamine were significantly lower in obesity, including tRNA uracil 4-sulfurtransferase (ThiI, P Wilcoxon = 0.001) and nucleoside-triphosphatase (NTPCR, P Wilcoxon = 0.006), both of which were positively associated with fecal thiamine.<br><br>CONCLUSION: Our study highlights the impairment of microbial thiamine production and its broad associations with gut microbiota dysbiosis and obesity-related phenotypes. Our findings provide a rationale for developing treatments that utilize thiamine to prevent obesity by modulating gut microbiota.}, }
@article {pmid40600141, year = {2025}, author = {Elbehery, AHA and Becker, K and Mishra, A and Ahmad, R}, title = {Editorial: Metagenomic approach for exploration of antimicrobial resistance in uncultivated microbiota.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1633252}, pmid = {40600141}, issn = {1664-302X}, }
@article {pmid40571179, year = {2025}, author = {Perrin, A and Clément, L and Szentiványi, T and Théou, P and López-Baucells, A and Bonny, L and Scaravelli, D and Glaizot, O and Christe, P}, title = {Bat phylogeny and geographic location, rather than bat individual characteristics, explains the pattern of trypanosome infection in Europe.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijpara.2025.06.008}, pmid = {40571179}, issn = {1879-0135}, abstract = {Understanding the drivers of parasite susceptibility provides valuable information, such as how parasites spread, what conditions favour their transmission, and what host characteristics make infections more likely. It can also reveal co-evolutionary dynamics and adaptation strategies between hosts and parasites. In this study, we investigated the infection patterns of several bat species across Europe by trypanosome parasites. We used phylogenetic generalised linear mixed models to investigate whether geographic location, individual characteristics (sex, body mass and body size) or species affect trypanosome infection. Additionally, we examined whether infection patterns were influenced by host phylogeny (similar prevalence among genetically close species) and tested for a cophylogenetic signal between bats and trypanosomes. Our results show that individual characteristics were poor predictors of trypanosome infection, whereas host phylogeny and geographic location significantly explained variation in infection. We also found a cophylogenetic congruence between bat species and trypanosome lineages, but this was primarily driven by the association between the bent-winged bat (Miniopterus schreibersii) and its trypanosome lineages. Overall, host phylogeny emerges as the main determinant of trypanosome infection in bats. These findings suggest that the probability of infection is governed by deterministic factors rather than random encounters between bats and their trypanosome parasites. However, the high host specificity and absence of a strong cophylogenetic signal indicate that random host switching, rather than co-speciation, is the dominant mechanism shaping bat-trypanosome associations.}, }
@article {pmid40170447, year = {2025}, author = {Veríssimo, J and Lopes-Lima, M and Amaral, F and Chaves, C and Fernandes, V and Kemanja, M and Teixeira, A and Martins, FMS and Beja, P}, title = {Navigating Methodological Trade-Offs in eDNA Metabarcoding Biodiversity Monitoring: Insights From a Mediterranean Watershed.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14082}, doi = {10.1111/1755-0998.14082}, pmid = {40170447}, issn = {1755-0998}, support = {2020.03608.CEECIND//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; COVID/BD/152600/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/133159/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/50027/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0048/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; NORTE-01-0246-FEDER-000063//European Regional Development Fund (ERDF)/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *DNA, Environmental/genetics ; *Metagenomics/methods ; Mediterranean Region ; *Vertebrates/classification/genetics ; *Environmental Monitoring/methods ; }, abstract = {Environmental DNA (eDNA) metabarcoding technologies promise significant advances in biodiversity monitoring, yet their application requires extensive optimisation and standardisation. Recent research demonstrated that increased sampling and analytical efforts are needed to improve biodiversity estimates, though fully optimising study designs is often hindered by resource constraints. Consequently, researchers must carefully navigate methodological trade-offs to design effective eDNA metabarcoding monitoring studies. We conducted a water eDNA survey of vertebrates in a Mediterranean watershed to identify key methodological factors influencing species richness and composition estimates. We examined the impacts of using high- versus low-capacity filtration capsules, varying levels of biological and technical replication, and the pooling of PCR replicates before indexing. The primary sources of variation identified were capsule filtration capacity and site replication across the watershed. While biological replication within sites and PCR replication also improved biodiversity estimates, their effects were comparatively smaller. Pooling PCR replicates before indexing performed more poorly than analysing them independently. Methodological impacts were stronger on terrestrial than on aquatic species. Based on these results, we recommend that priority should be given to high-capacity filtration and sampling across multiple sites. Site-level replication deserves lower priority, especially when filtering large water volumes. PCR replication is crucial for detecting rare species but should be balanced with increased site sampling and eventually site-level replication. Avoiding the pooling of PCR replicates is important to enhance sensitivity for rare species. Overall, we stress the importance of balancing methodological choices with resource constraints and monitoring goals, and we emphasise the need for research assessing methodological trade-offs in different study systems.}, }
@article {pmid40079420, year = {2025}, author = {Jurburg, SD}, title = {Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14102}, doi = {10.1111/1755-0998.14102}, pmid = {40079420}, issn = {1755-0998}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Metagenomics/methods ; Microbiota ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.}, }
@article {pmid40071381, year = {2025}, author = {da Silva, LP and Porto, M and Amorim, F and Beja, P and Mata, VA}, title = {Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14100}, doi = {10.1111/1755-0998.14100}, pmid = {40071381}, issn = {1755-0998}, support = {CEECIND/02064/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECIND/02547/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL57/2016/CP1440/CP1646/CT0018//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; NORTE-01-0246-FEDER-000063//European Regional Development Fund/ ; SR20/1575//British Ecological Society/ ; }, mesh = {*Chiroptera/physiology ; Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA, Plant/genetics/isolation &amp; purification ; Feces/chemistry ; *Plants/genetics/classification ; *Diet ; *Metagenomics/methods ; Arthropods ; }, abstract = {DNA metabarcoding is increasingly used in dietary studies, but it has limitations, such as detecting nonfood taxa. This issue is frequently mentioned in the literature but poorly understood, limiting interpretation of results and mitigation strategies. We evaluate the extent and sources of nonfood plant DNA in dietary metabarcoding, based on 281 faecal samples of a strictly insectivorous bat. We modelled plant taxa detections in relation to pollination syndromes, flowering and fruiting phenology and habitat associations, and we estimated co-occurrences between plants and arthropods. The bat arthropod diet was consistent with previous studies. Plants were detected in 82.9% of samples, representing 148 taxa, and all pollination syndromes evaluated. Plant detections were more frequent during their flowering periods, particularly for those with mixed pollination syndromes, suggesting a relationship between flowering and detectability. Fruiting had a positive, albeit weaker, effect. There was a tendency for more frequent detection of forest plants and less frequent detection of plants associated with riparian and agricultural habitats. Co-occurrences between arthropods and plants were weak and inconsistent. Our results highlight the potential for widespread detection of nonfood plant DNA in metabarcoding studies, calling for great care when analysing the plant component of diets. Specifically, we recommend: (i) implementing strategies for reducing plant contamination during field sampling; (ii) using multiple field and lab negative controls; and (iii) using ancillary information (e.g., sample visual inspection and literature review) to aid interpretation of metabarcoding results. Moreover, we recommend that studies reporting plant consumption results greatly diverging from dietary patterns obtained through other methods should include detailed explanations of methodological steps taken to exclude the confounding effects of nonfood plant DNA.}, }
@article {pmid40600049, year = {2025}, author = {Xu, H and Zhang, R and Zhang, X and Zhang, Z and Feng, Y and Lin, L}, title = {Pulmonary microbial spectrum of Burkholderia multivorans infection identified by metagenomic sequencing.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1577363}, pmid = {40600049}, issn = {2296-858X}, abstract = {PURPOSE: Burkholderia multivorans, a Gram-negative bacterium, often infect patients with severe immunocompromised and cystic fibrosis. B. multivorans infection is challenging to treat due to its ability to disrupt the action of multiple antimicrobial agents through intrinsic and acquired resistance mechanisms. A better understanding of the pulmonary microbial spectrum of B. multivorans infection is crucial for the prevention and treatment of B. multivorans.<br><br>CASE PRESENTATION: This case series reviewed the respiratory microbiome structure and alternations during the treatment of B. multivorans infection through metagenomic next-generation sequencing (mNGS). Analysis of mNGS data of 19 pharyngeal secretion samples collected from the 3 COVID-19 patients at different time points showed that the relative abundance of B. multivorans was fluctuated and eventually increased, indicating the possible development of drug resistance. A total of 40 antibiotic-resistant genes (ARGs) were detected. Significantly, the levels of CEOA, CEOB, and OPCM were consistent with the trends in the relative abundance of B. multivorans. Besides, we described nine previously uncharacterized non-synonymous mutations in PenA of B. multivorans. These mutations lead to amino acid changes Thr32Ala, Ala43Ser, Gln105Arg, Asn202Ser, Gln219Arg, Gly241Ala, Val259Ala, Thr279Ala, and Ser298Ile that may associate with resistance to &#x3b2;-lactam antibiotics.<br><br>CONCLUSION: This report shed light on the importance of rapidly diagnosis and treatment of B. multivorans infection. mNGS serve as a powerful microbial detection tool that provides a comprehensive, sensitive, and rapid method for pathogen detection and drug resistance analysis.}, }
@article {pmid40599704, year = {2025}, author = {Klimczuk, A and Chattoo, S and Izugbara, C and Klimczuk-Kochańska, M and Toczyski, P and Kumar, A and Kanozia, R and Gawron, GP and Ozair, A}, title = {Editorial: Towards 2030: sustainable development goal 3: good health and wellbeing. A sociological perspective.}, journal = {Frontiers in sociology}, volume = {10}, number = {}, pages = {1616878}, pmid = {40599704}, issn = {2297-7775}, }
@article {pmid40599650, year = {2025}, author = {Zhang, H and Zheng, X and Huang, Y and Zou, Y and Zhang, T and Repo, MA and Yin, M and You, Y and Jie, Z and Xu, WA}, title = {Novel potential biomarkers for predicting childhood caries via metagenomic analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1522970}, pmid = {40599650}, issn = {2235-2988}, mesh = {Humans ; *Dental Caries/diagnosis/microbiology ; Child ; *Biomarkers/analysis ; *Metagenomics/methods ; Saliva/microbiology ; Female ; Male ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; }, abstract = {BACKGROUND: Dental caries is a prevalent global health issue, particularly among children, with significant oral and overall health implications. The oral microbiome is considered a critical factor in caries development, with various microbial species implicated in the disease process.<br><br>OBJECTIVES: This study aims to explore the changes and interactions of oral microbiota in childhood caries using metagenomic analysis, and identify potential biomarkers for early caries detection and treatment.<br><br>METHODS: Saliva samples were collected from 241 children aged 6 to 9 years, categorized into caries-free (CF), low-caries (CL), and caries-severe (CS) groups. Metagenomic sequencing was performed to analyze the oral microbiome, followed by a series of statistical and functional analyses to characterize microbial diversity and function.<br><br>RESULTS: The study revealed significant differences in the microbial community composition among the groups, with the CS group exhibiting higher alpha and beta diversity than that of the CF group. Numerous unclassified microorganisms, such as Campylobacter SGB19347 and Catonella SGB4501, are intimately linked to dental caries and display intricate interaction networks, suggesting the potential formation of a distinct ecological network. In functional assessment, we identified a possible link between pectin and caries, suggesting that microorganisms that produce pectinase enzymes might play a role in the advancement of severe dental caries. Additionally, we identified 16 species as the best marker for severe dental caries, achieving an impressive AUC of 0.91.<br><br>CONCLUSION: The role of microbiota in dental caries is multifaceted, involving a complex interplay of microbial species and functions. Our findings enhance the understanding of the microbial basis of dental caries and offer potential diagnostic and therapeutic targets. The predictive capacity of the identified biomarkers warrants further investigation for early caries detection and intervention.<br><br>CLINICAL SIGNIFICANCE: The identification of novel biomarkers through metagenomic analysis enables early detection and targeted intervention for childhood caries, potentially transforming children dental care and significantly improving long-term oral health outcomes.}, }
@article {pmid40599424, year = {2025}, author = {Pérez-Valera, E and Elhottová, D}, title = {Dataset of 111 metagenome-assembled genomes from cattle manure, soil and manured soil samples.}, journal = {Data in brief}, volume = {61}, number = {}, pages = {111748}, pmid = {40599424}, issn = {2352-3409}, abstract = {This data report presents 111 metagenome-assembled genomes (MAGs) reconstructed from manure, soil and manured soil samples from microcosms after enriching for non-fermenting Gram-negative bacteria (NFGNB). Two independent microcosm experiments were conducted to investigate the spread of NFGNB from the fresh manure of dairy cows under antibiotic prophylaxis to the pasture soil of two organic farms. After sampling the microcosms on days 2, 14 and 28, the manure and soil samples were plated in duplicate on CHROMagar Acinetobacter medium for NFGNB enrichment and incubated at 28°C for 24 h. DNA was extracted from the cultures and sequenced using the Illumina NovaSeq 6000 platform with 150-bp paired-end reads. Reads were assembled with metaSPAdes both individually and by co-assembly. MAGs were reconstructed using MetaBAT, MaxBin, SemiBin2, COMEbin, and AVAMB, and then de-replicated at >95 % ANI (pairwise comparisons) using dRep. A total of 111 MAGs of at least medium quality (MIMAG standard) were obtained. These included 10 high-quality MAGs (>90 % completeness, <5 % contamination, rRNA genes and tRNA for at least 18 amino acids), 47 putative high-quality MAGs (>90 % completeness, <5 % contamination) and 54 medium-quality MAGs (>50 % completeness, <10 % contamination). The FASTA files of the MAGs as well as their taxonomic identifications, completeness and contamination, origin, genomic statistics and rRNA sequences are publicly available in a Zenodo dataset and the genomes in the NCBI database. The majority of MAGs (99) were assigned to Pseudomonadota, mainly Pseudomonas (28 MAGs), Stenotrophomonas (20 MAGs) and Acinetobacter (18 MAGs), while the remaining 12 MAGs belonged to Bacteroidota. Most MAGs (44) were of manure origin, followed by manured soil (38 MAGs) and soil (29 MAGs). High-quality MAGs were predominantly obtained from manure (6 high-quality, 21 putative high-quality), compared to manured soil (3 high-quality, 12 putative high-quality) and soil (1 high-quality, 14 putative high-quality). By providing their MAGs, this dataset offers a valuable resource for researchers investigating the genomic characteristics associated with the survival, environmental dispersal and ecological role of potentially hazardous NFGNB species in soil, particularly following the application of antibiotic-treated animal manure, and for comparative genomics studies in related environments.}, }
@article {pmid40598913, year = {2025}, author = {Ni, N and Qiu, J and Ge, W and Guo, X and Zhu, D and Wang, N and Luo, Y}, title = {Fibrous and Fragmented Microplastics Discharged from Sewage Amplify Health Risks Associated with Antibiotic Resistance Genes in Aquatic Environments.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c01335}, pmid = {40598913}, issn = {1520-5851}, abstract = {Wastewater treatment plants (WWTPs) are key sources of antibiotic resistance genes (ARGs) and microplastics (MPs) in aquatic environments. However, field data on ARG-MP copollution remain scarce, hindering environmental risk assessment of ARGs. This study used metagenomic sequencing and high-throughput qPCR to examine the composition and association of ARGs and MPs in sewage discharge-receiving waters. The results indicated that sewage discharge significantly increased the abundance of ARG-MP complexes in receiving waters, with fibrous and fragmented MPs exhibiting enhanced ARG enrichment and thereby serving as selective vectors for pathogens. Effluents promoted plasmid-mediated gene transfer and microbial functional shifts, driving intracellular ARG proliferation in the plastisphere. Fibrous and fragmented MPs showed strong co-occurrence patterns with ARGs, virulence factor genes, and mobile genetic elements, suggesting their role in antimicrobial resistance dissemination. A projection pursuit regression model indicated effluent-induced MP risk escalation at the estuary and downstream areas, which was associated with fragmented and polyamide MPs. Notably, WWTPs released substantial extracellular ARGs, with MPs potentially serving as a protective niche and a proliferative microenvironment. Here, we determined the role of WWTPs in shaping the aquatic resistome via MPs, which provides critical data for risk assessment and control strategies.}, }
@article {pmid40598608, year = {2025}, author = {Liu, F and McNally, J and Flemming, D and Ingham, AB and Hunt, PW and Li, RW}, title = {Escherichia coli is implicated in the development and manifestation of host susceptibility to the roundworm Trichostrongylus colubriformis infections in sheep.}, journal = {Veterinary research}, volume = {56}, number = {1}, pages = {133}, pmid = {40598608}, issn = {1297-9716}, support = {58-8042-3-022-F//Agricultural Research Service/ ; 242102311161//Henan Provincial Science and Technology Research Project/ ; }, mesh = {Animals ; *Sheep Diseases/parasitology/microbiology/immunology ; Sheep ; *Trichostrongylosis/veterinary/parasitology/immunology ; *Trichostrongylus/physiology ; *Escherichia coli/physiology ; *Gastrointestinal Microbiome ; Disease Susceptibility/veterinary/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; }, abstract = {Applied breeding for host resistance to gastrointestinal nematodes represents a cost-effective strategy for parasitic control. While resistance is under moderate genetic influences, gut microbial components involved in the development of resistance or susceptibility remain largely unknown. Here we characterize the structure and metabolic potential of the proximal colon microbiota in unique ovine populations bred for resistance and susceptibility using a full-length 16S rRNA gene sequencing-based microbiome approach. The resistant lambs produced significantly fewer parasite eggs than susceptible animals grazing on the same pasture. Further, the resistant lambs displayed a significant reduction in worm establishment in response to a Trichostrongylus colubriformis challenge infection (P < 0.0001; N = 20 per group). Among 32 bacterial species or strains displaying a significant difference in relative abundance between the resistant and susceptible group, E. coli was more abundant in susceptible lambs. E. coli was also ranked as the most important species in distinguishing the resistant and susceptible status. Moreover, a microbial signature or balance consisting of E. coli (Numerator) and Parabacteroides distasonis and Bacteroides thetaiotaomicron (Denominator) predicted the resistance status with high accuracy. The metagenome function prediction also revealed that several pathways related to infectious diseases, such as Shigellosis and pathogenic E. coli infection, were significantly altered between the two phenotypes. Our findings demonstrated that microbial signatures with a high predictive power for the resistance status can be developed as biomarkers to facilitate the selection for host resistance in sheep.}, }
@article {pmid40598447, year = {2025}, author = {Bulzu, PA and Henriques Vieira, H and Ghai, R}, title = {Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {154}, pmid = {40598447}, issn = {2049-2618}, support = {25-15920S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 24-11998S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-12496X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, mesh = {*Cryptophyta/virology/genetics ; Metagenomics ; Phylogeny ; Genome, Viral ; Photosynthesis ; *Giant Viruses/genetics/classification ; *DNA Viruses/genetics/classification ; }, abstract = {BACKGROUND: Polinton-like viruses (PLVs) are diverse eukaryotic DNA viral elements (14-40 kb) that often undergo significant expansion within protist genomes through repeated insertion events. Emerging evidence indicates they function as antiviral defense systems in protists, reducing the progeny yield of their infecting giant viruses (phylum Nucleocytoviricota) and influencing the population dynamics and evolution of both viruses and their hosts. While many PLVs have been identified within the genomes of sequenced protists, most were recovered from metagenomic data. Even with the large number of PLVs identified from metagenomic data, their host-virus linkages remain unknown owing to the scarcity of ecologically relevant protist genomes. Additionally, the extent of PLV diversification within abundant freshwater taxa remains undetermined. In order to tackle these questions, high-quality genomes of abundant and representative taxa that bridge genomic and metagenomic PLVs are necessary. In this regard, cryptophytes, which are among the most widely distributed, abundant organisms in freshwaters and have remained largely out of bounds of genomic and metagenomic approaches, are ideal candidates for investigating the diversification of such viral elements both in cellular and environmental context.<br><br>RESULTS: We leveraged long-read sequencing to recover large (200-600&#xa0;Mb), high-quality, and highly repetitive (>&#x2009;60%) genomes of representative freshwater and marine photosynthetic cryptophytes. We uncovered over a thousand complete PLVs within these genomes, revealing vast lineage-specific expansions, particularly in the common freshwater cryptophyte Rhodomonas lacustris. By combining deep sequence homology annotation with biological network analyses, we discern well-defined PLV groups defined by characteristic gene-sharing patterns and the use of distinct strategies for replication and integration within host genomes. Finally, the PLVs recovered from these cryptophyte genomes also allow us to assign host-virus linkages in environmental sequencing data.<br><br>CONCLUSIONS: Our findings provide a primer for understanding the evolutionary history, gene content, modes of replication and infection strategies of cryptophyte PLVs, with special emphasis on their expansion as endogenous viral elements (EVEs) in freshwater bloom-forming R. lacustris. Video Abstract.}, }
@article {pmid40598440, year = {2025}, author = {Lin, Z and Zhou, X and Lu, T and An, W and Chen, S and Li, S and Miao, H and Han, X}, title = {Co-cultivation of Lactobacillus acidophilus and Bacillus subtilis mediates the gut-muscle axis affecting pork quality and flavor.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {93}, pmid = {40598440}, issn = {1674-9782}, abstract = {BACKGROUND: Pork quality and flavor are critical determinants of consumer preference, yet the role of gut microbiota in shaping meat characteristics remains underexplored. In this study, we investigated how a probiotic consortium (FAM: Lactobacillus acidophilus and Bacillus subtilis) modulates the gut-muscle axis to enhance pork flavor.<br><br>RESULTS: In finishing pigs, FAM supplementation significantly increased flavor-associated nucleotides and umami-enhancing amino acids in longissimus dorsi muscle. Metagenomic analysis revealed FAM-driven enrichment of glycan-degrading Prevotella and short-chain fatty acid-producing Phascolarctobacterium, accompanied by reduced antibiotic resistance genes and virulence factors. Spearman correlation linked Prevotella copri abundance with elevated muscle amino acids, suggesting microbial-encoded CAZymes as key mediators.<br><br>CONCLUSIONS: This study provides the first evidence that probiotic-induced gut microbiota remodeling enhances pork flavor through metabolic cross-talk&#xa0;along the gut-muscle axis. The findings suggest a novel strategy for improving pork quality via dietary interventions targeting gut microbiota.}, }
@article {pmid40598319, year = {2025}, author = {Maeke, MD and Yin, X and Wunder, LC and Vanni, C and Richter-Heitmann, T and Miravet-Verde, S and Ruscheweyh, HJ and Sunagawa, S and Fabian, J and Piontek, J and Friedrich, MW and Hassenrück, C}, title = {Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {155}, pmid = {40598319}, issn = {2049-2618}, support = {EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; XJ2300006031//Start-up research fund of Hainan University, China/ ; LT0050/2023-L//Human Frontier Science Program/ ; 205320_215395//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 03F0814//German Federal Ministry of Education and Research (BMBF)/ ; 03F0848A//German Federal Ministry of Education and Research (BMBF)/ ; }, mesh = {Phylogeny ; *Geologic Sediments/microbiology ; *Archaea/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Data Mining/methods ; Metagenome ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Rare species, especially of the marine sedimentary biosphere, have long been overlooked owing to the complexity of sediment microbial communities, their sporadic temporal and patchy spatial abundance, and challenges in cultivating environmental microorganisms. In this study, we combined enrichments, targeted metagenomic sequencing, and extensive data mining to uncover uncultivated members of the archaeal rare biosphere in marine sediments.<br><br>RESULTS: In protein-amended enrichments, we detected the ecologically and metabolically uncharacterized class Candidatus Penumbrarchaeia within the phylum Thermoplasmatota. By screening more than 8000 metagenomic runs and 11,479 published genome assemblies, we expanded the phylogeny of Ca. Penumbrarchaeia by 3 novel orders. All six identified families of this class show low abundance in environmental samples characteristic of rare biosphere members. Members of the class Ca. Penumbrarchaeia were predicted to be involved in organic matter degradation in anoxic, carbon-rich habitats. All Ca. Penumbrarchaeia families contain high numbers of taxon-specific orthologous genes, highlighting their environmental adaptations and habitat specificity. Besides, members of this group exhibit the highest proportion of unknown genes within the entire phylum Thermoplasmatota, suggesting a high degree of functional novelty in this class.<br><br>CONCLUSIONS: In this study, we emphasize the necessity of targeted, data-integrative approaches to deepen our understanding of the rare biosphere and uncover the functions and metabolic potential hidden within these understudied taxa. Video Abstract.}, }
@article {pmid40597897, year = {2025}, author = {Wang, X and Xie, Y and Chen, M and Zhu, H and He, G and Yu, W and Qiao, D and Shen, Y and Song, L and Deng, Q}, title = {The complex diagnosis of post-dialysis fever: a case report and literature review of infective endocarditis in a dialysis patient.}, journal = {BMC nephrology}, volume = {26}, number = {1}, pages = {331}, pmid = {40597897}, issn = {1471-2369}, support = {2024-KHRCBZ-B15 and 2024-KHRCBZ-B08//Science and Technology plan project of the First People' s Hospital of Yunnan Province/ ; 82460150//National Natural Science Foundation of China/ ; 202401AU070048//Yunnan Fundamental Research Projects/ ; }, mesh = {Humans ; Male ; Aged ; *Renal Dialysis/adverse effects ; *Kidney Failure, Chronic/therapy ; *Fever/etiology/diagnosis/microbiology ; *Endocarditis, Bacterial/diagnosis/microbiology ; *Endocarditis/diagnosis ; }, abstract = {BACKGROUND: Post-dialysis fever is a common but diagnostically challenging issue in hemodialysis patients, with potential causes including dialysis-related infections, pulmonary infections, and cardiovascular complications.<br><br>CASE PRESENTATION: We report a 76-year-old male with end-stage renal disease (ESRD) on maintenance hemodialysis, coronary artery disease, and prior cardiac stent implantation, who presented with recurrent post-dialysis fever. Despite persistently negative conventional cultures, metagenomic next-generation sequencing (NGS) of pre-dialysis blood samples identified Pseudomonas aeruginosa (P. aeruginosa), Cutibacterium acnes (C. acnes; formerly Propionibacterium acnes), Staphylococcus epidermidis (S. epidermidis), and Corynebacterium accolens (C. accolens) and Epstein-Barr virus (EBV), while post-dialysis samples revealed only C. acnes and EBV. Given the temporal association with fever, these two pathogens were considered the primary causative agents. Subsequent transesophageal echocardiography (TEE) confirmed aortic valve vegetations, establishing the diagnosis of infective endocarditis (IE). Following targeted antimicrobial and antiviral adjustments based on NGS findings, the patient exhibited complete resolution of post-dialysis fever and was discharged. However, as the vegetation was not surgically removed, he was hospitalized multiple times over the following five months for recurrent infections and ultimately died of septic shock and multi-organ failure due to carbapenem-resistant Klebsiella pneumoniae.<br><br>CONCLUSIONS: This case underscores the complementary role of TEE and NGS in diagnosing IE in high-risk patients, enabling the detection of uncommon pathogens and informing targeted therapy to improve clinical outcomes.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40597620, year = {2025}, author = {Yang, L and Yan, Y and Shen, J and Xia, Y and Lang, F and Chen, C and Zou, W}, title = {Metagenomic insights into microbial community succession and its functional changes during the stage of acetic acid fermentation of shanxi aged vinegar.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {374}, pmid = {40597620}, issn = {1471-2180}, support = {20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; }, mesh = {*Acetic Acid/metabolism ; Fermentation ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Acetobacter/metabolism/genetics ; Metabolic Networks and Pathways ; *Microbiota/genetics ; Food Microbiology ; Metagenome ; }, abstract = {Traditional fermentation of Shanxi aged vinegar involves complex microbial interactions driving flavor synthesis, but the mechanisms underpinning metabolic adaptation and community succession remain poorly characterized. This study aimed to unravel stage-specific microbial dynamics and their functional contributions to flavor formation during Cupei fermentation. Metagenomic sequencing analyzed microbial communities and metabolic pathways at three fermentation stages (D3, D6, D9). Functional annotation (KEGG, CAZy) and species-level contribution assessments identified key taxa and genes linked to flavor biosynthesis. Microbial succession shifted from Lactobacillus dominance (64.68% at D3) to Acetobacter prevalence (48.04% at D9), with Lactobacillus acetotolerans persisting throughout (17.15-26.23%). Early-stage carbohydrate metabolism (GHs-driven: 60.38% at D3) transitioned to late-stage amino acid (15.62%) and cofactor synthesis (12.17%), activating valine, leucine, and histidine pathways critical for flavor compounds. Acetobacter oryzoeni and Acetobacter pomorum drove acetate (ALDH: 27.07-41.52%), valine (ilvE: 53.21-20.22%), and histidine (hisD: 41.83-33.30%) metabolism at D9. Low abundance species (Weissella confusa, 0.51%) and uncultured Limosilactobacillus sp. contributed via multi-gene networks (e.g., dat, ldh), which revealed an important functional contribution by overlooked low-abundance species. The study uncovers ecological coupling between microbial succession and metabolic adaptation, where dominant taxa and rare species synergistically govern flavor formation. These insights enable targeted microbial community design for flavor optimization in traditional fermented foods.}, }
@article {pmid40597432, year = {2025}, author = {Ehau-Taumaunu, H and Bell, TH and Sadeghi, J and Hockett, KL}, title = {Rapid and sustained differentiation of disease-suppressive phyllosphere microbiomes in tomato following experimental microbiome selection.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {77}, pmid = {40597432}, issn = {2524-6372}, support = {492F//PA Vegetable Growers Association/ ; 1016871//National Institute of Food and Agriculture/ ; }, abstract = {BACKGROUND: Microbial-based treatments to protect plants against phytopathogens typically focus on soil-borne disease or the aboveground application of one or a few biocontrol microorganisms. However, diverse microbiomes may provide unique benefits to phytoprotection in the phyllosphere, by restricting pathogen access to niche space and/or through multiple forms of direct antagonism. We previously showed that successive experimental passaging of phyllosphere microbiomes along with the phytopathogen Pseudomonas syringae pv. tomato (Pto), which causes bacterial speck in tomato, led to the development of a disease suppressive microbial community. Here, we used amplicon sequencing to assess bacterial and fungal composition at the end of each passage, as well as shotgun metagenomics at key passages based on observed disease-suppressive phenotypes, to assess differences in functional potential between suppressive and non-suppressive communities.<br><br>RESULTS: Bacterial composition changed and diversity declined quickly due to passaging and remained low, particularly in treatments with Pto present, whereas fungal diversity did not. Pseudomonas and Xanthomonas populations were particularily enriched in disease-suppressive microbiomes compared to conducive microbiomes. The relative abundance of Pseudomonas syringae group gemonosp. 3 (the clade to which the introduced pathogen belongs) in shotgun metagenomic data was similar to what we observed for Pseudomonas ASVs in the 16S rRNA gene dataset. We also observed an increase in the abundance of genes associated with microbial antagonism at Passage 4, corresponding to the highest observed disease severity.<br><br>CONCLUSIONS: Taxonomic richness and evenness were low within samples, with clustering occurring for suppressive or non-suppressive microbiomes. The relative abundance of genes associated with antagonism was higher for disease-suppressive phyllosphere microbiomes. This work is an important step towards understanding the microbe-microbe interactions within disease-suppressive phyllosphere communities.}, }
@article {pmid40597414, year = {2025}, author = {Kadyan, S and Park, G and Singh, TP and Patoine, C and Singar, S and Heise, T and Domeier, C and Ray, C and Kumar, M and Behare, PV and Chakrabarty, P and Efron, P and Sheffler, J and Nagpal, R}, title = {Microbiome-based therapeutics towards healthier aging and longevity.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {75}, pmid = {40597414}, issn = {1756-994X}, mesh = {Humans ; *Longevity ; *Gastrointestinal Microbiome ; *Healthy Aging ; *Aging ; *Microbiota ; Animals ; }, abstract = {The gut microbiome is our lifetime companion, regulating our health from birth throughout the lifespan. The gut microbiome composition changes continually with age, influencing both physiological and immunological development. Emerging evidence highlights the close association, and thus implication, of the microbiome with healthy disease-free aging and longevity. Accordingly, targeting the gut microbiome is emerging as a promising avenue to prevent, alleviate, and ameliorate aging-related disorders. Herein, we provide a prospective and inclusive framework of the close connection of the gut microbiome with human aging, while contemplating how this association is intertwined with age-related diseases. We delve into recently emerging and potential microbiome-based therapeutics that are projected to aid in alleviating myriad aging-related diseases, thereby enhancing the health and well-being of the aging population. Finally, we present a foundation and perspective underlining the prospects of microbiome-based therapeutics developed and tailored precisely for the elderly, with the overarching goal of promoting health and longevity.}, }
@article {pmid40597335, year = {2025}, author = {Drake, MJ and Pierdon, M and DeMers, G and Daniel, SG and Bittinger, K and Redding, LE}, title = {The effect of dietary zinc on the microbiome and resistome of the gestating sow and neonatal piglets.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {71}, pmid = {40597335}, issn = {2524-4671}, abstract = {Zinc is an important trace element for animal health and physiology, and it is routinely provided as a supplement in livestock diets. High levels of dietary zinc have been found to be beneficial for weanling pigs in preventing diarrhea and improving growth. It has also been associated with better reproductive performance in gestating sows and survival of neonatal piglets. However, little is known about zinc's effect on the microbiome of the gestating sow and her neonatal piglets. Even less is known about its effects on the sow and piglet resistome, which is important because dietary zinc can co-select for antimicrobial resistance. The goal of this randomized controlled dietary feeding trial was to assess the effect of high levels of dietary zinc in the last week of gestation on the microbiomes and resistomes of the gestating sow and her neonatal piglets. Seventy-three gestating sows were randomized to receive a diet with standard zinc levels (125 ppm) or high zinc levels (2500 ppm) approximately one week prior to their anticipated farrowing date. Fecal samples were collected from sows at enrollment and at farrowing and from piglets within 3 days of parturition. Fecal samples underwent 16sS rRNA gene sequencing, and a subset of samples underwent shotgun metagenomic sequencing. Statistically significant differences in richness, diversity and taxonomic composition were observed over time, and sows in the treatment group had significantly higher alpha diversity at farrowing (p = 0.04) and significantly altered levels of 3 taxa (Turicibacter, unclassified Clostridiaceae, and unclassified Christensenellaceae). Several antimicrobial resistance genes were significantly more abundant in the zinc group at farrowing compared to the control group, including tetracycline resistance genes [tet(O); tet(W); tet(32); tet(O/W)]; aminoglycoside resistance genes (APH(3')-IIIa), macrolide-lincosamide-streptogramin (MLS) resistance genes (lsaB; macB); and others (kdpE, Pseudomonas aeruginosa CpxR). No significant differences were observed in the piglet microbiomes or resistomes across sow treatment groups. Overall, high levels of dietary zinc had modest effects on the sow microbiome during the feeding trial. Increases in antimicrobial resistance genes in zinc supplemented sows suggest that supranutritional levels of dietary zinc should be avoided in gestating sows.}, }
@article {pmid40597307, year = {2025}, author = {Wang, Z and Wang, W and Wang, Y and Hu, H and Wang, B and Zhu, W and Li, X and Hou, X and Sun, W and Liu, Z and Lu, S and Chen, X}, title = {Mapping gut microbiota and metabolite alterations in patients with postmenopausal osteoporosis in the Beijing Community of China.}, journal = {European journal of medical research}, volume = {30}, number = {1}, pages = {539}, pmid = {40597307}, issn = {2047-783X}, support = {No.2020YFC2004900//National Key Research and Development Program of China/ ; H0608//National Natural Science Foundation of China/ ; No.81672201, 81871794//Natural Science Foundation of China/ ; No.7242065//Beijing Natural Science Foundation/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Osteoporosis, Postmenopausal/microbiology/metabolism/epidemiology ; Middle Aged ; Aged ; Bone Density ; Beijing ; China ; Feces/microbiology ; }, abstract = {INTRODUCTION: Postmenopausal osteoporosis (PMO) is a chronic disease in the elderly women, which has been shown to be related to the gut microbiota (GM) alternation in recent studies. Few studies have investigated which specific bacterial species and metabolites have an impact on postmenopausal osteoporosis patients, especially in urban communities.<br><br>METHODS: With the aim of comprehending GM features and metabolite variation in women suffering from PMO in the Beijing Community of China, we divided the 76 eligible participants into osteoporosis (OP) and health control (HC) groups taking into account the bone mineral density (BMD), and adopted 16 S rRNA gene sequencing and metagenomic sequencing to examine the GM compositions in the respective groups. Besides, the study adopted liquid chromatography and mass spectrometry (LC-MS) for the fecal metabolite analysis.<br><br>RESULTS: The OP group presented obviously changed bacterial &#x3b1;-diversity and &#x3b2;-diversity versus the HC group. GM at the genus level was differentially enriched in the OP or HC groups. Megamonas genus exhibited the strongest positive relevance to BMD and OC. Bacteroides genus had the strongest negative relevance to BMD and positive relevance to &#x3b2;-CTX. GM at the species level was also differentially enriched in OP or HC groups. After multiple linear regression analysis, Roseburia_intestinalis and Glycoursodeoxycholic acid were positively associated with BMD, hinting their beneficial effect in BMD. Corresponding signaling pathways also exhibited an obvious change, particularly in up-regulation Glycerol Phosphate Shuttle and down-regulation Malate-Aspartate Shuttle pathways.<br><br>CONCLUSIONS: According to the results of this study, GM and metabolites in women with PMO in the Beijing Community changed dramatically, which were significantly associated with BMD and bone turnover markers. Roseburia_intestinalis and Glycoursodeoxycholic acid levels were the most positively associated with BMD. All these assist in understanding the development mechanism of PMO from new perspectives and in developing novel therapeutic methods for improving bone health.}, }
@article {pmid40596882, year = {2025}, author = {Hekker, MD and Platteel, TN and Venekamp, RP and Top, J and Geerlings, SE and Schultsz, C and de Vos, MGJ and van de Wijgert, JHHM}, title = {Urinary tract infections in postmenopausal women revisited (UTIr): a prospective observational cohort study to explore the urobiomes of postmenopausal women with and without recurrent urinary tract infections.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {822}, pmid = {40596882}, issn = {1471-2334}, support = {OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; }, mesh = {Humans ; Female ; *Urinary Tract Infections/microbiology/epidemiology ; *Postmenopause ; Prospective Studies ; Middle Aged ; Recurrence ; Vagina/microbiology ; *Microbiota ; Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; }, abstract = {BACKGROUND: Recurrent urinary tract infections (RUTI) are prevalent, particularly among postmenopausal women, and place a significant burden on the affected individuals and the healthcare system. While Escherichia coli is the primary cause of most UTIs in premenopausal women, this may not hold true for postmenopausal women. To facilitate development of novel diagnostics, preventive interventions, and clinical management of RUTI in postmenopausal women, it is essential to strengthen the biological evidence base.<br><br>METHODS: This observational prospective cohort study will enrol 20 postmenopausal women without RUTI (controls) and approximately 30 with RUTI (cases), aiming to sample at least 50 UTI episodes. Questionnaires are completed, samples (urine, vulvoperineal and vaginal swabs, and faeces) are collected by participants or study staff at five scheduled time points over one year of follow-up, as well as during and after each UTI episode. All samples will undergo 16S rRNA amplicon sequencing, with selected urine samples also subjected to bacterial culturing, metagenomic sequencing, and metabolomics. Various urobiome comparisons will be conducted, such as between women with and without RUTI in the absence of a UTI, and over time during UTIs. Urobiomes will also be compared to vaginal, vulvoperineal, and gut microbiomes in the same women at the same time points. Finally, urine samples will be cultured to obtain bacterial isolates, which will be characterised and used for co-culture and urothelium organoid experiments.<br><br>DISCUSSION: The UTIr cohort study is an exploratory, hypothesis-generating study designed to improve understanding of the ecological mechanisms driving UTI onset, response to antibiotic treatment, and UTI recurrence in postmenopausal women. The data collected from each individual woman is longitudinal and comprehensive, which is instrumental for advancing the field. The study population consists of women over the age of 50 and the study procedures are demanding. Flexibility with protocol procedures has proven to be essential to maximise retention and minimise missing data. We recommend employing a sufficiently large recruitment team and/or planning for a sufficiently long recruitment period to accommodate the demanding nature of these types of in-depth studies with vulnerable populations.<br><br>TRIAL REGISTRATION: Not applicable.}, }
@article {pmid40596444, year = {2025}, author = {Li, YC and Liu, YX and Li, L and Wang, H and Zhao, ZR and Yao, ZY}, title = {Metagenomic next-generation sequencing (mNGS) versus tissue culture technique (TCT) in diagnosis of spinal infection: a systematic review and meta-analysis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20926}, pmid = {40596444}, issn = {2045-2322}, support = {2022K57//Quzhou Science and Technology Tackling Project/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Spinal Diseases/diagnosis/microbiology ; Sensitivity and Specificity ; }, abstract = {Spinal infections pose a significant clinical challenge due to the difficulty of early diagnosis. Traditional Tissue Culture Technique (TCT) has limitations, while Metagenomic Next-Generation Sequencing (mNGS) has emerged as a promising diagnostic tool. However, reports on the diagnostic performance of mNGS and TCT for spinal infections are inconsistent, and there has been a lack of systematic analysis of the evidence. This systematic review and meta-analysis included 10 studies involving a total of 770 patients to compare the diagnostic accuracy of mNGS and TCT. A comprehensive literature search was conducted using PubMed, Embase, Web of Science, Cochrane Library, and SinoMed to identify studies evaluating the diagnostic accuracy of mNGS and TCT for spinal infections. Data were analyzed using Review Manager 5.3 and Stata 16.0 to compute the sensitivity, specificity, and Area Under the Summary Receiver Operating Characteristic Curve (AUC). The meta-analysis revealed pooled estimates for mNGS with a sensitivity of 0.81 (95% CI, 0.74-0.87), specificity of 0.75 (95% CI, 0.48-0.91), and an AUC of 0.85 (95% CI, 0.82-0.88). In contrast, pooled estimates for TCT showed a sensitivity of 0.34 (95% CI, 0.27-0.43), specificity of 0.93 (95% CI, 0.79-0.98), and an AUC of 0.59 (95% CI, 0.55-0.63). While mNGS demonstrates higher sensitivity and overall diagnostic accuracy than TCT, its lower specificity suggests that it may be most effective when used alongside conventional methods to enhance diagnostic reliability in spinal infections.}, }
@article {pmid40596159, year = {2025}, author = {Bayatian, M and Pourbabaee, AA and Amoozegar, MA}, title = {Revealing the composition of bacterial communities in various oil-contaminated soils and investigating their intrinsic traits in hydrocarbon degradation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22016}, pmid = {40596159}, issn = {2045-2322}, mesh = {*Soil Microbiology ; *Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Bacteria/genetics/classification/metabolism ; *Soil Pollutants/metabolism ; RNA, Ribosomal, 16S/genetics ; *Petroleum/metabolism ; Soil/chemistry ; *Microbiota ; Petroleum Pollution ; Iran ; High-Throughput Nucleotide Sequencing ; Phylogeny ; }, abstract = {This study explores prokaryotic diversity and oil biodegradation potential in soils from three evaporation ponds in the Ahvaz and Maroon oil fields, Iran. Despite prior studies on prokaryotic diversity in contaminated soils, systematic comparisons within the same region remain limited. The analysis identified distinct physicochemical differences across sites. Ahvaz 1 soil, with a loamy silty clay texture, had the highest salinity (15.4%) and total petroleum hydrocarbons (TPH, 3.5%). Ahvaz 4 soil, loamy silty in texture, showed 7.49% salinity and 1% TPH, while Maroon 3 soil exhibited the lowest salinity (5.06%) and TPH (0.5%). Prokaryotic diversity and biodegradation traits were assessed using 16S rRNA next-generation sequencing (NGS) and qPCR, respectively. NGS revealed reduced prokaryotic diversity in all contaminated soils, with Bacillota dominating, whereas Pseudomonadota prevailed in all control samples. Maroon 3 soils had higher diversity, but Cyanobacteria and Actinomycetota, dominant in controls, were replaced by Chloroflexota, Gemmatimonadota, and Acidobacteriota in polluted soils. At the genus level, Bacillus, Lysinibacillus, Virgibacillus, Brevibacillus, and Paenibacillus showed increased abundance in contaminated soils. Real-time PCR of alkB and C23DO genes indicated enhanced hydrocarbon degradation potential. FAPROTAX and PICRUSt2 analyses revealed enhanced microbial capacity for hydrocarbon degradation in polluted soils, with enriched functions related to chemoheterotrophy, aromatic compound degradation, and increased levels of alkane 1-monooxygenase, alcohol dehydrogenase, and protocatechuate 4,5-dioxygenase subunits. The findings highlight crude oil's impact on microbial community structure, reducing archaea and emphasizing bacterial dominance while underscoring shifts in microbial responses and functional gene expression in hydrocarbon degradation.}, }
@article {pmid40595658, year = {2025}, author = {Zhang, Z and Liu, Y and Zhao, W and Liu, K and Chen, Y and Wang, F and Mao, G and Ji, M}, title = {Distinct genes and microbial communities involved in nitrogen cycling between monsoon- and westerlies-dominated Tibetan glaciers.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5926}, pmid = {40595658}, issn = {2041-1723}, support = {42421001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42330410//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20176//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Tibet ; *Nitrogen Cycle/genetics ; *Ice Cover/microbiology ; *Microbiota/genetics ; Nitrogen/metabolism ; Metagenome/genetics ; Climate Change ; Bacteria/genetics/metabolism/classification ; Temperature ; Nitrous Oxide/metabolism ; Nitrogen Fixation/genetics ; Transcriptome ; }, abstract = {The Tibetan Plateau (TP) glaciers are influenced by monsoon and westerlies. They are highly sensitive to climate change, with atmospheric nitrogen deposition significantly impacting microbial communities and functions. However, key uncertainties persist regarding biogeography and drivers of genes and microbial communities involved in nitrogen cycling. Here, we investigate the diversity and transcriptional activity of microbial communities and nitrogen-cycling genes using 85 metagenomes and 28 metatranscriptomes from the ablation zone of 21 TP glaciers. Our results show that over 90% of the glacial taxa possess the potential for nitrogen metabolism, with ~33% exhibiting transcriptional activity. Moreover, monsoon-dominated glaciers present greater microbial diversity and higher prevalence of nitrogen-fixing genes than westerlies-dominated glaciers, linked to higher temperatures. Comparatively, the latter show elevated genomic potential for nitrous oxide emissions, likely due to higher nitrate concentrations. These findings establish temperature-nitrogen co-regulation of microbial nitrogen transformations, critical for predicting climate feedback in the extreme environment.}, }
@article {pmid40595444, year = {2025}, author = {Minabou Ndjite, G and Jiang, AK and Ravel, CT and Grant, MR and Jiang, X and Hall, B}, title = {Gut microbial utilization of the alternative sweetener, D-allulose, via AlsE.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {970}, pmid = {40595444}, issn = {2399-3642}, support = {1R35GM155208-01//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Sweetening Agents/metabolism ; *Fructose/metabolism ; Adult ; *Clostridium/genetics/enzymology/metabolism ; }, abstract = {D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phosphate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE, but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3079 adult healthy human metagenomic samples that we analyzed contained alsE, suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE, supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE, and manage glycemic response while reducing gastrointestinal distress.}, }
@article {pmid40595289, year = {2025}, author = {Kador, SM and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Rahman, MS and Islam, OK and Islam, MT}, title = {Abundance and transmission of antibiotic resistance and virulence genes through mobile genetic elements in integrated chicken and fish farming system.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20953}, pmid = {40595289}, issn = {2045-2322}, support = {22-FoBST 05//Research Cell, Jashore University of Science and Technology/ ; SRG-221252//Special Research Grant, Ministry of Science and Technology, Bangladesh/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Interspersed Repetitive Sequences/genetics ; Aquaculture ; Fishes ; *Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/pathogenicity/drug effects ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Virulence/genetics ; Bangladesh ; }, abstract = {Integrated chicken and fish farming systems, common in Bangladesh, present significant public health risks due to the spread of antimicrobial resistance genes (ARGs) and virulence factors (VFGs) through mobile genetic elements (MGEs). This study employs metagenomic sequencing to explore the diversity and abundance of ARGs, VFGs, and MGEs in various environmental samples from these farming systems. A total of 384 ARGs were detected, with tetracycline resistance genes such as tetM and tetX being the most abundant, alongside macrolide-lincosamide-streptogramin and aminoglycoside resistance genes. Droppings harbored the highest proportion of ARGs (62.2%), whereas sediment served as a reservoir for multi-metal resistance genes. Virulence factors associated with immune modulation, such as pvdL and tssH, and biofilm formation genes like algC were particularly prevalent in sediment and droppings. Among MGEs, plasmids and transposons like Tn6072 and Tn4001 were the most abundant, playing a critical role in horizontal gene transfer. Bacterial genera including Bacteroides, Clostridium, and Escherichia were strongly associated with MGEs, indicating their role in the dissemination of resistance and virulence traits. Statistical analyses revealed significant differences in the abundance of ARGs, VFGs, and MGEs across sample types, with sediment and droppings identified as hotspots for gene exchange. These findings underscore the urgent need for improved antibiotic stewardship and waste management practices to limit the spread of antimicrobial resistance and pathogenic bacteria within integrated farming environments.}, }
@article {pmid40595004, year = {2025}, author = {Raina, TK and Gupta, M and Salgotra, RK}, title = {Metagenomic analysis to identify unique microbes in the rhizosphere of basmati rice (Oryza sativa L.) accessions.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22864}, pmid = {40595004}, issn = {2045-2322}, mesh = {*Oryza/microbiology/genetics ; *Rhizosphere ; *Metagenomics/methods ; Soil Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Odorants/analysis ; Microbiota ; }, abstract = {The captivating aroma of basmati rice is highly favoured by consumers across the globe. Unfortunately, the aroma of basmati rice has been gradually diminishing over time due to the excessive use of inorganic fertilizers and the impact of climate change. To understand the microbial community that plays a significant role in aroma enhancement in basmati rice accessions, a systematic study is required. A unique rhizobacteria of basmati rice associated with basmati rice were Actinobacteria, Bacillus subtilis, Burkholderia, Enterobacter, Klebsiella, Lactobacillus, Micrococcus, Pseudomonas, and Sinomonas. The biosynthesis of potential precursors (ornithine, putrescine, proline, and polyamines) of aroma in basmati rice involved various enzymes such as acetylornithine aminotransferase, acetylornithine deacetylase, N-acetylornithine carbomyltransferase, acetylornithine/succinyldiaminopimelate aminotransferase, and ornithine cyclodeaminase. These findings significantly contribute to the existing understanding of the rhizobacteria associated with basmati rice that play a crucial role in enhancing the aroma. The introduction of these cultures into the basmati rice growing areas has the potential to augment the plant growth and enhances the aroma. The present study explored the functional potential of the microbial community associated with aroma improvement in basmati rice. This will also enhance the export potential of the basmati rice in the region on sustainable basis.}, }
@article {pmid40594802, year = {2025}, author = {Deka, NC and Kumari, G and Nath, T}, title = {Microbial dynamics in rice ecosystem under supplementation of organic sources of nitrogen with inorganics and their concomitant impact on yield.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20473}, pmid = {40594802}, issn = {2045-2322}, }
@article {pmid40594590, year = {2025}, author = {Lan, N and Mao, C and Chen, M and Wang, X and Bai, S and Ren, J}, title = {Metagenomic insights into resistance trends related to microbial VB12 synthesis in eutrophic urban lakes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20599}, pmid = {40594590}, issn = {2045-2322}, support = {2023-YBSF-666//Scientific and Technological Research Foundation of Shaan'xi Province, Key Research and Development Project/ ; 2021A011//Shaanxi Provincial Key Research and Development Plan Project/ ; YXJLRH2022006//Basic and Clinical Integration Innovation Project of Xi' an Jiao tong University/ ; TQ202205//Nanjing Tianqing Scientific Research Fund of First Affliated Hospital of Xi'an Jiaotong University/ ; }, mesh = {*Lakes/microbiology ; *Metagenomics/methods ; *Metagenome ; *Vitamin B 12/biosynthesis/genetics ; Eutrophication ; Humans ; *Bacteria/genetics/metabolism ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Vitamin B12 (VB12) is essential for human health, and its deficiency can lead to various health issues, including anemia and neurological problems. Additionally, the presence of antibiotic resistance genes in various environments raises concerns about the spread of antibiotic resistance. This study aims to explore potential connections between these two functional gene categories in freshwater environments, which are closely intertwined with human health. We conducted a comprehensive metagenomic sequencing analysis across 23 sampling points from five different eutrophic urban lakes. The results highlight the dominance of the precorrin-2 synthesis pathway in the microbial synthesis of VB12 within urban lakes. Eutrophication may potentially enhance the precorrin-2 synthesis pathway while inhibiting others. The risk of antibiotic resistance is reduced in the anaerobic pathway of VB12 synthesis, while the abundance of metal resistance genes is increased. Binning analysis reveals that 26 metagenome-assembled genomes (MAGs) actively participate in VB12 synthesis, with at least 4 MAGs showing resistance during the VB12 synthesis process and demonstrating pathogenicity. These findings provide critical insights into the VB12 synthesis process and its implications for human health in terms of resistance risks.}, }
@article {pmid40594354, year = {2025}, author = {Flores, SS and Cordovez, V and Arias Giraldo, LM and Leon-Reyes, A and van 't Hof, P and Raaijmakers, JM and Oyserman, BO}, title = {Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22448}, pmid = {40594354}, issn = {2045-2322}, support = {CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; }, mesh = {*Solanum lycopersicum/microbiology/genetics ; *Microbiota/genetics ; Soil Microbiology ; Rhizosphere ; Ecuador ; Plant Roots/microbiology ; Biodiversity ; *Adaptation, Physiological ; Phylogeny ; }, abstract = {Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Just as the genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that similarly contribute to crop growth and health.}, }
@article {pmid40594317, year = {2025}, author = {Song, X and Li, JN and Wang, D and Han, ZY and Yan, XX and Yang, ZH and Xu, J and Wang, Q and Wu, D}, title = {Metagenomics reveals functional profiles of gut microbiota during the recovery phase of acute pancreatitis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20549}, pmid = {40594317}, issn = {2045-2322}, support = {32170788//National Natural Science Foundation of China/ ; 2022-PUMCH-B-023//National High Level Hospital Clinical Research Funding/ ; ZK108000//National Key Clinical Specialty Construction Project/ ; 7232123//Natural Science Foundation of Beijing/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Pancreatitis/microbiology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Acute Disease ; Bacteria/genetics/classification ; }, abstract = {Gut microbiota play a critical pathogenic role in acute pancreatitis (AP). This study aimed to investigate the composition and function of gut microbiota during the recovery phase of AP. Rectal swab samples obtained from 12 AP patients of varying severity during both the acute and recovery phases were sequenced using shotgun metagenomic sequencing. We analysed α-diversity, enterotypes, and the dominant microbiome composition, and performed differential analysis of gut microbiota composition and functional enrichment. During the recovery phase of AP, microbial diversity remained decreased, and minimal difference were observed in the structural diversity of the microbiome. There was an increasing tendency of beneficial bacteria (Bacteroidales) and a decreasing tendency of harmful bacteria (Firmicutes) in the recovery phase of mild AP (MAP). However, in the recovery phase of moderately severe AP (MSAP) and severe AP, Enterococcus abundance increased compared with that in the acute phase. Some signalling pathways showed opposite trends in the recovery phase of MAP and MSAP compared to the acute phase. These results suggested that gut microbiome composition and function are associated with AP recovery, which may inform strategies for the treatment and prognosis of AP.}, }
@article {pmid40594045, year = {2025}, author = {Bhamidipati, SV and Surathu, A and Chao, H and Agustinho, DP and Xiang, Q and Kottapalli, K and Santhanam, A and Momin, Z and Walker, K and Menon, VK and Weissenberger, G and Emerick, N and Mahjabeen, F and Meng, Q and Hu, J and Sucgang, R and Henke, D and Sedlazeck, FJ and Khan, ZM and Metcalf, GA and Avadhanula, V and Piedra, PA and Ramani, S and Atmar, RL and Estes, MK and Petrosino, JF and Gibbs, RA and Muzny, DM and Javornik, SC and Doddapaneni, H}, title = {Complete genomic characterization of global pathogens respiratory syntical virus and human norovirus using probe based capture enrichment.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20526}, pmid = {40594045}, issn = {2045-2322}, mesh = {Humans ; *Norovirus/genetics/isolation &amp; purification ; *Genome, Viral ; *Respiratory Syncytial Virus, Human/genetics ; *Caliciviridae Infections/virology ; Genomics/methods ; *Respiratory Syncytial Virus Infections/virology ; Genotype ; Phylogeny ; Gastroenteritis/virology ; Oligonucleotide Probes/genetics ; }, abstract = {Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children worldwide, while human noroviruses (HuNoV) are a leading cause of epidemic and sporadic acute gastroenteritis. Generating full-length genome sequences for these viruses is crucial for understanding viral diversity and tracking emerging variants. However, obtaining high-quality sequencing data is often challenging due to viral strain variability, quality, and low titers. Here, we present a set of comprehensive oligonucleotide probe sets designed from 1,570 RSV and 1,376 HuNoV isolate sequences in GenBank. Using these probe sets and a capture enrichment sequencing workflow, 85 RSV positive nasal swab samples and 55 (49 stool and six human intestinal enteroids) HuNoV positive samples encompassing major subtypes and genotypes were characterized. Samples with Ct values 17.0-29.9 for RSV, and 20.2-34.8 for HuNoV, with some HuNoV below the detection limit were sequenced. The percentage of reads mapped to viral genomes was 85.1% for RSV and 40.8% for HuNoV post-capture, compared to 0.08% and 1.15% in pre-capture libraries. Full-length genomes were obtained for all RSV positive samples and in 47/55 HuNoV positive samples-a significant improvement over genome recovery from pre-capture libraries. RSV transcriptome (subgenomic mRNAs) sequences were also characterized from this data.}, }
@article {pmid40593979, year = {2025}, author = {Chen, L and Chen, H and Lv, T and Guo, X and Wu, W and Zhao, D and Liu, F}, title = {Differences of the respiratory microbiota between children suffering from community acquired pneumonia with presence or absence of asthma.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20458}, pmid = {40593979}, issn = {2045-2322}, mesh = {Humans ; *Asthma/microbiology/complications ; *Community-Acquired Infections/microbiology/complications ; *Microbiota ; Male ; Female ; Child ; Child, Preschool ; *Pneumonia/microbiology/complications ; Infant ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Adolescent ; Community-Acquired Pneumonia ; }, abstract = {Recent advancements in respiratory microbiota research have progressively elucidated their pivotal role in pediatric respiratory pathologies. Alterations in airway microbial communities are intricately associated with diverse respiratory conditions and distinct disease states. This study conducted a comparative analysis of respiratory microecological profiles in pediatric cohorts diagnosed with community-acquired pneumonia (CAP), stratified by the presence or absence of comorbid bronchial asthma, from whom nasopharyngeal aspirates were obtained for metagenomic next-generation sequencing (mNGS). Analyses revealed comparable alpha-diversity indices between groups; however, beta-diversity metrics demonstrated marked compositional divergence. In the asthma-CAP cohort, Streptococcus pneumoniae and Rothia mucilaginosa emerged as predominant taxa, whereas Mycoplasmoides pneumoniae and Trichoderma citrinoviride dominated microbial profiles in uncomplicated CAP patients.}, }
@article {pmid40593735, year = {2025}, author = {Flores Ventura, E and Esteban-Torres, M and Gueimonde, M and van Sinderen, D and Koren, O and Hall, LJ and Segata, N and Valles-Colomer, M and Collado, MC}, title = {Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {121}, pmid = {40593735}, issn = {2055-5008}, support = {CEX2021-001189-S-20-1//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2022-139328OA-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 898088//European Union's Horizon 2020/ ; SFI/12/RC/2273-P1 and SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; 220876/Z/20/Z//Wellcome Trust Investigator/ ; Beatriz Galindo Junior Fellowship BG22/00172//Ministerio de Universidades/ ; 639226/ERC_/European Research Council/International ; }, mesh = {Female ; Humans ; Infant ; Infant, Newborn ; Pregnancy ; *Bifidobacteriales Infections/transmission/microbiology ; *Bifidobacterium/classification/genetics/isolation &amp; purification ; Gastrointestinal Microbiome ; *Infectious Disease Transmission, Vertical ; Metagenomics ; Mothers ; Vagina/microbiology ; }, abstract = {Early-life colonization is a critical developmental process influencing infant biological programming, with bifidobacteria playing a key role. This systematic review examines the transmissibility of Bifidobacterium strains from mothers to infants. Adhering to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, 31 articles from 2009 to 2024 were selected from 2825 screened titles and abstracts. Using a narrative synthesis and meta-analysis, the review focuses on studies employing strain-level metagenomic approaches (Protocol registry CRD: CRD42023490507). Ten studies using shotgun metagenomic sequencing identified specific strains of B. adolescentis, B. angulatum, B. bifidum, B. breve, B. pseudocatenulatum, B. catenulatum, and B. longum shared between mothers and infants. A meta-analysis of 810 mother-infant pairs revealed an overall species transmissibility estimate of 30% (95% CI: 0.17; 0.44), with B. longum strains persisting in infants' guts for up to 6 months. Strain transmissibility was higher in vaginally delivered infants compared to those delivered by caesarean section. This review highlights the high transmission rates of maternal Bifidobacterium strains in early-life gut seeding, particularly B. bifidum and B. longum. Despite ongoing research, uncertainties remain regarding the precise characteristics, transmission routes, and mechanisms of transmitted strains. Comprehensive approaches, including metagenomic sequencing and longitudinal studies, are needed to understand the role of vertical transmission in infant gut microbiome engraftment and its functional implications.}, }
@article {pmid40593605, year = {2025}, author = {Butcher, J and Villette, C and Zumsteg, J and Maurer, L and Barchietto, T and Rigo, R and Floch, K and Cseh, A and Buchet, S and Stintzi, A and Heintz, D}, title = {Microbial bioremediation of persistent organic pollutants in plant tissues provides crop growth promoting liquid fertilizer.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5768}, pmid = {40593605}, issn = {2041-1723}, support = {251174 and 199015//Agence de l'Eau Seine-Normandie/ ; 251174 and 199015//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; OGI-149//Genome Canada (G&#xe9;nome Canada)/ ; OGI-149//Ontario Genomics Institute (OGI)/ ; }, mesh = {*Fertilizers ; Biodegradation, Environmental ; Wetlands ; *Persistent Organic Pollutants/metabolism ; Bacteria/metabolism/genetics ; Fungi/metabolism/genetics ; *Crops, Agricultural/growth &amp; development/microbiology ; Wastewater ; Metagenomics ; }, abstract = {Constructed wetlands are used to clean domestic wastewater via phytoremediation, commonly involving the use of reeds. The process results in the production of large amounts of polluted plant tissues, which are then considered unusable waste products. In this study, the reusability of reeds and nettle-polluted tissues is investigated. Fermenting contaminated plant tissues to produce liquid fertilizer is a sustainable means to remove 87-95% of persistent organic pollutants. A multiomics approach combining metabolomics and amplicon metagenomics is used to analyze the mechanisms that occur during fertilizer production from polluted plant tissues and identify the microbes that are likely key for this transformation. A consortium of bacteria and fungi with cellulolytic activity is identified. In addition, the obtained liquid fertilizer positively impacts plant growth in the presence of pathogens and therefore exhibits potential application in farming. This approach may be a simple, commercially attractive solution for the management of contaminated plant tissues originating from constructed wetlands, which are currently considered problematic, useless waste products.}, }
@article {pmid40593262, year = {2025}, author = {Liu, L and Li, M and Qin, Y and Liu, Y and Li, M and Lian, B and Guo, R and Xiao, Y and Yin, C}, title = {Childhood obesity and insulin resistance is correlated with gut microbiome serum protein: an integrated metagenomic and proteomic analysis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {21436}, pmid = {40593262}, issn = {2045-2322}, support = {81903340//National Natural Science Foundation of China/ ; }, mesh = {Child ; Female ; Humans ; Male ; *Blood Proteins/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Insulin Resistance ; Metagenomics/methods ; *Pediatric Obesity/microbiology/blood/metabolism ; Proteomics/methods ; }, abstract = {The aim of this study was to investigate the changes in the gut microbiota and proteins related to metabolism and immunity caused by childhood obesity and insulin resistance (IR) and to assess the underlying relationship between the gut microbiota and IR in children. Nineteen children with obesity and sixteen healthy children were recruited. Children with obesity were divided into two groups: obese with IR and obese without IR. All of the obese children participated in a 1-month lifestyle-based weight loss program. Faecal metagenomics and serum Olink proteomics combined with clinical parameters were used to identify the metabolic alterations associated with childhood obesity and IR. The gut microbiota and serum protein were significantly altered in obese children with IR. The relative abundances of Akkermansia muciniphila, IGFBP1 and GP6 were decreased in obese children with IR. Butyricicoccus sp. AM29-23AC, DLK1, CD163, CCL16 and CTSD levels were recovered after IR improved. TNFR1 had a significant indirect effect on the interaction between s-Citrobacter.freundii and fasting insulin. In conclusion, obese children with IR have abnormal gut microbiota and serum proteins related to metabolism and immunity, which can be improved after weight loss. The gut microbiome of children with obesity may contribute to the development of IR by triggering metabolic inflammation.Clinical Trial Registration: This study was registered with the Chinese Clinical Trial Registry (Registration number: ChiCTR2300072179).}, }
@article {pmid40593191, year = {2025}, author = {Park, K and Lee, J and Kim, J and Kim, SG and Song, DH and Gu, SH and Lee, SH and Lee, D and Kim, WK and Song, JW}, title = {Discovery and genomic characterization of Ulleung virus harbored by Crocidura utsuryoensis on Ulleung Island in Republic of Korea.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {21748}, pmid = {40593191}, issn = {2045-2322}, support = {UE242006TD and 411FF5-912A01201//Agency for Defense Development/ ; }, mesh = {Animals ; Phylogeny ; *Shrews/virology ; Republic of Korea ; *Genome, Viral ; *Orthohantavirus/genetics/classification ; Genomics ; Haplotypes ; Islands ; }, abstract = {Hantaviruses are zoonotic RNA viruses that cause hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome, posing significant public health risks. This study reports the identification and genomic characterization of Ulleung virus (ULLEV), a newly discovered genetic lineage of Orthohantavirus jejuense harbored by Crocidura utsuryoensis, a shrew species endemic to Ulleung Island, Republic of Korea. In 2009, a surveillance effort involving 62 shrews revealed a molecular prevalence of 64.5%. Metagenomic next-generation sequencing identified four viral variants, with ULLEV Cu09-33 fully characterized. Comparative genomic and phylogenetic analyses confirmed ULLEV as a distinct subtype within O. jejuense and suggested that ULLEV and Jeju virus (JJUV) share a common ancestor, with divergence shaped by long-term co-evolution with their hosts and geographic isolation. Haplotype network analysis of mitochondrial DNA detected eight unique haplotypes in C. utsuryoensis, distinct from C. shantungensis populations, indicating genetic isolation. While incongruences among the tripartite genomes of ULLEV and JJUV suggested independent evolutionary trajectories, evidence for reassortment remains insufficient. These findings highlight the ecological significance of geographically isolated environments as reservoirs for unique hantavirus lineages and underscore the need for expanded genomic surveillance and phylogenetic studies to assess the zoonotic potential and public health implications of ULLEV.}, }
@article {pmid40593012, year = {2025}, author = {Sitko, K and Piotrowska, E and Podlacha, M and Zagórska, N and Starke, MD and Trzeciak, M and Tukaj, S}, title = {Topical application of the HSP90 inhibitor 17-AAG reduces skin inflammation and partially restores microbial balance: implications for atopic dermatitis therapy.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {21245}, pmid = {40593012}, issn = {2045-2322}, support = {2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; }, mesh = {*Benzoquinones/administration &amp; dosage/pharmacology ; *Lactams, Macrocyclic/administration &amp; dosage/pharmacology ; Animals ; *Dermatitis, Atopic/drug therapy/pathology/chemically induced/microbiology/metabolism ; *HSP90 Heat-Shock Proteins/antagonists &amp; inhibitors/metabolism ; Mice ; Humans ; Disease Models, Animal ; Administration, Topical ; *Skin/drug effects/pathology/microbiology ; Female ; Cytokines/metabolism ; Eosinophils/drug effects/metabolism ; Gastrointestinal Microbiome/drug effects ; Staphylococcus aureus/drug effects ; Inflammation/drug therapy ; Keratinocytes/drug effects/metabolism ; }, abstract = {Heat shock proteins belonging to the HSP90 family promote inflammation and are potential therapeutic targets in inflammatory and autoimmune diseases. Here the effects of the HSP90 inhibitor 17-AAG applied topically were evaluated in a DNCB-induced murine model of atopic dermatitis (AD). The use of 17-AAG improved clinical disease activity without causing toxicity in the animals. Topical application of 17-AAG resulted in reduced epidermal hyperplasia, decreased expression of TSLP, IL-5, and IL-6, as well as reduced activation of NF-κB in the skin. In addition, the eosinophil proportion in the blood and eosinophil peroxidase (EPX) activity in the skin were significantly reduced in 17-AAG-treated AD mice. The inhibitory effects of 17-AAG on the production of epidermal alarmins, T-helper cell-associated cytokines, and ROS release were demonstrated in cultures of activated human keratinocytes, CD4[+] T lymphocytes, and eosinophils, respectively. Finally, next-generation sequencing metagenomic approaches revealed that topical application of 17-AAG partially restored the normal gut microbiome in AD mice. Moreover, 17-AAG inhibited Staphylococcus aureus biofilm formation in vitro. The findings of this study, combined with the observed increase in HSP90 and EPX activity in the leukocytes of the analyzed cohort of AD patients, support the potential therapeutic use of HSP90 inhibitors in individuals with AD.}, }
@article {pmid40592825, year = {2025}, author = {Mali, N and Mali, S and Zhang, L and Fu, P}, title = {Interplay between gut microbiota and acute kidney injury: a review of their mutual influence and causation.}, journal = {Renal failure}, volume = {47}, number = {1}, pages = {2522976}, doi = {10.1080/0886022X.2025.2522976}, pmid = {40592825}, issn = {1525-6049}, mesh = {Humans ; *Acute Kidney Injury/microbiology/immunology/physiopathology ; *Gastrointestinal Microbiome/immunology/physiology ; Kidney/physiopathology/microbiology ; Animals ; }, abstract = {It is unclear, therefore, exactly how gut microbes and renal processes communicate. Recent developments in the field of microbiome research present chances to enhance our comprehension and management of acute kidney injury (AKI). This review highlights important ideas and suggests more research while giving a general summary of the microbiome's influence on kidney function and AKI. AKI is a complex condition that develops through a variety of pathways. Recent experimental research has highlighted the important role that the gut microbiota plays in the course of AKI. Our understanding of human biology has been completely transformed by the current increase in gut microbiota research. Amazing progress in DNA sequencing analysis, especially in the areas of metagenomics and metatranscriptomics, has greatly increased our ability to measure and track complex microbial populations. As such, we are now in a better position to look at how these communities affect human health and illness. As a result, the relationships between renal physiology and pathophysiology and the gut microbiota are now better understood. Both experimental AKI and chronic renal illness have been linked to changes in the intestinal microbiome. This succinct review attempts to examine our present knowledge of the immune-modulatory effects of the gut microbiota, how kidney disorders are influenced by it, and the possible reciprocal interaction between kidney diseases and the microbiota. Subsequent investigations ought to concentrate on delving deeper into the function of the gut microbiota in renal disorders and finding possible therapeutic strategies for adjusting it.}, }
@article {pmid40592271, year = {2025}, author = {Fan, Q and Bai, J and Jiao, T and Zhao, Z and Hou, F}, title = {Circular transmission network and reverse contribution pattern of antibiotic resistance genes in the Qinghai-Tibet Plateau ecosystem.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139054}, doi = {10.1016/j.jhazmat.2025.139054}, pmid = {40592271}, issn = {1873-3336}, abstract = {The dissemination of antibiotic resistance genes (ARGs) poses a major global public health challenge, yet transmission mechanisms within extreme ecosystems are poorly understood. Using metagenomics and metagenome-assembled genome (MAG) analysis, we investigated ARG composition, risk, and pathways across a complete Qinghai-Tibet Plateau food chain (soil, earthworm, herbage, yak, pika, snowfinch, herdsman). Contrary to conventional theory, ARG assemblages correlated negatively with microbial diversity. Our MAG-centric approach provided direct evidence that Horizontal Gene Transfer (HGT), including striking bacteria-archaea cross-domain transfer of 18 ARGs, predominates ARG dissemination, with specialized 'ARG reservoir' host phyla (e.g., Pseudomonadota) decoupling ARG functional diversity from overall microbial community structure. Earthworms function as 'ARG bioamplifiers', enriching 79.81 % of soil ARGs and contributing 49.43 % to herbage. Crucially, apex consumers (snowfinches, herdsmen) are not merely recipients; their feces drive a significant 'reverse contribution' of high-risk ARGs back into the ecosystem, establishing a complete circular ARG feedback network. Herdsman feces contained all Rank I-IV high-risk ARGs, while snowfinch feces held Rank II/IV, highlighting human activities' impact on escalating ARG risks in this extreme setting. These findings, particularly the novel HGT mechanisms and host specialization insights, challenge the traditional unidirectional transmission model, presenting a new paradigm for managing antibiotic resistance risks in extreme ecosystems within the One Health framework.}, }
@article {pmid40592243, year = {2025}, author = {Gao, Z and Liu, X and Yu, J and Li, Z and Shi, H and Zhang, G and Ling, J}, title = {Structural basis of immunomodulation by edible fungal polysaccharides: From molecular characteristics to action mechanisms.}, journal = {Carbohydrate research}, volume = {555}, number = {}, pages = {109591}, doi = {10.1016/j.carres.2025.109591}, pmid = {40592243}, issn = {1873-426X}, abstract = {Edible Fungal polysaccharides as Immunomodulators: A Systematic Review at the Crossroads of Immunology, Natural Products Chemistry, and Microbiology. The chemical structure-specifically molecular weight, branching degree, and functional group modifications-directly dictates immunological activity. For instance, high-molecular-weight β-glucans activate macrophage surface receptors through triple-helix conformations, whereas sulfation enhances electrostatic interactions with immune cells. Mechanistically, polysaccharides regulate macrophage polarization, dendritic cell maturation, and T/B cell activation, therebyengaging core signaling pathways such as TLR4/MyD88/NF-κB, NLRP3 inflammasome, and MAPK, This orchestrates synergistic enhancement of innate and adaptive immunity. Recent research further demonstrate that polysaccharides can also reshape the gut microbiota-immune metabolic axis by promoting the production of short-chain fatty acids (SCFAs) and activating receptors (e.g., GPR43), indirectly modulating systemic immune responses. Clinically, polysaccharides from Ganoderma lucidum and Lentinus edodes demonstrate efficacy in cancer adjuvant therapy by enhancing immune function and reducing radiotherapy/chemotherapy side effects. However, species-specific receptor recognition heterogeneity and lack of standardized preparation protocols impede clinical translation. Therefore,the implementing an integrated strategy of "polysaccharide structure-immunometabolic reprogramming-precision delivery" to overcome the existing bottlenecks. Combining multi-omics approaches (e.g., gut metagenomics and metabolomics) will advance therapeutics targeting microbiota-immune crosstalk. Such strategies aim to address chronic inflammatory inflammation", malignancies, and related pathologies with enhanced mechanistic specificity.}, }
@article {pmid40592211, year = {2025}, author = {Zhioua, S and Khan, I and Gonzalez, D and Junier, P and Sieber, S}, title = {Genomic and chemical characterization of cytotoxic Ahp-cyclodepsipeptides from Phormidium using Thamnocephalus platyurus bioassay.}, journal = {The Science of the total environment}, volume = {993}, number = {}, pages = {179750}, doi = {10.1016/j.scitotenv.2025.179750}, pmid = {40592211}, issn = {1879-1026}, abstract = {Toxic benthic cyanobacterial mats have been identified globally as a potential health hazard since they can produce potent cyanotoxins. Such mats have been connected to the death of mammals worldwide, with a significant fraction of recent cases associated to benthic cyanobacterial blooms producing anatoxin-a or its derivatives. A recent event involving the death of a dog led to monitoring of mats in the area and to the discovery of the first cyanopeptolin producer among the genus Phormidium. Using metagenomics, the genome of the dominant species in the cyanobacterial mats collected was reconstructed, but no evidence for the production of anatoxin-a or other congeners was obtained. In contrast, the biosynthetic gene cluster for cyanopeptolin was detected in the genome. Further chemical analysis of metabolites extracted from the same mats enabled the isolation and characterization of two novel cyanopeptolins with their truncated products. Toxicity was confirmed using the cytotoxic reporting organism Thamnocephalus platyurus. The untruncated cyanopeptolins had an LC50 as low as 6.4 μM while the truncated products did not exhibit cytotoxicity in the same assay. The presence of truncated analogues lacking cytotoxicity might suggest that other mat-associated microorganisms could degrade those compounds. While Phormidium may not be the direct cause of dog's death, our study provides the first evidence that Phormidium can produce cyanopeptolins. This highlights the underexplored variety of neglected cyanotoxin classes. These findings not only expand the known chemical diversity of cyanotoxins but also raise concerns regarding the potential ecological impact of toxic Ahp-cyclodepsipeptides in freshwater environments.}, }
@article {pmid40591894, year = {2025}, author = {Fu, S and Du, X and Xu, Z and Li, H and Yao, H and Tang, S and Zhao, W and Hao, M and Qiu, Z and Wang, Z}, title = {The potential of wastewater monitoring as a novel surveillance tool for early warning of Bordetella pertussis outbreaks.}, journal = {Emerging microbes &amp; infections}, volume = {}, number = {}, pages = {2528537}, doi = {10.1080/22221751.2025.2528537}, pmid = {40591894}, issn = {2222-1751}, abstract = {The prolonged latency period and delayed reporting of clinical surveillance data have led to a sluggish response to Bordetella pertussis outbreaks in China. Wastewater-based surveillance (WBS) provides real-time, cost-effective monitoring of various viruses. To confirm whether this approach can be applied to B. pertussis, 271 patients infected with B. pertussis were enrolled to evaluate the fecal shedding patterns of the bacterium. Concurrently, we collected wastewater samples in a typical northern (Xi'an) and southern city (Nanchang) in China, from September 2023 to July 2024. The concentrations of B. pertussis in the sewage were detected using quantitative polymerase chain reaction (qPCR). Additionally, metagenomic sequencing with pre-enrichment was employed to trace genotypes of B. pertussis. We report that 40.2% of cases tested positive for B. pertussis in fecal samples. Sewage surveillance identified two waves of B. pertussis infection in Xi'an and one wave of B. pertussis outbreak in Nanchang. The concentration of B. pertussis in sewage showed a strong correlation with the dynamics of diagnosed cases. Notably, each peak of sewage B. pertussis concentration occurred 10 days prior to clinical surveillance, underscoring the value of WBS in early warning. Additionally, both clinical and wastewater surveillance demonstrated consistency in the prevalence estimation of B. pertussis infection cases. Finally, relative to clinical surveillance, wastewater sequencing also revealed the same genotypes of B. pertussis. This study presents the first comprehensive analysis of the fecal shedding of B. pertussis, thereby establishing the potential for early detection of B. pertussis outbreaks through WBS.}, }
@article {pmid40591379, year = {2025}, author = {Orenburkina, OI and Rezbaeva, GN and Dudurich, VV and Babushkin, AE and Sogomonian, KS and Danilova, AA and Danilov, LG}, title = {[Microbiota of the ocular surface in children with myopia].}, journal = {Vestnik oftalmologii}, volume = {141}, number = {3}, pages = {5-12}, doi = {10.17116/oftalma20251410315}, pmid = {40591379}, issn = {0042-465X}, mesh = {Humans ; Child ; *Myopia/diagnosis/microbiology/physiopathology ; Male ; Female ; Adolescent ; *Microbiota ; *Conjunctiva/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; }, abstract = {UNLABELLED: A healthy ocular surface is characterized by relatively stable and comparatively low microbial diversity. However, pathological conditions can provoke shifts in the composition of bacterial taxa, which may be associated, among other factors, with the progression of myopia.<br><br>PURPOSE: This study compared the taxonomic diversity of the conjunctival microbiota in children with varying degrees of myopia and those without clinically confirmed myopia.<br><br>MATERIAL AND METHODS: Ocular surface samples were obtained from 29 children aged 6-17 years with myopia (58 eyes) and from 12 children of the control group aged 9-17 years (24 eyes). The taxonomic composition of the conjunctival microbiota was analyzed using 16S ribosomal RNA gene (rRNA) sequencing, followed by microbiome profiling through bioinformatics and statistical tools.<br><br>RESULTS: The ocular surface microbiota in children with myopia demonstrated higher alpha diversity compared to the control group. This was confirmed by values of the Chao (reflecting low-abundance taxa) and Shannon (reflecting overall bacterial diversity - higher diversity means higher index; optimal value; 3.1-4.2) indices. The results revealed a clear trend toward differentiation in bacterial composition between myopic and control groups. These differences were associated with changes in the relative abundance of opportunistic bacteria depending on the degree of myopia.<br><br>CONCLUSION: The taxonomic diversity of the ocular microbiota at the genus level in patients with varying degrees of myopia was characterized by a higher number of taxonomic units compared to the control group. The general trend is an increase in the biodiversity of the bacterial composition due to an increase in the relative representation of opportunistic microorganisms. Further research on the influence of the ocular microbiota on the progression of myopia is needed.}, }
@article {pmid40590722, year = {2025}, author = {Jin, H and Li, X and Wang, J and Cui, Y and Huang, S and Shi, K and Zhou, T and Yan, J}, title = {Draft genomes of Dehalococcoides mccartyi strain J1 and Trichlorobacter lovleyi strain J2 from a tetrachloroethene-dechlorinating consortium.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0048525}, doi = {10.1128/mra.00485-25}, pmid = {40590722}, issn = {2576-098X}, abstract = {Two metagenome-assembled genomes were recovered from an anaerobic consortium capable of complete reductive dechlorination of tetrachloroethene to ethene. The draft genomes, assigned to Dehalococcoides mccartyi strain J1 and Trichlorobacter lovleyi strain J2, are 1.37 and 3.84 Mb in size and encode 1,448 and 3,630 genes, respectively.}, }
@article {pmid40590427, year = {2025}, author = {Nalla, S and Ganta, S and Bukke, SPN and Bandaru, N and Onohuean, H and Alagbonsi, AI}, title = {Kaempferide and Norbergenin avert aluminium chloride-induced amyloid β accumulation and neurocognitive shutdown via oxidative and apoptotic mechanisms.}, journal = {International journal of immunopathology and pharmacology}, volume = {39}, number = {}, pages = {3946320251343687}, doi = {10.1177/03946320251343687}, pmid = {40590427}, issn = {2058-7384}, mesh = {Animals ; Aluminum Chloride ; Male ; *Apoptosis/drug effects ; Rats, Wistar ; *Oxidative Stress/drug effects ; *Neuroprotective Agents/pharmacology ; *Amyloid beta-Peptides/metabolism ; Rats ; *Cognition/drug effects ; Antioxidants/pharmacology ; Chlorides/toxicity ; Disease Models, Animal ; Aluminum Compounds ; }, abstract = {OBJECTIVE: To investigate the involvement of oxidative and apoptotic mechanisms in the possible neuroprotective effect of Kaempferide (KPD) and Norbergenin (NRG) against AlCl3-induced cognitive shutdown in rats.<br><br>INTRODUCTION: Aluminium chloride (AlCl3) is widely known as a neurotoxic agent that induces memory and cognitive shutdown via induction of oxidative stress and apoptosis. KPD is an O-methylated flavonol that possesses anti-oxidant, anti-inflammatory, anti-dementia and anti-depression properties, whereas NRG, a demethylated compound derived from bergenin, possesses an anti-oxidant property and has neuroprotective effects. Both alleviate D-galactose-induced neurotoxicity in rats.<br><br>METHODS: Eighty-four male Wistar rats were randomly divided into two experimental models: prophylactic (pre-treatment with donepezil, KPD or NRG; n&#x2009;=&#x2009;42) and curative (post-treatment with donepezil, KPD, or NRG; n&#x2009;=&#x2009;42). In each of these models, the animals were divided into seven groups (n&#x2009;=&#x2009;6 per group): group 1 (normal saline), group 2 (200&#x2009;mg/kg AlCl3), group 3 (donepezil + AlCl3), group 4 (5&#x2009;mg/kg KPD + AlCl3), group 5 (10&#x2009;mg/kg KPD + AlCl3), group 6 (5&#x2009;mg/kg NRG + AlCl3) and group 7 (10&#x2009;mg/kg NRG + AlCl3)Results:Kaempferide and Norbergenin averted the increase in TBARS, NO and AChE, and decrease in the number of crossings, time spent and distance moved in the target quadrant, latency of fall, speed, paw withdrawal threshold (PWT), SOD, CAT, GPx, GR and GSH induced by AlCl3. These agents also averted the upregulation of A&#x3b2;1-41, p-Tau, caspase-3, Bax and downregulation of Akt, p-CREB, SOD1 and BCl-2 induced by AlCl3Conclusion:The neuroprotective effects of KPD and NRG against AlCl3-induced A&#x3b2; accumulation and cognitive shutdown are mediated via suppression of oxidative stress and apoptosis.}, }
@article {pmid40590044, year = {2025}, author = {Zhang, L and Rao, Y and Li, Z and Fan, M and Xiang, Z and Wang, J}, title = {The Advance and Clinical Practice on Lung Disease Caused by Mycobacterium abscessus.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {3103-3115}, pmid = {40590044}, issn = {1178-6973}, abstract = {Mycobacterium abscessus (M. abscessus) lung disease has gradually become a common clinical condition, with its incidence rate continuously rising, especially among patients with weakened immune function or those with chronic lung diseases. Given the high resistance of M. abscessus to antibiotics, the options for antibiotics are very limited. Additionally, long treatment times and poor patient compliance lead to low cure rates and high recurrence rates, making it one of the significant public health challenges threatening global health. This article presents two cases of patients diagnosed with M. abscessus lung disease using next-generation metagenomic sequencing technology. It reviews and analyzes the current research on M. abscessus along with details from these cases. Furthermore, this article emphasizes the necessity of timely, regular, and comprehensive treatment for M. abscessus lung disease. Meanwhile, we call for the formulation of robust prevention strategies, the optimization and innovation of treatment regimens, and the enhancement of follow-up management after cure to improve the understanding and handling capabilities of M. abscessus lung disease, thereby addressing the increasing clinical challenges.}, }
@article {pmid40589867, year = {2025}, author = {Xu, W and Han, D and Chen, T and Wang, Q}, title = {Infected pericardial effusion caused by Prevotella intermedia: a rare diagnosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1612282}, pmid = {40589867}, issn = {2235-2988}, mesh = {Humans ; *Pericardial Effusion/microbiology/diagnosis ; *Prevotella intermedia/isolation &amp; purification/genetics ; *Bacteroidaceae Infections/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing ; China ; Male ; Metagenomics ; Anti-Bacterial Agents/therapeutic use ; Female ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prevotella intermedia is a Gram-negative bacterium that thrives in anaerobic environments. It presents challenges in detection through routine laboratory assays, and hitherto, there has been no documented instance of detecting this bacterium in pericardial effusion in China. Metagenomic Next-Generation Sequencing (mNGS) can boost the detection rate of this pathogen and furnish early guidance for clinical management.}, }
@article {pmid40589860, year = {2025}, author = {Nimnoi, P and Pongsilp, N}, title = {Insights into the metagenomic and metabolomic compositions of the bacterial communities in Thai traditional fermented foods as well as the relationships between food nutrition and food microbiomes.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19606}, pmid = {40589860}, issn = {2167-8359}, mesh = {*Fermented Foods/microbiology ; Thailand ; *Food Microbiology ; *Bacteria/genetics/classification/metabolism ; *Microbiota ; Metagenomics ; Metabolomics ; Fermentation ; }, abstract = {Five Thai traditional fermented foods, including khao-mak (sweet fermented sticky rice), pak-kard-dong (sour salt-fermented mustard greens), nor-mai-dong (sour salt-fermented bamboo sprouts), moo-som (sour salt-fermented pork), and pla-som (sour salt-fermented fish), were analyzed for their food nutrition and bacterial community structures. Sour salt-fermented bamboo sprouts possessed the highest unique amplicon sequence variables (ASVs), which were 3,476, as well as the highest bacterial diversity and richness, while in contrast, sweet fermented sticky rice possessed the lowest such indices. The phylum Firmicutes accounted for the largest proportions in both sour salt-fermented meats and sweet fermented sticky rice whereas the Proteobacteria occupied the largest proportions in both sour salt-fermented vegetables. The bacterial community structures of both sour salt-fermented meats were similar in terms of composition at class level, while the dominant genera compositions were totally different among all foods. Gene functions, enzymes, and metabolic pathways annotated from the bacterial communities in all foods were those involved in growth metabolisms, genetic information processing, environmental information processing, and cellular signaling. Sour salt-fermented bamboo sprouts had the highest numbers of unique annotated genes, enzymes, and metabolic pathways.}, }
@article {pmid40589579, year = {2025}, author = {Zhang, YH and Hu, YQ and Zeng, YX and Hu, T and Han, W and Du, Y and Hu, Z and Meng, SS}, title = {Bacterial community composition and function in different habitats in Antarctic Fildes region revealed by high-throughput sequencing.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1524681}, pmid = {40589579}, issn = {1664-302X}, abstract = {INTRODUCTION: Pristine soil, ornithogenic soil, intertidal sediment, and marine sediment represent four of typical habitats in the Fildes region, maritime Antarctica. However, information on bacterial community composition and function in these Antarctic habitats remain limited.<br><br>METHODS: In this study, using a combination of 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing, 12 samples collected from various habitats in the region were analyzed.<br><br>RESULTS AND DISCUSSION: Bacterial community compositions in terrestrial habitats (i.e., pristine and ornithogenic soils) were found to be distinct (p < 0.01) from those in marine habitats (i.e., marine and intertidal sediments). Organic carbon (p < 0.01) and pH (p < 0.01) were two major environmental factors affecting the bacterial community composition in the diverse habitats. Proteobacteria (represented by Gamma-, Alpha-, and Betaproteobacteria; > 30%), Actinobacteria (represented by Actinobacteria; > 20%), and Bacteroidetes (represented by Flavobacteriia; > 10%) were dominant in bacteria related to carbon, nitrogen, and sulfur metabolism across all samples. Though most metabolic pathways were common in both terrestrial and marine habitats, terrestrial samples showed more diverse metabolic pathways than marine samples. However, among the top 15 abundant metabolic pathways, genes related to 11 metabolic pathways were relatively more abundant in marine habitats than in terrestrial habitats (p < 0.05). More abundant genes related to methane metabolism (e.g., pmoA), nitrification (e.g., amoA and hao), reductive citrate cycle pathway (e.g., frdA), repair of DNA damage (e.g., lexA and uvrB), salt and osmotic stress tolerance (e.g., betB, gltB, and treS), and aromatic hydrocarbon degradation (e.g., bcrC and bssA) were detected in pristine and/or ornithogenic soils, whereas genes related to sulfur metabolism (e.g., soxY, fccB, dsrAB, and sat), nitrogen fixation (e.g., nifH), acetyl-CoA metabolism (e.g., acsB, cdhD, and cdhE), carbohydrate degradation (e.g., amyA and chiA), and cold adaptation (e.g., cspA, deaD and recQ) were in higher abundance in marine and/or intertidal sediments. The influence of penguin feces on soil bacterial community composition and ecological function was observed in this study. The study findings will improve our understanding of bacterial community composition and function in various habitats in maritime Antarctica under the background of global climate change.}, }
@article {pmid40589577, year = {2025}, author = {Dong, W and Lun, Y and Sun, J and Liu, B}, title = {Lactobacillus plantarum SAL delays aging-associated oxidative stress and gut microbiota dysbiosis in mice.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1607824}, pmid = {40589577}, issn = {1664-302X}, abstract = {INTRODUCTION: Lactobacillus plantarum SAL, isolated from multidrug-resistant patients' feces, exhibits superior in vitro probiotic traits including bile salt resistance, gastric acid tolerance, and potent antioxidant capacity. While Lactobacillus plantarum generally enhances gut microbiota structure/function, improving health and lifespan in model organisms, the in vivo effects, mechanisms, and potential anti-aging properties of the SAL strain remain unexplored. This study addresses this critical research gap.<br><br>METHODS: Twenty-four SPF KM male mice were divided into a control group (CON), model group (MOD), and a SAL strain intervention group (SAL). MOD and SAL groups received d-gal-induced aging models. SAL group was orally administered SAL strain suspension daily, while MOD and CON groups received saline for 10 weeks. After the intervention, serum and liver tissues were collected to detect aging biomarkers (&#x3b2;-galactosidase) and oxidative stress markers.Colon tissue histopathological examination was performed, and fresh fecal samples were subjected to metagenomic sequencing and analysis. Additionally, Spearman correlation analysis was conducted to evaluate the relationships between genuslevel differential gut microbiota and oxidative stress markers in serum and liver tissues.<br><br>RESULTS: Compared with the MOD group, the SAL group exhibited significantly reduced MDA levels in serum and liver tissues (all p < 0.05), elevated activities of SOD and T-AOC (all p < 0.05), and increased serum GSH-Px and CAT activities (all p < 0.05). Colon histology showed structural improvements, including increased crypt numbers, restored architecture, reduced submucosal space, and upregulated expression of ZO-1, Occludin, and Muc2 (all p < 0.05). Gut microbiota analysis revealed increased abundances of Firmicutes and Verrucomicrobia, decreased Bacteroidetes, and elevated Firmicutes/Bacteroidetes (F/B) ratio (p < 0.05). Differential genera Lactobacillus and Mucispirillum showed significant negative correlations with MDA levels (all p < 0.05), while Lactobacillus positively correlated with SOD, GSH-Px, and T-AOC activities.<br><br>DISCUSSION: The SAL strain intervention significantly improved redox homeostasis, restored intestinal barrier integrity, and reversed gut dysbiosis, highlighting its dual regulatory role in anti-aging mechanisms. These findings demonstrate the potential of L. plantarum SAL as an anti-aging probiotic and establish a theoretical framework for microbiota - targeted interventions to alleviate age-related pathologies.}, }
@article {pmid40588758, year = {2025}, author = {Wang, Y and Lu, Z and Hu, J and Yuan, X and Chen, W and Lu, S and Pan, Y and Chen, Q and Hu, S and Zhang, W and Xiong, C}, title = {The silent spread: uncovering the diversity and evolution of poxviruses in ticks across Western China's host landscapes.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {214}, pmid = {40588758}, issn = {1743-422X}, support = {Grant No. GWVI-11.1-03//the Shanghai New Three-year Action Plan for Public Health/ ; }, abstract = {BACKGROUND: Poxviruses are a diverse group of pathogens with significant implications for both human and animal health. Ticks, as hematophagous arthropods, are capable of switching hosts during their life cycle. Although previous research has suggested the potential for parapoxviral transmission via ticks, the poxviral transmission dynamics remain poorly understood, particularly regarding the role of ticks as vectors.<br><br>METHODS: Tick samples were collected from western China, followed by metagenomic sequencing. The diversity of potential blood-feeding hosts and the prevalence of poxviruses were assessed using BWA. Poxviral sequences were assembled using MetaSPAdes and TGICL, and phylogenetic analysis was conducted to examine the origin of prevalent poxviruses and the unblasted poxviral fragments in ticks.<br><br>RESULTS: A total of 61 poxvirus species across 22 genera were identified, with 387 distinct poxviral sequences assembled. Of these, viral and host abundance were relatively higher in Tibet than in samples from Shaanxi and Gansu. Notably, unblasted gene fragments were identified within the assembled poxviral genomes, originating from a broad range of hosts, including mammals (e.g., rodents), fish, and arthropods. Phylogenetic analysis of the parapoxviruses revealed ongoing mutations, particularly in the Parapoxvirus orf, suggesting an increase in adaptability and potential pathogenicity. The results indicate that environmental factors such as altitude, host availability and host sensitivity may significantly shape viral diversity and transmission dynamics.<br><br>CONCLUSIONS: Ticks may contribute to the ecological circulation of poxviruses by switching hosts during their life cycle, potentially influencing viral genetic diversity. It underscores the risks of zoonotic spillover, particularly in regions with frequent human-animal interactions.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12985-025-02844-1.}, }
@article {pmid40588733, year = {2025}, author = {Zhang, H and Fu, Y and Cao, C and Jiang, H and Tang, R and Dai, Z and Zhang, W}, title = {Identification and characterization of novel CRESS-DNA viruses in the human respiratory tract.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {211}, pmid = {40588733}, issn = {1743-422X}, support = {82341106//National Natural Science Foundation of China/ ; 2023YFD1801301 and 2022YFC2603801//National Key Research and Development Programs of China/ ; JLY2021151//Clinical Medicine Science and Technology Development Foundation of Jiangsu University/ ; }, mesh = {Humans ; Phylogeny ; *DNA Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; *Respiratory System/virology ; Computational Biology ; *Nasopharynx/virology ; DNA, Viral/genetics ; Female ; Male ; Adult ; }, abstract = {CRESS-DNA viruses are small, circular, single-stranded DNA viruses that have been identified in diverse environments and hosts, including vertebrates, invertebrates, and environmental samples. However, their diversity and role in the human respiratory tract remain poorly understood. In this study, we employed viral metagenomics to analyze 140 nasopharyngeal swab samples from asymptomatic individuals. High-throughput sequencing and bioinformatics analyses were used to identify and characterize novel CRESS-DNA viruses. Phylogenetic relationships were inferred based on Rep protein sequences using maximum likelihood analysis. We identified and characterized eight novel CRESS-DNA viruses, which were classified into the families Endolinaviridae and Naryaviridae, with one potentially representing a novel viral family. These viruses exhibited typical circular genomic structures encoding Rep and Cap proteins, with conserved motifs associated with rolling circle replication. Phylogenetic analysis showed that some viruses were closely related to sequences from vertebrate hosts or environmental samples, suggesting a diverse ecological distribution. Our findings expand the known diversity of CRESS-DNA viruses in the human respiratory tract and highlight their potential ecological and evolutionary significance. Further studies are needed to explore their host specificity, replication mechanisms, and potential roles in human health and disease.}, }
@article {pmid40588688, year = {2025}, author = {Svetina, M and Kunej, T and Korošec, P and Rijavec, M}, title = {Towards a Multi-omics Understanding of Anaphylaxis: Insights into Pathogenesis and Biomarker Identification.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {68}, number = {1}, pages = {61}, pmid = {40588688}, issn = {1559-0267}, support = {P3-0360//The Slovenian Research and Innovation Agency/ ; J3-50114//The Slovenian Research and Innovation Agency/ ; P3-0360//The Slovenian Research and Innovation Agency/ ; P3-0360//The Slovenian Research and Innovation Agency/ ; }, mesh = {Humans ; *Anaphylaxis/etiology/diagnosis/metabolism/genetics ; *Biomarkers/metabolism ; Metabolomics/methods ; Genomics/methods ; Proteomics ; Epigenomics ; Transcriptome ; Animals ; Genetic Predisposition to Disease ; Multiomics ; }, abstract = {Anaphylaxis is a severe, life-threatening hypersensitivity reaction that presents significant challenges in both clinical practice and scientific research. While individual omics studies have provided valuable insights into the genetic predisposition, immune dysregulation, and metabolic alterations associated with anaphylaxis, a comprehensive understanding of its full pathophysiology remains elusive. Multi-omics integration, which combines genomics, epigenomics, transcriptomics, proteomics, and metabolomics, has the potential to uncover novel mechanisms, biomarkers, and therapeutic targets. However, studies employing comprehensive multi-omics approaches in anaphylaxis are still limited. This review of 107 studies published between 2000 and 2024-including genomics (43), metagenomics (2), epigenomics (2), transcriptomics (20), proteomics (26), and metabolomics (14)-synthesizes findings from existing single-omics studies on human anaphylaxis, identifies key interconnections across omics layers, and underscores the critical need for large-scale, integrative research. Advancing this type of research is essential to advance our understanding of anaphylaxis, improve risk prediction, and enhance both diagnosis and treatment strategies.}, }
@article {pmid40588027, year = {2025}, author = {Zhang, J and Yu, Z and Gao, Y and Li, Y and Hu, X and Gu, H and Tang, C and Liu, J and Liu, J and Zhang, S and Sima, X and Wang, G and Liu, P and Rui, Y and Franks, A and Liu, X and Jin, J}, title = {Warming-induced unstable microbial community metabolically lowers straw-carbon sequestration in paddy soils.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.06.075}, pmid = {40588027}, issn = {2090-1224}, abstract = {INTRODUCTION: Growing academic attention has been given to the crucial role of soil microorganisms in the net loss of soil organic carbon (SOC) under climate warming and the effectiveness of straw-C sequestration to replenish the SOC stock. However, the lack of empirical investigations in anaerobic paddy soils hinders accurate estimation of the global soil C-climate feedback and development of countermeasures.<br><br>OBJECTIVES: This study aimed to unravel the impact of warming on the complexity of the microbial community network of the paddy soil in response to warming, and correspondent changes of microbial metabolic functions relevant to the transformation of straw-C in SOC pools.<br><br>METHODS: We amended [13]C/[15]N-labeled rice straw into a long-term paddy soil and incubated under three temperature treatments (25, 35 and 45&#x202f;&#xb0;C) for 140&#x202f;days to quantify straw-C sequestration in various SOC fractions, and further deployed metagenomic sequencing and solid-state [13]C NMR analyses to explore relevant biochemical mechanisms.<br><br>RESULTS: Warming (35&#x202f;&#xb0;C and 45&#x202f;&#xb0;C vs. 25&#x202f;&#xb0;C) enhanced SOC decomposition, but straw amendment did not replenish the loss C in mineral-associate C, a major SOC fraction of this soil, especially at 45&#x202f;&#xb0;C. Compared to 25&#x202f;&#xb0;C, temperature increases to 35&#x202f;&#xb0;C and 45&#x202f;&#xb0;C led to decreases in microbial diversity indices by an average of 19&#x202f;% and 43&#x202f;%, respectively. Warming also destabilized the microbial community network with less connectivity and keystone nodes in the paddy soil. Furthermore, warming decreased the abundances of organic C- and N-mineralization genes. Those genes encode enzymes involved in the degradation of both labile and recalcitrant organic compounds, including starch, cellulose, hemicellulose, chitin, pectin and aromatics, as well as in N mineralization, such as glutamate dehydrogenase and glutamate synthase. A subsequent deficiency in the synthesis of those enzymes appeared to suppress the transformation of straw-C and N, thereby reducing their sequestration efficiency in the mineral-associate C fraction in the paddy soil.<br><br>CONCLUSION: The detrimental impact of warming on the microbial metabolic profiles lowered the role of straw amendment in sustaining SOC stability under warming. An improved understanding of the warming-induced loss of microbial community diversity and correspondent weakening metabolic functions for the turnover of exogenous C should be accounted for global mitigation practices in paddy fields under climate warming.}, }
@article {pmid40587929, year = {2025}, author = {Chen, J and Guo, Y and Lin, Y and Zhang, Y and Qian, Q and Zhang, X and Lin, P and Chen, C and Xie, S}, title = {Fate, mobility and pathogenicity of antibiotic resistome in a full-scale drinking water treatment plant: Highlighting the chlorination risks.}, journal = {Journal of environmental management}, volume = {390}, number = {}, pages = {126425}, doi = {10.1016/j.jenvman.2025.126425}, pmid = {40587929}, issn = {1095-8630}, abstract = {Drinking water treatment plants (DWTPs) serve as the last barrier in preventing the spread of antibiotic resistance genes (ARGs) into tap water, yet the distribution and dissemination mechanisms of ARGs in DWTPs remain unclear. In this study, the antibiotic resistome of a full-scale DWTP using Nansi Lake (an important node of the South-to-North Water Diversion Project's eastern route, China) as water source was investigated based on metagenomic analysis. The results showed that coagulation and chlorination were the two crucial processes increasing the relative abundance of ARGs in the DWTP, and the former predominantly enhanced that of sulfonamide RGs, while the latter increased that of bacitracin, aminoglycoside and multidrug RGs. ARG hosts and mobile genetic elements (MGEs) both played significant roles in ARG compositions. The persistence of Sphingorhabdus during the conventional treatment stages and the dissemination potential of plasmids accounted for the relative abundance of sulfonamide RGs, while the chlorine and multidrug resistance of Acinetobacter, Acidovorax, and Pseudomonas, along with the coexistence of various MGEs, suggested the persistence and transmission risk of ARGs after chlorination. Ozonation and activated carbon filtration could eliminate some human-pathogenic bacteria (HPB), but the chlorination process significantly increased the relative abundance of HPB. The multidrug-resistant HPB such as Acinetobacter calcoaceticus and Acinetobacter haemolyticus were the key targets for risk control in the DWTP. Our findings provide new insights into the fate, mobility, and pathogenicity of ARGs in a typical DWTP, offering beneficial guidance for decision-making in the risk control of ARGs in DWTPs.}, }
@article {pmid40586794, year = {2025}, author = {Chadd, EF and Ergunay, K and Kumsa, B and Bourke, BP and Broomfield, BS and Long, LS and Linton, YM}, title = {Nanopore sequencing reveals a diversity of microorganisms in ticks from Ethiopia.}, journal = {Parasitology research}, volume = {124}, number = {7}, pages = {73}, pmid = {40586794}, issn = {1432-1955}, support = {FY23 Award # 23-101//Deployed Warfighter Protection (DWFP) Program/ ; Award # P0031_21_WR//Armed Forces Health Surveillance Division/ ; }, mesh = {Animals ; Ethiopia ; *Nanopore Sequencing ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Ticks/microbiology ; Rickettsia/genetics/isolation &amp; purification ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenome ; Phylogeny ; *Biodiversity ; }, abstract = {Ethiopia is home to a diverse group of ixodid ticks that are known to transmit disease to both animals and humans. Recent advances in metagenome sequencing show there is more microorganism diversity found in ticks than previously known. Compared to amplicon-based gene identification methods, agnostic metagenomic sequencing provides broader insights into the diversity of microorganisms in ticks, providing knowledge that will better enable public health measures in preventing the spread of zoonotic disease. In the present study, metagenomic sequencing was used to look at the microbial diversity of ticks collected from livestock in Ethiopia. This study identified six bacterial genera (Coxiella, Francisella, spotted-fever group (SFG) Rickettsia, Spiroplasma, Ehrlichia, and Borrelia), one genus of eukaryotic parasite (Babesia sp.), and one virus species (Parapoxvirus bovinestomatitis) from 154 tick pools representing 22 species of ticks among four genera (Amblyomma, Haemaphysalis, Hyalomma, and Rhipicephalus). We were able to differentiate between pathogenic and nonpathogenic microorganisms, highlighting concerns among traditional gene-targeted screening methods. Among all pooled samples, the predominant microorganisms included Coxiella-like endosymbionts (55.2%), SFG Rickettsia (38.3%), and nonpathogenic Francisella spp. (26.0%). Rickettsia africae was the predominant pathogenic agent detected, and phylogenetic analysis of two samples from A. gemma and A. variegatum confirmed the presence of R. africae. This study highlights the power of metagenomics applied to potential vectors of zoonotic disease, and it expands the knowledge on tick-pathogen associations in Ethiopia.}, }
@article {pmid40586686, year = {2025}, author = {Goens, M and Mouton, W and Oriol, G and Cheynet, V and Restier, L and Bal, A and Brengel-Pesce, K and Rozières, A and Viret, C and Nancey, S and Faure, M and Trouillet-Assant, S and Duclaux-Loras, R}, title = {Deep Characterisation of Circulating Torque Teno Virus DNA Load in Crohn's Disease Patients.}, journal = {Journal of medical virology}, volume = {97}, number = {7}, pages = {e70473}, doi = {10.1002/jmv.70473}, pmid = {40586686}, issn = {1096-9071}, support = {//This study was suported by an Appel d'offre jeune chercheur des Hospices Civils de Lyon and bioM&#xe9;rieux./ ; }, mesh = {Humans ; *Torque teno virus/genetics/isolation &amp; purification ; *Crohn Disease/virology ; Male ; *DNA, Viral/blood/genetics ; *Viral Load ; Female ; Adult ; Middle Aged ; *DNA Virus Infections/virology ; Real-Time Polymerase Chain Reaction ; Young Adult ; Metagenomics ; Aged ; Recurrence ; }, abstract = {Torque teno virus (TTV) DNA load in plasma is suggested as a marker for immunosuppression post-transplantation. Crohn's disease (CD) arises from genetic susceptibility, environmental factors, and dysbiosis, causing immune responses. This study examines TTV DNA load in CD patients in remission and its correlation with relapse. Using quantitative real-time polymerase chain reaction (PCR) and metagenomic analysis, the dynamic of plasma TTV DNA load was analyzed from a cohort of CD patients (n = 39) over 1 year and compared with controls (n = 49). At inclusion, TTV DNA was significantly higher in CD patients compare to control (Median [IQR]: 3.27 [2.43-3.67] and 2.05 [1.28-2.80] Log copies/mL, p = 0.0004). Plasma TTV DNA load failed to predict disease relapse in CD patients. Augmented plasma TTV DNA levels in CD patients correlated with diminished circulating CD3 + T cells and especially CD4 + T cells. No preferential representation of TTV subspecies or Anelloviridae genera was detected in CD patients' plasma. This study revealed elevated TTV DNA levels in CD patients' plasma compared to healthy controls, underscoring the intriguing potential of TTV blood sampling as a biomarker in CD.}, }
@article {pmid40586597, year = {2025}, author = {Khatib, L and Song, SJ and Dilmore, AH and Sanders, JG and Brennan, C and Hernandez, AR and Myers, T and Oles, R and Farmer, S and Cowart, C and Birmingham, A and Diaz, EA and Nizet, O and Gilbert, K and Litwin, N and Das, P and Nowinski, B and Bryant, M and Tribelhorn, C and Sanders-Bodai, K and Chaumont, S and Knol, J and Roeselers, G and Laiola, M and Shetty, SA and Veiga, P and Tap, J and Derrien, M and Koutnikova, H and Cotillard, A and Lay, C and Tovar, AR and Torres, N and Arteaga, L and González, A and McDonald, D and Bartko, A and Knight, R}, title = {A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0054425}, doi = {10.1128/msystems.00544-25}, pmid = {40586597}, issn = {2379-5077}, abstract = {UNLABELLED: Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been made to identify general patterns linking diet to the gut microbiome, much of this research has been concentrated on a small number of countries. Additionally, both diet and the gut microbiome have highly complex and individualized configurations, and there is growing evidence that tailoring diets to individual gut microbiota profiles may optimize the path toward improving or maintaining health and preventing disease. Using fecal metagenomic data from 1,177 individuals across three countries, we examine the relationship between diet and bacterial genera, focusing on Prevotella and Faecalibacterium, which have gained significant attention for their potential roles in human health and strong associations with dietary patterns. We find that these two genera in particular show significant associations with many aspects of diet but these associations vary in scale and direction, depending on the level of metagenomic resolution (i.e., genus level by reads and strain level by metagenome-assembled genomes) and the contextual population. These results highlight the growing importance of building metagenomic data sets that are standardized, comprehensive, and representative of diverse populations to increase our ability to tease apart the complex relationship between diet and the microbiome.<br><br>IMPORTANCE: An analysis of fecal microbiome data from individuals in the United States, United Kingdom, and Mexico shows that associations with dietary components vary both by country and by level of resolution (i.e., genus and strain). Our work sheds light on why there may be conflicting reports regarding microbial associations with diet, disease, and health.}, }
@article {pmid40586571, year = {2025}, author = {Jiang, Y and An, Z and Li, W and Xia, S and Ding, Q and Zhong, J and Wang, H and Xu, Y and Chen, K and Shen, Y}, title = {Integrated multi-omics reveals the impact of ruminal keystone bacteria and microbial metabolites on average daily gain in Xuzhou cattle.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0076925}, doi = {10.1128/spectrum.00769-25}, pmid = {40586571}, issn = {2165-0497}, abstract = {UNLABELLED: The rumen microbiome plays a crucial role in determining the metabolic and digestive efficiency of livestock. Despite its crucial role, the impact of the rumen microbiome on average daily gain (ADG) in Xuzhou cattle remains underexplored. Xuzhou cattle is a well-known breed in China, renowned for rapid growth and superior meat quality. We selected 10 individuals from the Xuzhou cattle population and categorized Xuzhou cattle into High-ADG and Low-ADG groups and analyzed their rumen microbiota. Through comprehensive metagenomic and metabolomic analyses, we characterized the microbial diversity and functional composition of the rumen microbiome, uncovering distinct taxonomic and functional alterations associated with ADG. Thirteen kingdoms, 224 phyla, and over 16,000 species were identified, and principal coordinates analysis (PCoA) indicated significant microbial differentiation between the two groups on phylum, genus, and species levels (P < 0.05). Notably, Lentisphaerae, along with several other genera and species, presented a higher abundance in High, suggesting a potential connection with enhanced growth performance. Further functional annotation revealed that the High group displayed enriched carbohydrate and amino acid metabolism pathways, with a greater abundance of carbohydrate-active enzymes (CAZymes), particularly those involved in the degradation of complex carbohydrates. The Low-ADG group exhibited reduced metabolic activity in these pathways. Metabolomic analysis revealed 10 significantly altered metabolites, including gamma-glutamyltyrosine and N-acetylaspartic acid, which were upregulated in the High-ADG group, indicating their potential role in growth promotion. Spearman's rank correlation analysis further uncovered significant interactions between key microbiomes and metabolites, which correlated with ADG. Random forest analysis identified Victivallales and Lentisphaerae as key taxa, with gamma-glutamyltyrosine and Asp-Phe emerging as predictive biomarkers for ADG.<br><br>IMPORTANCE: This study identifies key microbiota (Victivallales and Lentisphaerae) and metabolites (gamma-glutamyltyrosine, Asp-Phe, N-acetylaspartic acid, Gly-Phe) that positively regulate average daily gain (ADG) in Xuzhou cattle through amino acid metabolism. This fundamental information is vital for the development of potential manipulation strategies to improve the daily gain level through precision feeding.}, }
@article {pmid40586543, year = {2025}, author = {Begmatov, S and Beletsky, AV and Mardanov, AV and Lukina, AP and Glukhova, LB and Karnachuk, OV and Ravin, NV}, title = {Novel lineages of bacteria with reduced genomes from the gut of farm animals.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0029425}, doi = {10.1128/msphere.00294-25}, pmid = {40586543}, issn = {2379-5042}, abstract = {Genome reduction and associated metabolic deficiencies have been described in various lineages of parasitic and symbiotic microorganisms that obtain essential nutrients from their partners, and in some free-living microorganisms that inhabit stable environments. The animal gut is a relatively stable ecosystem, characterized by an abundance of organic substances and a high concentration of microorganisms, which provides favorable conditions for the survival of microorganisms with reduced genomes. Metagenomic analysis of 49 samples of feces of farm animals (cows, sheep, yaks, and horses) revealed uncultured lineages of bacteria with reduced genomes (<1 Mbp): family UBA1242 (Christensenellales, Firmicutes), order Rs-D84 (Alphaproteobacteria), and family UBA9783 (Opitutales, Verrucomicrobiota), defined in genome-taxonomy database. Analysis of the genomes showed that these bacteria lacked pathways for the biosynthesis of amino acids, nucleotides, lipids, and many other essential metabolites. The UBA9783 genomes encoded a near-complete Embden-Meyerhof glycolytic pathway and the non-oxidative phase of the pentose phosphate pathway, while in UBA1242 and Rs-D84, these pathways are incomplete. All bacteria are limited to fermentative metabolism and lack aerobic and anaerobic respiratory pathways. All UBA9783 and some Rs-D84 genomes encoded F0F1-type ATP synthase and pyrophosphate-energized proton pump; they also can import and utilize peptides and some amino acids. While UBA9783 bacteria could thrive as specialized free-living organisms in the organic-rich gut environment, the UBA1242 and Rs-D84 lineages appear to have adopted the lifestyle of an obligate symbiont/parasite, obtaining metabolites from other cells.IMPORTANCEThe microbiota of the animal gastrointestinal tracts is a complex community of microorganisms which interact in a synergistic or antagonistic relationship and play key nutritional and metabolic roles. However, despite its importance, the gut microbiota of farm animals, especially its uncultured majority, remains largely unexplored. We performed a metagenomic analysis of the gut microbiome of farm animals and characterized three uncultured lineages of bacteria with reduced genomes (<1 Mbp) from the phyla Firmicutes, Proteobacteria, and Verrucomicrobiota. These bacteria were predicted to possess key metabolic deficiencies such as the inability to synthesize essential cell metabolites, suggesting their adaptation to the lifestyle of a symbiont/parasite, or a scavenger obtaining nutrients from the organic-rich gut environment. This study shows that genome reduction with metabolic specialization and adaptation to a partner-dependent lifestyle occurred through convergent evolution in several phylogenetically distant lineages of gut microbiota.}, }
@article {pmid40586542, year = {2025}, author = {Bruno, JS and Heidrich, V and Restini, FCF and Alves, TMMT and Miranda-Silva, W and Knebel, FH and Cóser, EM and Inoue, LT and Asprino, PF and Camargo, AA and Fregnani, ER}, title = {Dental biofilm serves as an ecological reservoir of acidogenic pathobionts in head and neck cancer patients with radiotherapy-related caries.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0025725}, doi = {10.1128/msphere.00257-25}, pmid = {40586542}, issn = {2379-5042}, abstract = {UNLABELLED: Radiotherapy-related caries (RRC) is an aggressive and debilitating oral toxicity that affects half of the patients who undergo radiotherapy for head and neck cancer. However, the etiology of RRC is not fully established, and there are no clinically validated methods for preventing it. To gain a better understanding of the risk factors and the microbiome's role in causing RRC, we compared clinicopathological characteristics, oncological treatment regimens, oral health condition, and the oral microbiota at three different oral sites of radiotherapy-treated patients with (RRC+) and without radiotherapy-related caries (RRC-). We observed no significant differences between these groups in the clinicopathological characteristics and treatment regimens. However, RRC+ patients were older and had poorer oral health conditions at the start of the radiotherapy treatment, with a lower number of teeth and a higher proportion of rehabilitated teeth. RRC+ patients had lower microbiota diversity and the dental biofilm of RRC+ patients displayed striking alterations in microbiome composition compared to RRC- patients, including enrichment of acidogenic species and altered metabolic potential, with a higher abundance of genes linked to energy-related pathways associated with the synthesis of amino acids and sugars. We also compared the microbiota of RRC+ tissue with conventional caries tissue, revealing lower bacterial diversity and enrichment of Lactobacillaceae members in RRC+. The insights into the irradiated oral microbiota enhance the understanding of RRC etiology and highlight the potential for microbial-targeted therapies in its prevention and treatment.<br><br>IMPORTANCE: This study focuses on a dedicated collection of diverse oral sites to comprehensively investigate microbial differences between patients who develop RRC and those who do not. RRC is a severe oral disease that profoundly impacts on the oral health and overall quality of life of cancer survivors. Leveraging shotgun metagenomics, we characterize the unique microbial variations in in vivo irradiated dental biofilms, unveiling novel insights into the microbial ecology of radiotherapy-treated patients. Furthermore, this research integrates extensive data on oral health and oncological profiles, providing a comprehensive understanding of the intricate relationship between oral microbial communities and the outcomes of radiotherapy-induced toxicity.}, }
@article {pmid40586540, year = {2025}, author = {Bulka, O and Edwards, EA}, title = {Complete metagenome-assembled genome sequence of Solidesulfovibrio sp. DCME from a dichloromethane dechlorinating microbial community.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0051525}, doi = {10.1128/mra.00515-25}, pmid = {40586540}, issn = {2576-098X}, abstract = {Here, we announce the closed genome of Solidesulfovibrio sp. DCME, assembled from metagenomic sequencing of an anaerobic dichloromethane mineralizing enrichment culture. The Solidesulfovibrio genus is known to cycle hydrogen, a key process for facilitating dichloromethane mineralization, which nominates this microbe as an important player in its microbial community.}, }
@article {pmid40586419, year = {2025}, author = {Dason, MS and Corà, D and Re, A}, title = {Sequence modeling tools to decode the biosynthetic diversity of the human microbiome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0033325}, doi = {10.1128/msystems.00333-25}, pmid = {40586419}, issn = {2379-5077}, abstract = {Understanding the biosynthetic potential of the human microbiome remains a significant challenge with far-reaching scientific and translational implications. Analyses of human-associated (meta)genomic sequencing data undeniably show that the biosynthetic diversity encoded in these genomes is largely underexplored. A crucial step in studying specialized metabolites involves the sequence-based identification of genes encoding biosynthetic pathways, typically organized into biosynthetic gene clusters (BGCs). In this review, we provide a concise and updated overview of the widening range of computational approaches that have effectively addressed the sequence-based identification of BGCs across both isolated genomes and complex microbial communities. These advancements are set to deepen our understanding of the biosynthetic potential and diversity of microorganisms residing in different human body sites.}, }
@article {pmid40586263, year = {2025}, author = {Bonham, KS and Margolis, ET and Fahur Bottino, G and Sobrino, AC and Patel, F and McCann, S and Zieff, MR and Miles, M and Herr, D and Davel, L and Bosco, C and ,  and Huttenhower, C and Pini, N and Alexander, DC and Jones, DK and Williams, SCR and Amso, D and Gladstone, M and Fifer, WP and Donald, KA and Gabard-Durnam, LJ and Klepac-Ceraj, V}, title = {Codevelopment of gut microbial metabolism and visual neural circuitry over human infancy.}, journal = {mBio}, volume = {}, number = {}, pages = {e0083525}, doi = {10.1128/mbio.00835-25}, pmid = {40586263}, issn = {2150-7511}, abstract = {Infancy is a time of elevated neuroplasticity supporting rapid brain and sensory development. The gut microbiome, also undergoing extensive developmental changes in early life, may influence brain development through the metabolism of neuroactive compounds. Here, we leverage longitudinal data from 194 South African infants across the first 18 months of life to show that microbial genes encoding enzymes that metabolize molecules playing a key role in modulating early neuroplasticity are associated with visual cortical neurodevelopment, measured by the Visual-Evoked Potential (VEP). Neuroactive compounds included neurotransmitters GABA and glutamate, the amino acid tryptophan, and short-chain fatty acids involved in myelination, including acetate and butyrate. Microbial gene sets around 4 months of age were strongly associated with the VEP from around 9-14 months of age and showed more associations than concurrently measured gene sets, suggesting that microbial metabolism in early life may affect subsequent neural plasticity and development.IMPORTANCEOver the past decade, extensive research has revealed strong links between the gut microbiome and the brain, at least in adults or those with neuropsychiatric disorders. This study explores how these associations emerge in early development using a longitudinal sample of 194 infants with repeated microbiome metabolism and electroencephalography (EEG) measures during the critical early period of visual cortex neuroplasticity. We examined microbial genes encoding enzymes for neuroactive compounds (e.g., GABA, glutamate, tryptophan, and short-chain fatty acids) and their association with the visual-evoked potential (VEP). Genes from 4-month stool samples strongly correlated with VEP features between 9 and 14 months, suggesting that early microbial metabolism influences later visual neurodevelopment. These prospective associations were more numerous than the concurrent ones. Our findings suggest that early gut microbiome metabolic potential plays a crucial role in shaping neural plasticity and visual neurodevelopment.}, }
@article {pmid40585302, year = {2025}, author = {Louca, S}, title = {Machine learning models for delineating marine microbial taxa.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {2}, pages = {lqaf090}, pmid = {40585302}, issn = {2631-9268}, mesh = {*Machine Learning ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Metagenome ; Phylogeny ; Genome, Bacterial ; *Aquatic Organisms/genetics/classification ; }, abstract = {The relationship between gene content differences and microbial taxonomic divergence remains poorly understood, and algorithms for delineating novel microbial taxa above genus level based on multiple genome similarity metrics are lacking. Addressing these gaps is important for macroevolutionary theory, biodiversity assessments, and discovery of novel taxa in metagenomes. Here, I develop machine learning classifier models, based on multiple genome similarity metrics, to determine whether any two marine bacterial and archaeal (prokaryotic) metagenome-assembled genomes (MAGs) belong to the same taxon, from the genus up to the phylum levels. Metrics include average amino acid and nucleotide identities, and fractions of shared genes within various categories, applied to 14 390 previously published non-redundant MAGs. At all taxonomic levels, the balanced accuracy (average of the true-positive and true-negative rate) of classifiers exceeded 92%, suggesting that simple genome similarity metrics serve as good taxon differentiators. Predictor selection and sensitivity analyses revealed gene categories, e.g. those involved in metabolism of cofactors and vitamins, particularly correlated to taxon divergence. Predicted taxon delineations were further used to de novo enumerate marine prokaryotic taxa. Statistical analyses of those enumerations suggest that over half of extant marine prokaryotic phyla, classes, and orders have already been recovered by genome-resolved metagenomic surveys.}, }
@article {pmid40584717, year = {2025}, author = {Shao, J and Xu, X and Xie, X and Fan, Y and Zhang, D and Tang, W}, title = {A case report of septic shock caused by opportunistic infections associated with anti-interferon-γ autoantibody positivity: diagnostic and therapeutic challenges.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1592152}, pmid = {40584717}, issn = {2296-858X}, abstract = {BACKGROUND: Since 2004, there has been an increasing number of reports on severe, persistent, or recurrent Salmonella infections in adults with adult immunodeficiency associated with anti-gamma interferon antibody positivity (AIGA). AIGA patients experience rapid disease progression upon infection with opportunistic pathogens, high mortality rates, and strong disease latency, posing significant challenges for diagnosis and treatment. This article discusses the diagnosis and treatment strategies for AIGA with opportunistic pathogen infection through the diagnosis and treatment process of a 61-year-old male patient.<br><br>METHODS: The patient presented with diarrhea and fever for 2&#x202f;weeks and was diagnosed with non-typhoidal Salmonella infection at an external hospital. The condition progressed to shock and the patient was transferred to our EICU. After admission, the pathogens were confirmed through chest CT, blood culture, blood metagenomic next-generation sequencing (mNGS), and bronchoalveolar lavage fluid (BALF) mNGS, and cell immune function screening and anti-gamma interferon antibody testing were completed. The anti-infective treatment regimen was adjusted based on the test results, and immunoglobulin therapy was administered.<br><br>RESULTS: The patient's blood culture was positive for non-typhoidal Salmonella, and blood mNGS confirmed non-typhoidal Salmonella and Legionella pneumophila; BALF mNGS showed Enterococcus faecium, Legionella pneumophila, Candida tropicalis, Candida glabrata, HSV1, and CMV mixed infection. Immune function screening indicated a significant decrease in CD4&#x202f;+&#x202f;T cells (303 cells/&#x3bc;L) and a significant increase in anti-gamma interferon antibody (163.78&#x202f;ng/mL), confirming the diagnosis of AIGA. After treatment with meropenem, linezolid, doxycycline, ganciclovir, and caspofungin combined with anti-infective and immunoglobulin therapy, the patient's condition significantly improved and was discharged.<br><br>CONCLUSION: AIGA patients experience rapid disease progression after infection with opportunistic pathogens. Early identification of anti-gamma interferon antibody and mixed infection pathogens is crucial for treatment.}, }
@article {pmid40584560, year = {2025}, author = {Billard, H and Fuster, M and Enault, F and Carrias, JF and Fargette, L and Carrouée, M and Desmares, P and Delmont, TO and Nogaret, P and Bigeard, E and Tanguy, G and Baudoux, AC and Christaki, U and Sime-Ngando, T and Colombet, J}, title = {Unexpected diversity and ecological significance of uncultivable large virus-like particles in aquatic environments.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf098}, pmid = {40584560}, issn = {2730-6151}, abstract = {The discovery of jumbo phages and giant viruses of microeukaryotes has transformed our perception of the virosphere. Metagenomic and metatranscriptomic data further highlight their diversity and ecological impact. Nevertheless, sequence-based approaches fail to take into account the morphological diversity of non-cultivated viruses, resulting in our fragmented understanding of their nature and role in the environment. Here, we combined flow cytometry and electron microscopy to uncover both previously unsuspected morphological diversity and significant abundances of large virus-like particles in aquatic environments. We discovered new viral morphotypes, all likely to be associated with microeukaryotes. We also obtained insights into the multi-year dynamics of the abundances of both giant microeukaryotic virus-like particles and jumbo phage-like particles. This work deepens our understanding of large virus and reveals their key role as regulators of microbial communities.}, }
@article {pmid40584555, year = {2025}, author = {Li, W and Fan, Q and Yang, Y and Xiao, X and Li, J and Zhang, Y}, title = {Benchmarking and optimizing qualitative and quantitative pipelines in environmental metatranscriptomics using mixture controlling experiments.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf090}, pmid = {40584555}, issn = {2730-6151}, abstract = {Metatranscriptomic analysis is increasingly performed in environments to provide dynamic gene expression information on ecosystems, responding to their changing conditions. Many computational methods have undergone remarkable development in the past years, but a comprehensive benchmark study is still lacking. There are concerns regarding the accuracies of the qualitative and quantitative profilers obtained from metatranscriptomic analysis, especially for the microbiota in extreme environments, most of them are unculturable and lack well-annotated reference genomes. Here, we presented a benchmark experiment that included 10 single-species and their cell or RNA-admixtures with the predefined species compositions and varying evenness, simulating the low annotation rate and high heterogeneity. In total, 1 metagenome sample and 24 metatranscriptome were sequenced for the comparisons of 36 combination of analysis methods for tasks ranging from sample preparation, quality control, rRNA removal, alignment strategies, taxonomic profiling, and transcript quantification. For each part of the workflow mentioned above, corresponding metrics have been established to serve as standards for assessment and comparison. Evaluation revealed the performances and proposed an optimized pipeline named MT-Enviro (MetaTranscriptomic analysis for ENVIROnmental microbiome). Our data and analysis provide a comprehensive framework for benchmarking computational methods with metatranscriptomic analysis. MT-Enviro is implemented in Nextflow and is freely available from https://github.com/Li-Lab-SJTU/MT-Enviro.}, }
@article {pmid40584035, year = {2025}, author = {Li, X and Li, D and Wang, C and Li, Q and Nie, Y and Zhang, L and Xu, J and Ma, Y}, title = {Metagenomic insights into the effects of Chive seed flavonoid on intestinal fermentation, morphology, and microbiota composition in sheep.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1590400}, pmid = {40584035}, issn = {1664-302X}, abstract = {Chive seed flavonoid (CSF) exhibits antioxidant, digestive, and immunomodulatory properties, yet their effects on ruminant intestinal development and microbial ecosystems remain underexplored. This study systematically evaluated CSF supplementation (0.25% of concentrate) on intestinal morphology, volatile fatty acids (VFAs) dynamics, and microbiota composition in 16 weaned Hu lambs (3 months; 19.57 ± 1.56 kg initial weight) using histomorphometry, VFA quantification, and full-length 16S rRNA sequencing. Animals were randomly allocated to a control (basal diet) or CSF-supplemented group (T), following a 7-day adaptation and 90-day experimental protocol. Key findings revealed: (1) The T group demonstrated increased jejunal and ileal villus length (p < 0.05), elevated villus height-to-crypt depth ratio (V/C; p < 0.05), thickened muscular layers (p < 0.05), and reduced crypt depth (p < 0.05). (2) CSF supplementation significantly elevated acetate, propionate, butyrate, and total VFAs (p < 0.05) in ileum, cecum, colon, and rectum, with notable jejunal propionate and total VFAs increases (p < 0.05). (3) Upregulated expression of ileal and cecal genes (IGF1, CD81, CTNNBL1, SLC39A8) linked to tissue morphogenesis and VFAs absorption was observed in the T group (p < 0.01). (4) Full-length 16S analysis demonstrated CSF-enhanced microbial diversity and selective enrichment of Cyanobacteriota, Bacillus, Acetobacterium, and Streptomyces [Linear Discriminant Analysis Effect Size (LEfSe) analysis]. Regional microbial shifts included Bacteroidota proliferation in the small intestine and rectum, Actinomycetota dominance in duodenum/cecum/colon, and ileal enrichment of Bacillota, Clostridium, and Streptomyces. KEGG pathway analysis confirmed CSF-driven enhancements in carbohydrate/energy metabolism, immune regulation, and intestinal barrier pathways (p < 0.05). In conclusion, dietary supplementation with 0.25% CSF improved intestinal morphology, increased the production of VFAs, and optimized microbial composition, thereby promoting intestinal health in sheep. This study provides a theoretical basis for the application of CSF in promoting healthy production in sheep.}, }
@article {pmid40584012, year = {2025}, author = {Li, Y and Zhu, J and Li, Q and Hong, H and Li, T and Jia, H and Hou, B and Lu, H and Li, Y and Xie, J and Wang, F and Ye, H and Liu, K and Lu, A and Zhao, J}, title = {Non-linear frequency-doubling up-conversion in sulfide minerals enables deep-sea oxygenic photosynthesis.}, journal = {National science review}, volume = {12}, number = {6}, pages = {nwaf219}, pmid = {40584012}, issn = {2053-714X}, abstract = {Visible light emission exceeding purely thermal radiation has been imaged at deep-sea hydrothermal vents, yet the underlying mechanisms remain unexplained. Here, we show that visible light can be produced from geothermal infrared radiation via nonlinear frequency-doubling up-conversion in sulfide minerals that are abundant in hydrothermal vents. Chalcopyrite exhibits significant second harmonic generation, which is further amplified under high pressure, yielding a 400-700 nm photon flux three orders of magnitude greater than blackbody emission. When exposed to 1064 nm of irradiation, chalcopyrite induces fluorescence responses in the cyanobacterium Synechococcus sp. PCC 7002 at 656 and 685 nm, suggesting that the up-converted 532 nm light is absorbed by phycobilisomes and transferred to photosystem II. Metagenomic analysis reveals a strong correlation between cyanobacteria and high-temperature, chalcopyrite-rich vents. Similar up-conversion processes have also been observed in other sulfide minerals, emitting wavelengths covering the entire visible spectrum. These findings unveil a novel mineral-mediated photonic mechanism that generates biologically relevant visible light at hydrothermal vents, which can be harnessed by oxygenic photosynthetic cyanobacteria in Earth's deep biosphere and possibly beyond.}, }
@article {pmid40583454, year = {2025}, author = {Aldrian, D and Pollio, A and Mayerhofer, C and Diederen, K and Jacobs, JP and Pai, N and Szamosi, JC and Hart, L and Turner, D and Del Chierico, F and Cardile, S and Grigoryan, Z and Chen, LA and Hurych, J and Cinek, O and Taddei, CR and Schwerd, T and Wine, E and Griffiths, AM and Müller, T and Vogel, GF}, title = {Fecal Microbial Community Profiling Allows Discrimination of Phenweotype and Treatment Response in Pediatric Crohn's Disease and Ulcerative Colitis-An International Meta-Analysis.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izaf135}, pmid = {40583454}, issn = {1536-4844}, abstract = {BACKGROUND AND AIMS: The pathophysiology of pediatric inflammatory bowel disease (PIBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is not entirely understood. Dysregulation of the intestinal microbiome is recognized as both a disease-driving and a potential therapeutic target. This study aimed to systematically analyze gut microbiome compositions and its applicability as a biomarker for disease progress and treatment response.<br><br>METHODS: Bibliographic and nucleotide databases were searched. Raw 16S-rRNA sequencing reads were subjected to a uniform downstream dada2/phyloseq pipeline to extract taxonomy, community structure, and abundance information. Patient metadata were extracted from publications, and study authors were contacted for further details if required.<br><br>RESULTS: Twenty-six studies comprising 3956 stool samples (CD 41%, UC 36%, 23% healthy) were included in the analyses. Median age of individuals was 12 (interquartile range 4). Sex distribution was comparable. Alpha diversity was reduced between the healthy and both UC and CD treatment-na&#xef;ve groups (P&#x2005;<&#x2005;.001) and further reduced with increasing clinical disease activity. Beta diversity revealed altered community structure in treatment-na&#xef;ve children with PIBD (P&#x2005;<&#x2005;.001). This alteration remained in patients in clinical remission (P&#x2005;<&#x2005;.001). Machine learning models discriminated between treatment-na&#xef;ve patients with CD or UC with an area under the receiver operating characteristics curve (AUROC) of 98%. Microbial communities differed between patient responders versus nonresponders to treatment (P&#x2005;<&#x2005;.001). Further, microbial community profiling distinguished treatment response (eg, steroid, nutrition, or TNF&#x3b1;) with AUROCs of 82%-90%.<br><br>CONCLUSIONS: Gut microbial community structure is substantially altered in active and inactive PIBD and may be utilized as a biomarker for differentiating PIBD subtype and predicting treatment response.}, }
@article {pmid40582827, year = {2025}, author = {Han, RQ and Shi, Y and Song, YC and Song, RX and Xue, NN}, title = {[Distribution Characteristics of Soil Resistance Genes in Cotton Fields with Different Continuous Cropping Years].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {6}, pages = {3934-3941}, doi = {10.13227/j.hjkx.202405127}, pmid = {40582827}, issn = {0250-3301}, mesh = {*Gossypium/growth &amp; development/genetics ; Soil/chemistry ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Agriculture/methods ; China ; }, abstract = {With the continuous development of intensive agriculture， the crop rotation index has increased. Continuous planting of a single type of crop introduces specific environmental selective pressures that may lead to changes in the soil resistome. Therefore， investigating the composition and characteristics of antibiotic resistance genes （ARGs） and metal resistance genes （MRGs） in soil with different degrees of continuous cropping is of great significance for promoting the green development of agriculture. In this study， we employed metagenomics techniques to examine the profile of ARGs in cotton field soils across different levels of continuous cropping years in the Xinjiang Arid Region. Our findings revealed that the types and abundance of ARGs and MRGs in cotton field soils differed with the length of continuous cropping periods. A total of 1 181 ARGs and 506 MRGs were found in the present study. Continuous cropping led to the emergence of some new ARGs and MRGs. Network and Procrustes analysis indicated a significant correlation between the composition of ARGs and MRGs. Additionally， the actP gene was the key node connecting ARGs and MRGs. Mantel tests demonstrated that ARGs and MRGs were not correlated with soil pH， alkali-hydrolyzable nitrogen， total nitrogen， or total potassium levels. However， a strong positive correlation was observed between these genes and soil electrical conductivity （Mantels' P=0.001） and a significant but weak correlation with the continuous cropping years （Mantels' P < 0.05）.}, }
@article {pmid40582607, year = {2025}, author = {Páez-Triana, L and Luna, N and Cruz-Saavedra, L and Ramírez, AL and Medina, JE and Castañeda, S and Gómez, M and Garcia-Corredor, DJ and Medellín, MOP and Patiño, LH and Muñoz, M and Ramirez, JD}, title = {Characterizing the diversity of Rhipicephalus sanguineus sensu lato (s.l) virome in Colombia.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107715}, doi = {10.1016/j.actatropica.2025.107715}, pmid = {40582607}, issn = {1873-6254}, abstract = {Ticks within the species complex Rhipicephalus sanguineus sensu lato are carriers for various pathogens worldwide. Among them are some RNA viruses, who have gained increased attention due to their potential for interaction between pathogenic and non-pathogenic organism, shifts in tick distribution, and the emergence of diseases transmitted by ticks to human populations. Our study aimed to investigate the RNA virus composition in R. sanguineus s.l. (also known as R. linnaei) ticks collected from the Santander and Casanare regions in eastern Colombia. We employed Oxford Nanopore sequencing technology coupled with viral enrichment procedures. Thirty-nine adult ticks, removed from dogs, were sequenced with Oxford Nanopore sequencing. These reads underwent two distinct analyses: one focused on sequencing reads utilizing Centrifuge/BLAST for direct assignment, and one involved assembly of viral metagenomic assembled genomes (vMAGs) using the Genome Detective Tool program. Our investigation showed the presence of six distinct viruses within the tick virome: Trinbago virus, Mivirus sp., Bole tick virus 4, Brown dog tick phlebovirus 2, Totiviridae sp., Ixodes scapularis totilike virus, and Brown dog tick phlebovirus 1. Notably, we successfully assembled the genomes for the latter two species, enabling phylogenetic and comparative analyses with genomes from various global regions. Only the category of sex yield significant differences in alpha diversity. We described viruses with potential pathogenicity but also with endosymbiotic potential. The latter group holds promise for developing biotechnological tools to aid future tick vector control strategies. Furthermore, our research offered valuable insights into the predominant viruses found in R. sanguineus s.l. ticks in two previously unexplored regions within Colombia.}, }
@article {pmid40582470, year = {2025}, author = {Bolloré, K and Tinto, B and Charriat, F and Pisoni, A and Exbrayat, A and Gutierrez, S and Simonin, Y and Tuaillon, E}, title = {Investigation of the viral causes of febrile jaundice in Burkina Faso through metagenomic sequencing.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106541}, doi = {10.1016/j.jinf.2025.106541}, pmid = {40582470}, issn = {1532-2742}, abstract = {OBJECTIVES: Yellow fever virus (YFV) is a key concern in West Africa, often associated with febrile jaundice. However, many patients with this syndrome test negative for YFV, raising questions about other potential viral etiologies. This study aimed to characterize the viral landscape in YFV-negative febrile jaundice cases using metagenomic next-generation sequencing (mNGS).<br><br>METHODS: Serum samples were collected in 2019 from 152 febrile jaundice patients in Burkina Faso who tested negative for both YFV and malaria. A random subset of 100 samples was analyzed by mNGS to identify viral sequences. Bioinformatic pipelines were applied to classify viral reads, and findings were validated by quantitative PCR (qPCR) and serological assays. Additional specimens from the same cohort, as well as from febrile patients without jaundice, were tested to assess the prevalence of the key viral findings.<br><br>RESULTS: mNGS revealed 58 viral species, including four human pathogens: HIV-1 (n=1), YFV (n=1), hepatitis A virus (HAV, n=16), and hepatitis B virus (HBV, n=18). qPCR confirmed 75% of HAV and 67% of HBV cases. Serological testing on additional samples confirmed comparable HAV and HBV prevalence among jaundiced patients, but significantly lower rates among those without jaundice.<br><br>CONCLUSION: mNGS uncovered undiagnosed viral infections, demonstrating its value for differential diagnosis and surveillance in resource-limited settings.}, }
@article {pmid40582136, year = {2025}, author = {Song, L and Hu, C and Zhang, X and Liu, Y and Song, G and Wu, J and Wang, Z and Sun, M}, title = {Effects of feeding on microbial community structure and pathogen abundance in marine aquaculture ponds.}, journal = {Marine environmental research}, volume = {210}, number = {}, pages = {107319}, doi = {10.1016/j.marenvres.2025.107319}, pmid = {40582136}, issn = {1879-0291}, abstract = {Microbial communities in aquaculture ponds play a vital role in regulating water quality, driving nutrient cycling, and maintaining ecological balance. In 2023, we conducted a study to evaluate how feeding affects microbial communities by comparing the microbial composition and water quality in both fed and unfed aquaculture ponds. Metagenomic sequencing indicated that feeding significantly elevated the relative abundance of bacteria within the microbial community. Ecological similarity analysis showed that bacterial community in the ponds predominantly originated from internal pond sources, rather than from adjacent coastal waters. Furthermore, the relative abundance of pathogenic bacteria was significantly higher in fed ponds, with Vibrio parahaemolyticus levels reaching 1.6 times those in unfed ponds. In addition, water quality assessments further showed that feeding elevated nutrient concentrations, leading to eutrophication. Analyses of redundancy and correlation showed a notable positive link (p < 0.05) between the levels of pathogenic bacteria and the concentration of organic nutrients. These results suggest that excessive feeding contributes to eutrophication, which promotes the growth of bacteria, including pathogenic strains, thereby increasing the risk of disease outbreaks in aquaculture systems.}, }
@article {pmid40581627, year = {2025}, author = {Nørgaard, JC and Marandi, RZ and Ilett, EE and Gulay, A and Paredes, R and Lundgren, JD and Jørgensen, M and Sengeløv, H}, title = {The gut microbiome and its resistome as predictors of clinical infections and phenotypic antibiotic resistance in hematopoietic stem cell transplant recipients.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiaf330}, pmid = {40581627}, issn = {1537-6613}, abstract = {A relationship between the gut microbiome composition, its resistome, and risk of clinical infections may exist and was explored here using 663 shotgun-sequenced fecal samples from 276 stem cell transplant patients. E. faecium, E. coli, and E. faecalis were the three most prevalent causes of clinical infection, with vancomycin resistance in E. faecium as the most common antibiotic resistance feature. Associations between the gut microbiome, resistome, and clinical infections were tested, with significant findings (FDR<0.05) evaluated in multivariable analysis. A 10% increase in gut abundance of E. faecium was positively associated with subsequent clinical infection with E. faecium (OR=1.14, p=0.02). Additionally, a 1% increase in vanA gene abundance was positively associated with vancomycin-resistant E. faecium infection (OR=1.27, p<0.01). Here we used metagenomics to enhance the understanding of infectious sources and to identify patients at risk of clinical infection with antibiotic-resistant bacterial strains.}, }
@article {pmid40581162, year = {2025}, author = {Haider, SA and Jamal, Z and Ammar, M and Hakim, R and Afrough, B and Kreku, A and Inamdar, L and Salman, M and Umair, M}, title = {Genomic characterization of the Coxsackievirus A24 variant in the Acute Hemorrhagic Conjunctivitis outbreak (2023) in Islamabad, Pakistan through metagenomic next generation sequencing.}, journal = {Journal of virological methods}, volume = {338}, number = {}, pages = {115213}, doi = {10.1016/j.jviromet.2025.115213}, pmid = {40581162}, issn = {1879-0984}, abstract = {Pakistan experienced a significant outbreak of Acute Hemorrhagic Conjunctivitis (AHC) in 2023. To identify the cause, in the absence of targeted diagnostic tests, the National Institute of Health, Islamabad, studied 15 conjunctivitis patients from Islamabad in September 2023. Metagenomic Next Generation Sequencing (mNGS) was performed on 10 samples collected within 48 h of symptom onset. The human Coxsackievirus A24 variant (CV-A24v), genotype IV, was detected in three samples. Phylogenetic analysis showed ∼99 % similarity with recent strains from China and 94 % similarity with the 2015 France outbreak. Mutation analysis revealed mostly non-synonymous substitutions, particularly in the VP1 region (n = 14), and differences in 2 C and 3D regions of nonstructural proteins. Comparison with 2005 Pakistan outbreak sequences showed divergence in the VP1 region, with two distinct mutations ("L16I" and "L25H"), with L16I being a rare mutation observed only in strain from China and India in 2023. Structural modeling of VP1 proteins indicated conformational differences between the 2023 and 2005 strains, suggesting potential impacts on viral infectivity and immune escape. These findings indicate the reemergence of CV-A24v in Pakistan and highlight the importance of adaptable diagnostic strategies to respond to emerging infectious threats.}, }
@article {pmid40581059, year = {2025}, author = {Shi, Y and Zuo, S and Zhang, Z and Li, A and Ji, B}, title = {Mechanistic insights into nitrogen source influence on microalgal-bacterial granular sludge: Community dynamics and metabolic functions.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132895}, doi = {10.1016/j.biortech.2025.132895}, pmid = {40581059}, issn = {1873-2976}, abstract = {This study investigated the effects of nitrogen source (different ammonia to urea ratios) on pollutant removal, microbial community evolution and function in the MBGS system. Results showed that a higher ammonia proportion significantly enhanced total nitrogen removal during the initial 7-day operation compared to urea (p < 0.05). However, this nitrogen source-dependent effect adapted and diminished during the subsequent 14 days (p > 0.05). Microbial analysis revealed that urea enriched Proteobacteria (specifically Alphaproteobacteria including Roseomonas), while ammonia stimulated Firmicutes (specifically Clostridia including Acetoanaerobium), Betaproteobacteria, and Cyanophyceae. Metagenomic analysis identified that Alphaproteobacteria played a dominant role in key genes (ureA/B/C, GLUD, gltB) involved in nitrogen metabolism. Robust correlations between nitrogen source composition and microbial population dynamics underscores the self-regulating capacity of the MBGS system. These comprehensive findings demonstrate the excellent adaptability of the MBGS to varying nitrogen compositions through microbial community regulation.}, }
@article {pmid40580838, year = {2025}, author = {Mirzaei, S and Gorczyca, B and Uyaguari-Diaz, M and Sparling, R and Maksimova, E}, title = {Microbial consortia in full-scale pre-ozonated biologically active filters treating a high-DOC water: Effects of seasonal and operational variations.}, journal = {Water research}, volume = {285}, number = {}, pages = {124065}, doi = {10.1016/j.watres.2025.124065}, pmid = {40580838}, issn = {1879-2448}, abstract = {This study investigated the microbial dynamics in full-scale biologically active anthracite/silica sand (BAS) and granular activated carbon (BAC) filters used to treat high-DOC coagulated softened water. By analyzing these filter types across two seasons (winter and summer), we examined the impact of operational conditions-including temperature (1 °C vs. 25 °C), backwashing cycle (72 h vs. two weeks), and empty bed contact time (10 vs. 24 min in BAC and 4 vs. 10 min in BAS)-on organic matter removal, biological activity, and bacterial taxonomy and functionality. The highest DOC (19.1 %) and BDOC (34.8 %) removal rates were observed in BAC during summer and post-backwashing, whereas BAS in both seasons and BAC in the winter showed minimal effects on the organic matter concentration. No direct correlation was found between ATP levels, bacterial 16S rRNA bacterial gene copy numbers, and DOC/BDOC removal in BAC. However, an optimal condition of 13 × 10[-6] ATP per bacterial gene copy number in BAC during summer post-backwashing coincided with the highest DOC and BDOC removal. Bacterial taxa with established associations to DOC degradation accounted for over 60 % of the total bacterial orders identified in both BAS and BAC across seasons. The BAC environment appeared to selectively enrich consortia capable of transforming complex DOC fractions, likely facilitated by its greater surface area, extended EBCT, and less frequent backwashing. These conditions supported the persistence and activity of specific bacterial orders, including Actinomycetales, Myxococcales, Planctomycetales, and Rhizobiales. Subsystem-level metagenomic analysis indicated a significant enrichment of genes associated with metabolic functions linked to enzymes such as decarboxylase, N-methylhydantoinase A, cyclic beta-1,2-glucan synthase, carbon monoxide dehydrogenase, cell division protein FtsH, N-methylhydantoinase B, and UDP-glucose 4-epimerase in BAC samples. This study deepens our understanding of the BAF microbiome's role in natural organic matter removal and its relationship with operational parameters, addressing critical gaps in drinking water biological treatment.}, }
@article {pmid40580736, year = {2025}, author = {Peng, C and Li, M and Wang, J and Zhang, J and Liu, X and Wang, L}, title = {Metagenomic and metabolomic insight into microplastic-derived inhibition of tetracycline degradation in sediments.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139045}, doi = {10.1016/j.jhazmat.2025.139045}, pmid = {40580736}, issn = {1873-3336}, abstract = {Microplastics (MPs) have been extensively reported to affect organic compound metabolism and nutrient cycling in the ecosystem, particularly in aquatic sediments. However, the specific microbial pathways and underlying mechanisms governing these impacts remain incompletely understood. Herein, this study integrates field investigations and simulation experiments to demonstrate the inhibitory effects of MP contamination on tetracycline (TC) biodegradation in sediments. Our findings reveal three distinct TC biotransformation pathways in sediments, with monooxygenase-mediated hydroxylation emerging as the predominant pathway. Comparative analysis revealed significant reductions in monooxygenase abundance (56.6 %), host bacterial populations (38.5 %), and TC biodegradation efficiency (23.8 %) in MP-amended sediments compared with the control after 28 days (p < 0.05). MPs reduce microbial metabolic activity and cooperative relationships among microorganisms, which inhibit cooperative metabolism of complex organic compounds (including tetracycline). Ultimately, MPs occupy interstitial spaces within sediment matrices, thereby altering redox conditions and promoting microbial succession toward taxa less efficient in TC metabolism. Moreover, the plastisphere exhibits significantly reduced metabolic capacity for TC transformation compared with inorganic mineral-associated biofilms, thereby impeding TC biotransformation within sediments. This finding further implies that continuous MP accumulation may exacerbate interference with biogeochemical cycles.}, }
@article {pmid40580733, year = {2025}, author = {Du, S and Tang, H and Wang, Z and Chen, H and Fang, X and Sun, J and Niu, Z and Liu, Y and Hu, Y and Su, W and Zhang, Z and Prapamontol, T and Nakayama, SF and Huang, J and Norback, D and Wu, Q and Tan, Y and Zhao, Z}, title = {Children's home environments as reservoirs of antimicrobial resistance: Divergent urban-rural risks from antibiotic resistance genes and pathogens.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139053}, doi = {10.1016/j.jhazmat.2025.139053}, pmid = {40580733}, issn = {1873-3336}, abstract = {Antibiotic resistance genes(ARGs) and pathogens pose a global health challenge, particularly for vulnerable children. However, limited knowledge is on their existence in home environments where children spend majority of time, even less on urban-rural differences. We collected settled dust from children's homes in urban(n = 31) and rural (n = 34) areas of Shanghai, China, and analyzed microbiomes, ARGs and pathogens through metagenomic sequencing. Home dust microbial compositions differed significantly between urban and rural environment. ARGs were widely detected in home environment (rural:758 subtypes; urban:733). Significant urban-rural differences were also observed in ARGs and pathogens composition, diversity, co-occurrence patterns, assembly processes and drivers. Specifically, rural dust was enriched with more differentially abundant ARG subtypes. Urban dust was enriched with clinically critical multidrug-resistant pathogens (e.g. Acinetobacter baumannii), contrasting with rural areas enriched in plant-associated pathogens. Stochastic processes dominated the assembly of ARGs and pathogens, while environmental factors partially explained their variations. Temperature was positively associated with total ARG abundance in both areas. Residential greenness had a positive relationship with ARG abundance in rural but negative in urban settings. Our findings indicated children's homes as reservoirs of antimicrobial resistance, urging vigilance against rural ARG enrichment and urban multidrug-resistant pathogen risks for pediatric health.}, }
@article {pmid40580323, year = {2025}, author = {Callejas, C and Guerrero, L and Erijman, L and López, I and Borzacconi, L}, title = {Microbiota and methanogenic activities in an anaerobic internal circulation reactor: insights into biogas production from brewery wastewater.}, journal = {Biodegradation}, volume = {36}, number = {4}, pages = {56}, pmid = {40580323}, issn = {1572-9729}, support = {2019//Comisi&#xf3;n Sectorial de Investigaci&#xf3;n Cient&#xed;fica/ ; 2019//Comisi&#xf3;n Sectorial de Investigaci&#xf3;n Cient&#xed;fica/ ; 2019//Comisi&#xf3;n Sectorial de Investigaci&#xf3;n Cient&#xed;fica/ ; }, mesh = {*Bioreactors/microbiology ; *Methane/metabolism ; *Microbiota ; *Biofuels/microbiology ; *Wastewater/microbiology ; Anaerobiosis ; Archaea/metabolism/genetics/classification ; Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; }, abstract = {In this study, we analyzed the prokaryotic community and methanogenic activities in sludge samples collected from a full-scale internal circulation (IC) reactor used to treat brewery wastewater. The reactor performance was monitored over 15 months, and specific methanogenic activities were periodically measured in fresh sludge samples using CO2/H2 or acetate as substrates. The maximum hydrogenotrophic activities were consistently higher than maximum acetoclastic activities, suggesting the relevance of hydrogenotrophic methanogens in the sludge. Over six months, the prokaryotic community present in four sludge samples was analyzed using amplicon libraries and metagenomics. V4-16S rRNA amplicon libraries revealed the presence of a diverse microbial community dominated by Firmicutes and Bacteroidetes among bacterial phyla, and Halobacterota and Euryarchaeota among archaea. Furthermore, the 16S libraries constructed with cDNA were consistent with the methanogenic activity assays. A genome-centric metagenomics approach was used to assemble 42 high-quality metagenome-assembled genomes (MAGs), among which Methanothrix and Methanobacterium were the dominant archaeal members, and Acidobacteriota, Synergistota, Krumholzibacteriota, and Nitrospirota phyla were among the bacteria. Potential acetogenic members were explored via the fths gene; 15 MAGs contained this marker gene. A combination of methanogenic activity tests, amplicon libraries, and MAG analysis was used to gain insights into the prokaryotic structure and functional potential of the microbial community driving methane production in the reactor.}, }
@article {pmid40580246, year = {2025}, author = {Mauduit, O and Kumar, P and Scholand, KK and Aksan, E and Schaefer, L and Abu-Romman, A and Delcroix, V and Yu, Z and Sindikubwabo, AI and Korstanje, R and Makarenkova, HP and de Paiva, CS}, title = {Exploring the transformative effects of calorie restriction on the lacrimal gland in adult mice.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {40580246}, issn = {2509-2723}, support = {EY035333/EY/NEI NIH HHS/United States ; EY026202/EY/NEI NIH HHS/United States ; EY002520/EY/NEI NIH HHS/United States ; T32 EY007001/EY/NEI NIH HHS/United States ; AG038070//National Institute of Aging/ ; }, abstract = {Advanced age is one of the most recognizable risk factors for dry eye. Dry eye disease affects millions worldwide and can result from age-related lacrimal gland dysfunction, which correlates with a decline in lacrimal gland secretory cell function and chronic inflammation. This study investigated the potential of calorie restriction to maintain lacrimal gland and ocular surface health. Adult female C57BL/6 J mice were subjected to a 40% calorie restriction for 4 months, starting at 6-7 months and continuing until 10-11 months. These mice were compared to controls fed ad libitum. Bulk RNA sequencing of lacrimal glands, conjunctiva, and cornea subjected to calorie restriction compared to ad libitum revealed significant differentially expressed genes (DEGs). Pathways enriched in the upregulated DEGs indicate enhanced circadian rhythm, secretory functions, and lipid metabolism. These findings were confirmed using individual qRT-PCR and western blotting. In contrast, pathways enriched in the downregulated DEGs were associated with immune cell activation, adaptive immune responses, extracellular matrix remodeling, and metalloproteinase activity. Histological sections of calorie-restricted lacrimal glands revealed reduced mononuclear cell infiltration and fewer positive cells for CD4, CD19, and MHC II than in ad libitum lacrimal glands. Calorie restriction also prevented age-related corneal barrier dysfunction and mitigated age-related conjunctival goblet cell loss, hallmarks of dry eye disease. These findings suggest that calorie restriction supports lacrimal gland and ocular surface health by reducing inflammation and extracellular matrix remodeling and by enhancing the lacrimal gland's secretory function.}, }
@article {pmid40580234, year = {2025}, author = {Biessy, L and Sissons, J and Kihika, JK and Wood, SA and Pearman, JK}, title = {Microbial adaptations to acidic, nutrient- and metal-rich lakes in Aotearoa New Zealand.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {2}, pages = {24}, pmid = {40580234}, issn = {1433-4909}, mesh = {*Lakes/microbiology/chemistry ; New Zealand ; *Microbiota ; *Adaptation, Physiological ; Geologic Sediments/microbiology ; *Metals/analysis ; Nutrients/analysis ; Bacteria/genetics/metabolism ; }, abstract = {Four lakes in the same region of Aotearoa New Zealand were investigated to characterize sediment microbial communities and functions under contrasting environmental conditions. Two lakes, an acidic lake (Rototai) and a lake with elevated metals and nutrients (Killarney) were impacted by extreme stressors, while the lowland mesotrophic lake (Kaihoka East) and an alpine lake (Peel) were used as reference lakes. Using metabarcoding and metagenomics analysis, we profiled community composition, functional pathways, and resistance mechanisms in the lake sediments. Rototai contained high abundances of genes involved in sulfur cycling (assimilatory and dissimilatory sulfate reduction, sulfur oxidation) and acid tolerance (kdp potassium-transport system, ClcA antiporters). In contrast, Killarney had elevated abundances of genes involved in methanogenesis, however despite high metal concentrations, no enrichment of metal-resistance genes was detected. Kaihoka East contained the highest prokaryotic diversity and an elevated abundance of genes involved in nitrification. Although community taxonomic differences were modest across lakes, functional analyses revealed distinct metabolic adaptations. These findings highlight the utility of using metagenomic approaches to identify biogeochemical processes and stress-response strategies in lakes. Improved understanding of microbial functional diversity in surface sediments has implications for lake management, particularly in systems impacted by acidification, high nutrient loading, and metal contamination.}, }
@article {pmid40580061, year = {2025}, author = {Rathour, R and Ma, Y and Xiong, J and Wang, XW and Petersen, J and Zhang, X}, title = {Hemolymph microbiota and host immunity of crustaceans and mollusks.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf133}, pmid = {40580061}, issn = {1751-7370}, abstract = {None declared.Conflicts of interestCrustaceans and mollusks have major economic importance and are also key players in aquatic biogeochemical cycles. However, disease outbreaks, temperature fluctuations, pollutants, and other stressors have severely threatened their global production. Invertebrates generally rely on their innate immune system as the primary defence mechanism, operating at cellular and humoral levels to protect against pathogens. The hemolymph plays a vital role in immune responses, containing microbial communities that interact with the host's immune processes. Significant advances in molecular methods such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics have revealed the presence of a resident hemolymph microbiome and delineated its potentially vital role in immune homeostasis and overall host health. Accordingly, understanding the composition and role of the hemolymph microbiota, alongside innate immune responses, has become a key focus in recent research aimed at unravelling disease resistance mechanisms and supporting sustainable aquaculture practices. Here, we summarize the latest advancements in understanding the host and environmental factors that shape hemolymph microbiota diversity in various crustaceans and mollusks species. We also consider the innate immune responses of the hosts, as these modulate interactions between hosts, microbes, and environments. Interactions within the hemolymph microbiome significantly affect host health, providing critical insights for advancing sustainable aquaculture.}, }
@article {pmid40579799, year = {2025}, author = {Zamparo, S and Brocca, G and Marroni, F and Radovic, S and Castellano, C and Torge, D and Bianchi, S and Groman, D and Macchiarelli, G and Muscatello, LV and Volpatti, D and Orioles, M}, title = {Metabarcoding Reveals a Potentially Undescribed Columnaris-Causing Bacterium in Peracute Skin Disease of Rainbow Trout (Oncorhynchus mykiss, Walbaum).}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e70004}, doi = {10.1111/jfd.70004}, pmid = {40579799}, issn = {1365-2761}, abstract = {Columnaris-causing bacteria (CCB) represent a group of four Flavobacterium species, previously classified under Flavobacterium columnaris, causing a threatening condition in salmonid farming characterised by cutaneous and gill lesions, commonly referred to as 'saddleback disease'. A peracute skin disease outbreak with high mortality in rainbow trout (Oncorhynchus mykiss) farms in Northern Italy was investigated. The disease presented with skin discoloration and scale lifting without internal organ abnormalities, leading to a weekly cumulative mortality of up to 80%. The disease was successfully managed with Oxytetracycline treatment, with no relapses observed. Conventional investigation methods produced inconsistent results, prompting additional analyses. Metagenomic sequencing of the 16S rRNA identified Flavobacterium species differing from the classical CCB based on the alignment of the V3 and V4 regions, with best matches to Flavobacterium bernardetii, Flavobacterium aquicola, and Flavobacterium hiemivividum. Histopathology and SEM confirmed epidermal necrosis and bacterial infiltration in the dermis, with filamentous bacteria resembling Flavobacterium morphology yet differing from classical CCB lesions. These findings point to a previously undescribed Flavobacterium-related skin disease with significant economic implications, supporting the value of metagenomic in investigating microbial dynamics in aquaculture diseases, especially in sites exposed to external environments. Further research is required to clarify the pathogenic mechanisms and guide effective management strategies for future outbreaks.}, }
@article {pmid40578342, year = {2025}, author = {Wong, KK and Wu, BG and Chung, M and Li, Q and Darawshy, F and Tsay, JJ and Holub, M and Barnett, CR and Kwok, B and Kugler, MC and Chung, C and Natalini, JG and Singh, S and Li, Y and Schluger, R and Ficaro, L and Carpenito, J and Collazo, D and Perez, L and Kyeremateng, Y and Chang, M and Czachor, A and Singh, R and Mccormick, C and Campbell, CD and Keane, R and Askenazi, M and Hansbro, PM and Weiden, MD and Huang, YJ and Stringer, KA and Clemente, JC and Li, H and Jones, D and Ghedin, E and Segal, LN and Sulaiman, I}, title = {Microbial contribution to metabolic niche formation varies across the respiratory tract.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2025.06.002}, pmid = {40578342}, issn = {1934-6069}, abstract = {Variations in the airway microbiome are associated with inflammatory responses in the lung and pulmonary disease outcomes. Regional changes in microbiome composition could have spatial effects on the metabolic environment, contributing to differences in the host response. Here, we profiled the respiratory microbiome (metagenome/metatranscriptome) and metabolome of a patient cohort, uncovering topographical differences in microbial function, which were further delineated using isotope probing in mice. In humans, the functional activity of taxa varied across the respiratory tract and correlated with immunomodulatory metabolites such as glutamic acid/glutamate and methionine. Common oral commensals, such as Prevotella, Streptococcus, and Veillonella, were more functionally active in the lower airways. Inoculating mice with these commensals led to regional increases in several metabolites, notably methionine and tyrosine. Isotope labeling validated the contribution of Prevotella melaninogenica in generating specific metabolites. This functional characterization of microbial communities reveals topographical changes in the lung metabolome and potential impacts on host responses.}, }
@article {pmid40578105, year = {2025}, author = {Wang, C and Luan, X and Zhang, J and Zhang, H and Zhang, Y and Yang, M and Tian, Z}, title = {Responses of viral communities in aerobic biofilms under antibiotic stress.}, journal = {Water research}, volume = {285}, number = {}, pages = {124099}, doi = {10.1016/j.watres.2025.124099}, pmid = {40578105}, issn = {1879-2448}, abstract = {Bacteriophages are pivotal in shaping microbial communities, but their structural and functional responses to antibiotic stress in aerobic biofilms remain underexplored. This study aims to fill this void by providing a comprehensive understanding of how viral communities in aerobic biofilms adapt to increasing antibiotic pressures through interactions with their bacterial hosts. Three lab-scale aerobic biofilm systems were established and operated for 577 days, two of those were exposed to increasing influent concentrations of oxytetracycline (OTC) and streptomycin (STM), respectively. The dynamics of the biofilm virome under antibiotic stress was revealed by metagenomic sequencing. Results showed that the virome in aerobic biofilms displayed a high percentage (98.7 %) of unknown bacteriophages, indicating considerable viral diversity. As for the hosts of phages, a total of 1741 bacteriophage contigs were associated with 660 distinct bacterial hosts. In antibiotic-treated systems, broad-host-range generalist bacteriophages accounted for over 17.95 % (STM) and 17.90 % (OTC), compared to 14.32 % in the control. Furthermore, viral community did not carry diverse antibiotic resistance genes, which only accounted for 0.34 % of the resistome. Additionally, it did not regulate the number of resistant bacteria by activating the lytic and lysogenic cycles in this study. This indicated that the contribution of transduction to the horizontal spread of resistant determinants is very limited in the aerobic biofilm. Under antibiotic stress, viral auxiliary metabolic genes compensated for incomplete metabolic pathways in host cells, particularly those related to carbohydrate, amino acid, and cofactor metabolism. These genes likely offer dual benefits to bacterial hosts by repairing antibiotic-induced cellular damage and supporting energy generation, thereby providing adaptive advantages for bacterial survival and proliferation under antibiotic selection pressure. This study uncovers the complex interactions between bacteriophages, their hosts, and environmental pressures. It suggests that viral communities in these environments compensate for functional metabolism rather than promote resistance development under antibiotic stress, providing new insights into the potential roles of bacteriophages in the regulation of microbial-driven processes.}, }
@article {pmid40578104, year = {2025}, author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L}, title = {Resistome and microbiome shifts in catfish rearing water: the influence of temperature and antibiotic treatments.}, journal = {Water research}, volume = {285}, number = {}, pages = {124074}, doi = {10.1016/j.watres.2025.124074}, pmid = {40578104}, issn = {1879-2448}, abstract = {The increasing reliance on aquaculture for sustainable protein production highlights the need for responsible antibiotic use to manage bacterial infections, particularly in intensive farming systems. This study investigated the effects of three FDA-approved antibiotics (Aquaflor®, Romet®, Terramycin®) at common fish bacterial disease outbreak temperatures (20 °C, 25 °C, and 30 °C) on the microbiome and resistome of aquaculture water using a catfish model system. Metagenomic analyses evaluated the abundance, diversity, and mobility of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). The impact of temperature on Aquaflor- and Romet-induced changes in ARG abundance, richness, and resistome composition followed a U-shaped trend, with the least effect observed at 25 °C. Of the three antibiotics tested, Terramycin exerted the most significant influence on the water microbiome and resistome, enriching tetracycline resistance genes and co-selecting for floR, sul, and dfrA genes. Temperature also induced notable shifts in the ARB population, with Mantel tests revealing strong correlations between ARG profiles and changes in the overall bacterial community and ARB populations. While certain ARG classes consistently remained associated with specific host phyla, others shifted, highlighting the potential for horizontal gene transfer (HGT) as a critical mechanism for disseminating resistance genes like tet(C), particularly after antibiotic treatment. This is further supported by the observed reduction in plasmid numbers following treatment, which coincided with increased HGT events. Our findings highlight the pivotal role of temperature in influencing resistome dynamics, emphasizing the importance of accounting for environmental factors when applying antibiotics to effectively mitigate antimicrobial resistance in aquaculture systems.}, }
@article {pmid40578039, year = {2025}, author = {Wen, Y and Li, M and Hao, Y and Peng, J and Wei, X and Zhang, Z and Liu, B and Wang, Y and Peng, T and Ma, Y}, title = {HDAC/NF-κB signaling pathway mediates gut microbiota dysbiosis in rheumatoid arthritis: Intervention mechanisms of Fengshining decoction.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {145}, number = {}, pages = {156976}, doi = {10.1016/j.phymed.2025.156976}, pmid = {40578039}, issn = {1618-095X}, abstract = {BACKGROUND: Gut microbiota dysbiosis has been associated with the development of rheumatoid arthritis (RA). Fengshining (FSN) is a traditional Chinese medicine decoction that can effectively alleviate RA. However, how FSN modulates the gut microbiota to mitigate RA has not been comprehensively studied. This study evaluated the gut microecological mechanisms underlying FSN's effects on RA, focusing on the impact of gut-derived short-chain fatty acids (SCFAs), specifically butyrate, in RA treatment.<br><br>METHODS: The pharmacological effects of FSN on type II collagen-induced arthritis (CIA) in mice were assessed via pathological indicators, metagenomics, and metabolomics analyses. Furthermore, the impact of FSN on gut microbiota and metabolic profiles was also evaluated. Moreover, a pseudo-germ-free CIA model was established to validate whether exogenous butyrate alleviates RA. This study also elucidated whether fecal microbiota transplantation (FMT) from FSN-treated mice could mitigate RA symptoms.<br><br>RESULTS: The data showed that FSN markedly alleviated CIA symptoms and reduced serum inflammatory cytokine levels. Metagenomic and metabolomic analyses revealed that FSN-enriched SCFA-producing bacteria, including Butyrivibrio, Faecalicatena, and Lacrimispora. Furthermore, FSN increased the activity of carbohydrate metabolism-related enzymes and upregulated the expression patterns of homologous protein families. Moreover, exogenous butyrate supplementation suppressed pro-inflammatory factors, modulating immune responses, and enhanced intestinal barrier function. Further, Western blot analysis validated that FSN inhibited the HDAC/NF-&#x3ba;B pathway.<br><br>CONCLUSION: This study indicated that the gut microecological mechanism of FSN might be associated with its herbal components, which regulate gut microbiota diversity, restore the intestinal barrier, and boost microbial metabolite production. Furthermore, butyrate was observed to modulate intestinal mucosa, inhibit inflammatory responses, repair the intestinal barrier, and mitigate joint damage, thus alleviating RA symptoms.}, }
@article {pmid40577874, year = {2025}, author = {Li, Y and Zhu, Z and Li, S and Tan, Y and Xu, H and Sheng, X and Qi, B and Wu, J and Li, L and Zhao, Z}, title = {Phase-specific microbial relay strategy enhances lipid degradation and humification in aerobic composting of lipid-rich food waste.}, journal = {Journal of environmental management}, volume = {390}, number = {}, pages = {126342}, doi = {10.1016/j.jenvman.2025.126342}, pmid = {40577874}, issn = {1095-8630}, abstract = {Lipid-rich food waste poses significant challenges in aerobic composting owing to oil-induced physicochemical barriers (>10 % oil content reduces porosity by 32-45 % and suppresses microbial activity). To bridge this gap, we designed a phase-specific microbial relay strategy integrating Pseudomonas aeruginosa DO1 with thermophilic consortia derived from agricultural soils (CK3). The results demonstrated that DO1 achieved 25 % lipid degradation within 96 h (mesophilic phase, <45 °C) through lipase secretion (121.18-131.45 U/mL) and enzymatic emulsification of lipids, after which its abundance decreased (from 26.99 % to 8.41 %). Subsequently, CK3-derived thermophilic bacteria (Bacillus, 38.54 %; Thermoactinomyces, 2.53 %) and fungi (Wallemia, 21.12 %) dominated the thermophilic phase (>50 °C for >5 d), driving β-oxidation-mediated lipid degradation to 91.91 % and enhancing humification with 92.74 % humic substances. Metagenomic analysis confirmed the enrichment of lipolytic pathways (ko00071, p < 0.01) and the upregulation of ammonia-assimilation genes (glsA/gdhB), reducing nitrogen loss to 25.1 %. This temperature-phased relay strategy enables the efficient in situ degradation of high-lipid waste (>15 % oil), offering a scalable solution for industrial composting.}, }
@article {pmid40577531, year = {2025}, author = {Duxbury, SJN and Raguideau, S and Cremin, K and Richards, L and Medvecky, M and Rosko, J and Coates, M and Randall, K and Chen, J and Quince, C and Soyer, OS}, title = {Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf126}, pmid = {40577531}, issn = {1751-7370}, abstract = {Understanding how microbial communities maintain stable compositional diversity is a key question in microbial ecology. Studies from pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence diversity, but the relevance of these factors in more complex communities is unclear. Here we used a cyanobacterial enrichment community that consistently forms millimetre-scale granular structures, to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found stable co-existence of 17 species belonging to diverse bacterial phyla. Metagenomic analysis revealed polysaccharide breakdown genes and complementary vitamin biosynthesis pathways in these species. Supporting these findings, we show growth of several isolated species on cyanobacterial slime components and experimentally verify vitamin exchanges between two members of the community. Several species had genes for (an)oxygenic photosynthesis and sulfur cycling, the expression of which we verified via meta transcriptomics. Consistent with this, we found that the granular structures displayed oxygen gradients with anoxic interiors. Cyanobacteria and other bacteria were distributed on the periphery and insides of these structures, respectively. Perturbation of the community via glucose addition resulted in fold increases of the heterotrophs, whereas disturbing the community by continual shaking led to fold reductions in several heterotrophs, including anoxygenic phototrophs. In contrast, removal of vitamins supplementation did not consistently alter species coverages, due to predicted vitamin sharing amongst community members. Taken together, these findings indicate that spatial organisation, microenvironment niche formation and metabolic interactions contribute to community compositional diversity and stability.}, }
@article {pmid40577477, year = {2025}, author = {Li, B and Jiang, L and Johnson, T and Wang, G and Sun, W and Wei, G and Jiao, S and Gu, J and Tiedje, J and Qian, X}, title = {Global health risks lurking in livestock resistome.}, journal = {Science advances}, volume = {11}, number = {26}, pages = {eadt8073}, pmid = {40577477}, issn = {2375-2548}, mesh = {*Livestock/microbiology ; Animals ; *Global Health ; Humans ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Risk Assessment ; *Metagenome ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Livestock farming consumes more than 70% of global antibiotics annually, making livestock manures an important vector of anthropogenically influenced antibiotic resistance genes (ARGs). The global pattern of the livestock resistome, its driving mechanisms, and transmission potential to the clinic are not well assessed. We analyzed 4017 livestock manure metagenomes from 26 countries and constructed a comprehensive catalog of livestock ARGs and metagenome-assembled genomes. Livestock resistome is a substantial reservoir of known (2291 subtypes) and latent ARGs (3166 subtypes) and is highly connectable to human resistomes. We depicted the global pattern of livestock resistome and prevalence of clinically critical ARGs, highlighting the role of farm and human antibiotic stewardship in shaping livestock resistome. We developed a risk-assessment framework by integrating mobility potential, clinical significance, and host pathogenic relevance, and prioritized higher risk livestock ARGs, producing a predictive global map of livestock resistome risks that can help guide research and policy.}, }
@article {pmid40576662, year = {2025}, author = {Goldschmidt, I and Kramer, M and Junge, N and Ouro-Djobo, N and Poets, A and Rathert, M and Geffers, R and Baumann, U and Hartleben, B and Schulze, KD and Woltemate, S and Vital, M}, title = {Short- and long-term development of gut microbiota in children after liver transplantation - a prospective observational trial.}, journal = {Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society}, volume = {}, number = {}, pages = {}, doi = {10.1097/LVT.0000000000000659}, pmid = {40576662}, issn = {1527-6473}, abstract = {In children, little is known on gut microbiota (GM) in end-stage liver disease and its association with graft function after pediatric liver transplantation (pLT). We analyzed GM composition and function in children before pLT, longitudinally post-pLT and in long-term survivors (LT-pLT) in order to assess the impact of disease severity, treatment and pLT on GM and delineate associations with graft and patient health. Fecal samples (FS) of 29 children (17f, age 2.6 [0.2-15.7] years) awaiting pLT were included with longitudinal follow-ups until 12M post-transplant in 18, and compared with 38 LT-pLT (21f, age 11 [2.7-17.7] years, 7.8 [1.0-17.0] years post-pLT) and 94 healthy controls (HC). Samples were analyzed using quantitative 16S rRNA gene analyses combined with shotgun metagenomics (subset of samples). Pre-pLT patients showed reduced alpha-diversities and altered GM composition compared with LT-pLT and HC, associated with disease severity and anti-pruritic treatment with Rifampicin. Dysbiosis increased after pLT and started to recover after 3M. Although bacterial concentrations, alpha diversity and gene richness increased post-pLT, levels remained below those of HC. Abundances of key functions, e.g. the capacity to synthesize butyrate, also remained reduced. Quantitative analyses revealed true extent of differences between patients and HC that were underestimated using relative abundance data. GM diversity and functional capacities correlated negatively with transaminase levels mid- and long-term after pLT. Random Forest analyses based on GM were able to predict hepatocellular damage at high accuracy (AUC: 0.89). We provide comprehensive, quantitative insights into GM composition and function before and after pLT. A link between GM alterations with (long-term) graft health was uncovered providing possible targets to modulate GM function in order to increase graft and patient health.}, }
@article {pmid40576316, year = {2025}, author = {Lui, LM and Nielsen, TN and Smith, HJ and Chandonia, J-M and Kuehl, JV and Song, F and Sczesnak, A and Hendrickson, A and Hazen, TC and Fields, MW and Arkin, AP}, title = {Sediment and groundwater metagenomes from subsurface microbial communities from the Oak Ridge National Laboratory Oak Ridge Reservation, Oak Ridge, Tennessee, USA.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0001425}, doi = {10.1128/mra.00014-25}, pmid = {40576316}, issn = {2576-098X}, abstract = {We report 26 subsurface sediment and 9 groundwater metagenomes from the Oak Ridge Reservation at Oak Ridge, TN, USA. Samples were collected from various depths and phases (attached vs planktonic) to study subsurface microbial metabolism, the effect of contamination on microbial communities, and differences across groundwater and sediment microbial communities.}, }
@article {pmid40575481, year = {2025}, author = {Chen, L and Li, Z and Yuan, D and Chen, Y and Xu, Y and Tang, W and Liu, C}, title = {Microorganism changes in the gut of Apis mellifera surviving for the long term in Camellia oleifera forests.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1608835}, pmid = {40575481}, issn = {2235-2988}, mesh = {Animals ; Bees/microbiology ; *Camellia ; *Gastrointestinal Microbiome ; Oligosaccharides/metabolism ; Forests ; Metabolomics ; Metagenomics ; *Gastrointestinal Tract/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {Alpha-galactosides (oligosaccharides) in C. oleifera nectar and pollen cause honey bee larval rot and worker bloats. Honey bee colonies surviving in C. oleifera forests for a long period have low rates of larval rot and worker bloats; however, the mechanism of oligosaccharide metabolism is unclear. In this study, we used metagenomics and metabolomics to investigate the structure and function of the gut flora and the digestion characteristics of oligosaccharides in the gut of A. mellifera foragers (CN group) that had been in the C. oleifera forest for a long period (continuously for 14 years), and those that had not been pollinated with C. oleifera (N group) after 24 h of consumption of C. oleifera honey. The results revealed that the abundance of Gilliamella apicola up to 24.08%, which can metabolize α-galactoside (α-Gal), was significantly higher (P < 0.05) in the gut of foragers in the CN group than in the N group. Additionally, the gut flora of foragers in the CN group carried a significantly higher (P < 0.05) abundance of genes encoding α-galactosidase (Glycoside hydrolase family 4, GH4) than the N group. Similarly, metabolomic results indicated that the three toxic oligosaccharides in C. oleifera honey were lower in the gut of CN group foragers. These results suggest that the gut flora of A. mellifera, which inhabits oil tea forests for long periods of time, changes and adapts to the predominant ecological niche, enhancing the host's ability to metabolize toxic oligosaccharides. This important discovery provides positive guidance for the subsequent directions for breeding of A. mellifera (G. apicola enrichment and GH4 upregulation), specialized in pollinating C. oleifera.}, }
@article {pmid40575480, year = {2025}, author = {Tang, Y and Tang, S and Zhang, Y and Lin, Z and Shan, S}, title = {The significance of metagenomic next-generation sequencing and targeted next-generation sequencing in the diagnostic evaluation of patients with suspected pulmonary infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1552236}, pmid = {40575480}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Aged ; Sensitivity and Specificity ; *Respiratory Tract Infections/diagnosis/microbiology ; Adult ; Bacteria/genetics/isolation &amp; purification/classification ; Aged, 80 and over ; }, abstract = {OBJECTIVE: To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in identifying pathogens in patients with pulmonary infections.<br><br>METHODS: A retrospective analysis was conducted on 155 patients with suspected lung infections who underwent alveolar lavage and were admitted to the Department of Respiratory and Critical Care Medicine at Baodi Hospital, Tianjin Medical University, from July 2023 to December 2023. The bronchoalveolar lavage fluid (BALF) samples obtained were subjected to mNGS, tNGS and culture methods to compare their diagnostic efficacy in identifying lung infection pathogens.<br><br>RESULTS: The results indicated that both tNGS and mNGS methods exhibit comparable detection efficiencies in identifying pathogens in patients with pulmonary infections, significantly outperforming BALF culture approach. In terms of diagnostic accuracy, tNGS exhibited a higher sensitivity than mNGS, with rates of 96.1% and 75.7% respectively (P>0.05). However, the specificity of tNGS was slightly lower than that of mNGS, with rates of 59.1% and 68.2% respectively (P>0.05). It is noteworthy that this difference in specificity was not statistically significant.<br><br>CONCLUSION: tNGS exhibits a diagnostic efficacy comparable to mNGS, particularly in its sensitivity for identifying lung infections, as evidenced by expert insights and clinical applications. Furthermore, tNGS offers advantages in convenience, time efficiency, and cost-effectiveness, hinting at its potential to serve as an alternative to mNGS in clinical settings.}, }
@article {pmid40575430, year = {2025}, author = {Brar, AS and Vemula, SL and Yanamaladoddi, V and Sodhi, S and Hatwal, J and Sohal, A and Batta, A}, title = {Impact of gut microbiome on atrial fibrillation: Mechanistic insights and future directions in individualized medicine.}, journal = {World journal of cardiology}, volume = {17}, number = {6}, pages = {107386}, pmid = {40575430}, issn = {1949-8462}, abstract = {Atrial fibrillation (AF) is a growing global health burden, with a prevalence of over 52.55 million cases. Rising disability-adjusted life-years, increasing age, and disparities in care have contributed to the worsening severity and mortality of AF. Modifiable risk factors, such as hypertension, obesity, and diabetes mellitus, are associated with alterations in gut microbiota, making the gut-heart axis a potential therapeutic target. Gut dysbiosis influences AF pathogenesis through inflammation, metabolic disruption, and autonomic dysfunction. Key mechanisms include gut barrier dysfunction, short-chain fatty acid (SCFA) depletion, lipopolysaccharides (LPS)-induced inflammation, and ferroptosis-mediated atrial remodeling. Trimethylamine N-oxide, bile acids, and tryptophan metabolites contribute to arrhythmogenic remodeling. Emerging evidence suggests that dietary interventions, including prebiotics and probiotics, as well as gut surveillance, may help mitigate AF progression. Clinical implications of gut modulation in AF include personalized dietary strategies, microbiome assessment through metagenomic sequencing, and targeted interventions such as SCFA-based therapies and ferroptosis inhibition. Metabolite surveillance, including LPS and indoxyl sulfate monitoring, may influence the effectiveness of anticoagulant and antiarrhythmic therapy. Despite growing mechanistic evidence linking gut dysbiosis to AF, clinical applications remain unexplored. This review summarizes the current understanding of the gut microbiome's role in AF.}, }
@article {pmid40575134, year = {2025}, author = {Foulkes, DM and Cooper, DM and Westland, C and Byrne, DP}, title = {Regulation of bacterial phosphorelay systems.}, journal = {RSC chemical biology}, volume = {}, number = {}, pages = {}, pmid = {40575134}, issn = {2633-0679}, abstract = {In terms of biomass, bacteria are the most successful organisms on earth. This is partly attributed to their tremendous adaptive capabilities, which allows them to sense and rapidly organise responses to changing environmental stimuli. Using complex signalling mechanisms, bacteria can relay cellular information to fine-tune their metabolism, maintain homeostasis, and trigger virulence processes during infection. Across all life, protein phosphorylation represents the most abundant signalling mechanism, which is controlled by a versatile class of enzymes called protein kinases and their cognate phosphatases. For many years, histidine kinase (HK)-containing two-component systems (TCSs) were considered the canonical instruments of bacterial sensing. However, advances in metagenomics has since proven that bacterial phosphorelay is in fact orchestrated by a functionally diverse array of integrated protein kinase types, including Ser, Thr, Tyr and Arg-targeting enzymes. In this review, we provide an up-to-date appraisal of bacterial kinase signalling, with an emphasis on how these sensing pathways are regulated to modulate kinase output. Finally, we explore how selective kinase inhibitors may be exploited to control infections and combat the looming health emergency of multidrug resistant bacteria.}, }
@article {pmid40574876, year = {2025}, author = {Odenwald, MA and Ramaswamy, R and Lin, H and Lehmann, C and Moran, A and Mullowney, MW and Sidebottom, AM and Hernandez, A and McMillin, M and Rose, A and Moran, D and Little, J and Sulakhe, D and D'Souza, M and Woodson, C and Tanveer, T and de Porto, A and Dylla, N and Sundararajan, A and Burgo, V and Cantoral, J and Jadczak, C and Adler, E and Aronsohn, A and Pamer, EG and Rinella, ME}, title = {Fecal Butyrate and Deoxycholic Acid Concentrations Correlate With Mortality in Patients With Liver Disease.}, journal = {Gastro hep advances}, volume = {4}, number = {8}, pages = {100695}, pmid = {40574876}, issn = {2772-5723}, abstract = {BACKGROUND AND AIMS: The intestinal microbiome produces metabolites, including short chain fatty acids (SCFAs) and secondary bile acids (BAs), that impact host physiology. Loss of intestinal microbiome diversity is associated with cirrhosis progression, but the impact of microbiome-associated metabolites on liver disease remains largely undefined. We aimed to correlate fecal metabolite concentrations with the severity and progression of liver disease.<br><br>METHODS: In this cross-sectional study, fecal samples from patients hospitalized with liver disease were analyzed by shotgun metagenomic sequencing to determine microbiome compositions and targeted mass spectrometry to quantify SCFAs and BAs. Random survival forest and logistic regression models identified clinical, metagenomic, and metabolomic features associated with rehospitalization and survival.<br><br>RESULTS: This cross-sectional study included 24 chronic liver disease, 18 compensated cirrhosis, 225 decompensated cirrhosis and 40 acute-on-chronic liver failure patients and 27 control fecal donors. Microbiome sequencing and metabolite profiling correlated microbial diversity and SCFA and BA concentrations with liver disease severity. Butyrate and deoxycholic acid (DCA) were more important features than individual microbial species in random survival forest models predicting 30-day transplant-free survival, and low butyrate and DCA were associated with 30-day mortality (P < .0001). After controlling for model for end stage liver disease (MELD)-sodium score, disease stage, age and gender, low fecal concentrations of butyrate and DCA remained significant risk factors for death (Cox 1.38, P = .027). Bacterial species associated with butyrate and DCA concentrations included Bifidobacterium spp. and F. prausnitzii.<br><br>CONCLUSION: Mass spectrometry rapidly identifies patients with low fecal butyrate and DCA concentrations who are at increased risk of 30-day mortality. These findings set the stage for clinical trials of microbiome reconstitution with butyrate and DCA-producing bacterial species.}, }
@article {pmid40574752, year = {2025}, author = {Zhang, X and Li, R and Lu, R and Wu, C and Liang, Z and Zhang, Z and Huang, B and Yang, Y and Qi, Z and Zhang, D and Zhai, D and Wang, Q and Tan, W}, title = {Transition of D3c branch and novel recombination events contribute to the diversity of Coxsackievirus A6 in Beijing, China, from 2019 to 2023.}, journal = {Virus evolution}, volume = {11}, number = {1}, pages = {veaf036}, pmid = {40574752}, issn = {2057-1577}, abstract = {Coxsackievirus A6 (CVA6) is a major pathogen responsible for numerous outbreaks of hand, foot, and mouth disease (HFMD) worldwide. This study investigates the molecular evolution and recombination of CVA6 in Beijing, China. Full-length sequences of 54 CVA6 from Beijing (2019-2023) were obtained through metagenomic next-generation sequencing and Sanger sequencing. These sequences were compared with representative sequences from GenBank to analyse their phylogenetic characteristics, recombination diversity, and evolutionary dynamics. The 54 CVA6 strains co-circulated with those from multiple provinces in China, as well as from South Korea and Japan. Phylogenetic analysis revealed a novel D3c branch, with the VP1 T283A amino acid mutation identified as a key change in its formation. One sequence belonged to the D3a branch, while 53 sequences belonged to the D3c branch. Recombination analysis identified RF-A (46, 85.1%) and three novel recombinant forms (RFs): RF-Z (1, 1.9%), RF-AA (1, 1.9%), and RF-AB (6, 11.1%). Bayesian phylogenetic analysis estimated that the most recent common ancestor of D3c emerged in August 2013 (95% highest probability density (HPD): May 2012 to September 2014), with recombination events occurring in RF-Z (2017-2019), RF-AA (2019-2023), and RF-AB (2021-2023). In conclusion, we revealed a globally circulating CVA6 D3c branch and identified three novel RFs, providing valuable insights for the intervention and control of HFMD.}, }
@article {pmid40574064, year = {2025}, author = {Varut, RM and Ciolofan, MS and Veronica, ME and Radivojević, K and Trasca, DM and Popescu, C and Diaconu, O and Singer, CE}, title = {Cyclodextrins as Modulators of Gut Microbiota: Pharmaceutical Applications and Impact on Intestinal Health.}, journal = {Pharmaceutics}, volume = {17}, number = {6}, pages = {}, pmid = {40574064}, issn = {1999-4923}, abstract = {Background/Objectives: Cyclodextrins (CDs) have garnered increasing attention in pharmaceutical research due to their ability to enhance drug solubility, bioavailability, and therapeutic efficacy. Meanwhile, the gut microbiota, a key regulator of human health, has emerged as an important target in evaluating the safety and broader implications of pharmaceutical excipients. This review aims to synthesize current knowledge regarding the effects of CDs on the composition and function of the gut microbiota. Methods: A literature search following PRISMA guidelines was conducted in PubMed, ScienceDirect, and Google Scholar to identify studies on cyclodextrins and their interactions with gut microbiota. Results: Cyclodextrins, particularly α-, β-, and γ-CDs, demonstrated the capacity to modulate gut microbiota composition, promoting the growth of beneficial bacteria such as Bifidobacterium and Akkermansia. Supplementation with CDs was also associated with an increased production of short-chain fatty acids (SCFAs), which are essential for maintaining intestinal homeostasis and metabolic health. Moreover, CDs exhibited potential in lowering lipid levels and improving postprandial glycemic control without enhancing insulin secretion. Although generally recognized as safe, the toxicological profile of CDs varies depending on their type, dosage, and route of administration. Conclusions: Cyclodextrins hold considerable promise not only as pharmaceutical excipients but also as modulators of gut microbial communities, suggesting a dual therapeutic and prebiotic role. Future studies integrating metagenomic and metabolomic approaches are necessary to further elucidate the molecular mechanisms underlying CD-microbiota interactions and to optimize their application in enhancing drug delivery efficiency and promoting intestinal health.}, }
@article {pmid40573878, year = {2025}, author = {Ullah, F and Ali, S and Siraj, M and Akhtar, MS and Zaman, W}, title = {Plant Microbiomes Alleviate Abiotic Stress-Associated Damage in Crops and Enhance Climate-Resilient Agriculture.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {40573878}, issn = {2223-7747}, abstract = {Plant microbiomes, composed of a diverse array of microorganisms such as bacteria, fungi, archaea, and microalgae, are critical to plant health and resilience, playing key roles in nutrient cycling, stress mitigation, and disease resistance. Climate change is expected to intensify various abiotic stressors, such as drought, salinity, temperature extremes, nutrient deficiencies, and heavy metal toxicity. Plant-associated microbiomes have emerged as a promising natural solution to help mitigate these stresses and enhance agricultural resilience. However, translating laboratory findings into real-world agricultural benefits remains a significant challenge due to the complexity of plant-microbe interactions under field conditions. We explore the roles of plant microbiomes in combating abiotic stress and discuss advances in microbiome engineering strategies, including synthetic biology, microbial consortia design, metagenomics, and CRISPR-Cas, with a focus on enhancing their practical application in agriculture. Integrating microbiome-based solutions into climate-smart agricultural practices may contribute to long-term sustainability. Finally, we underscore the importance of interdisciplinary collaboration in overcoming existing challenges. Microbiome-based solutions hold promise for improving global food security and promoting sustainable agricultural practices in the face of climate change.}, }
@article {pmid40573780, year = {2025}, author = {Zhang, S and Luo, Z and Peng, J and Wu, X and Meng, X and Qin, Y and Zhu, F}, title = {Analysis of Cadmium Accumulation Characteristics Affected by Rhizosphere Bacterial Community of Two High-Quality Rice Varieties.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {40573780}, issn = {2223-7747}, support = {2024YFD2301400//the National Key Research and Development Program of China/ ; 2024CX09//the Agricultural Science and Technology Innovation Project of Hunan Province, China/ ; }, abstract = {Cadmium-contaminated rice poses serious health risks through the bioaccumulation of Cd (cadmium) from soil to edible grains. Cd contamination disrupts soil microbial ecology and alters microbial diversity. However, the role of cultivar-specific rhizosphere microbial communities in modulating Cd uptake remains unclear. In this study, we aimed to elucidate the mechanism underlying variety-dependent rhizosphere microecological remodeling and Cd accumulation in two independently selected late rice varieties, Yuzhenxiang (YZX) and Xiangwanxian 12 (XWX12). Combining physiological and metagenomic analyses, we revealed variety-specific correlations between root Cd accumulation and dynamic changes in soil pH, soil available phosphorus, and rhizosphere bacteria. The key bacterial genera (Variibacter, Nitrospira) showed differential enrichment patterns under Cd stress. In contrast, Galella and Anaeromyxobacter likely reduce Cd bioavailability by modulating phosphorus availability. Overall, this study elucidates that rice cultivars indirectly shape Cd accumulation patterns via rhizosphere microbial remodeling, providing novel insights for microbial remediation strategies in Cd-contaminated farmland.}, }
@article {pmid40573768, year = {2025}, author = {Giménez-Valero, C and Maciá-Vázquez, AA and Núñez-Gómez, D and Conesa, A and Lidón, V and Melgarejo, P}, title = {Evolution of the Soil Bacterial Community as a Function of Crop Management: A Metagenomic Study in Orange Tree (Citrus sinensis) Plantations.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {40573768}, issn = {2223-7747}, support = {AGROALNEXT program (AGROALNEXT 2022/013, SIRIS Project)//European Union/ ; }, abstract = {Soil management significantly influences the structure and diversity of soil bacterial communities, affecting biodiversity and ecosystem functions. In semi-arid regions, water efficiency strategies like anti-weed netting are implemented, but their impact on soil microbial communities remains underexplored. This study evaluates the temporal evolution of soil bacterial communities in orange tree (Citrus sinensis (L.) Osbeck) plantations under two conditions: with and without anti-weed netting. Soil samples were collected at three time points over a period of 18 months since the establishment of the crop and analyzed using high-throughput 16S rRNA sequencing, assessing alpha and beta diversity, taxonomic composition, and functional pathways via KEGG analysis. The results indicate that weed control netting contributes to stabilizing bacterial diversity over time and increases the relative abundance of dominant phyla such as Planctomycetota, Proteobacteria, Bacteroidota, and Acidobacteriota. Functional predictions revealed significant differences in metabolic pathways, including those associated with nitrogen fixation and organic matter degradation. These findings suggest that anti-weed netting not only influences the taxonomic composition of soil bacterial communities but also modulates their functional potential, with implications for sustainable agriculture in semi-arid environments. This study provides new insights into the interaction between soil management and soil bacterial communities, offering valuable information for optimizing agricultural practices and soil conservation strategies.}, }
@article {pmid40573458, year = {2025}, author = {Sim, G and Choi, CH and Lee, M and Lee, HS and Kim, SY and Lee, SH and Lee, HI and Chung, YS}, title = {Discovery of a Novel Parahenipavirus, Parahenipavirus_GH, in Shrews in South Korea, 2022.}, journal = {Viruses}, volume = {17}, number = {6}, pages = {}, pmid = {40573458}, issn = {1999-4915}, support = {6331-301-210-13//Korea Disease Control and Prevention Agency/ ; }, mesh = {Animals ; *Shrews/virology ; Republic of Korea/epidemiology ; Phylogeny ; Rodentia/virology ; Genome, Viral ; *Henipavirus/genetics/isolation &amp; purification/classification ; Zoonoses/virology ; Kidney/virology ; }, abstract = {Highly pathogenic henipaviruses (Nipah and Hendra viruses) and parahenipaviruses (Langya virus) have demonstrated significant zoonotic potential. We aimed to identify Henipavirus or Parahenipavirus species in rodents and shrews in South Korea to underline the potential zoonotic transmission risk. Kidney and lung tissues from 285 rodents and shrews were screened for Henipavirus and Parahenipavirus using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) targeting the Gamak virus and Daeryong virus (DARV) sequences. Based on the qRT-PCR results, 75 out of the 285 individuals tested positive, with the highest viral loads in the kidneys of Apodemus agrarius, Crocidura lasiura, and Crocidura shantungensis. A kidney sample from C. shantungensis that exhibited the lowest Ct value was further analyzed using PCR, Sanger sequencing, and metagenomic analysis, yielding a near-complete genome of a novel Parahenipavirus, designated Parahenipavirus_GH (PHNV-GH), which is phylogenetically related to DARV and Jingmen virus but exhibits distinct genomic features. Ixodes granulatus ticks were also identified on the host shrew. The identification of PHNV-GH in southern South Korea expands the known geographical distribution range of parahenipaviruses and highlights the ongoing risk of zoonotic transmission. Given the uncertain transmission dynamics and pathogenic potential of parahenipaviruses, comprehensive environmental surveillance and characterization of emerging parahenipaviruses are essential for preventing future outbreaks.}, }
@article {pmid40492061, year = {2025}, author = {Lynch, KF and Triplett, EW and Hyöty, H and Ahrens, AP and Laiho, JE and Petrosino, JF and Lloyd, RE and Agardh, D}, title = {A case-cohort longitudinal study for the analysis of microbial associations and viruses on the risk of celiac disease (MAVRiC).}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {40492061}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; U01 DK128847/DK/NIDDK NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; R01 DK124581/DK/NIDDK NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; U01 DK124166/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; }, abstract = {Celiac disease etiopathogenesis requires genetic predisposition and exposure to gluten before a child can develop the chronic autoimmune disorder. However, these factors alone are not sufficient. Even a child with persistent tissue transglutaminase autoantibodies (tTGA), i.e., celiac disease autoimmunity (CDA), does not necessarily develop celiac disease. Larger longitudinal studies are needed to determine the impact of time-varying infections and gut microorganisms on the subsequent and specific risk of celiac disease. The aim was to design a celiac disease case-cohort longitudinal study using The Environmental Determinants of Diabetes in the Young (TEDDY) study. Following the TEDDY cohort up age 3-years, CDA was confirmed in 704 of the 6132 genetically at-risk children. Celiac disease onset was defined as the age CDA developed when followed by a biopsy-proven diagnosis. A competing risk analysis was performed on celiac disease onset cases (CD-onset) as well as CDA children with no diagnosis (CDA-only) and results show genetic factors (additional HLA-DR3-DQ2 haplotype, higher non-HLA polygenic risk score, sex-girl) and a more rapid increase in gluten-consumption correlate with significant increased risk of both outcomes. However, reports of virus-related respiratory infections in August to October during follow-up correlated with an increased risk of a CD-onset but not with CDA-only. To create a case-cohort study, a sub-cohort of 561 children (9% sampling fraction) was first randomly selected to represent the TEDDY cohort over time while at risk of CDA. It included 483 children followed until age 3-years and 78 children followed before developing CDA (CDA-only n=41/78, CD-onset n=37/78). All incident CD-onset children (N=306) were included to form the case group. This case-cohort will be utilized to analyze virus antibodies and bacteriome from longitudinal plasma and stool samples (the Microbial Associations and Viruses on the Risk of Celiac disease study, MAVRiC).}, }
@article {pmid40573435, year = {2025}, author = {Ajileye, TG and Akinleye, TE and Faleye, TOC and De Coninck, L and George, UE and Onoja, AB and Agbaje, ST and Ifeorah, IM and Olayinka, OA and Oni, EI and Oragwa, AO and Popoola, BO and Olayinka, OT and Osasona, OG and George, OA and Ajayi, PG and Suleiman, AA and Muhammad, AI and Komolafe, I and Adeniji, AJ and Matthijnssens, J and Adewumi, MO}, title = {Ten Previously Unassigned Human Cosavirus Genotypes Detected in Feces of Children with Non-Polio Acute Flaccid Paralysis in Nigeria in 2020.}, journal = {Viruses}, volume = {17}, number = {6}, pages = {}, doi = {10.3390/v17060844}, pmid = {40573435}, issn = {1999-4915}, mesh = {Humans ; *Feces/virology ; Nigeria/epidemiology ; Phylogeny ; *Genotype ; Child ; Child, Preschool ; *Picornaviridae/genetics/classification/isolation &amp; purification ; Genome, Viral ; Infant ; *Picornaviridae Infections/virology/epidemiology ; Genetic Variation ; Adolescent ; Female ; Male ; Metagenomics ; *Paralysis/virology ; }, abstract = {Since its discovery via metagenomics in 2008, human cosavirus (HCoSV) has been detected in the cerebrospinal fluid (CSF) and feces of humans with meningitis, acute flaccid paralysis (AFP), and acute gastroenteritis. To date, 34 HCoSV genotypes have been documented by the Picornaviridae study group. However, the documented genetic diversity of HCoSV in Nigeria is limited. Here we describe the genetic diversity of HCoSV in Nigeria using a metagenomics approach. Archived and anonymized fecal specimens from children (under 15 years old) diagnosed with non-polio AFP from five states in Nigeria were analyzed. Virus-like particles were purified from 55 pools (made from 254 samples) using the NetoVIR protocol. Pools were subjected to nucleic acid extraction and metagenomic sequencing. Reads were trimmed and assembled, and contigs classified as HCoSV were subjected to phylogenetic, pairwise identity, recombination analysis, and, when necessary, immuno-informatics and capsid structure prediction. Fifteen pools yielded 23 genomes of HCoSV. Phylogenetic and pairwise identity analysis showed that all belonged to four species (eleven, three, three, and six members of Cosavirus asiani, Cosavirus bepakis, Cosavirus depakis, and Cosavirus eaustrali, respectively) and seventeen genotypes. Ten genomes belong to seven (HCoSV-A3/A10, A15, A17, A19, A24, D3, and E1) previously assigned genotypes, while the remaining thirteen genomes belonged to ten newly proposed genotypes across the four HCoSV species, based on the near-complete VP1 region (VP1*) of the cosavirus genome. Our analysis suggests the existence of at least seven and eight Cosavirus bepakis and Cosavirus eaustrali genotypes, respectively (including those described here). We report the first near-complete genomes of Cosavirus bepakis and Cosavirus depakis from Nigeria, which contributes to the increasing knowledge of the diversity of HCoSV, raising the number of tentative genotypes from 34 to over 40. Our findings suggest that the genetic diversity of HCoSV might be broader than is currently documented, highlighting the need for enhanced surveillance.}, }
@article {pmid40573403, year = {2025}, author = {Zhang, X and Fan, IX and Xu, Y and Rule, J and Tse, LPV and Pourkarim, MR and Lee, WM and Di Bisceglie, AM and Fan, X}, title = {Novel Viral Sequences in a Patient with Cryptogenic Liver Cirrhosis Revealed by Serum Virome Sequencing.}, journal = {Viruses}, volume = {17}, number = {6}, pages = {}, doi = {10.3390/v17060812}, pmid = {40573403}, issn = {1999-4915}, support = {1R21AI175438-24/NH/NIH HHS/United States ; }, mesh = {Humans ; *Liver Cirrhosis/virology ; *Virome/genetics ; Male ; Middle Aged ; Female ; *Viruses/genetics/classification/isolation &amp; purification ; Genome, Viral ; Metagenomics ; Aged ; Sequence Analysis, DNA ; Adult ; *Serum/virology ; }, abstract = {Clinical studies indicate the etiology of liver disease to be unknown in 5% to 30% of patients. A long-standing hypothesis is the existence of unknown viruses beyond hepatitis A through E virus. We conducted serum virome sequencing in nine patients with cryptogenic liver disease and identified eight contigs that could not be annotated. One was determined to be a contaminant, while two of seven contigs from an individual (Patient 3) were validated by reverse transcription and polymerase chain reaction (RT-PCR) and Sanger sequencing. The possibility of contamination was completely excluded through PCR, with templates extracted using different methods from samples taken at different time points. One of the contigs, Seq260, was characterized as negative-sense single-stranded DNA via enzymatic digestion and genome walking. Digital-droplet PCR revealed the copy number of Seq260 to be low: 343 copies/mL. Seq260-based nested PCR screening was negative in 200 blood donors and 225 patients with liver disease with/without known etiologies. None of the seven contigs from Patient 3 was mapped onto 118,713 viral metagenomic data. Conclusively, we discovered seven unknown contigs from a patient with cryptogenic liver cirrhosis. These sequences are likely from a novel human virus with a negative-sense, linear single-stranded DNA genome.}, }
@article {pmid40573397, year = {2025}, author = {Wang, W and Wang, Q and Cao, R and Li, Y and Liu, Z and Xue, Z and Wang, X and Liu, Z}, title = {Metagenomic Investigation of Pathogenic RNA Viruses Causing Diarrhea in Sika Deer Fawns.}, journal = {Viruses}, volume = {17}, number = {6}, pages = {}, doi = {10.3390/v17060803}, pmid = {40573397}, issn = {1999-4915}, support = {CAAS-ASTIP-2021-ISAPS//Science and Technology Innovation Project of the Chinese Academy of Agricultural Sciences/ ; 2023YFD1800704//National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Deer/virology ; *Diarrhea/virology/veterinary ; Metagenomics ; Feces/virology ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; Genome, Viral ; China/epidemiology ; Rotavirus/genetics ; Metagenome ; Cattle ; }, abstract = {Diarrhea is a common disease in sika deer. The causes of diarrhea in sika deer are complex and involve a variety of pathogens. Additionally, new virulent pathogens are continuously emerging, which poses a serious threat to deer's health and particularly affects fawns' survival rate. In the present study, feces samples were collected from fawns with diarrhea in Jilin Province, in the northeast of China. The viral communities were investigated using the metagenomic method. Viral metagenome data revealed that the viruses in the fecal samples were mainly from 21 families in 14 orders. The major viruses in high abundance were astrovirus, rotavirus, coronavirus, and bovine viral diarrhea virus. In addition, a large number of phages, which mainly belonged to the family Siphoviridae, were identified. Then, the known causative virus species were investigated via RT-qPCR. The results showed that the infection rates of bovine coronavirus, bovine rotavirus, and bovine viral diarrhea virus were 59.44%, 58.89%, and 21.67%, respectively, and mixed infections were commonly seen in the samples. A bovine rotavirus strain was successfully isolated from the positive samples. Whole-genome sequencing revealed that the genotype of the strain was G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H3, indicating the recombination of rotavirus. This study revealed the profiles and characteristics of viruses that cause sika deer diarrhea, which will be helpful for understanding diarrhea diseases in sika deer.}, }
@article {pmid40573349, year = {2025}, author = {Hernández-Villegas, EN and Castelán-Sánchez, HG and Moreira-Soto, A and Vigueras-Galván, AL and Jiménez-Rico, MA and Rico-Chávez, O and Rodríguez-González, S and Tolsá-García, MJ and Roiz, D and Martínez-Duque, P and Arana-Guardía, R and García-Súarez, O and Jiménez, MZ and Falcón, LI and Roche, B and Sarmiento-Silva, RE and Arnal, A and Drexler, JF and Suzán, G}, title = {Characterization of the Virome in Mosquitoes Across Distinct Habitats in the Yucatán Peninsula, Mexico.}, journal = {Viruses}, volume = {17}, number = {6}, pages = {}, doi = {10.3390/v17060758}, pmid = {40573349}, issn = {1999-4915}, mesh = {Animals ; Mexico ; *Culicidae/virology ; *Ecosystem ; *Virome ; *Mosquito Vectors/virology ; *Viruses/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Genome, Viral ; Biodiversity ; }, abstract = {Human activities and land use changes have a major impact on the distribution and diversity of mosquito vectors and their associated viruses. This study describes the diversity and differential abundance of viruses associated with mosquito species from four habitats of the Yucatan Peninsula, Mexico. Using next-generation sequencing (NGS), we analyzed 61 genomic libraries belonging to 20 mosquito species to characterize the viral community. A total of 16 viral species were identified, representing 14 different viral families. Most identified viruses were associated with insects, plants, and fungi. Additionally, vertebrate associated viral families, including Herpesviridae, Peribunyaviridae, Nairoviridae, and Arenaviridae, were detected in mosquitoes from urban habitats. Notably, insect-associated viruses like Hubei mosquito virus 4 and Hubei virga-like virus 2 were identified, along with the first report of Mercadeo virus in Mexico. Variations in viral community composition were primarily driven by mosquito species, with species of the same genus maintaining similar viromes despite occupying different habitats. These findings reinforce that intrinsic traits of mosquito species play a key role in shaping viral community composition. To our knowledge, this is the first study that describes the viral community in mosquitoes in Yucatan Peninsula, Mexico. This study provides essential baseline data for the surveillance of mosquitoes and associated viruses from a biodiverse tropical region that faces strong land use modifications.}, }
@article {pmid40573347, year = {2025}, author = {Pardo, I and Finamor, LPS and Marra, PS and Ferreira, JMG and Gutfreund, MC and Hsieh, MK and Li, Y and Pinho, JRR and Rizzo, LV and Kobayashi, T and Diekema, DJ and Edmond, MB and Bispo, PJM and Marra, AR}, title = {Metagenomic Next-Generation Sequencing for the Diagnosis of Infectious Uveitis: A Comprehensive Systematic Review.}, journal = {Viruses}, volume = {17}, number = {6}, pages = {}, doi = {10.3390/v17060757}, pmid = {40573347}, issn = {1999-4915}, mesh = {Humans ; *Metagenomics/methods ; *Uveitis/diagnosis/virology/microbiology/parasitology ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Toxoplasma/genetics ; }, abstract = {Background: Infectious uveitis is a potentially sight-threatening condition that requires timely and accurate pathogen identification to guide effective therapy. However, conventional microbiological tests (CMTs) often lack sensitivity and the inclusiveness of pathogen detection. Metagenomic next-generation sequencing (mNGS) offers an unbiased approach to detecting a broad range of pathogens. This review evaluates its diagnostic performance in detecting infectious uveitis. Methods: A systematic search across multiple databases identified studies assessing the use of mNGS for diagnosing infectious uveitis. The included studies compared mNGS to CMTs, including polymerase chain reaction (PCR), culture, serology, and the IGRA (Interferon-Gamma Release Assay). The study characteristics; the detection rates; and the sensitivity, specificity, and predictive values were extracted. The sensitivity and specificity of mNGS were calculated using CMTs as a reference. Results: Twelve studies comprising 859 patients were included. The sensitivity of mNGS compared to that of CMTs ranged from 38.4% to 100%, while specificity varied between 15.8% and 100%. The commonly detected pathogens included varicella-zoster virus, cytomegalovirus, Toxoplasma gondii, and herpes simplex virus. In some cases, mNGS outperformed PCR in viral detection, aiding diagnosis when the standard methods failed. However, contamination risks and inconsistent diagnostic thresholds were noted. Conclusions: mNGS enables the diagnosis of infectious uveitis, particularly for viral causes, but its variable performance and standardization challenges warrant further investigation.}, }
@article {pmid40573336, year = {2025}, author = {Žuštra, A and Howard, A and Schwartz, K and Day, R and Dietrich, J and Sobotyk, C and Kraberger, S and Varsani, A}, title = {Three Distinct Circovirids Identified in a Tapeworm Recovered from a Bobcat (Lynx rufus).}, journal = {Viruses}, volume = {17}, number = {6}, pages = {}, doi = {10.3390/v17060745}, pmid = {40573336}, issn = {1999-4915}, mesh = {Animals ; Phylogeny ; *Cestoda/virology ; Genome, Mitochondrial ; Genome, Viral ; Metagenomics ; Feces/virology ; }, abstract = {Bobcats (Lynx rufus) are an iconic North American predator; however, there is limited knowledge regarding their associated parasites. In this case study, we used a metagenomic approach to identify associated viruses and helminth species from a deceased bobcat. We determined the full mitochondrial genome of the bobcat and three helminths, i.e., tapeworm (Taenia sp.), stomach worm (Physaloptera sp.), and lung worm (Metathelazia sp.). Furthermore, we identified four circovirids; two (identified in a tapeworm and fecal swab) are members of the genus Circovirus and share 96.7% genome-wide identity between isolates and 87.4-88.6% identity with members of the species Circovirus miztontli. These appear to infect vertebrate species common to the Sonoran Desert, which could be a rodent preyed upon by the bobcat, and/or bobcat itself. The other two circovirids are novel members of the genus Cyclovirus (both identified in a tapeworm), one sharing 99.8% with those in the species Cyclovirus misi from a rodent and the other <67.3% with all other Cycloviruses. Our data support that these two Cycloviruses are likely tapeworm-infecting; however, more studies are needed to confirm the host. These findings enhance our understanding of viruses and helminths in bobcats, emphasizing the need for further research to unravel the ecology of parasites in these elusive predators.}, }
@article {pmid40573190, year = {2025}, author = {Ruiz-Álvarez, BE and Cattero, V and Desjardins, Y}, title = {Prebiotic-like Effects of Proanthocyanidin-Rich Aronia Extract Supplementation on Gut Microbiota Composition and Function in the Twin-M-SHIME[®] Model.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {18}, number = {6}, pages = {}, doi = {10.3390/ph18060793}, pmid = {40573190}, issn = {1424-8247}, support = {NSERC-Symrise Industrial Chair on prebiotic Effects of Fruits and Vegetables//Symrise/ ; }, abstract = {Background: Phenolic compounds, particularly anthocyanins and proanthocyanidins (PACs), are poorly absorbed in the upper digestive tract and reach the colon largely intact, where they may influence gut microbiota (GM) composition and, in turn, impact host health. We hypothesized that a PAC-rich aronia extract would beneficially modulate the GM, promote the growth of health-associated bacteria, and enhance short-chain fatty acid (SCFA) production across different colon sections, with partial reversion effects after supplementation ends. Methods: The Twin-M-SHIME[®] system was used to simulate the digestion and colonic fermentation in two donors with contrasting microbiota profiles. The experimental design included four phases: stabilization (14 days), control (7 days), treatment with 500 mg/day PAC-rich aronia extract (21 days), and wash-out (10 days). SCFA production was monitored, and changes in microbiome composition were assessed using 16S rRNA gene sequencing. Results: PAC-rich aronia extract significantly modulated SCFA levels, increasing butyrate and reducing acetate, with some inter-donor variability. SCFA concentrations tended to return to baseline after the wash-out (WO) period. Metagenomic analysis revealed a decrease in Collinsella, Sutterella, Selenomonas, and Parabacteroides-genera linked to low-fiber diets and gut inflammation-while promoting Proteobacteria (e.g., Escherichia-Shigella, Klebsiella) and butyrate-associated Firmicutes such as Lactiplantibacillus. Although some microbial shifts partially reverted during the wash-out (e.g., Akkermansia, Bacteroides, and Bifidobacterium), other changes persisted. Conclusions: These findings suggest that PAC-rich aronia extract beneficially modulates GM and SCFA production, but continuous intake may be necessary to maintain these effects over time.}, }
@article {pmid40572226, year = {2025}, author = {Cho, HE and Kim, MJ and Choi, J and Sohn, YH and Lee, JJ and Park, KS and Cho, SY and Park, KH and Kim, YJ}, title = {Shotgun Metagenomic Sequencing Analysis as a Diagnostic Strategy for Patients with Lower Respiratory Tract Infections.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572226}, issn = {2076-2607}, support = {RS-2023-00246999//National Research Foundation of Korea/ ; }, abstract = {Conventional diagnostic methods (CDMs) for lower respiratory infections (LRIs) have limitations in detecting causative pathogens. This study evaluates the utility of shotgun metagenomic sequencing (SMS) as a complementary diagnostic tool using bronchoalveolar lavage (BAL) fluid. Sixteen BAL fluid samples from pneumonia patients with positive CDM results-including bacterial/fungal cultures; PCR for Mycobacterium tuberculosis or cytomegalovirus; and the BioFire[®] FilmArray[®] Pneumonia Panel (BioFire Diagnostics LLC, Salt Lake City, UT, USA)-underwent 10 Gb SMS on the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA). Reads were aligned to the NCBI RefSeq database; with fungal identification further supported by internal transcribed spacer (ITS) analysis. Antibiotic resistance genes (ARGs) were annotated using the Comprehensive Antibiotic Resistance Database. Microbial reads accounted for 0.00002-0.04971% per sample. SMS detected corresponding bacteria in 63% of cases, increasing to 69% when subdominant taxa were included. Fungal reads were low; however, Candida species were identified in four samples via ITS. No viral reads were detected. ARGs meeting perfect match criteria were found in two cases. This is the first real-world study comparing SMS with CDMs, including semiquantitative PCR, in BAL fluid for LRI. SMS shows promise as a supplementary diagnostic method, with further research needed to optimize its performance and cost-effectiveness.}, }
@article {pmid40572225, year = {2025}, author = {Jiang, Y and Li, W and Li, J and Hu, J and Wei, Y and Wang, Y and Yang, H and Zhou, Y and Wu, Y and Zhang, S}, title = {Co-Inoculating Burkholderia vietnamiensis B418 and Trichoderma harzianum T11W Reduced Meloidogyne incognita Infestation of Tomato Plants.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572225}, issn = {2076-2607}, support = {ZR2021MC085//Shandong Provincial Natural Science Foundation/ ; 2022TSGC2370//Shandong Provincial Innovation Capability Promotion Project for Sci-tech Small and Medium-sized Enterprises/ ; 2024GH15//Innovation Pilot Project of Integration of Science, Education, and Industry of Shandong Academy of Sciences (International Scientific and Technology Cooperation)/ ; }, abstract = {Root-knot nematodes (RKNs; Meloidogyne incognita) pose a significant threat to tomato crops, necessitating sustainable control methods. This study investigated the inoculation efficacy of co-cultured Burkholderia vietnamiensis B418 and Trichoderma harzianum T11W compared with single-strain treatments for RKNs suppression and their influence on the structure and function of the rhizosphere microbiome. Co-inoculation with B418 + T11W achieved a 71.42% reduction in the disease index, significantly outperforming single inoculations of B418 (54.46%) and T11W (58.93%). Co-inoculation also increased plant height by 38.51% and fresh weight by 76.02% compared to the RKNs infested plants control, promoting robust tomato growth. Metagenomic analysis reveals that co-inoculation enhanced bacterial diversity, with 378 unique bacterial species and a high Shannon index, while fungal diversity decreased with Trichoderma dominance (83.31% abundance). Actinomycetota (46.42%) and Ascomycota (97.92%) were enriched in the co-inoculated rhizosphere, showing negative correlations with RKNs severity. Functional analysis indicates enriched metabolic pathways, including streptomycin and unsaturated fatty acid biosynthesis, enhancing microbial antagonism. Single inoculations altered pathways like steroid degradation (B418) and terpenoid biosynthesis (T11W), but co-inoculation uniquely optimized the rhizosphere microenvironment. These findings highlight co-inoculation with B418 + T11W effectively suppressing RKNs and fostering plant health by reshaping microbial communities and functions, offering a promising approach for sustainable agriculture.}, }
@article {pmid40572188, year = {2025}, author = {Asao, K and Hashida, N}, title = {Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572188}, issn = {2076-2607}, support = {23K15906 [to K.A.]//the Japan Society for the Promotion of Science/ ; 21K09695 [to N.H.]//the Japan Society for the Promotion of Science/ ; }, abstract = {This review outlines technological advances in pathogen identification and describes the development and evolution of next-generation sequencers that can be applied to the ocular microbiome. Traditional methods such as culture and PCR have limitations in detecting the full spectrum of resident microorganisms, prompting a transition toward metagenomic analysis. As microbiome research expands across body systems, the comprehensive identification of ocular bacteria, fungi, and viruses has become possible. The commensal ocular microbiome may influence disease development through changes in the immune system and ocular environment. Next-generation sequencing enables detailed microbial profiling, aiding in disease diagnosis and treatment selection. Alterations in the microbiome may also induce metabolic changes, offering insights into novel treatment methods. This review outlines the evolution of next-generation sequencing technology, summarizes current knowledge of microorganisms found on the ocular surface and in intraocular fluid, and discusses future challenges and prospects. However, the large volume of microbiome data obtained must be interpreted with caution due to possible analytical biases. Furthermore, determining whether the microbiome is truly pathogenic requires comprehensive interpretation beyond the clinical findings and results of traditional identification methods.}, }
@article {pmid40572136, year = {2025}, author = {Shi, M and Zhang, L and Sun, H and Ji, S and Cui, H and Wan, W and Liu, X and Tian, A and Yang, W and Wang, X and Yang, F and Jin, S}, title = {The Plant Growth-Promoting Bacterium Bacillus cereus LpBc-47 Can Alleviate the Damage of Saline-Alkali Stress to Lilium pumilum.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572136}, issn = {2076-2607}, support = {([2023] 1197)//Heilongjiang Province Agriculture Research System-Ecological Agriculture/ ; [LJGXCG2023-036]//Heilongjiang Province "Double First Class" Discipline Collaborative Innovation Achievement Project/ ; }, abstract = {Soil salinization severely impacts plant cultivation. Lilium pumilum (L. pumilum) exhibits tolerance to saline-alkali stresses. One Bacillus cereus strain, LpBc-47, possesses the ability of growth promotion and saline-alkali tolerance. The microbial diversity of L. pumilum was assessed through metagenomic sequencing. LpBC-47 obtained from L. pumilum was subjected to physiological and biochemical analyses and whole-genome sequencing. The effects of endophytic bacteria on plants were evaluated by measuring growth parameters, physiological indices, antioxidant enzyme activities, and ROS content. Microbial diversity analysis revealed that the abundance of endophytic bacteria in L. pumilum decreased under saline-alkali conditions, whereas the abundance of Bacillus cereus increased. Physiological and biochemical analysis showed that LpBC-47 has the characteristics of promoting growth and reducing plant damage caused by salt-alkali stress, such as phosphorus solubilization, nitrogen fixation, siderophore production, IAA, and ACC deaminase synthesis. Genomic analysis revealed that LpBC-47 contains growth-associated and stress-alleviation genes. GFP indicated the colonization of LpBc-47 in the roots and bulbs of L. pumilum. The LpBc-47 inoculant plant increased leaf length and dry weight, elevated proline and chlorophyll levels, enhanced antioxidant enzyme activity, and reduced oxidative damage. This study highlights the potential of LpBc-47 for improving plant growth under saline-alkali conditions.}, }
@article {pmid40572128, year = {2025}, author = {Strike, W and Faleye, TOC and Lubega, B and Rockward, A and Torabi, S and Noble, A and Banadaki, MD and Keck, J and Mugerwa, H and Scotch, M and Berry, S}, title = {Implementing Wastewater-Based Epidemiology for Long-Read Metagenomic Sequencing of Antimicrobial Resistance in Kampala, Uganda.}, journal = {Microorganisms}, volume = {13}, number = {6}, pages = {}, pmid = {40572128}, issn = {2076-2607}, support = {1U01DA053903-01/NH/NIH HHS/United States ; 1P30ES026529-01/NH/NIH HHS/United States ; BAA 75D301-20-R-68024/CC/CDC HHS/United States ; 2154934//U.S. National Science Foundation/ ; 2412446//U.S. National Science Foundation/ ; }, abstract = {Antimicrobial resistance (AMR) is an emerging global threat that is expanding in many areas of the world. Wastewater-based epidemiology (WBE) is uniquely suited for use in areas of the world where clinical surveillance is limited or logistically slow to identify emerging threats, such as in Sub-Saharan Africa (SSA). Wastewater was analyzed from three urban areas of Kampala, including a local HIV research clinic and two informal settlements. Wastewater extraction was performed using a low-cost, magnetic bead-based protocol that minimizes consumable plastic consumption followed by sequencing on the Oxford Nanopore Technology MinION platform. The majority of the analysis was performed using cloud-based services to identify AMR biomarkers and bacterial pathogens. Assemblies containing AMR pathogens were isolated from all locations. As one example, clinically relevant AMR biomarkers for multiple drug classes were found within Acinetobacter baumannii genomic fragments. This work presents a metagenomic WBE workflow that is compatible with areas of the world without robust water treatment infrastructure. This study was able to identify various bacterial pathogens and AMR biomarkers without shipping water samples internationally or relying on complex concentration methods. Due to the time-dependent nature of wastewater surveillance data, this work involved cross-training researchers in Uganda to collect and analyze wastewater for future efforts in public health development.}, }
@article {pmid40572043, year = {2025}, author = {Yang, C and Sun, J and Li, L and Zheng, J and Wang, C and Zhao, Y and Yun, D and Jia, M and Wu, Z and Liang, H and Li, W and Hu, T and Guo, R and Xiao, L and Zou, Y and Liu, Z}, title = {Synbiotics of Lactobacillus suilingensis and inulin alleviates cognitive impairment via regulating gut microbiota indole-3-lactic acid metabolism in female AD mice.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {21}, number = {7}, pages = {e70406}, doi = {10.1002/alz.70406}, pmid = {40572043}, issn = {1552-5279}, support = {2022ZD0208100//National Science and Technology Innovation 2030-Major Program of Brain Science and Brain-Like Research/ ; 32241012//National Natural Science Foundation of China/ ; 32472351//National Natural Science Foundation of China/ ; JCYJ20220818102810022//Shenzhen Science and Technology Program/ ; XMHT20220104017//Shenzhen Municipal Government of China/ ; 2022A1515110717//Regional Consolidated Fund-Youth Fund Project in Guangdong Province/ ; BGIRSZ20220009//open project of BGI-shenzhen/ ; //China Biotechnology Development Center/ ; //Shenzhen Science and Technology Innovation Commission/ ; //Shenzhen Municipal Government/ ; //Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Inulin/pharmacology/administration &amp; dosage ; Female ; *Cognitive Dysfunction/metabolism ; Mice ; *Synbiotics/administration &amp; dosage ; *Indoles/metabolism ; *Alzheimer Disease/metabolism ; Humans ; Tryptophan/metabolism ; Disease Models, Animal ; Receptors, Aryl Hydrocarbon/metabolism ; Probiotics ; }, abstract = {INTRODUCTION: Recent studies have found that gut microbial tryptophan metabolism is altered in Alzheimer's disease (AD) patients. However, the functional consequences of these changes and their therapeutic potential remain unclear.<br><br>METHODS: The metagenomic data of 49 preclinical AD patients and 115 healthy controls were analyzed. A synbiotic with targeted metabolic functions was formulated based on in vitro testing, and its effect on AD was evaluated using female 5&#xd7;FAD mice.<br><br>RESULTS: Indole lactic acid (ILA) synthesis was downregulated in AD patients. Synbiotic treatment combining Lactobacillus suilingensis and inulin outperformed probiotic treatment alone in enhancing tryptophan metabolism, and increasing ILA biosynthesis. Increased ILA could reduce A&#x3b2; accumulation and significantly alleviate cognitive impairment in female AD mice by inhibiting neuroinflammation through activation of the aryl hydrocarbon receptor (AhR) signaling pathway.<br><br>DISCUSSION: This study highlights the therapeutic potential of targeting gut microbial tryptophan metabolism in AD and provides a rationale for future precision strategies aimed at modulating microbiota-derived metabolic pathways.<br><br>HIGHLIGHTS: Gut metagenomic analysis reveals reduced indole lactic acid (ILA) biosynthesis genes in preclinical AD patients. Screening and formulating ILA-producing synbiotic by using whole-genome analysis. Synbiotic treatment alleviates cognitive impairment and promotes ILA synthesis in female 5&#xd7;FAD mice. ILA alleviates neuroinflammation in female 5&#xd7;FAD mice by activating aryl hydrocarbon receptor (AhR) in the brain. Synbiotic targeting tryptophan metabolism provides a novel approach for Alzheimer's intervention.}, }
@article {pmid40571109, year = {2025}, author = {Chen, H and Qiu, X and Lei, S and Zhao, Y and Zhang, M and Gao, M and Guo, R and Di, H and Huang, J and Yu, Z}, title = {Gut vs. Vaginal Microbiome in Diabetes Progression: Key Microbial Shifts and Implications.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107833}, doi = {10.1016/j.micpath.2025.107833}, pmid = {40571109}, issn = {1096-1208}, abstract = {BACKGROUND: Dysiosis in gut and vaginal microbiome is implicated in type 2 diabetes (T2D) pathogenesis, but their contributions remain unclear. This study aims to compare their alterations and clinical relevance in diabetes development.<br><br>METHODS: Metagenomic sequencing was performed on vaginal and fecal samples from T2D patients. Differential feature selection and correlation model were used to dissect microbial contributions to diabetic markers.<br><br>RESULTS: Gut microbiota exhibited reduced diversity in T2D patients, with enrichment of Desulfovibrio desulfuricans and Adlercreutzia equolifaciens validated in public cohorts. Vaginal microbiota diversity remained unaffected. Furthermore, structural equation modeling revealed stronger gut microbiota associations with blood glucose and HbA1c. Notably, Romboutsia ilealis-derived pgm was enriched in the diabetes group, which could catalyze the production of glucose, suggesting that it may be involved in the progression of T2D.<br><br>CONCLUSION: Our findings establish the gut microbiome as the dominant driver of T2D progression, with R. ilealis emerging as a potential therapeutic target. This highlights the priority of gut-centric microbiota interventions in diabetes management.}, }
@article {pmid40571107, year = {2025}, author = {Chen, J and Chen, Z and Xu, B and Huang, Z and Zhang, C}, title = {Skin microbiome of Asian elephants with skin diseases during seasonal transitions.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107832}, doi = {10.1016/j.micpath.2025.107832}, pmid = {40571107}, issn = {1096-1208}, abstract = {INTRODUCTION: Wild Asian elephants (Elephas maximus), which are an endangered species, often suffer from skin diseases during seasonal transitions, which seriously affect their health. Understanding the pathogenesis of such skin diseases is critical for their prevention and treatment. It is known that skin microorganisms are closely related to host skin health.<br><br>OBJECTIVE: To compare the microbiotas and microbiomes of diseased and healthy skin of Asian elephants.<br><br>METHODS: DNA was extracted from skin swab samples from diseased and healthy Asian elephants for metagenomic sequencing. Various bioinformatic tools were used to process the raw sequencing data and identify gene sequences for functional annotation and species identification as well as to determine species abundance. Antibiotic resistance genes and virulence factors were also identified using DIAMOND.<br><br>RESULTS: Staphylococcus was highly enriched in the microbiota of diseased skin, whereas Leuconostoc predominated in that of healthy skin. Moreover, substantial differences existed between the two elephant skin groups in terms of metabolic pathways related to ATP-binding cassette transporters and TCSs and the abundance of antibiotic resistance genes and Staphylococcus-associated toxins. The substantial difference in Staphylococcus-related virulence factors was likely due to the significant enrichment of Staphylococcus in the diseased skin samples, suggesting that this bacterial genus is the causative agent of skin diseases in Asian elephants. Additionally, Leuconostoc mesenteroides, which was enriched in the healthy skin samples, has anti-inflammatory, antimicrobial, and other beneficial effects that have promising applications in the prevention, diagnosis, and treatment of skin diseases.<br><br>CONCLUSION: This study reveals the cause of skin diseases in Asian elephants and provides a theoretical basis for improving the skin health of wild animals and expanding wildlife conservation methods and technologies.}, }
@article {pmid40570964, year = {2025}, author = {Fishman, JA and El Khoury, J and Kawai, T and Riella, LV and Elias, N and Williams, W and Crisalli, KA and Hashimoto, D and Bercovici, S and Lindner, M and Noll, N and Balasundaram, G and Getchell, K and Low, S and Scales, B and Chhangawala, S and Marett, A and Curtis, M and Yeung, V}, title = {Infectious Disease Surveillance and Management in Clinical Xenotransplantation: Experience with the First Human Porcine Kidney Transplant.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajt.2025.06.016}, pmid = {40570964}, issn = {1600-6143}, abstract = {The success and safety of clinical xenotransplantation are determined by technical aspects of surgery, the nature and intensity of immunosuppression, xenograft function, and the ability to avoid immunologic, hematologic, infectious and malignant complications. In clinical xenotransplantation from swine, infectious challenges relate to the potential spread of pig pathogens to immunosuppressed humans as well as manifestations of infections of the recipient from prior exposures to common human organisms. Robust strategies are required for donor screening, recipient monitoring, and infection prevention. This report outlines the comprehensive infectious disease management strategy deployed in the first living human recipient of a genetically modified pig kidney, including (1) donor screening and pathogen mitigation, (2) pre- and post-transplant infection monitoring of the recipient, (3) infectious complications and management, with (4) implications for future xenotransplantation protocols.}, }
@article {pmid40570762, year = {2025}, author = {Pateriya, D and Malwe, AS and Sharma, VK}, title = {CRCpred: An AI-ML tool for colorectal cancer prediction using gut microbiome.}, journal = {Computers in biology and medicine}, volume = {195}, number = {}, pages = {110592}, doi = {10.1016/j.compbiomed.2025.110592}, pmid = {40570762}, issn = {1879-0534}, abstract = {Colorectal cancer (CRC) is a leading cause of death worldwide. A plethora of research shows the alteration of the gut microbiome and the association of bacterial taxa with CRC. Gaining insights into the health status through microbiome-based diagnosis is a rapidly growing area of research. Many studies have utilized machine learning (ML) to leverage gut microbial dysbiosis for CRC screening, yet most have been limited by their training data and algorithms. Here, using 1728 publicly available metagenomic samples from 11 studies across eight countries, we developed a web-based tool, "CRCpred," employing ML and deep learning-based hybrid algorithms for CRC prediction. The XGBoost algorithm demonstrated the highest performance, achieving an average area under the curve (AUC) of 0.90 on the test and 0.91 on the validation datasets. Our results highlight the utility of CRCpred in predicting CRC and healthy status using gut bacterial species relative abundance profile. CRCpred is publicly available at https://metabiosys.iiserb.ac.in/crcpred.}, }
@article {pmid40570628, year = {2025}, author = {Hu, F and Zhang, W and Chen, P and Yuan, Z and Ye, J and Xu, Z}, title = {Glucose as a dual-functional co-substrate in intimately coupled photocatalysis and biodegradation systems: Synergistic enhancement of refractory organics mineralization and nitrate removal.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {138975}, doi = {10.1016/j.jhazmat.2025.138975}, pmid = {40570628}, issn = {1873-3336}, abstract = {Nitrate contamination threatens water quality and human health; however, conventional denitrification treatment strategies struggle in complex wastewater due to the low bioavailability of refractory organics. The intimately coupled photocatalysis and biodegradation (ICPB) system addresses this by transforming recalcitrant compounds into usable electron donors, enabling simultaneous nitrate and organic pollutant removal. This study demonstrates that adding a small dose of glucose (50 mg/L chemical oxygen demand) to the ICPB system enhanced performance by increasing organic mineralization from 53 % to 81 % and total nitrate and nitrite removal from 40 % to 93 %. Supplementing the ICPB system with glucose significantly stimulated microbial activity. The heightened activity accelerated the mineralization of photocatalytically-derived intermediates, preventing toxic byproduct accumulation. Microbial inhibition was reduced from 68 % to 20 %, further enhancing the pollutant removal efficiency of the ICPB system. Additionally, glucose functioned as an auxiliary electron donor, concurrently enhancing denitrification. Metagenomic analysis suggested that riboflavin biosynthesis upregulation may have promoted electron transfer, potentially boosting system efficiency. This strategy offers a simple and effective means to optimize the synergistic removal of refractory organics and nitrate during wastewater treatment.}, }
@article {pmid40570627, year = {2025}, author = {Li, YQ and Zhang, CM and Ma, H and Shao, KJ and Yuan, PH and Jiang, HY}, title = {Antiallergic drugs drive the alteration of microbial community and antibiotic resistome in surface waters: A metagenomic perspective.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139028}, doi = {10.1016/j.jhazmat.2025.139028}, pmid = {40570627}, issn = {1873-3336}, abstract = {Antiallergic drugs (AADs) are emerging contaminants of global concern due to their environmental persistence and potential ecological impacts. This study investigated the effects of seven AADs (chlorpheniramine, diphenhydramine, cetirizine, loratadine, desloratadine, sodium cromoglicate and calcium gluconate) at environmentally relevant concentrations on antibiotic resistome and bacterial community structures in water using microcosm experiments and metagenomic sequencing. The results showed that AADs increased the abundance of antibiotic-resistant bacteria (ARB) by 1.24- to 7.78-fold. Community structure shifts indicated that chlorpheniramine, diphenhydramine, and cetirizine promoted Actinobacteria (e.g., Aurantimicrobium), while the other four AADs favored Proteobacteria (e.g., Limnohabitans). AADs also significantly altered the relative abundance of antibiotic resistance genes (ARGs), with Actinobacteria and Proteobacteria identified as key ARB components and potential hosts of ARGs (e.g., evgS, mtrA, RanA). Host analysis showed ARGs were primarily carried by Actinobacteria (e.g., Aurantimicrobium) under chlorpheniramine, diphenhydramine, and cetirizine exposure, but by Proteobacteria (e.g., Limnohabitans) under the other four AADs. Furthermore, AADs facilitated the horizontal transfer of ARGs (e.g., evgS) within microbial communities, contributing to antibiotic resistance dissemination. This study highlights the ecological risks of AADs in promoting antibiotic resistance spread and provides new insights into their impact on microbial communities and resistome dynamics in aquatic environments.}, }
@article {pmid40570498, year = {2025}, author = {Zhang, X and Jiao, P and Li, B and Zhang, XX and Ma, L}, title = {Phage lysis-mediated reduction of antibiotic-resistant bacteria alleviates micro/nanoplastic-driven antimicrobial resistance dissemination in anaerobic digestion.}, journal = {Water research}, volume = {285}, number = {}, pages = {124046}, doi = {10.1016/j.watres.2025.124046}, pmid = {40570498}, issn = {1879-2448}, abstract = {Micro/nanoplastics (MPs/NPs) prevalent in anaerobic digestion (AD) have posed escalating threats to antimicrobial resistance (AMR) dissemination, yet mechanistic insights remain insufficient. Here we investigated polypropylene (PP)-MPs (200 μm) and PP-NPs (100 nm) at environmentally relevant concentrations (10, 50, and 100 mg/g TS) on antibiotic resistance gene (ARG) dynamics and transfer mechanisms using metagenomics and bioinformatic modeling. PP-MPs/NPs significantly elevated (6.4-17.8 %, p < 0.05) ARG abundance through selective enrichment of aminoglycoside, mupirocin, multidrug, polymyxin, sulfonamide, tetracycline, and novobiocin ARGs. Metagenomic assembly revealed the particle-induced ecological niche specialization of antibiotic-resistant bacteria (ARB), notably the multi-resistant ESKAPE pathogen Enterobacter hormaechei (53.4-69.4 % enrichment, p < 0.05), which harbored mobile aadA, qacEdelta1, and sul1 via conjugative plasmids. Mechanistically, MPs/NPs facilitated horizontal gene transfer (HGT) through synergism of plasmids and phages. The enhanced abundance of conjugation elements, enriched plasmid-borne ARGs, and extensive HGT events promoted plasmid-conjugative transfer, while the strongly correlated ARG-carrying lysogenic phage-host pairs highlighted phage-mediated transfer under MPs/NPs. The significant increase of phage-to-host-ratio (1.0-1.2 folds) revealed the underestimated role of phages lysing ARB under MPs/NPs stress, thereby contributing to ARG load reduction. A novel risk assessment framework prioritizing prevalence, enrichment, mobility, and host pathogenicity identified dfrA3, mefB, OXA-347, and tet44 as high-risk biomarkers and quantified 1.5-9.9 % increased health risks in digestate-exposed scenarios. These findings reveal the neglected role of phage lysis driving ARG reduction, providing actionable targets for mitigating plastic-driven resistance in AD.}, }
@article {pmid40570497, year = {2025}, author = {Thornton, M and Eder, G and Amman, F and Pantielieieva, A and Vierheilig, J and Bergthaler, A}, title = {Comparative wastewater virome analysis with different enrichment methods.}, journal = {Water research}, volume = {285}, number = {}, pages = {123985}, doi = {10.1016/j.watres.2025.123985}, pmid = {40570497}, issn = {1879-2448}, abstract = {Wastewater-based epidemiology (WBE) has proven its value for public health. Physical concentration of virus particles is a crucial step for WBE to permit a sensitive and unbiased characterization of the catchment virome. Here we evaluate five different virion concentration techniques, including polyethylene glycol precipitation (PEG), vacuum-based direct capture (VDC), ultrafiltration (UF), NanoTrap® (NT), and membrane adsorption (MEM) for their suitability to concentrate a wide variety of viral taxa from raw wastewater for PCR detection and sequencing-based metagenomic readouts. We found that to capture a taxonomically diverse virome from wastewater, PEG and VDC outperform all other methods tested in enrichment rates, reproducibility, species detection, and captured nucleotide diversity. We observed that different methods exhibit variable concentration efficiencies across taxonomic groups in a reproducible manner, though we could not identify common physiochemical attributes driving this difference. We conclude that both PEG and VDC are equally capable at detecting and enriching a broad range of viral taxa, boosting the genomic information potential and reducing blind spots relative to other tested methods. These results advance WBE towards capturing the complex wastewater virome and help guide protocol choices for potential future viral threats.}, }
@article {pmid40570415, year = {2025}, author = {Yin, Z and Cao, K and Duan, N and Zhang, Z}, title = {Microbial community dynamics and functional potential during the natural fermentation of rose: A metagenomic and volatile compound analysis.}, journal = {Enzyme and microbial technology}, volume = {190}, number = {}, pages = {110703}, doi = {10.1016/j.enzmictec.2025.110703}, pmid = {40570415}, issn = {1879-0909}, abstract = {This study investigates the dynamics of microbial communities and their functional characteristics during the natural fermentation of roses. Utilizing metagenomic sequencing and volatile compound analysis, the research elucidates the succession of microbial communities and their relationship with the flavor compound production. The findings indicate that Klebsiella and Pichia are predominant in the early stages of fermentation, while Acetobacter and Cyberlindnera become more abundant in the middle and later stages. The glycosyltransferase (GT) family is identified as the primary carbohydrate-active enzyme (CAZy) family involved in fermentation, with GT1 and GT2 exhibiting a higher gene abundance. Functional genes are predominantly associated with the carbohydrate and amino acid metabolism. Analysis of volatile compounds reveals that substances such as phenethyl acetate and (S,S)-2,3-Butanediol are closely related to the structure of the microbial community. These findings contribute to a deeper understanding of the mechanisms underlying rose fermentation and offer a theoretical foundation for technological advancements in the rose product industry.}, }
@article {pmid40570391, year = {2025}, author = {Holm, RH and Chigwechokha, P and Strike, WD and Nyirenda, RL and Tandwe, C and Noble, A and Keck, J and Berry, S}, title = {Multi-pathogen wastewater surveillance in Malawi: An assessment of culture-based, RT-PCR, and long-read metagenomics methods with multiple ongoing outbreaks.}, journal = {The Science of the total environment}, volume = {992}, number = {}, pages = {179946}, doi = {10.1016/j.scitotenv.2025.179946}, pmid = {40570391}, issn = {1879-1026}, abstract = {There is little infrastructure for human disease testing apart from rapid malaria diagnostic tests in many low- and middle-income countries of sub-Saharan Africa outside major referral hospitals, and animal testing is also limited. Eight pathogens were studied in wastewater and environmental surveillance (WES) sites in Malawi with identified locally relevant disease prevalence: influenza A virus, influenza B virus, measles virus, respiratory syncytial virus, Salmonella Typhi, SARS-CoV-2, Vibrio cholerae, and yellow fever virus. Culture-based inoculation onto plates, single-plex RT-PCR, and/or Oxford Nanopore Technologies MinION genomics methods were used for a real-world assessment. This analysis included 20 grab samples from three locations over 4-weeks. Three samples tested positive for V. cholerae using culture-based methods, the only pathogen analyzed using this method. In 14 of the 20 samples, at least one pathogen was detected using PCR. Genomic analysis was conducted on 12 samples; V. cholerae was detected in eight samples, but Salmonella Typhi was not detected. V. cholerae was a clear case of disconnection between methods for the same sample during an outbreak period: 3/20 detected by culture, 1/20 detected by PCR (ctxAB), 3/20 detected by PCR (hlyA), and 8/12 detected by genomics. S. Typhi was the most frequently detected pathogen via PCR (10/20 detections) but was not detected by genomics. Influenza B, measles, SARS-CoV-2, and yellow fever viruses were determined to not be detected (Ct > 40) in the samples studied. This study demonstrated discrepancies in multi-pathogen WES detection across the three methods and highlights the need for further investigation into the limitations of their portability in local, low-resource, laboratories. This presents a valuable learning opportunity in regions experiencing ongoing outbreaks.}, }
@article {pmid40570246, year = {2025}, author = {Ma, C and Bao, Y and Hereid, S and Zhang, H and Bai, X and Bai, Q and Zhao, L and Zhang, X and Lian, H and Dai, L and Bao, X and Bao, L}, title = {Mechanistic Elucidation of Tricholoma mongolicum Polysaccharides in Treating MAFLD via Regulation of the Gut Microbiota-Metabolite-Ferroptosis Axis: A Multi-Omics Perspective.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c05877}, pmid = {40570246}, issn = {1520-5118}, abstract = {This study aimed to elucidate the modulatory effects and underlying molecular mechanisms of Tricholoma mongolicum polysaccharide (TMP) in the context of metabolic dysfunction-associated fatty liver disease (MAFLD). High-performance gel permeation chromatography (HPGPC) analysis indicated a bimodal molecular weight distribution. Monosaccharide composition profiling revealed a predominance of glucose and galactose among other constituents. Scanning electron microscopy (SEM) illustrated a porous, aggregated colloidal microstructure. In a model of MAFLD, TMP intervention significantly attenuated serum levels of TC, TG, and AST, ALT, accompanied by notable histological improvements, including reduced hepatic steatosis and inflammatory cell infiltration. Metagenomic analysis demonstrated that TMP substantially enhanced gut microbial α-diversity, restructured microbial community composition, decreased the Firmicutes/Bacteroidetes ratio, enriched SCFAs-producing genera, and suppressed the excessive proliferation of pro-inflammatory bacterial genera. Integrated proteomic and lipidomic analyses revealed that TMP inhibited hepatic immune-inflammatory responses and ferroptosis pathways, enhanced pathways associated with metabolic homeostasis. Furthermore, TMP modulated hepatic iron metabolism by upregulating the Nrf2/GPx4 antioxidant axis and FPN1 while downregulating TFR1, thereby alleviating oxidative stress and iron overload. These findings demonstrate that TMP exerts therapeutic efficacy through a bidirectional gut-liver regulatory mechanism involving microbial modulation, ferroptosis inhibition, metabolic reprogramming, and activation of antioxidant defenses. This research provides novel insights and molecular targets for the development of natural polysaccharide-based interventions for MAFLD.}, }
@article {pmid40570071, year = {2025}, author = {Savelieva, EI and Shachneva, MD}, title = {Problems and prospects of metabolomic studies in the alteration of the gut microbiome.}, journal = {Biomeditsinskaia khimiia}, volume = {71}, number = {3}, pages = {195-208}, doi = {10.18097/PBMCR1556}, pmid = {40570071}, issn = {2310-6972}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metabolome ; Animals ; Bile Acids and Salts/metabolism ; *Renal Insufficiency, Chronic/microbiology/metabolism ; Fatty Acids, Volatile/metabolism ; }, abstract = {The review summarizes existing knowledge on the relationship between certain diseases and alteration (degeneration) of the intestinal microbiome. We consider major microbial metabolites firmly recognized as signaling molecules acting in communication between the microbiome and the host organism. These include short-chain fatty acids, bile acids, amines, amino acids, and their metabolites. Special attention is paid to metabolomic studies of the microbiome in chronic kidney diseases, in particular, immunoglobulin A nephropathy. The arguments supporting a concept of the microbiome of blood, previously considered an exclusively sterile environment in healthy humans, are considered. Metagenomic methods plays a key role in characterization of both the composition and potential physiological effects of microbial communities. The advantages and limitations of metabolomic analysis of blood serum/plasma and feces have been analyzed. Since the potential of clinical studies of the mutual impact of the microbiome-metabolome is limited by genetic and external factors, preclinical studies still employ both germ-free models and models based on the effects of antibiotics. The review considers the problems and prospects of metabolomics in studying the nature and mechanisms of the mutual impact of the microbiome and metabolome.}, }
@article {pmid40569902, year = {2025}, author = {Belheouane, M and Kalsdorf, B and Niemann, S and Gaede, KI and Lange, C and Heyckendorf, J and Merker, M}, title = {Serratia sp. traits distinguish the lung microbiome of patients with tuberculosis and non-tuberculous mycobacterial lung diseases.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0325362}, pmid = {40569902}, issn = {1932-6203}, mesh = {Humans ; *Microbiota/genetics ; Male ; Middle Aged ; *Lung/microbiology ; RNA, Ribosomal, 16S/genetics ; Female ; Adult ; *Serratia/genetics/isolation &amp; purification/classification ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Mycobacterium Infections, Nontuberculous/microbiology ; Nontuberculous Mycobacteria/genetics ; *Tuberculosis, Pulmonary/microbiology ; *Lung Diseases/microbiology ; }, abstract = {BACKGROUND: Pathogenic mycobacteria, such as Mycobacterium tuberculosis complex (Mtbc), and non-tuberculous mycobacteria (NTMs) can cause severe chronic pulmonary infections. However, not all infected patients develop active disease, and it remains unclear whether key lung microbiome taxa play a role in the pathogenesis of tuberculosis (TB) and NTM lung diseases (LD). Here, we aim to further define the lung microbiome composition in TB, and NTM-LD prior to the initiation of therapy.<br><br>STUDY DESIGN: We employed 16S rRNA amplicon sequencing to characterize the baseline microbiome in bronchoalveolar lavage fluid (BALF) from patients diagnosed with TB (n&#x2009;=&#x2009;23), NTM-LD (n&#x2009;=&#x2009;19), or non-infectious inflammatory disease (n&#x2009;=&#x2009;4). We applied depletion of human cells, removal of extracellular DNA, implementation of a decontamination strategy, and exploratory whole-metagenome sequencing (WMS) of selected specimens.<br><br>RESULTS: Genera Serratia and unclassified Yersiniaceae dominated the lung microbiome of most patients with a mean relative abundance of >15% and >70%, respectively. However, at the sub-genus level, as determined by amplicon sequence variants (ASVs), TB-patients exhibited increased community diversity, and distinct signatures of ASV_7, ASV_21 abundances which resulted in a significant association with disease state. Exploratory WMS, and ASV similarity analyses suggested the presence of Serratia liquefaciens, Serratia grimesii, Serratia myotis and/or Serratia quinivorans in TB and NTM-LD patients.<br><br>CONCLUSIONS: The lung microbiome of TB-patients harbored a distinct, and heterogenous structure, with specific occurrences of certain Serratia traits. Some of these traits may play a role in understanding the microbial interactions in the lung microbiome of patients infected with Mtbc.}, }
@article {pmid40569694, year = {2025}, author = {Kasmanas, JC and Magnúsdóttir, S and Zhang, J and Smalla, K and Schloter, M and Stadler, PF and de Leon Ferreira de Carvalho, ACP and Rocha, U}, title = {Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40569694}, issn = {2047-217X}, support = {2019/03,396-9//S&#xe3;o Paulo Research Foundation/ ; 2022/03,534-5//S&#xe3;o Paulo Research Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; //International Development Research Centre/ ; }, mesh = {*Plasmids/genetics ; Humans ; *Genomics/methods ; Virulence/genetics ; *Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome/genetics ; Virulence Factors/genetics ; Computational Biology/methods ; Software ; Genome, Bacterial ; *Bacteria/genetics/pathogenicity/drug effects ; }, abstract = {BACKGROUND: Comparative genomics, genetic spread analysis, and context-aware ranking are crucial in understanding microbial dynamics' impact on public health. gSpreadComp streamlines the path from in silico analysis to hypothesis generation. By integrating comparative genomics, genome annotation, normalization, plasmid-mediated gene transfer, and microbial resistance-virulence risk-ranking into a unified workflow, gSpreadComp facilitates hypothesis generation from complex microbial datasets.<br><br>FINDINGS: The gSpreadComp workflow works through 6 modular steps: taxonomy assignment, genome quality estimation, antimicrobial resistance (AMR) gene annotation, plasmid/chromosome classification, virulence factor annotation, and downstream analysis. Our workflow calculates gene spread using normalized weighted average prevalence and ranks potential resistance-virulence risk by integrating microbial resistance, virulence, and plasmid transmissibility data and producing an HTML report. As a use case, we analyzed 3,566 metagenome-assembled genomes recovered from human gut microbiomes across diets. Our findings indicated consistent AMR across diets, with diet-specific resistance patterns, such as increased bacitracin in vegans and tetracycline in omnivores. Notably, ketogenic diets showed a slightly higher resistance-virulence rank, while vegan and vegetarian diets encompassed more plasmid-mediated gene transfer.<br><br>CONCLUSIONS: The gSpreadComp workflow aims to facilitate hypothesis generation for targeted experimental validations by the identification of concerning resistant hotspots in complex microbial datasets. Our study raises attention to a more thorough study of the critical role of diet in microbial community dynamics and the spread of AMR. This research underscores the importance of integrating genomic data into public health strategies to combat AMR. The gSpreadComp workflow is available at https://github.com/mdsufz/gSpreadComp/.}, }
@article {pmid40569093, year = {2025}, author = {Brown, L and Hoa, NT and Ly, VT and Li, L and Cao, C and Youngchim, S and Chayakulkeeree, M and Bicanic, T and Chan, JF and Yuen, KY and Le, T}, title = {Recent Advances in the Diagnosis of Talaromycosis.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf253}, pmid = {40569093}, issn = {1537-6591}, support = {//National Institute for Health Research/ ; //Federation of European Microbiological Societies/ ; //Dowager Countess Eleanor Peel Trust/ ; //British Society for Medical Mycology/ ; //Wingate Foundation/ ; R01 AI181764-01//National Institutes of Allergy and Infectious Diseases/ ; R01AI177098-02//National Institutes of Allergy and Infectious Diseases/ ; R01-AI143409-05//National Institutes of Allergy and Infectious Diseases/ ; U01AI169358-03//National Institutes of Allergy and Infectious Diseases/ ; }, abstract = {Talaromycosis is an invasive fungal disease endemic to Southeast Asia. While culture is essential in identification, susceptibility testing, and typing, the low sensitivity and long turnaround times limit its clinical utility. Several promising monoclonal antibody-based (MAb) antigen-detection assays have been evaluated in large patient cohorts. This includes the MAb-Mp1p and MAb-4D1 enzyme immunoassays and their point-of-care platforms. Quantitative polymerase chain reaction (qPCR) assays targeting the 5.8S or 18S region of ribosomal RNA have been developed. These antigen and qPCR assays are highly specific and more sensitive than blood culture, making them excellent rapid rule-in tests for talaromycosis in people with a compatible clinical syndrome. Metagenomic next-generation sequencing is emerging as a promising tool for non-bias detection of talaromycosis. Host-based diagnostics targeting antibodies, interferon-gamma release, and transcriptomics are being actively developed. This review summarizes recent advances in the diagnosis of talaromycosis and provides expert recommendations on the application of these novel tests to improve the diagnostic algorithm and management of talaromycosis.}, }
@article {pmid40568985, year = {2025}, author = {Zhao, J and Brandt, G and Gronniger, JL and Wang, Z and Li, J and Hunt, DE and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT}, title = {Quantifying the contribution of the rare biosphere to natural disturbances.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf129}, pmid = {40568985}, issn = {1751-7370}, abstract = {Understanding how populations respond to disturbances represents a major goal for microbial ecology. While several hypotheses have been advanced to explain microbial community compositional changes in response to disturbance, appropriate data to test these hypotheses is scarce, due to the challenges in delineating rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we operationally define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to identify rare populations, and by borrowing the proportional similarity index (PS index) from macroecology to identify generalists. We applied these concepts to time-series (field) metagenomes from the Piver's Island Coastal Observatory (PICO) to establish that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm temperature events, in part due to the response of rare populations. Therefore, these results provide support for the insurance hypothesis [i.e., the rare biosphere has the buffering capacity to mitigate the effects of disturbance]. Additionally, generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis [i.e., disturbance favors generalists]. Several of these findings were also observed in replicated laboratory mesocosms that aimed to simulate disturbances such as a rain-driven washout of microbial cells and a labile organic matter release from a phytoplankton bloom. Taken together, our results advance understanding of the mechanisms governing microbial population dynamics under changing environmental conditions and have implications for ecosystem modeling.}, }
@article {pmid40568706, year = {2025}, author = {Mu, X and Luo, H and Li, H and Chen, S and Han, Y and Zhang, L and Liu, W and Qiao, W and Zheng, S and Huang, Z}, title = {Pathogen detection and antibiotic use in granulomatous lobular mastitis: a comparison of mNGS and culture.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1570776}, pmid = {40568706}, issn = {2235-2988}, mesh = {Humans ; Female ; Retrospective Studies ; *Anti-Bacterial Agents/therapeutic use ; Adult ; *Granulomatous Mastitis/microbiology/drug therapy/diagnosis ; Corynebacterium/isolation &amp; purification/genetics ; High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Sensitivity and Specificity ; Young Adult ; Metagenomics/methods ; Bacteriological Techniques/methods ; *Bacteria/isolation &amp; purification/genetics/classification ; Corynebacterium Infections/diagnosis/drug therapy/microbiology ; }, abstract = {OBJECTIVE: This study aimed to evaluate the clinical microbial profile of patients with granulomatous lobular mastitis (GLM) and compare various detection methods to identify the most effective approach for pathogen detection, which could help enhance clinical diagnosis and treatment.<br><br>METHODS: We retrospectively analyzed data from 84 patients diagnosed with GLM, assessed the composition of pathogenic microorganisms in these patients, and compared the effectiveness of different sampling methods and detection techniques.<br><br>RESULTS: Corynebacterium kroppenstedtii (C. kroppenstedtii) was identified as the predominant microorganism among GLM patients. The positivity rate was low in skin swabs (10%) but similar in pus (40%) and tissue samples (37%). After antibiotic treatment, the pathogen detection rate of metagenomic next-generation sequencing (mNGS) (54.55%) was found to be higher than that of culture-based methods (27.27%). Among the GLM cases with pathogenic infection, although mNGS demonstrated higher sensitivity (75.0%) than culture tests (50.0%), both methods exhibited 100.0% specificity. However, the time for obtaining results with mNGS was significantly shorter (1.2 &#xb1; 0.41 days) compared to bacterial culture (5.5 &#xb1; 0.64 days) (P < 0.05).<br><br>CONCLUSIONS: Our findings indicate that pus was the most suitable sample type for microbial evidence collection in patients with GLM. mNGS demonstrated superior performance compared to culture in distinguishing infectious from non-infectious cases, with reduced antibiotic interference, faster turnaround time, and higher accuracy. Based on our single-center experience, empirical cephalosporin treatment may be appropriate for these patients. Additionally, surgical intervention remains the most efficient approach for rapid and complete resolution.}, }
@article {pmid40568699, year = {2025}, author = {Hu, H and Li, K and Jin, Z and Wang, K and Liu, B}, title = {Rapidly progressive pulmonary abscess initially misdiagnosed as lung cancer: the role of Peptostreptococcus stomatis and Parvimonas micra.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1590220}, pmid = {40568699}, issn = {2235-2988}, mesh = {Humans ; *Peptostreptococcus/isolation &amp; purification/genetics ; *Lung Abscess/microbiology/diagnosis/pathology/drug therapy ; *Lung Neoplasms/diagnosis ; *Gram-Positive Bacterial Infections/diagnosis/microbiology/pathology/drug therapy ; *Diagnostic Errors ; *Firmicutes/isolation &amp; purification/genetics ; Male ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; Middle Aged ; }, abstract = {Pulmonary abscess is a serious infectious disease characterized by localized lung tissue necrosis, primarily caused by anaerobic or facultative anaerobic bacterial infections. While the Streptococcus anginosus group (SAG) is a well-established pathogen in pulmonary abscess formation, recent findings suggest that strict anaerobes such as Peptostreptococcus stomatis and Parvimonas micra can also contribute to deep-seated infections. However, their role in rapidly progressive pulmonary abscesses has not been previously documented. Here, we present a case of a rapidly progressive pulmonary abscess caused by Peptostreptococcus stomatis and Parvimonas micra in an immunocompetent patient, initially misdiagnosed as lung cancer. This case highlights the importance of differentiating infectious lung lesions from malignancies and underscores the clinical utility of metagenomic next-generation sequencing (mNGS) in diagnosing rare anaerobic infections, offering valuable insights for precise diagnostic and therapeutic strategies.}, }
@article {pmid40568670, year = {2025}, author = {Iqbal, NT and Sawatzki, K and Ahmed, K and Tisoncik-Go, J and Smith, E and Voss, K and Cornelius, J and Wang, L and Spaulding, AB and Serebryannyy, L and Douek, DC and Syed, MA and Mahmood, SF and Khan, E and Van Voorhis, WC and Gale, M}, title = {Metagenomic investigation of febrile illness in Pakistan reveals global transmission and co-circulation of Zika and Dengue viruses.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.10.25322803}, pmid = {40568670}, abstract = {We report the first identification of Zika virus in Pakistan following genomic and serological analyses of blood samples from 20 patients with febrile illness. In November 2021, an outbreak of dengue-like illness occurred in the metropolitan city of Karachi. Viral genome capture and sequencing of seven patients revealed six cases of dengue virus serotype 2 and two Zika virus infections, including one dengue and Zika virus co-infection. The next year, following severe flooding, 13 suspected dengue patients were screened by real time qRT-PCR and serology, and 92% (12/13) had evidence of current or recent Zika virus infection. Phylogenetic analyses revealed the Zika viruses originated from Brazil. The most recent observed ancestor dates to 2016, suggesting a prior importation event and ongoing circulation. Our results suggest that Zika virus may be circulating and contributing to disease burden during seasonal Dengue outbreak.}, }
@article {pmid40568302, year = {2025}, author = {Ostrzinski, A and Kunath, BJ and Soares, AR and Laczny, CC and Halder, R and Kallmeyer, J and di Primio, R and Wilmes, P and Probst, AJ and Trautwein-Schult, A and Becher, D}, title = {Systematic evaluation of protein extraction for metaproteomic analysis of marine sediment with high clay content.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf074}, pmid = {40568302}, issn = {2730-6151}, abstract = {Marine sediments harbor extremely diverse microbial communities that contribute to global biodiversity and play an essential role in the functioning of ecosystems. However, the metaproteome of marine sediments is still poorly understood. The extraction of proteins from environmental samples is still a challenge, especially from marine sediments, due to the complexity of the matrix. Therefore, methods for protein extraction from marine sediments need to be improved. To develop an effective workflow for protein extraction for clayey sediments, we compared, combined and enhanced different protein extraction methods. The workflow presented here includes blocking of protein binding sites on sediment particles with high concentrations of amino acids, effective cell lysis by ultrasonic capture, electro-elution, and simultaneous fractionation of proteins. To test the protocol's efficacy, we added Escherichia coli cells to sediment samples before protein extraction. By using our refined workflow, we were able to identify a comparable number of E. coli proteins from the supplemented sediment to those from pure E. coli cultures. This new protocol will enable future studies to identify active players in clay-rich marine sediments and accurately determine functional biodiversity based on their respective protein complements.}, }
@article {pmid40568210, year = {2025}, author = {Chen, M and Zeng, SY and Lu, SJ and Shi, M and Zhang, QQ}, title = {Early re-examination of chest CT may be unnecessary when patients with psittaci pneumonia at low and intermediate risk on Pneumonia Severity Index present with response to initial treatment.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1574706}, pmid = {40568210}, issn = {2296-858X}, abstract = {BACKGROUND: Chlamydia parrot pneumonia (CPS) is a rare community-acquired pneumonia (CAP) caused by Chlamydia parrot infection. With the development of metagenomic second-generation sequencing technology (mNGS), its diagnostic rate has improved in recent years. However, there are few clinical studies on Chlamydia parrot pneumonia, especially for patients with low and intermediate pneumonia severity index (PSI), and the necessity of early review of chest computed tomography (CT) is not clear. This study aimed to explore the clinical significance of early review of chest CT in patients with low and intermediate risk of Chlamydia parrot pneumonia with PSI after initial treatment was effective.<br><br>METHODS: Retrospective analysis of 8 patients with Chlamydia psittaci pneumonia diagnosed by metagenomic next-generation sequencing (mNGS) admitted to Zhejiang Provincial Tongde Hospital from January 2020 to December 2022 (PSI score &#x2264; 130 points). All patients had improved clinical symptoms and inflammatory markers after receiving antibiotic treatment, and chest CT was reexamined within 5-12 days. Evaluate the correlation between imaging changes before and after treatment and clinical symptoms and inflammatory indicators (CRP, PCT, WBC, etc.).<br><br>RESULTS: After treatment, the patient's body temperature, CRP, PCT and other indicators decreased significantly (P < 0.05). However, early CT reexamination showed that imaging progressed in 5 cases (62.5%), was stable in 2 cases (25%), and only 1 case (12.5%) showed partial improvement (P > 0.05). Nevertheless, none of the patients had a deterioration in their condition later on and finally achieved imaging recovery. Clinicians did not adjust the treatment plan when imaging progressed, and only 1 case was given glucocorticoid additionally.<br><br>CONCLUSION: For patients with low- intermediate risk Chlamydia psittaci pneumonia with low PSI, if clinical symptoms and inflammatory markers improve, early reexamination of chest CT may have no additional clinical value and does not affect treatment decisions. Therefore, it is not recommended to routinely perform early CT re-examination for such patients to reduce unnecessary consumption of medical resources. Larger sample studies are needed in the future for further verification.<br><br>CLINICAL TRIAL REGISTRATION: https://www.medicalresearch.org.cn/login, identifier MR-33-25003507.}, }
@article {pmid40567259, year = {2025}, author = {Li, Q and Jiang, J and Li, J and Zhang, W and Xin, Y and He, B and He, S and Tu, C and Guo, Y and Gong, W}, title = {Complexity of Diarrhea-Associated Viruses in Stunted Pigs Identified by Viral Metagenomics.}, journal = {Transboundary and emerging diseases}, volume = {2025}, number = {}, pages = {1974716}, pmid = {40567259}, issn = {1865-1682}, mesh = {Animals ; Swine ; *Swine Diseases/virology/epidemiology ; *Diarrhea/veterinary/virology/epidemiology ; Metagenomics ; Phylogeny ; China/epidemiology ; }, abstract = {Viral diarrhea poses a severe threat to the health and growth of piglets, especially when caused by co-infection with multiple diarrhea-associated viruses. In this study anal swabs were collected from pigs older than 3 months from a farm in Gansu province, China, and subjected to viral metagenomic analysis. They had been suffering from diarrhea and their growth was significantly retarded. A total of 18 viruses were identified by high-throughput sequencing (HTS) in pooled samples from 22 stunted pigs and (separately) three healthy pigs. They included 15 diarrhea-associated RNA viruses with five porcine rotaviruses (PoRVs), porcine epidemic diarrhea virus (PEDV), a torovirus, and a sapelovirus present only in the stunted pigs. Among the identified PoRVs, PoRVBs showed a much greater genetic diversity than other PoRVs with multiple variant gene sequences identified in segments VP1 (2), VP2 (3), VP3 (4), VP4 (5), VP7 (5), NSP1 (2), NSP3 (3), NSP4 (2), and NSP5 (4), with 1-3 new genotypes being defined within each segment except NSP5. Unexpectedly, PoRVF was identified for the first time in pigs, with all gene segments exhibiting low nucleotide (56.5%-79.4%) and amino acid sequence identities (46.2%-92.0%) with previously identified avian RVF reference strains. Phylogenetic analysis showed that multiple variant strains of PAstV2 (6) and PAstV4 (13) were found in stunted pigs, and other enteric viruses were highly homologous with reference strains. Overall, the findings indicate that the stunted pigs may serve as a hotbed for the propagation of diarrhea-associated viruses and that they should be isolated and treated as early as possible.}, }
@article {pmid40566942, year = {2025}, author = {Kara, K and Yilmaz Öztaş, S and Baytok, E}, title = {In Vitro Ruminal Metagenomic Profiles and Ruminal Fermentation Variables of Aromatic Plant Pulps.}, journal = {Veterinary medicine and science}, volume = {11}, number = {4}, pages = {e70447}, doi = {10.1002/vms3.70447}, pmid = {40566942}, issn = {2053-1095}, support = {TSA-2023-13007//Erciyes University Scientific Research Projects Unit/ ; }, mesh = {*Fermentation ; *Rumen/microbiology/metabolism/physiology ; Animals ; Cattle ; Metagenomics ; Animal Feed/analysis ; *Metagenome ; Gastrointestinal Microbiome ; Digestion ; }, abstract = {BACKGROUND: Aromatic plant residues remaining after aromatic oil extraction represent a promising alternative feed source due to their rich bioactive compound content and fibrous structure. However, their fermentative behaviour and microbial degradability in the rumen require evaluation.<br><br>OBJECTIVE: This study aimed to determine the nutrient composition, in vitro ruminal gas production, digestibility characteristics and fermentation end-products of aromatic plant pulps (sage, thyme, lavender and yarrow) obtained via hydrodistillation.<br><br>METHODS: Dried pulps were analysed for nutrient contents and subjected to in vitro ruminal fermentation for 24&#xa0;h. Gas production estimated metabolizable energy (ME), net energy for lactation (NEL), organic matter digestibility (OMd), ammonia nitrogen (NH3-N) and short-chain fatty acid (SCFA) profiles were evaluated. Microbial community composition was assessed via 16S rRNA-based metagenomics.<br><br>RESULTS: Yarrow pulp had the highest gas production, ME, NEL, OMd and SCFA concentrations (AA, BA, IVA, T-SCFA) (p&#xa0;<&#xa0;0.05). Thyme pulp exhibited the highest NH3-N levels (75.14&#xa0;mg/L), suggesting high rumen-degradable protein content. Sage pulp had the lowest NH3-N levels (60.93&#xa0;mg/L). Microbial composition shifted with fibre content; higher lignin (in lavender) was associated with lower Bacteroidota and higher Firmicutes abundance. Methanogenic archaea (Methanobrevibacter) were least abundant in thyme pulp (p&#xa0;<&#xa0;0.05).<br><br>CONCLUSION: Due to their fermentability and favourable microbial responses, aromatic plant pulps, particularly yarrow, show promise as functional ruminant feed ingredients. These byproducts may enhance ruminal fibre utilization while modulating microbial ecology and reducing methane-associated archaea.}, }
@article {pmid40566543, year = {2025}, author = {von Känel, G and Steinmann, LY and Mauz, B and Lukesch, R and Küenzi, P}, title = {It Is Useless to Resist: Biofilms in Metalworking Fluid Systems.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/life15060890}, pmid = {40566543}, issn = {2075-1729}, support = {n.a.//Blaser Swisslube AG/ ; }, abstract = {Biofouling, the undesirable deposition of microorganisms on surfaces, is ubiquitous in aqueous systems. This is no different for systems running with water-miscible metalworking fluids (MWFs), which additionally contain many organic chemicals that create favorable conditions for growth and metabolism. Biofilm formation is thus inevitable, as there is no shortage of wetted surfaces in metalworking systems. MWF manufacturers tried in vain to offer resistance by using biocides and biostatic compounds as ingredients in concentrates and as tank-side additives. We report here that such elements, alone or as components of MWFs, did not prevent biofilm formation and had negligible effects on pre-established laboratory biofilms. Moreover, biofilms in metalworking systems are interwoven with residues, sediments, and metal swarfs generated during machining. Again, co-incubation of such "real" biofilms with MWFs had no significant effect on population size-but on population composition! The implications of this finding are unclear but could provide a starting point for the treatment of biofouling, as biofilm population structure might be of importance. Finally, we show that bacteria gain function in biofilms and that they were able to degrade a toxic amine in MWFs, which the same bacteria were unable to do in planktonic form.}, }
@article {pmid40565719, year = {2025}, author = {Landi, N and Scognamiglio, M and Muscariello, L and Marasco, R and Palazzo, A and De Chiara, I and Ragucci, S and Pedone, PV and Fiorentino, A and Di Maro, A}, title = {Chemical Traits and Microbial Population Characterization of 'Asprinio' Grape Must, a Local Vine Cultivated in Campania Region (Italy).}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, doi = {10.3390/foods14122110}, pmid = {40565719}, issn = {2304-8158}, support = {CUP B53C22001790006//"ITACA.SB" (Project No. IR0000009) funded by the European Union's NextGenerationEU under the MUR call 3264/2021 PNRR M4/C2/L3.1.1./ ; CUP E25I22000010007//'Rigenerazione culturale e sociale dei borghi storici del Matese - Castello del Matese e Letino', (Unione europea - NextGenerationEU)/ ; }, abstract = {'Asprinio' grape is used to produce a white wine from the Campania region, known as 'Asprinio' (DOC since 1993). A plethora of approaches was adopted to characterize the organic compounds (e.g., free amino acids and other metabolites) and microbial population (bacteria and fungi) in 'Asprinio' grape must by collecting samples from three different vineyards cultivated with the 'alberata' training system. The average free amino acid content of 'Asprinio' grape must showed quantitative variations, but no significant statistical differences were found. On average, proline was the most abundant free amino acid (~282 mg/L; 47.9%), followed by arginine (~66 mg/L; 11.5%) and glutamine (~25.2 mg/L; 4.2%). On the other hand, the total polyphenol content (TPC) of 'Asprinio' grape must was different, like their antioxidant activity, which increased when the TPC content was higher. Moreover, 1D and 2D NMR spectra highlighted the presence of high sugars amount (in particular glucose) as well as trans-caftaric acid, trans-coutaric acid, trans-fertaric acid, and the cis-isomers of these cinnamate esters. Finally, the evaluation of the microbial communities in the 'Asprinio' grape must revealed the presence of several representative bacterial phyla-mainly Bacteroidota, Proteobacteria, and Actinobacteriota-as well as various fungal genera, including Cladosporium, Hanseniaspora, Aspergillus, and Saccharomyces. Notably, these microorganisms, which contribute to the fermentation process and influence the final wine flavor, have been found in different proportions in the grape musts analyzed. Our results contribute to increasing knowledge of the 'Asprinio' grape, an indigenous vine of Southern Italy.}, }
@article {pmid40565014, year = {2025}, author = {Monareng, NJ and Ncube, KT and van Rooi, C and Modiba, MC and Mtileni, B}, title = {A Systematic Review on Microbial Profiling Techniques in Goat Milk: Implications for Probiotics and Shelf-Life.}, journal = {International journal of molecular sciences}, volume = {26}, number = {12}, pages = {}, doi = {10.3390/ijms26125551}, pmid = {40565014}, issn = {1422-0067}, support = {PMDS240528221992//National Research Foundation/ ; }, mesh = {Goats ; Animals ; *Milk/microbiology ; *Probiotics ; *Microbiota ; *Food Microbiology ; Humans ; }, abstract = {Due to its high digestibility, rich nutrient profile, and potential probiotic content, goat milk is an essential nutritional resource, particularly for individuals with cow milk allergies. This review summarises the current state of microbial diversity in goat milk, emphasising the implications for quality, safety, and probiotic potential. This systematic review adhered to PRISMA guidelines, conducting a comprehensive literature search across PubMed, ScienceDirect, and Google Scholar using keywords related to microbial profiling in goat milk. The inclusion criteria targeted English-language studies from 2000 to 2025 that utilised high-throughput or next-generation sequencing methods. Out of 126 articles screened, 84 met the eligibility criteria. The extracted data focused on microbial diversity, profiling techniques, and their respective strengths and limitations in evaluating probiotic potential and spoilage risks. The review addresses the challenges linked to microbial spoilage and the composition and functional roles of microbial communities in goat milk. With species such as Bacillus and Pseudomonas playing crucial roles in fermentation and spoilage, key findings emphasise the prevalence of microbial phyla, including Proteobacteria, Firmicutes, and Actinobacteria in goat milk. The review also explores the probiotic potential of the goat milk microbiota, highlighting the health benefits associated with strains such as Lactobacillus and Bifidobacterium. Significant discoveries underline the necessity for advanced multi-omics techniques to thoroughly define microbial ecosystems and the substantial gaps in breed-specific microbiota research. Important findings illustrate the need for enhanced multi-omics techniques, given the challenges of host RNA and protein interference, low microbial biomass, and limited goat-specific reference databases, for optimising probiotic development, spoilage prevention strategies, and integrating metagenomics, metabolomics, metaproteomics, and metatranscriptomics to improve milk quality and safety as some of the future research objectives. This study emphasises the importance of understanding goat milk microbiology to advance dairy science and enhance human health.}, }
@article {pmid40564305, year = {2025}, author = {Rodriguez, AE and Britez, JD and Pisón-Martínez, ML and Delgado, FO and Balbiani, F and Berardo, CC and Gramaglia, C and Cuba, F and Poklepovich, TJ and Moreno, C and Francinelli, G and Morici, G and Arias, M and Schapiro, J and Barbano, P and Tomazic, ML}, title = {Evaluating Good Husbandry Practices and Organic Fermented Additives for Coccidiosis Control in a Pilot Study Using Slow-Growing Broilers.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {12}, pages = {}, doi = {10.3390/ani15121752}, pmid = {40564305}, issn = {2076-2615}, support = {FONTAGRO ATN/RF 18136 RG//Inter-American Development Bank/ ; PNSA PDL01-I113 and PE-I078//INSTITUTO NACIONAL DE TECNOLOG&#xcd;A AGROPECUARIA/ ; }, abstract = {The Argentine Campero-INTA slow-growing chicken, a widely used breed in family poultry farming, faces high coccidiosis prevalence, impairing productivity. Control often relies on management and drugs due to vaccination costs. This pilot study assessed the breed's susceptibility to local Eimeria and the impact of good animal welfare practices (AWPs) and an organic fermented additive, locally produced, combined with AWPs (OF-AWPs). Two trials evaluated productive (body weight gain and feed conversion), infection (oocyst excretion and lesion score), and histopathological parameters (villus height and crypt depth). The productivity (PI) and anticoccidial (ACI) indexes were calculated. Metagenomic analysis of the additive was also conducted. Mild to moderate coccidiosis significantly reduced PI (7.99-16.83 vs. 29.29 in unchallenged controls). In the second trial, AWPs showed good anticoccidial efficacy (ACI 173.9), while OF-AWPs demonstrated high efficacy, especially in birds of 28 days (ACI 180.6), improving productive parameters, reducing oocyst shedding, and enhancing the villus height to crypt depth ratio. Over a 75-day cycle, the OF-AWP increased the PI by 24.44% compared to untreated chickens (108.8 vs. 87.43). Lactic acid bacteria were the main component of the organic fermented additive. This research highlights the potential of an agroecological strategy to manage coccidiosis in Campero-INTA chickens.}, }
@article {pmid40564077, year = {2025}, author = {Theis, BF and Park, JS and Kim, JSA and Zeydabadinejad, S and Vijay-Kumar, M and Yeoh, BS and Saha, P}, title = {Gut Feelings: How Microbes, Diet, and Host Immunity Shape Disease.}, journal = {Biomedicines}, volume = {13}, number = {6}, pages = {}, doi = {10.3390/biomedicines13061357}, pmid = {40564077}, issn = {2227-9059}, abstract = {The human gut microbiome is intricately linked to systemic and organ-specific immune responses and is highly responsive to dietary modulation. As metagenomic techniques enable in-depth study of an ever-growing number of gut microbial species, it has become increasingly feasible to decipher the specific functions of the gut microbiome and how they may be modulated by diet. Diet exerts both supportive and selective pressures on the gut microbiome by regulating a multitude of factors, including energy density, macronutrient and micronutrient content, and circadian rhythm. The microbiome, in turn, contributes to local and systemic immune responses by providing colonization resistance against pathogens, shaping immune cell activity and differentiation, and facilitating the production of bioactive metabolites. Emerging research has strengthened the connections between the gut microbiome and cardiometabolic disorders (e.g., cardiovascular disease, obesity, type-2 diabetes), autoimmune conditions (e.g., type-1 diabetes, rheumatoid arthritis, celiac disease), respiratory disease, chronic kidney and liver disease, inflammatory bowel disease, and neurological disorders (e.g., Alzheimer's, Parkinson's disease, depressive disorders). Here, we outline ways in which dietary factors impact host response in diseases through alterations of gut microbiome functionality and composition. Consideration of diet-mediated microbial effects within the context of the diseases discussed highlights the potential of microbiome-targeted treatment strategies as alternative or adjunct therapies to improve patient outcomes.}, }
@article {pmid40563973, year = {2025}, author = {Qumsani, AT}, title = {Gut Microbiome Engineering for Diabetic Kidney Disease Prevention: A Lactobacillus rhamnosus GG Intervention Study.}, journal = {Biology}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/biology14060723}, pmid = {40563973}, issn = {2079-7737}, abstract = {The gut microbiota has emerged as a critical modulator in metabolic diseases, with substantial evidence supporting its role in attenuating diabetes-related nephropathy. Recent investigations demonstrate that strategic manipulation of intestinal microflora offers novel therapeutic avenues for safeguarding renal function against diabetic complications. This investigation sought to determine the nephroprotective potential of Lactobacillus rhamnosus GG (LGG) administration in diabetic nephropathy models. Six experimental cohorts were evaluated: control, probiotic-supplemented control, diabetic, diabetic receiving probiotic therapy, diabetic with antibiotics, and diabetic treated with both antibiotics and probiotics. Diabetic conditions were established via intraperitoneal administration of streptozotocin (50 mg/kg) following overnight fasting, according to validated protocols for experimental diabetes induction. Probiotic therapy (3 × 10[9] CFU/kg, bi-daily) began one month before diabetes induction and continued throughout the study duration. Glycemic indices were monitored at bi-weekly intervals, inflammatory biomarkers, renal function indices, and urinary albumin excretion. The metabolic profile was evaluated through the determination of HOMA-IR and the computation of metabolic syndrome scores. Microbiome characterization employed 16S rRNA gene sequencing alongside metagenomic shotgun sequencing for comprehensive microbial community mapping. L. rhamnosus GG supplementation substantially augmented microbiome richness and evenness metrics. Principal component analysis revealed distinct clustering of microbial populations between treatment groups. The Prevotella/Bacteroides ratio, an emerging marker of metabolic dysfunction, normalized following probiotic intervention in diabetic subjects. Results: L. rhamnosus GG administration markedly attenuated diabetic progression, achieving glycated hemoglobin reduction of 32% compared to untreated controls. Pro-inflammatory cytokine levels (IL-6, TNF-α) decreased significantly, while anti-inflammatory mediators (IL-10, TGF-β) exhibited enhanced expression. The renal morphometric analysis demonstrated preservation of glomerular architecture and reduced interstitial fibrosis. Additionally, transmission electron microscopy confirmed the maintenance of podocyte foot process integrity in probiotic-treated groups. Conclusions: The administration of Lactobacillus rhamnosus GG demonstrated profound renoprotective efficacy through multifaceted mechanisms, including microbiome reconstitution, metabolic amelioration, and inflammation modulation. Therapeutic effects suggest the potential of a combined probiotic and pharmacological approach to attenuate diabetic-induced renal pathology with enhanced efficacy.}, }
@article {pmid40563865, year = {2025}, author = {Zhao, L and Dong, XN and Cui, H and Sun, LY and Mu, R and Nie, M and Kang, JM and Bu, N and Zhang, YS and Qi, ZH and Li, ZX and Zhang, ZL and Zhang, XY and Ding, YL and Wang, R and Wang, Y and Liu, YH}, title = {Comparative Analysis of Microbial Communities in Each Developmental Stage of Dermacentor nuttalli in Two Regions in Inner Mongolia, China.}, journal = {Biology}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/biology14060613}, pmid = {40563865}, issn = {2079-7737}, support = {32260887//National Natural Science Foundation of China/ ; }, abstract = {Dermacentor is the most widely distributed tick genus in China. Dermacentor nuttalli, a predominant tick species in Inner Mongolia, can carry and transmit pathogenic microorganisms. Here, D. nuttalli were collected from Ordos (O-D) and Hinggan League (H-D) in the Inner Mongolia. D. nuttalli specimens at different developmental stages were subsequently reared under identical laboratory conditions. Sample processing, nucleic acid extraction, high-throughput sequencing, and microbial community analyses were conducted. Bacterial communities in O-D and H-D were annotated to 8 phyla, 145 genera and 16 phyla, 141 genera, respectively, with Proteobacteria showing the highest relative abundance. Differences in dominant bacterial genera were observed across developmental stages between the two regions. The most abundant bacterial species were Arsenophonus_uncultured_bacterium in O-D and Rickettsia japonica in H-D. Viral communities were annotated to 4 orders, 25 families, 61 genera, and 126 species in O-D and 6 orders, 28 families, 49 genera, 135 species in H-D. Notable difference in the viral genera with >1% abundance were identified at different developmental stages in the two regions. To our knowledge, this is the first study to compare microbial community compositions of D. nuttalli across developmental stages in two Inner Mongolian regions under under identical rearing conditions and to report the presence of R. japonica, Tacheng Tick Virus-2, and bovine viral diarrhea virus in D. nuttalli.}, }
@article {pmid40563782, year = {2025}, author = {Hong, SH and Roh, HW and Nam, YJ and Kim, TW and Cho, YH and Son, SJ and Hong, CH}, title = {Age- and Sex-Specific Gut Microbiota Signatures Associated with Dementia-Related Brain Pathologies: An LEfSe-Based Metagenomic Study.}, journal = {Brain sciences}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/brainsci15060611}, pmid = {40563782}, issn = {2076-3425}, support = {2024-ER0505-00//Korea National Institute of Health (KNIH)/ ; GRRCAjou2023-B02//Gyeonggi-do Regional Research Center program of Gyeonggi province/ ; RS-2022-KH130309//Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health &amp; Welfare, Republic of Korea/ ; RS-2021-KH113821//Korea Health Technology R&amp;D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health &amp; Welfare, Republic of Korea/ ; }, abstract = {BACKGROUND/OBJECTIVES: Emerging evidence suggests that gut microbiota composition is influenced by both age and sex and may contribute to dementia-related brain pathologies. However, comprehensive microbiome-based biomarker discovery stratified by these factors remains limited.<br><br>METHODS: We performed a metagenomic analysis of the gut microbiota of participants stratified by sex (female vs. male) and age (<75 vs. &#x2265;75 years). Alpha diversity (observed operational taxonomic unit, Chao1, Shannon, and Simpson) and linear discriminant analysis effect size analyses were conducted to identify dominant taxa associated with Alzheimer's pathology, vascular pathology, and dementia-related structural brain changes.<br><br>RESULTS: Females and non-elderly participants (aged < 75 years) exhibited higher gut microbial diversity, characterized by an increased abundance of Bifidobacterium spp. and Blautia spp., whereas males and elderly participants (aged &#x2265; 75 years) exhibited increased levels of Bacteroides spp. and Bacteroidia, which have been associated with inflammation and dysbiosis. Several taxa, including Bifidobacterium spp. were consistently identified as potential protective biomarkers, while Bacteroides spp. was linked to a higher risk of dementia-related brain pathologies.<br><br>CONCLUSIONS: Our findings demonstrate distinct age- and sex-specific differences in gut microbiota composition that may be closely associated with the pathophysiology of dementia-related brain pathologies. These results demonstrate that gut microbiota may serve as potential biomarkers for monitoring cerebrovascular conditions, potentially contributing to the development of personalized therapeutic strategies.}, }
@article {pmid40563710, year = {2025}, author = {Kazen, AB and Umfleet, LG and Aboulalazm, FA and Cohen, AD and Terhune, S and Mason, L and Obarski, S and Franczak, M and Kindel, TL and Wang, Y and Kirby, JR}, title = {Gut Microbiota and Neurovascular Patterns in Amnestic Mild Cognitive Impairment.}, journal = {Brain sciences}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/brainsci15060538}, pmid = {40563710}, issn = {2076-3425}, support = {1R21AG075501-24A1/NH/NIH HHS/United States ; }, abstract = {Background/Objectives: The interplay between the gut microbiome (GMB) and neurovascular function in neurodegeneration is unclear. The goal of this proof-of-concept, cross-sectional study is to identify relationships between the GMB, neurovascular functioning, and cognition in amnestic mild cognitive impairment (aMCI), the prototypical prodromal symptomatic stage of Alzheimer's disease (AD). Methods: Participants (n = 14 aMCI and 10 controls) provided fecal samples for GMB sequencing (16S and shotgun metagenomics), underwent MRI, and completed cognitive testing. Cerebral vascular reactivity (CVR), cerebral blood flow (CBF), and arterial transit time (ATT) were assessed. Statistical analyses evaluated the relationships between discriminatory taxa, cerebrovascular metrics, and cognition. Results: Sequencing revealed differentially abundant bacterial and viral taxa distinguishing aMCI from controls. Spearman correlations revealed that bacteria known to induce inflammation were negatively associated with CVR, CBF, and cognition, and positively associated with ATT. A reciprocal pattern emerged for the association of taxa with gut health. Conclusions: Our results provide preliminary evidence that pro-inflammatory gut bacterial and viral taxa are associated with neurovascular dysfunction and cognitive impairment in prodromal AD, highlighting their potential as candidate microbial biomarkers and targets for early intervention.}, }
@article {pmid40563261, year = {2025}, author = {Gao, J and Zhu, H and Gao, J and Xu, G}, title = {Characteristics of Intestinal Microbiota and Host Gene Regulation in Coilia nasus Responding to Stress.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/antiox14060626}, pmid = {40563261}, issn = {2076-3921}, support = {32302976//the National Natural Science Foundation of China/ ; BK20230179//the Natural Science Foundation of Jiangsu Province/ ; 2022YFD2400904//the National Key Research and Development Program of China/ ; JSGS [2021]134//the Jiangsu Province seed industry revitalization "revealing-list" project/ ; }, abstract = {Transport stress in aquaculture poses significant challenges to fish health by inducing oxidative stress and intestinal damage. This study investigated the effects of transport stress on intestinal microbiota, host gene regulation, and metabolic responses in Coilia nasus. The fish were subjected to simulated transport conditions, followed by an analysis of their intestinal antioxidant capacity, inflammatory factors, transcriptome sequencing, metagenomic profiling, and metabolomic assays. The results revealed that transport stress significantly suppressed antioxidant enzyme activities (e.g., catalase, superoxide dismutase, glutathione peroxidase) and elevated oxidative damage (malondialdehyde, lipid peroxidation) alongside upregulating pro-inflammatory cytokines. The transcriptomic analysis identified differentially expressed genes enriched in the lipid metabolism and ferroptosis pathways, with the increased lipid peroxidation and iron overload activating ferroptosis. The metagenomic data showed an altered gut microbiota composition, including increased Aeromonas and reduced beneficial metabolites (e.g., propionic acid, bile acids). Correlation analyses linked the microbial shifts and metabolite changes to ferroptosis and barrier dysfunction. These findings demonstrate that transport stress disrupts intestinal redox balance, induces ferroptosis, and reshapes gut microbiota, collectively compromising intestinal integrity and health in C. nasus.}, }
@article {pmid40563104, year = {2025}, author = {Trutschel, L and Kruger, B and Czaja, A and Brueck, M and Sackett, J and Druschel, G and Rowe, A}, title = {Sulfide Oxidation Products Support Microbial Metabolism at Interface Environments in a Marine-Like Serpentinizing Spring in Northern California.}, journal = {Geobiology}, volume = {23}, number = {4}, pages = {e70026}, doi = {10.1111/gbi.70026}, pmid = {40563104}, issn = {1472-4669}, support = {80NSSC21K0482/NASA/NASA/United States ; }, mesh = {Oxidation-Reduction ; California ; *Sulfides/metabolism ; *Bacteria/metabolism/classification/genetics ; *Natural Springs/microbiology/chemistry ; Microbiota ; }, abstract = {Interface environments between extreme and neutrophilic conditions are often hotspots of metabolic activity and taxonomic diversity. In serpentinizing systems, the mixing of high pH fluids with meteoric water, and/or the exposure of these fluids to the atmosphere can create interface environments with distinct but related metabolic activities and species. Investigating these systems can provide insights into the factors that stimulate microbial growth, and/or what attributes may be limiting microbial physiologies in native serpentinized fluids. To this aim, changes in geochemistry and microbial communities were investigated for different interface environments at Ney Springs-a marine-like terrestrial serpentinization system where the main serpentinized fluids have been well characterized geochemically and microbially. We found that reduced sulfur species from Ney Springs had large impacts on the community changes observed at interface environments. Oxygen availability at outflow environments resulted in a relative increase in the taxa observed that were capable of sulfur oxidation, and in some cases light-driven sulfur oxidation. A combination of cultivation work and metagenomics suggests these groups seem to predominantly target sulfur intermediates like polysulfide, elemental sulfur, and thiosulfate as electron donors, which are present and abundant to various degrees throughout the Ney system. Fluid mixing with meteoric water results in more neutral pH systems which in turn select for different sulfur-oxidizing taxa. Specifically, we see blooms of taxa that are not typically observed in the primary Ney fluids, such as Halothiobacillus in zones where fluids mix underground with meteoric water (~pH 10) or the introduction of Thiothrix into the nearby creek as fluids enter at the surface (~pH 8). This work points to the potential importance of oxidants for stimulating microbial respiration at Ney Springs, and the observation that these serpentinized fluids act as an important source of reduced sulfur, supporting diverse taxa around the Ney Springs system.}, }
@article {pmid40562730, year = {2025}, author = {Vetterli, D and Zennaro, M and Tacchini, V and Lobrinus, JA and Prendki, V and Lazarevic, V and Schrenzel, J}, title = {Next-Generation Sequencing Techniques to Diagnose Culture-Negative Subacute Native Aortic Endocarditis.}, journal = {Emerging infectious diseases}, volume = {31}, number = {7}, pages = {1478-1481}, doi = {10.3201/eid3107.241739}, pmid = {40562730}, issn = {1080-6059}, mesh = {Humans ; Male ; *Aortic Valve/microbiology ; *Endocarditis/diagnosis/microbiology ; *Endocarditis, Bacterial/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Streptococcus gordonii/genetics/isolation &amp; purification ; Aged, 80 and over ; }, abstract = {Next-generation sequencing might improve diagnosis of infective endocarditis. A case in Switzerland was initially attributed to Solobacterium moorei bacteria. Metagenomic analysis of the affected heart valve detected Streptococcus gordonii, but not S. moorei, illustrating that the results of molecular detection can vary depending on sampling time and anatomic site.}, }
@article {pmid40562294, year = {2025}, author = {Zhang, J and Zhan, H and Xu, H and Wang, R and Li, Z and Feng, F and Wu, H and Xu, Z and Wang, S and Guo, Y and Li, Y}, title = {Infectious agents in dilated cardiomyopathy: Genetic interactions, autoimmunity, mechanisms, and therapeutic approaches.}, journal = {Autoimmunity reviews}, volume = {}, number = {}, pages = {103860}, doi = {10.1016/j.autrev.2025.103860}, pmid = {40562294}, issn = {1873-0183}, abstract = {Dilated cardiomyopathy (DCM) is a heterogeneous myocardial disorder characterized by left ventricular dilation and systolic dysfunction in the absence of ischemic, hypertensive, or valvular heart disease. Although its precise etiology remains unclear, it is widely recognized as a multifactorial disease arising from complex interactions between genetic predisposition and environmental triggers. Among these, infectious agents have been implicated in the pathogenesis of various subtypes, particularly inflammatory and idiopathic DCM. These agents can contribute to disease onset and progression through direct cardiomyocyte injury, immune-mediated chronic inflammation, and other yet-to-be-defined mechanisms. Infection-driven autoimmune activation is another potential key contributor to DCM, potentially linking infectious exposure to sustained myocardial damage. However, the precise role of various infectious agents in DCM initiation and progression, as well as their interactions with genetic predisposition and autoimmune activation, is inadequately understood. Improving understanding of infection-related etiologies could facilitate development of targeted therapeutic strategies; however, significant challenges persist in identifying causative and novel pathogens, and translating this into clinical practice. Therefore, this review explores the complex interactions between infectious agents, genetic predisposition, and autoimmune responses in DCM pathogenesis. We summarize current evidence on the role of infectious agents in DCM and emerging therapeutic strategies aimed at treating infection-related DCM. Finally, we outline future research directions to advance understanding of infection-associated DCM and improve patient outcomes. We reveal that a deeper understanding of host-microbe interactions, immune pathways, and genetic predisposition is essential for advancing DCM research. Furthermore, integrating genomics, metagenomics, and antibody and immunological profiling is crucial for developing personalized therapeutic strategies for this complex disease.}, }
@article {pmid40562247, year = {2025}, author = {Yang, X and Wang, W and Liu, X and Xie, S and Feng, J and Lv, J}, title = {Nitrogen metabolism functional shifts of indigenous bacteria and effect on nitrogen removal in microalgae-based municipal wastewater treatment system across aeration modes.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132881}, doi = {10.1016/j.biortech.2025.132881}, pmid = {40562247}, issn = {1873-2976}, abstract = {Although the effect of aeration intensity on the performance of microalgae-based wastewater treatment systems has been widely studied, the impact of aeration mode has received less attention. This study explored how different aeration modes influence nitrogen metabolism in microalgae-based wastewater systems using metagenomic analysis. Both continuous aeration (CA) and intermittent aeration (IA) supported rapid bacterial growth and effective pollutant removal. Compared to CA, IA and no-aeration modes significantly enhanced bacterial nitrification and denitrification. Key nitrogen-metabolizing genera such as Paracoccus, Acidovorax, and Rhizobium played major roles in nitrogen cycling. Their abundances were closely associated with NH4[+]-N, NO3[-]-N, NO2[-]-N, total phosphorus, chemical oxygen demand, dissolved oxygen, bacterial number, and total biomass. Overall, environmental changes induced by different aeration modes significantly shaped indigenous bacterial communities involved in nitrogen metabolism, thereby influencing the abundances of nitrogen metabolism-related genes and, ultimately, nitrogen removal performance.}, }
@article {pmid40562089, year = {2025}, author = {Gu, P and Xu, Y and Li, X}, title = {Chronic Low-Dose Cadmium Exposure Disrupts Gut Microbiota and Lipid Metabolism to Induce Liver Injury.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {}, number = {}, pages = {115603}, doi = {10.1016/j.fct.2025.115603}, pmid = {40562089}, issn = {1873-6351}, abstract = {Cadmium (Cd) is a widespread environmental pollutant linked to liver injury and metabolic dysfunction, yet the gut-liver axis mechanisms remain unclear. We investigated chronic low-dose Cd exposure (100 nM CdCl2, 12 weeks) in mice using integrated metagenomic and metabolomic profiling. Despite intact intestinal morphology, Cd exposure induced hepatic inflammation, steatosis, and elevated transaminases. Shotgun metagenomics revealed gut microbiota shifts, with enrichment of Prevotella and depletion of Turicibacter. Fecal metabolomics showed disrupted bile acid detoxification and lipid remodeling. Functional analysis indicated upregulation of microbial fatty acid metabolism genes, suggesting compensatory but dysregulated responses. These findings demonstrate that chronic Cd exposure perturbs gut microbiota and metabolic outputs, driving liver injury via microbiota-mediated mechanisms. Our study highlights the gut-liver axis as a key target of Cd toxicity and points to microbiota-based interventions as potential therapies.}, }
@article {pmid40561629, year = {2025}, author = {Deng, Z and Xie, Y and Yu, H and Zhang, X and Tan, T and Kuang, W and Han, Z and Li, Y and Wang, H and Zhang, N and Zhang, C}, title = {Harnessing deep-sea cold seep microbiomes for reductive dehalogenation: from culturomics and genomics insights.}, journal = {Water research}, volume = {285}, number = {}, pages = {124072}, doi = {10.1016/j.watres.2025.124072}, pmid = {40561629}, issn = {1879-2448}, abstract = {Deep-sea cold seeps harbor a rich and diverse repertoire of reductive dehalogenase-encoding genes (rdhA), yet their potential for reductive dehalogenation remains largely unexplored. In this study, we investigated the microbial debromination of 2,4,6-tribromophenol (TBP) in cold seep sediment microcosms. By optimizing culture conditions with different nutrient sources and substrate concentrations, we established a highly efficient debrominating microbial consortium capable of completely degrading 50 μM TBP within 72 h. Metagenomic analysis revealed Bin3, a novel bacterium affiliated with Peptococcaceae, as a key dehalogenator harboring multiple rdhA genes. Microbial community analysis demonstrated that nutrient availability significantly influenced beta diversity (community composition) but had only a minor effect on alpha diversity. Through degradation kinetics, co-occurrence network analysis, normalized stochasticity ratio analysis, and metagenomic quantification, we found that supplementing lactate along with 0.05 % yeast extract significantly enhanced TBP degradation efficiency and facilitated the targeted enrichment of key dehalogenating microbes (with relative abundance increasing from <1 % to 32 %). Comparative genomic analysis indicated that Bin3 has undergone specific adaptations through expansion of gene families involved in pili formation, cell motility, nutrient acquisition, and diverse metabolic pathways, potentially enhancing its competitiveness in deep-sea cold seep environments. This study advances our understanding of deep-sea dehalogenating microbiomes and their adaptation to extreme environments, providing insights into their ecological significance and potential applications in pollutant bioremediation.}, }
@article {pmid40561623, year = {2025}, author = {Zhang, Y and Wang, M and Wu, H and Cheng, W and Zhao, L and Yu, G and Ren, J}, title = {Hydroperiodic dynamics of microbial-mediated nitrogen cycling and its multi-element coupling effect in the Weihe River.}, journal = {Water research}, volume = {285}, number = {}, pages = {124057}, doi = {10.1016/j.watres.2025.124057}, pmid = {40561623}, issn = {1879-2448}, abstract = {The aquatic ecosystem is affected by both human activities and climate change, and the excessive input and imbalance of nitrogen (N) have become an environmental issue of global concern. In this study, based on metagenomic sequencing, network analysis, random forest and structural equation model were used to investigate the hydroperiod dynamics, driving mechanisms of N cycling and the coupling effects of N, carbon (C) and sulfur (S) cycling in the Weihe River. The results showed that the nitrogen concentration and pathways exhibited heterogeneity during the high, normal and low water periods. Nitrogen fixation and organic nitrogen mineralization were abundant during the high water period, and nitrification, anammox were dominant during the low water period. The co-occurrence network of bacteria and nitrogen cycling genes was dominated by positive correlations, and Limnohabitans, Flavobacterium, and Polynucleobacter showed diverse metabolic potentials. Redundancy analysis showed that nitrogen cycling genes were more sensitive to substrate changes in the high and low water periods, and dependent on basic physicochemical conditions during the normal water period. A structural equation model revealed that climatic conditions, water properties, and microbial communities had positive effects on nitrogen cycling genes (standard effects of 0.154, 0.347, 0.603), with microbial-gene collaboration driving core functionality. The strong positive correlation of the co-occurrence network of C, N, and S functional genes revealed the elemental synergies. The multi-element coupled cycling networks showed more complex and stronger interactions during the normal water periods, and the efficiency of cross-element metabolism was reduced during low water periods. This study holds significance in understanding the ecological effects of microbial-mediated nitrogen cycling and multi-element coupled cycling in rivers, and provides a theoretical basis for nutrient control in micro-polluted rivers.}, }
@article {pmid40560512, year = {2025}, author = {Pramanik, K and Sen, A and Dutta, S and Mandal, GS and Paramanik, B and Das, A and Chatterjee, N and Ghorai, AK and Ali, MN}, title = {Microbial populations under fluoride stress: a metagenomic exploration from Indian soil.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {7}, pages = {221}, pmid = {40560512}, issn = {1573-0972}, mesh = {*Soil Microbiology ; *Fluorides/analysis ; India ; Metagenomics ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Soil/chemistry ; Fungi/genetics/classification/drug effects/isolation &amp; purification ; Archaea/genetics/classification/drug effects/isolation &amp; purification ; Metagenome ; Phylogeny ; Microbiota/drug effects ; }, abstract = {Fluoride exposure, even at a low concentration, significantly impairs crop growth and productivity by inhibiting metabolic enzymes and disrupting photosynthesis. Addressing this challenge, microbial de-fluoridation emerges as a vital strategy to improve soil health, enhance crop growth, and ensure agricultural sustainability. This study analyzed topsoil samples (0-0.2 m depth) from rice fields in three blocks of Purulia district, West Bengal-Arsha, Jhalda-I, and Joypur. Fluoride content in the samples ranged from 58.76 ± 0.76 mg/kg to 282.9 ± 4.9 mg/kg (total) and 1.57 ± 0.02 mg/kg to 2.97 ± 0.03 mg/kg (available). The metagenomic analysis of the collected soil samples revealed diverse microbial communities comprising archaea, bacteria, fungi, and viruses, with Actinobacteria (phylum), Hyphomicrobiales (order), and Nocardioidaceae (family) being the dominant prokaryotes. Arsha soil with comparatively low fluoride contamination exhibited the highest microbial diversity (11,891 taxa), followed by Joypur (11,528 taxa) and Jhalda-I (11,358 taxa), with Arsha showing nearly double the unique microbial taxa compared to the other locations. Clusters of orthologous groups of proteins functional analysis identified 60,898 genes in Arsha, 63,403 genes in Jhalda-I, and 73,334 genes in Joypur, while Kyoto encyclopedia of genes and genomes analysis revealed 9,385, 9,104, and 10,633 genes, respectively. Key genes associated with fluoride metabolism-inorganic pyrophosphatase, divalent metal cation transporter mntH, and putative fluoride ion transporter crcB-were abundant across all sites, highlighting the influence of fluoride on microbial community structure. This study provides the first comprehensive report on soil microbial communities in fluoride-rich areas, highlighting the potential of native fluoride-tolerant microbes to mitigate fluoride toxicity in agricultural soils and offer sustainable, microbe-based solutions to fluoride contamination.}, }
@article {pmid40559797, year = {2025}, author = {Hai, C and Gong, H and Xu, Y and Liu, X and Bai, C and Su, G and Yang, L and Li, G}, title = {Loss of Myostatin Alters Gut Microbiota and Carbohydrate Metabolism to Influence the Gut-Muscle Axis in Cattle.}, journal = {Veterinary sciences}, volume = {12}, number = {6}, pages = {}, pmid = {40559797}, issn = {2306-7381}, support = {2023ZD0404803//Scientific and Technological Innovation 2030/ ; 32360837, 32341052//National Natural Science Foundation of China/ ; 2022JBGS0025//Inner Mongolia Open Competition Projects/ ; 2022LJRC0006//Inner Mongolia Science and Technology Leading Team/ ; 2021ZD0009, 2021ZD0008, 2022ZD0008, 2023KJHZ0028//Inner Mongolia Science and Technology Major Projects/ ; NJYT23138//Inner Mongolia Young Talents Projects/ ; 2023MS03004//Inner Mongolia Natural Science Foundation/ ; 2022ZY0212//Central Government Guides Development/ ; NK2022130203//National Agricultural Science and Technology Project/ ; XTCX2023-06//Collaborative Innovation among Universities in Hohhot/ ; JYBGCSYS2022//Ministry of Education Engineering Centre Project/ ; 2023A02011-1//Xinjiang Uygur Science and Technology Major Project/ ; }, abstract = {The gut-muscle axis plays a vital role in host metabolism and health. Although the MSTN gene is a well-known negative regulator of muscle growth, its role in intestinal function and metabolism remains unclear. Understanding this connection is crucial for revealing the systemic impact of MSTN gene editing and its potential to improve metabolic efficiency in livestock. In this study, we investigated the influence of MSTN deletion on gut microbiota composition and carbohydrate metabolism in the cecum and colon of cattle. Using integrated metagenomic, metabolomic, serum biochemical, and muscle transcriptomic analyses, we found significant alterations in microbial communities and key metabolic pathways. Hallella and Escherichia in the colon, as well as Alishewanella in the cecum, were closely linked to carbohydrate metabolism. Differential microbes and metabolites influenced key metabolic pathways, including glycolysis/gluconeogenesis and lipopolysaccharide biosynthesis. Functional gene analysis identified Bacteroides as the most critical bacterium affecting glycolysis/gluconeogenesis. Additionally, genes related to carbohydrate esterases were upregulated. These changes correlated with reduced serum glucose and insulin levels while increasing muscle gene expression related to glucose-to-lactose conversion. Overall, MSTN gene editing alters gut microbiota composition and carbohydrate metabolism in the cecum and colon, thereby influencing host glucose metabolism and energy homeostasis.}, }
@article {pmid40559651, year = {2025}, author = {Wimmer, BC and Dwan, C and De Medts, J and Duysburgh, C and Rotsaert, C and Marzorati, M}, title = {Undaria pinnatifida Fucoidan Enhances Gut Microbiome, Butyrate Production, and Exerts Anti-Inflammatory Effects in an In Vitro Short-Term SHIME[®] Coupled to a Caco-2/THP-1 Co-Culture Model.}, journal = {Marine drugs}, volume = {23}, number = {6}, pages = {}, pmid = {40559651}, issn = {1660-3397}, support = {n.a.//Marinova Pty Ltd., 249 Kennedy Drive, Cambridge, TAS 7170, Australia/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/isolation &amp; purification ; *Undaria/chemistry ; *Anti-Inflammatory Agents/pharmacology ; Caco-2 Cells ; Coculture Techniques ; *Butyrates/metabolism ; THP-1 Cells ; Colon/microbiology/drug effects ; Feces/microbiology ; Cytokines/metabolism ; Adult ; Fatty Acids, Volatile/metabolism ; Edible Seaweeds ; }, abstract = {Fucoidans have demonstrated a wide range of bioactivities including immune modulation and benefits in gut health. To gain a deeper understanding on the effects of fucoidan from Undaria pinnatifida (UPF) on the colonic microbiome, the short-term Simulator of the Human Intestinal Microbial Ecosystem[®], a validated in vitro gut model, was applied. Following a three-week intervention period on adult faecal samples from three healthy donors, microbial community activity of the colonic microbiota was assessed by quantifying short-chain fatty acids while composition was analysed utilising 16S-targeted Illumina sequencing. Metagenomic data were used to describe changes in community structure. To assess the secretion of cytokines, co-culture experiments using Caco-2 and THP1-Blue™ cells were performed. UPF supplementation over a three-week period had a profound butyrogenic effect while also enriching colonic microbial diversity, consistently stimulating saccharolytic genera, and reducing genera linked with potentially negative health effects in both regions of the colon. Mild immune modulatory effects of UPF were also observed. Colonic fermentation of UPF showed anti-inflammatory properties by inducing the secretion of the anti-inflammatory cytokines IL-6 and IL-10 in two out of three donors in the proximal and distal colon. In conclusion, UPF supplementation may provide significant gut health benefits.}, }
@article {pmid40559609, year = {2025}, author = {Mziray, SR and Githinji, G and de Laurent, ZR and Mbelele, PM and Mohammed, KS and Wadugu, BD and Grundy, BS and Heysell, SK and Mpagama, SG and Chilongola, JO}, title = {Deploying Metagenomics to Characterize Microbial Pathogens During Outbreak of Acute Febrile Illness Among Children in Tanzania.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, pmid = {40559609}, issn = {2076-0817}, support = {TMA2016SF-1463-REMODELTZ//European &amp; Developing Countries Clinical Trials Partnership/ ; }, mesh = {Humans ; Tanzania/epidemiology ; Child ; *Metagenomics/methods ; Male ; Female ; *Disease Outbreaks ; *Fever/microbiology/epidemiology ; Cross-Sectional Studies ; *Bacteria/genetics/classification/isolation &amp; purification ; Child, Preschool ; Adolescent ; High-Throughput Nucleotide Sequencing ; Acute Disease ; }, abstract = {Outbreaks of infectious diseases contribute significantly to morbidity and mortality in resource-limited settings, yet the capacity to identify their etiology remains limited. We aimed to characterize microbes and antimicrobial resistance (AMR) genes in Tanzanian children affected by an acute febrile illness (AFI) outbreak using metagenomic next-generation sequencing (mNGS). A cross-sectional study was conducted on archived blood samples from children who presented with AFI between 2018 and 2019. Total nucleic acids were extracted from 200 µL of blood, and complementary DNA (cDNA), along with enriched pathogenic DNA, was sequenced using the Illumina MiSeq platform. mNGS data were analyzed using CZ-ID Illumina mNGS bioinformatics pipeline v7.0. Results were obtained from 25 participants (mean age: 11.6 years; SD ± 5), of whom 36% had a moderate to high-grade fever. The following five potential microbial causes of AFI were identified: Escherichia coli (n = 19), Paraclostridium bifermentans (n = 2), Pegivirus C (n = 2), Shigella flexneri (n = 1) and Pseudomonas fluorescens (n = 1), with E. coli being the most prevalent. Twelve AMR genes were detected, including mdtC, acrF, mdtF, and emrB. E. coli harbored most of the AMR genes previously associated with resistance to commonly used antibiotics. mNGS offers a promising complementary approach to conventional diagnostics for identifying pathogens and AMR profiles in vulnerable populations.}, }
@article {pmid40559526, year = {2025}, author = {Kim, M and Fida, M and Abu Saleh, OM and Ranganath, N}, title = {From Culture-Negative to DNA-Positive: The Molecular Revolution in Infective Endocarditis Diagnosis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, pmid = {40559526}, issn = {2076-0817}, mesh = {Humans ; *Endocarditis/diagnosis/microbiology ; *Molecular Diagnostic Techniques/methods ; DNA, Bacterial/genetics ; Metagenomics/methods ; }, abstract = {Infective endocarditis (IE) remains a diagnostic challenge, particularly in cases where microbiological diagnosis is not established. Advances in molecular diagnostics have expanded the ability to identify causative pathogens beyond traditional culture-based methods. This review explores the role of molecular assays, including pathogen-specific PCR, multiplex PCR, broad-range PCR, and shotgun metagenomic sequencing, in diagnosing IE. These molecular techniques enhance pathogen detection, especially in patients with prior antibiotic exposure, and improve diagnostic accuracy in culture-negative IE. Broad-range PCR assays and metagenomic sequencing offer the untargeted detection of a wide spectrum of organisms. Despite their advantages, limitations such as availability, interpretation challenges, and a lack of antimicrobial susceptibility testing remain. A multimodal approach integrating molecular diagnostics with conventional methods is essential to optimize patient management. Further research is needed to refine diagnostic algorithms and improve cost-effectiveness in clinical practice.}, }
@article {pmid40559436, year = {2025}, author = {Domilescu, I and Miutescu, B and Horhat, FG and Popescu, A and Nica, C and Ghiuchici, AM and Gadour, E and Sîrbu, I and Hutanu, D}, title = {Gut-Microbiome Signatures Predicting Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer: A Systematic Review.}, journal = {Metabolites}, volume = {15}, number = {6}, pages = {}, pmid = {40559436}, issn = {2218-1989}, abstract = {BACKGROUND AND OBJECTIVES: Rectal cancer management increasingly relies on watch-and-wait strategies after neoadjuvant chemoradiotherapy (nCRT). Accurate, non-invasive prediction of pathological complete response (pCR) remains elusive. Emerging evidence suggests that gut-microbiome composition modulates radio-chemosensitivity. We systematically reviewed primary studies that correlated baseline or on-treatment gut-microbiome features with nCRT response in locally advanced rectal cancer (LARC).<br><br>METHODS: MEDLINE, Embase and PubMed were searched from inception to 30 April 2025. Eligibility required (i) prospective or retrospective human studies of LARC, (ii) faecal or mucosal microbiome profiling by 16S, metagenomics, or metatranscriptomics, and (iii) response assessment using tumour-regression grade or pCR. Narrative synthesis and random-effects proportion meta-analysis were performed where data were homogeneous.<br><br>RESULTS: Twelve studies (n = 1354 unique patients, median sample = 73, range 22-735) met inclusion. Four independent machine-learning models achieved an Area Under the Receiver Operating Characteristic curve AUROC &#x2265; 0.85 for pCR prediction. Consistently enriched taxa in responders included Lachnospiraceae bacterium, Blautia wexlerae, Roseburia spp., and Intestinimonas butyriciproducens. Non-responders showed over-representation of Fusobacterium nucleatum, Bacteroides fragilis, and Prevotella spp. Two studies linked butyrate-producing modules to radiosensitivity, whereas nucleotide-biosynthesis pathways conferred resistance. Pooled pCR rate in patients with a "butyrate-rich" baseline profile was 44% (95% CI 35-54) versus 21% (95% CI 15-29) in controls (I[2] = 18%).<br><br>CONCLUSIONS: Despite heterogeneity, convergent functional and taxonomic signals underpin a microbiome-based radiosensitivity axis in LARC. Multi-centre validation cohorts and intervention trials manipulating these taxa, such as prebiotics or live-biotherapeutics, are warranted before clinical deployment.}, }
@article {pmid40559193, year = {2025}, author = {Anselmo, A and Rizzo, F and Gervasi, E and Corrent, L and Ciammaruconi, A and Fillo, S and Fortunato, A and Marella, AM and Costantini, S and Baldassari, L and Lista, F and Ciervo, A}, title = {Tropheryma whipplei and Giardia intestinalis Co-Infection: Metagenomic Analysis During Infection and the Recovery Follow-Up.}, journal = {Infectious disease reports}, volume = {17}, number = {3}, pages = {}, pmid = {40559193}, issn = {2036-7430}, support = {B1519 ESM4 GP//Italian General Secretariat of Defense and the National Armaments Directorate within the "Eu-ropean Biodefence Laboratory Network 2 (EBLN2) project",/ ; }, abstract = {BACKGROUND: Whipple's disease (WD) is a rare infection caused by Tropheryma whipplei. Diagnosis is challenging and requires a combination of several data sets, such as patient history, clinical and laboratory investigations, and endoscopy with histology analyses. While persistent diarrhea is a common symptom, WD can affect multiple organs.<br><br>CASE DESCRIPTION: We present the case of a 66-year-old immunocompetent patient with WD and a history of Helicobacter pylori infection who developed chronic diarrhea. Colonoscopy and histopathological analysis revealed the presence of foamy macrophages with periodic acid-Schiff-positive particles. Subsequently, molecular methods confirmed the clinical WD diagnosis and metagenomic analyses further identified a co-infection with Giardia intestinalis. The patient fully recovered after 14 months of antibiotic therapy. During pharmacological treatment, clinical and laboratory follow-ups were conducted at 6 and 12 months, and microbiome profiles were also analyzed to identify the most abundant species in the samples.<br><br>CONCLUSION: The metagenomic analyses showed the eradication of the two pathogens and a progressive restoration to a healthy/balanced status after antibiotic therapy.}, }
@article {pmid40559130, year = {2025}, author = {Chaple-Gil, AM and Santiesteban-Velázquez, M and Urbizo Vélez, JJ}, title = {Association Between Oral Microbiota Dysbiosis and the Risk of Dementia: A Systematic Review.}, journal = {Dentistry journal}, volume = {13}, number = {6}, pages = {}, pmid = {40559130}, issn = {2304-6767}, abstract = {Background/Objectives: Growing evidence suggests that oral microbiota dysbiosis may contribute to the development of systemic conditions, including neurodegenerative diseases. This dysregulation promotes immunoinflammatory responses that are increasingly associated with dementia. This systematic review aimed to evaluate the association between oral microbiota dysbiosis and the risk of dementia in older adults. Methods: Eligible studies evaluated oral microbial composition using validated methods such as genetic sequencing, bacterial culture, or metagenomic analysis. Following PRISMA guidelines and a PICO framework, the review included cohort, case-control, and cross-sectional studies. Searches were conducted across PubMed, Scopus, Web of Science, Embase, and Cochrane Library. Two independent reviewers screened and selected studies, resolving disagreements through a third evaluator. Results: This systematic review revealed that Tannerella forsythia, Fusobacterium nucleatum, Porphyromonas, Prevotella, Leptotrichia, Fusobacteriota, Peptostreptococcaceae, and Candida spp. were consistently associated with Alzheimer's disease and mild cognitive impairment, indicating their potential role in neurodegeneration. In contrast, Streptococcus gordonii, Gemella haemolysans, Rothia, Neisseria, and Haemophilus were reduced in cognitively impaired individuals, suggesting a link with healthy cognition. Studies also showed decreased microbial diversity in Alzheimer's disease and the possible modifying effect of the APOE4 allele. Oral health interventions improved microbial composition and slowed cognitive decline, supporting the diagnostic and therapeutic potential of oral microbiota modulation. Conclusions: The findings suggest that oral microbiota dysbiosis may not only result from cognitive decline but also contribute to its pathogenesis. Future studies with larger and more diverse cohorts are recommended to validate these associations.}, }
@article {pmid40558984, year = {2025}, author = {Crane, YM and Crane, CF and Subramanyam, S and Schemerhorn, BJ}, title = {Shotgun Metagenome Analysis of Two Schizaphis graminum Biotypes over Time With and Without Carried Cereal Yellow Dwarf Virus.}, journal = {Insects}, volume = {16}, number = {6}, pages = {}, pmid = {40558984}, issn = {2075-4450}, support = {5020-21000-000-D//USDA-ARS Research Project/ ; }, abstract = {The greenbug aphid (Schizaphis graminum (Rondani)) is a major pest of wheat and an important vector of wheat viruses. An RNA-seq study was conducted to investigate the microbial effects of two greenbug genotypes, the presence or absence of cereal yellow dwarf virus, and the condition of the wheat host over a 20-day time course of unrestricted greenbug feeding. Messenger RNA reads were mapped to ca. 47,000 bacterial, 1218 archaeal, 14,165 viral, 571 fungal, and 94 protozoan reference or representative genomes, plus greenbug itself and its wheat host. Taxon counts were analyzed with QIIME2 and DESeq2. Distinct early (days 1 through 10) and late (days 15 and 20) communities differed in the abundance of typical enteric genera (Shigella, Escherichia, Citrobacter), which declined in the late community, while the ratio of microbial to greenbug read counts declined 50% and diversity measures increased. The nearly universal aphid endosymbiont, Buchnera aphidicola, accounted for less than 25% of the read counts in both communities. There were 302 differentially expressed (populated) genera with respect to early and late dates, while 25 genera differed between the greenbug genotypes and nine differed between carrier and virus-free greenbugs. The late community was likely responding to starvation as the wheat host succumbed to aphid feeding. Our results add to basic knowledge about aphid microbiomes and offer an attractive alternative method to assess insect microbiomes.}, }
@article {pmid40558870, year = {2025}, author = {Abreu, CM and Carneiro, GHF and Costa, MRD and Barroso, GM and Duque, TS and Silva, JMS and Santos, JBD}, title = {Avena sativa as a Multifunctional Tool for Phytoremediation and Bioenergy Production in Sulfentrazone Contaminated Soils.}, journal = {Journal of xenobiotics}, volume = {15}, number = {3}, pages = {}, pmid = {40558870}, issn = {2039-4713}, support = {APQ 01151-23; APQ 00694-23 and, APQ 004955-23//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 001//National Council for Scientific and Technological Development/ ; }, abstract = {Phytoremediation using Avena sativa offers a sustainable strategy for mitigating sulfentrazone contamination while integrating bioenergy production. This study proposes an analysis of the bioenergy potential and the microbial metagenomic profile associated with Avena sativa in the presence and absence of sulfentrazone, aiming at the synergistic bioprospecting of microbial communities capable of biodegradation and remediation of contaminated environments. Using a randomized block design, we evaluated the bioenergy potential and rhizospheric microbial dynamics of A. sativa in soils with and without sulfentrazone (600 g ha[-1]). Herbicide residues were quantified via UHPLC-MS/MS, and metagenomic profiles were obtained through 16S rRNA gene and ITS region sequencing to assess shifts in rhizospheric microbiota. Microbial diversity was analyzed using the Shannon and Gini-Simpson Indices, complemented by Principal Component Analysis (PCA). Bioenergy yields (biogas and ethanol) were estimated based on plant biomass. Over 80 days, the cultivation of A. sativa promoted a 19.7% dissipation of sulfentrazone, associated with rhizospheric enrichment of plant growth-promoting taxa (Bradyrhizobium, Rhodococcus, and Trichoderma), which increased by 68% compared to uncontaminated soils. Contaminated soils exhibited reduced microbial diversity (Gini-Simpson Index = 0.7), with a predominance of Actinobacteria and Ascomycota, suggesting adaptive specialization. Despite herbicide-induced stress (39.3% reduction in plant height and 60% reduction in grain yield), the biomass demonstrated considerable bioenergy potential: 340.6 m[3] ha[-1] of biogas and 284.4 L ha[-1] of ethanol. The findings highlight the dual role of A. sativa in soil rehabilitation and renewable energy systems, supported by plant-microbe synergies. Scalability challenges and regulatory gaps in ecotoxicological assessments were identified, reinforcing the need to optimize microbial consortia and implement region-specific management strategies. These results support the integration of phytoremediation into circular bioeconomy models, balancing ecological recovery with agricultural productivity. Future research should focus on microbial genetic pathways, field-scale validation, and the development of regulatory frameworks to advance this green technology in global soil remediation efforts.}, }
@article {pmid40558084, year = {2025}, author = {Brumfield, KD and Enke, S and Swan, BK and Carrasquilla, L and Lee, MD and Stern, DB and Gieser, L and Hasan, NA and Usmani, M and Jutla, AS and Huq, A and Caviness, K and Goodrich, JS and Bull, R and Colwell, RR}, title = {Hybridization capture sequencing for Vibrio spp. and associated virulence factors.}, journal = {mBio}, volume = {}, number = {}, pages = {e0051625}, doi = {10.1128/mbio.00516-25}, pmid = {40558084}, issn = {2150-7511}, abstract = {Proliferation of Vibrio spp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundance Vibrio spp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69 Vibrio spp. and 162 Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition, Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenic Vibrio spp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specific Vibrio spp., yielded significantly greater metagenomic insight, notably a variety of other Vibrio spp., including detection of Vibrio cholerae, Vibrio fluvialis, and Vibrio aestuarianus, in addition to Vibrio parahaemolyticus and Vibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios.IMPORTANCEThe increasing prevalence of pathogenic Vibrio spp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundance Vibrio spp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing of Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples. Results suggest pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.}, }
@article {pmid40558050, year = {2025}, author = {Phan, J and Jain, S and Nijkamp, JF and Sasidharan, R and Agarwal, A and Bird, JK and Spooren, A and Wittwer Schegg, J and Ver Loren van Themaat, E and Mak, TN}, title = {Gut health predictive indices linking gut microbiota dysbiosis with healthy state, mild gut discomfort, and inflammatory bowel disease phenotypes using gut microbiome profiling.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0027125}, doi = {10.1128/spectrum.00271-25}, pmid = {40558050}, issn = {2165-0497}, abstract = {Despite the complexity of the gut microbiome, several scores that use taxonomic characteristics exist that attempt to identify a healthy gut or gastrointestinal disease. Two systems in use are the metagenomic aerotolerant predominance index (MAPI) and keystone scores. The aim of this analysis was to compare different gut microbiome scores, specifically MAPI and a keystone species score, on two cross-sectional data sets and to investigate correlations of these scores with self-reported gut discomfort and gastrointestinal disease. The first data set is a commercial data set (Sun Genomics data set) with whole-genome shotgun sequencing samples from 5,372 customers. The second data set is curated from publicly available data (public data set) with 2,415 samples from participants in human studies with gut-related taxonomic profiles. MAPI scores and keystone species scores were calculated using standard methodology. The MAPI score was significantly lower in men for the public data set. There was a graded response for both the MAPI and keystone scores between healthy subjects, subjects with mild gastrointestinal discomfort, and patients with gastrointestinal disease: the MAPI score was higher, and the keystone score was lower in subjects with gastrointestinal discomfort or with inflammatory bowel disease patients. The keystone and MAPI scores have the potential to help identify factors associated with gut microbial dysbiosis and gastrointestinal discomfort or disease. Furthermore, given the functional link of the MAPI score to oxidative stress in the microbiome, the scores can help to identify conditions where oxidative stress is one of the hallmarks of dysbiosis.IMPORTANCEGut bacteria play a role in both mild gastrointestinal discomfort, which includes bloating and constipation, and inflammatory bowel disease. There are many different types of bacteria in the gut, and gut microbiome composition differs greatly between different people. Therefore, it is difficult to predict who has a gut microbiome associated with a healthy gut and who might develop disease or experience gut discomfort. Several scoring systems have been developed to categorize gut health states. This analysis compared two different scoring systems using data from two different sources to see how well they could identify people with gastrointestinal disease, gastrointestinal complaints, or a healthy gut. The scoring systems showed similar trends according to gut health status: groups of people with gut bacteria imbalance or gut disease had a different score than groups of people with healthy gut bacteria.}, }
@article {pmid40557789, year = {2025}, author = {Jones, KS and Pilliod, DS and Aunins, AW}, title = {Metabarcoding Analysis of Arthropod Pollinator Diversity: A Methodological Comparison of eDNA Derived From Flowers and DNA Derived From Bulk Samples of Insects.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70003}, doi = {10.1111/mec.70003}, pmid = {40557789}, issn = {1365-294X}, support = {//U.S. Bureau of Land Management/ ; //U.S. Geological Survey/ ; }, abstract = {Limitations of traditional insect sampling methods have motivated the development and optimisation of new non-lethal methods capable of quantifying diverse arthropod communities. Environmental DNA (eDNA) metabarcoding using arthropod-specific primers has recently been investigated as a novel way to characterise arthropod communities from the DNA they deposit on the surface of plants. This sampling method has had demonstrated success, but pollinators-especially bees-are oddly underrepresented in these studies. To evaluate this inconsistency, we investigated the limitations of eDNA metabarcoding for bees and other pollinators. We compared pollinator diversity derived from eDNA extracted from flowers and DNA extracted from pulverised bulk samples of insects collected from vane traps deployed at the same sites using three metabarcoding primers, two of which target arthropods generally (COI-Jusino and 16S-Marquina) and one that targets bumblebees (Bombus spp., COI-Milam). Across methods, we detected 77 insect families from 9 orders. The COI-Jusino marker amplified the highest taxonomic diversity compared to 16S-Marquina and COI-Milam. More amplicon sequence variants (ASVs) were recovered from vane traps (blue: 1357, yellow: 1542) than flowers (245), but only 23% of families and 13% of genera were shared among methods, indicating that flowers and blue and yellow vane traps may each sample different parts of the available arthropod community. Of 29 flower samples with known bee visitations, only 10 samples had bee detections from eDNA, and incomplete reference databases hindered assignment to species. Although our study provides additional evidence for the usefulness of eDNA metabarcoding for characterising arthropod communities, significant challenges remain when using eDNA metabarcoding methods to identify and quantify pollinator communities, especially bees.}, }
@article {pmid40557508, year = {2025}, author = {Schroeder, TH and Vanwynsberghe, M and Dervishi, A and Stäudle, H}, title = {Detection of pathogenic microorganisms using metagenomic next generation sequencing for patients with suspected infection presenting in the emergency department.}, journal = {European journal of emergency medicine : official journal of the European Society for Emergency Medicine}, volume = {32}, number = {4}, pages = {288-290}, doi = {10.1097/MEJ.0000000000001239}, pmid = {40557508}, issn = {1473-5695}, }
@article {pmid40557420, year = {2025}, author = {Girard, M and Vandamme, L and Cazaux, B and Limasset, A}, title = {OReO: optimizing read order for practical compression.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf128}, pmid = {40557420}, issn = {2635-0041}, abstract = {MOTIVATION: Recent advances in high-throughput and third-generation sequencing technologies have created significant challenges in storing and managing the rapidly growing volume of read datasets. Although more than 50 specialized compression tools have been developed, employing methods such as reference-based approaches, customized generic compressors, and read reordering, many users still rely on common generic compressors (e.g. gzip, zstd, xz) for convenience, portability, and reliability, despite their low compression ratios. Here, we introduce Optimizing Read Order (OReO), a simple read-reordering framework that achieves high compression performance without requiring specialized software for decompression. By grouping overlapping reads together before applying generic compressors, OReO exploits inherent redundancies in sequencing data and achieves compression ratios on par with state-of-the-art tools. Moreover, because it relies only on standard decompressors, OReO avoids the need for dedicated installations and maintenance, removing a key barrier to practical adoption.<br><br>RESULTS: We evaluated OReO on both Oxford Nanopore Technologies (ONT) and HiFi genomic and metagenomic datasets of varying sizes and complexities. Our results demonstrate that OReO provides substantial compression gains with comparable resource usage and outperforms dedicated methods in decompression speed. We propose that future compression strategies should focus on reordering as a means to let generic compression tools fully exploit data redundancy, offering an efficient, sustainable, and user-friendly solution to the growing challenges of sequencing data storage.<br><br>The OReO code is open source and available at github.com/girunivlille/oreo.}, }
@article {pmid40557317, year = {2025}, author = {Ding, Y and Jing, C and Wei, J and Wang, D and Li, W and Wang, M and Zhou, J and Qian, Q and Sun, W}, title = {Comparison of the diagnostic capabilities of tNGS and mNGS for pathogens causing lower respiratory tract infections: a prospective observational study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1578939}, pmid = {40557317}, issn = {2235-2988}, mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; Male ; Prospective Studies ; Female ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Sensitivity and Specificity ; Aged ; Adult ; China ; *High-Throughput Nucleotide Sequencing/methods ; Bacteria/isolation &amp; purification/genetics/classification ; Fungi/isolation &amp; purification/genetics ; *Molecular Diagnostic Techniques/methods ; }, abstract = {AIMS: Pathogens in lower respiratory tract infections(LRTI) are complex. Conventional microbiological testings(CMTs) are time-consuming and inaccurate. mNGS is widely used to overcome these issues. tNGS, as an emerging NGS technology, has uncertain diagnostic efficacy.<br><br>MATERIALS AND METHODS: 136 suspected LRTI patients were included from January 2022 to February 2024 from the Department of Respiratory and Critical Care Medicine at Jiangsu Province People's Hospital,China.We simultaneously submitted the bronchoalveolar lavage fluids (BALFs) for mNGS, tNGS and conventional microbial testing (CMTs) and compared the pathogen diagnostic efficacy of mNGS, and tNGS.<br><br>RESULTS: A total of 136 patients were included, and there was no statistically significant difference in the detection sensitivity(74.75% VS 78.64%, p>0,05) and specificity(81.82% vs 93,94%,p>0.05) between mNGS and tNGS. However, tNGS has a higher sensitivity(27.94% vs 17.65%,p=0.043)and specificity(88.78% vs 84.82%,p=0.048) for fungi. According to our diagnostic criteria, tNGS successfully identified 3 cases of Pneumocystis jirovecii(P. jirovecii) individually. In addition, both tNGS and mNGS detected chlamydia psittaci whereas CMTs were unable to detect it.<br><br>CONCLUSIONS: tNGS demonstrates diagnostic efficacy for pathogens in lower respiratory tract infections that is comparable to mNGS. However, tNGS has specific advantages in the detection of fungi. Considering the cost-effectiveness of tNGS, it is recommended to implement tNGS clinically for patients with lower respiratory tract infections.}, }
@article {pmid40557154, year = {2025}, author = {Bai, X and Raju, SC and Knudsen, AD and Thudium, RF and Arentoft, NS and Gelpi, M and Heidari, SL and Kunisaki, KM and Kristiansen, K and Hov, JR and Nielsen, SD and Trøseid, M}, title = {Microbiome profiling reveals gut bacterial species associated with rapid lung function decline in people with HIV.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1555441}, pmid = {40557154}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *HIV Infections/microbiology/complications/physiopathology ; Middle Aged ; Dysbiosis ; *Lung/physiopathology ; *Bacteria/genetics/classification ; Adult ; *Lung Diseases/microbiology ; Respiratory Function Tests ; Aged ; }, abstract = {BACKGROUND: People with HIV (PWH) have an increased risk of pulmonary comorbidities compared to people without HIV. The gut microbiome regulates host immunity and is altered in PWH. This study aims to determine potential associations between gut microbiome, lung function decline, and airflow limitation in PWH.<br><br>METHODS: PWH from the Copenhagen Comorbidity in HIV Infection (COCOMO) Study with available lung function testing and microbiome data were included (n=385). The gut microbiome was characterized using shotgun metagenomic sequencing. Associations between gut microbiome, rapid lung function decline, and airflow limitation were analysed in multivariable logistic regressions adjusted for traditional and HIV-associated risk factors for lung disease.<br><br>RESULTS: Several bacterial species were significantly enriched in PWH with rapid lung function decline, including opportunistic pathogenic bacterial species Bacteroides coprophilus, Klebsiella michiganensis, and Clostridium perfringens. A gut microbial dysbiosis index based on compositional changes was associated with rapid lung function decline (adjusted odds ratio (aOR) 1.18, 95% confidence interval (CI) [1.11-1.27], p<0.001), and airflow limitation (aOR 1.16, 95% CI [1.04-1.29], p=0.007) in adjusted multivariable logistic regression analyses.<br><br>CONCLUSION: Associations between the gut dysbiosis index and rapid lung function decline and airflow limitation suggest a potential role of certain gut bacterial species in the pathogenesis of pulmonary comorbidities in PWH.}, }
@article {pmid40556944, year = {2025}, author = {Chen, Y and Fan, B and Zeng, J and Zou, Y and Tao, C and Chen, C and Zhang, P and Liang, J and Qi, F and Tang, H and Lu, L}, title = {Single-Cell RNA Transcriptomics and Multi-omics Analyses Reveal the Clinical Effects of Acupuncture on Methadone Reduction.}, journal = {Research (Washington, D.C.)}, volume = {8}, number = {}, pages = {0741}, pmid = {40556944}, issn = {2639-5274}, abstract = {Opioid use disorders (OUDs) pose a substantial global health burden, with methadone maintenance treatment (MMT) widely adopted as an intervention; however, MMT is associated with immunosuppression, metabolic disturbances, and dysbiosis of the gut microbiota. Despite the potential of acupuncture in reducing methadone dosages and opioid addiction, the underlying biological mechanisms remain unclear. Therefore, we aimed to integrate clinical trial data with multi-omics analysis, including single-cell sequencing, transcriptomics, metabolomics, and metagenomics, to evaluate the effects of acupuncture in patients undergoing MMT. We collected peripheral blood mononuclear cells, plasma, and fecal samples from 48 MMT participants in a randomized, placebo-controlled trial. Participants were divided into acupuncture (n = 25) and sham-acupuncture (n = 23) groups. After 8 weeks of intervention, 84% of patients in the acupuncture group achieved ≥20% reduction in methadone dosage, compared to 39% in the sham-acupuncture group (P < 0.01). Our findings revealed that acupuncture may activate the defense response to viruses, with altered immune cell functions in classical monocytes correlating with clinical responses to reduced methadone doses. Acupuncture might ameliorate intestinal microbial disruptions caused by OUD by up-regulating Bilophila and modulating bile acid metabolism. Furthermore, acupuncture up-regulated galectin-9 (LGALS9)-mediated intercellular communication between classical monocytes and other immune subsets. To further validate the mechanistic link between bile acid metabolism and immune regulation, we conducted in vitro experiments using THP-1 monocytes treated with cholic acid. The results showed that bile acid exposure suppressed galectin-9 and IFN-γ expression, while low-dose bile acid (simulating acupuncture effects) partially reversed this effect. These findings support a bile acid-galectin-interferon axis that may be modulated by acupuncture in OUD. Collectively, our results provide clinical and mechanistic evidence supporting acupuncture as a potential adjunct therapy to mitigate the adverse effects of long-term opioid use.}, }
@article {pmid40556900, year = {2025}, author = {Zhang, Q and Wang, X and Cheng, P and Huo, S and Liu, C and Yu, Z}, title = {Editorial: Recent advances in agricultural waste recycling by microorganisms and their symbiosis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1631828}, doi = {10.3389/fmicb.2025.1631828}, pmid = {40556900}, issn = {1664-302X}, }
@article {pmid40556899, year = {2025}, author = {Ning, T and Zheng, X and Liang, J and Wang, W and Zhang, G and Wei, X and Tan, L}, title = {Effect of different bulking agents on the quality, microbial community structure and metabolic functions during human feces composting in foam composting device.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1556537}, pmid = {40556899}, issn = {1664-302X}, abstract = {Aerobic composting represents an efficacious strategy for the disposal of human feces, yet investigations into the effects of different bulking agents on this process remain limited. This study investigated the effects of composting human feces with four types of bulking agents-wheat straw, corn straw, millet straw, and sawdust-in a foam composting device, as well as the impacts of the process on the microbial community structure and metabolic functions adopting sequencing data analysis and metagenomic analysis. The results demonstrate that aerobic composting can safely treat human feces, resulting in a mature compost product. Comparative assessments of compost quality and microbial profiles with various bulking agents indicated superior performance of corn straw compost, surpassing those produced with wheat straw, millet straw, and sawdust in terms of humification level (HA/FA = 2.9), peak temperature reached (71.2°C), composting duration (20 days), and nutrient composition (TN 42.87 g/kg). Additionally, the diversity and dominance of certain microbial colonies (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidota) were significantly higher in composts formulated with corn straw. The metagenomic data analysis reveals significant differences in the abundance of "carbon metabolism" and "microbial metabolism" among different groups, further indicating that the addition of different bulking agents affects the utilization of metabolic products, amino acids, and carbohydrates as carbon sources by microbes in human feces compost. Consequently, leveraging corn straw as a bulking agent, given its abundant availability, could potentially improve the efficiency and outcome of the human feces composting process.}, }
@article {pmid40556897, year = {2025}, author = {Lu, L and Huang, X and Zheng, P and Wei, S and Jiao, N and Zhang, R and Li, X and Yang, Y}, title = {Two novel phages infecting Erythrobacter isolated from the epipelagic ocean.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1592355}, pmid = {40556897}, issn = {1664-302X}, abstract = {Erythrobacter, an aerobic anoxygenic photoheterotrophic bacterial genus, plays a vital role in carbon and energy cycling in marine environments. However, their phage predators remain poorly understood, with only two strains previously reported. This study isolated and characterized a novel Erythrobacter phage, vB_EauS-R34L1 (R34L1), and its sub-strain vB_EauS-R34L2 (R34L2), from coastal seawater. Both phages exhibit long-tailed, icosahedral morphologies and relatively narrow but slightly different host ranges. One-step growth curve analysis revealed a 160-min latent period and burst sizes of 81 and 91 PFU/cell for R34L1 and R34L2, respectively. Genomic analysis showed that the phages possess dsDNA genomes of 56,415 bp (R34L1) and 54,924 bp (R34L2), with G + C contents of 61.60 and 61.19%, respectively. Both phages harbor a suite of unique genes, including GapR and GH19, which are crucial for host interaction and ecological functionality. Blastn analysis indicated a 99.73% genome similarity between them. Taxonomic and phylogenetic analyses positioned them in a novel viral genus cluster, Eausmariqdvirus, under the family Casjensviridae, indicating a distant evolutionary relationship with known phages. Metagenomic queries suggested that R34L1- and R34L2-like phages are exclusively abundant in temperate and tropical epipelagic zones. This study expands our understanding of Erythrobacter phages and provides insights into their ecological roles in marine ecosystems.}, }
@article {pmid40556523, year = {2025}, author = {Huang, J and Liang, W and Zhang, R and Zhao, Y and Shi, R and Chen, X and Zheng, Y and Li, X and Liu, D and Wang, H and Liu, J and Liao, Y and Zhang, X and Jiang, Z and Fu, C and Huang, T and Shan, X and Wang, W and Bu, J and Peng, T and Shen, E}, title = {Pou2af1 Deficiency Aggravates DSS-Induced Colitis via Impaired Germinal Center Responses and Altered Gut Microbiota.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izaf089}, pmid = {40556523}, issn = {1536-4844}, support = {//The Affiliated Qingyuan Hospital/ ; 202301-316//Guangzhou Medical University/ ; JCXKJS2021C11//Discipline from School of Basic Medicine of Guangzhou Medical University/ ; 2021KTSCX090//Department of Education of Guangdong Province/ ; //Guangzhou Medical University 2022 Student Innovation Ability Improvement Program/ ; }, abstract = {BACKGROUND: Bob1 plays a critical role in immune system regulation, particularly in the function of B cells. Its deficiency in the context of colitis remains underexplored. This study investigates the effects of Bob1 (Pou2af1) deficiency on colitis, particularly focusing on immune responses and gut microbiota alterations in a murine model.<br><br>METHODS: In this study, we employed Pou2af1 knockout (KO) and wild-type (WT) mice to investigate the role of Bob1 in dextran sodium sulfate (DSS)-induced colitis. Colitis was induced by administering 2.5% DSS in drinking water for 7 days. Mice were monitored daily for weight loss, stool consistency, and rectal bleeding to calculate the disease activity index (DAI). Colon length was measured, and colon tissues were collected for histological analysis using hematoxylin and eosin (H&amp;E) staining. Flow cytometry was performed to assess germinal center responses as well as the proportion of T helper (Th)1 and Th17 cells in the colonic lamina propria. Metagenomic sequencing was conducted on fecal samples to evaluate gut microbiota composition.<br><br>RESULTS: Pou2af1-deficient mice exhibited significantly exacerbated colitis compared to WT mice. This was evidenced by greater weight loss, elevated disease activity index, reduced colon length, and more severe pathological changes. Immune analysis revealed an impaired germinal center response, diminished generation of IgA&#x207a; plasma cells, and decreased Th17 cells in the colonic lamina propria in Pou2af1-deficient mice. Additionally, microbiota analysis indicated dysbiosis in the Pou2af1-deficient group, with a notable decrease in Bacteroides species and an increase in pro-inflammatory microbes.<br><br>DISCUSSION: The findings suggest that Pou2af1 deficiency exacerbates DSS-induced colitis by impairing immune responses, particularly the germinal center reaction, and altering gut microbiota composition. These alterations contribute to increased disease severity, highlighting the importance of Pou2af1 in maintaining intestinal immune homeostasis.}, }
@article {pmid40556381, year = {2025}, author = {Zhao, S and Xu, Q and Li, M and Chen, J and Francis, F and Dai, X and Tan, J and Kong, Z}, title = {Exploring the Impact of Dinotefuran Residue on Microbial Community and Flavor Generation in Huangjiu Fermentation.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c02308}, pmid = {40556381}, issn = {1520-5118}, abstract = {Pesticide residues create food safety hazards while negatively affecting the quality of fermented foods, but the mechanisms of the deterioration response have been a mystery. In this study, headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) and metagenomics sequencing analyses were employed to investigate the effect of dinotefuran residue on the aroma profile and microbial community of Huangjiu. The presence of dinotefuran led to a reduction in the overall concentration of volatile compounds, and some floral, fruity, and sweet aromas such as piperitenol, citronellyl isobutyrate, and trans-2-decenal were no longer detected. Meanwhile, the levels of certain acidic volatiles, including formic acid, propionic acid, and heptanoic acid, increased and contributed to off-flavors. Dinotefuran affected the Huangjiu flavor by modifying the abundance and structure of key genera such as Saccharomyces, Lactococcus, and Cyberlindnera. These changes were associated with disturbances in 16 KEGG tertiary metabolic pathways, including glycolysis, pyruvate metabolism, and amino acid biosynthesis. These results provided some reference for further studies on how pesticide residues affect the flavor and microbial characteristics of traditional fermented beverages like Huangjiu.}, }
@article {pmid40555957, year = {2025}, author = {Gonçalves, OS and Fernandes, AS and de Sousa, TGG and Santana, MF and Barreto, CC}, title = {From cultivation challenges of Acidobacteriota to biotechnological promises - unveiling what is needed to fully harness their potential.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {7}, pages = {208}, pmid = {40555957}, issn = {1573-0972}, support = {00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 5.10/2022//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 402644/2021-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-02381-21//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*Biotechnology/methods ; Biodegradation, Environmental ; Genome, Bacterial ; Industrial Microbiology ; Genomics ; }, abstract = {Acidobacteriota are currently well-known for their ubiquity and metabolic versatility. Their environmental importance is the subject of many studies, but their biotechnological applications still need to be explored. Although they are considered hard-to-culture bacteria, many genomes are available, which reveals promising biotechnological potential. Despite these promising features, the application of Acidobacteriota in biotechnology remains underexplored. In this context, we review key findings regarding the potential applications of Acidobacteriota, emphasizing advancements derived from genomic, metagenomic, and culture-based studies. We specifically focus on their ability to produce enzymes and other bioactive molecules, their antimicrobial properties, and their potential applications in agriculture and bioremediation. Furthermore, we discuss strategies to overcome the challenges associated with culturing and manipulating these bacteria, such as heterologous expression and other emerging techniques related to -omics and computational approaches. These strategies could provide deeper insights into Acidobacteriota's metabolism, including their biosynthetic pathways and interactions within microbial consortia. Ultimately, this understanding could lead to broader applications of Acidobacteriota in environmental and industrial biotechnology.}, }
@article {pmid40555791, year = {2025}, author = {Lin, S and Sun, Z and Zhu, X and Wang, M and Zhang, Q and Qian, J and Zhang, H and Mei, Z and Pu, Y and Kong, M and Guo, P and Zhou, X and Li, J and Sun, X and Ma, L and Zhang, X and Zhao, F and Nie, J and Hong, S and Chen, J and Wang, X and Li, X and Zheng, Y}, title = {Segatella copri and gut microbial ammonia metabolism contribute to chronic kidney disease pathogenesis.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40555791}, issn = {2058-5276}, abstract = {Alterations in gut microbiota have been linked to chronic kidney disease (CKD), but large-scale studies and mechanistic insights are limited. Here we analysed gut metagenome data from 1,550 older individuals (aged 65-93 years) with comprehensive kidney function measurements. Segatella copri was positively associated with kidney function through microbial ammonia metabolism-related pathways and the asnA gene, which encodes an ammonia-assimilating enzyme. These associations were replicated in two external studies. In mice, ammonia supplementation increased serum levels of creatinine and blood urea nitrogen, accelerating CKD progression. In vitro cultures of S. copri or asnA-overexpressing Escherichia coli reduced ammonia concentrations, which was markedly attenuated in asnA-knockout S. copri. Gavage of either S. copri or asnA-overexpressing E. coli, but not asnA-knockout S. copri, mitigated ammonia-induced CKD progression in mice. These findings highlight the role of gut microbial ammonia metabolism in CKD pathogenesis and underscore the therapeutic potential of microbial-based interventions.}, }
@article {pmid40555747, year = {2025}, author = {Jarman, JB and Torres, PJ and Stromberg, S and Sato, H and Stack, C and Ladrillono, A and Pace, S and Jimenez, NL and Haselbeck, RJ and Insel, R and Van Dien, S and Culler, SJ}, title = {Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {867}, pmid = {40555747}, issn = {2399-3642}, mesh = {Humans ; *Bifidobacterium/isolation &amp; purification/genetics ; *Gastrointestinal Microbiome ; *Dysbiosis/epidemiology/microbiology ; Infant ; United States/epidemiology ; Female ; Male ; Infant, Newborn ; Metagenomics ; }, abstract = {The composition of the infant gut microbiome is critical to immune development and noncommunicable disease (NCD) trajectory. However, a comprehensive evaluation of the infant gut microbiome in the United States is lacking. The My Baby Biome study, designed to address this knowledge gap, evaluated the gut microbiomes of 412 infants (representative of U.S. demographic diversity) using metagenomics and metabolomics. Regardless of birth mode and/or feeding method, widespread Bifidobacterium deficit was observed, with approximately 25% of U.S. infants lacking detectable Bifidobacterium. Bifidobacterium-dominant microbiomes exhibit distinct features when compared to microbiomes with other dominant microbial compositions including reduced antimicrobial resistance and virulence factor genes, altered carbohydrate utilization pathways, and altered metabolic signatures. In C-section birth infants, Bifidobacterium tended to be replaced in the human milk oligosaccharide utilization niche with potentially pathogenic species. Longitudinal health outcomes from these infants suggest that the disappearance of key Bifidobacterium may contribute to the development of atopy.}, }
@article {pmid40555322, year = {2025}, author = {Ying, S and Zhang, Z and Xiang, R}, title = {Metagenomic and Whole-Genome Characterization of Carbapenem-Resistant Acinetobacter baumannii Carrying blaOXA-23 Gene within the Tn2006 Transposon Among ICU Patients.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2025.06.009}, pmid = {40555322}, issn = {2213-7173}, abstract = {PURPOSE: To characterize carbapenem-resistant Acinetobacter baumannii carrying blaOXA-23 genes within the Tn2006 transposon using metagenomic and whole-genome sequencing, focusing on their genetic features, antimicrobial resistance, and potential for clonal spread and horizontal gene transfer among ICU patients.<br><br>METHODS: Bronchoalveolar lavage fluid samples from 28 ICU patients were analyzed using mNGS to detect pathogens and resistance genes. A. baumannii isolates underwent whole-genome sequencing for genetic diversity assessment. Antimicrobial susceptibility testing and comparative genomic analysis were performed.<br><br>RESULTS: mNGS revealed mixed infections in 71.4% of patients, identifying multiple bacteria, viruses, fungi, and mycoplasma species. A. baumannii was detected in 25 samples, often alongside other pathogens. All isolates harbored blaOXA-23 within Tn2006 on the chromosome and belonged to sequence type ST2, indicating clonal dissemination despite significant genetic diversity (up to 2,969 SNP differences). The isolates were highly resistant to multiple antibiotics but remained susceptible to tigecycline and colistin. Comparative genomic analysis with 238 global CRAB genomes confirmed the prevalence of the Tn2006 transposon carrying blaOXA-23 in ST2 strains, emphasizing the potential for rapid spread of this resistance mechanism.<br><br>CONCLUSION: The widespread presence of multidrug-resistant A. baumannii carrying blaOXA-23 within Tn2006 among ICU patients poses a significant public health concern. The high rate of mixed infections and the potential for horizontal gene transfer complicate infection management in critically ill patients. Enhanced infection control measures, continuous surveillance, and targeted interventions are urgently needed to prevent further dissemination of these resistant strains in hospital settings.}, }
@article {pmid40555025, year = {2025}, author = {Lin, Z and Pang, S and Wu, Y and Xu, T and Zhou, YL and Li, H and Zhang, C and Qian, PY and Zhang, S}, title = {Biodiversity and nitrogen metabolism in the plastisphere impacted by urban nitrogen loading from a coastal mega-city.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {139012}, doi = {10.1016/j.jhazmat.2025.139012}, pmid = {40555025}, issn = {1873-3336}, abstract = {The plastisphere, recognized for vast biomass and critical role in nitrogen cycling, is becoming a pertinent component of marine ecosystems. The relationship between plastisphere and increased nitrogen inputs from urban wastewater in coastal zones remains poorly understood. Through metagenomics, metatranscriptomics and metabolomics, this research sought to elucidate the plastisphere's reaction to elevated nitrogen loading and pinpoint key microbial resources that can be harnessed. Although the archaeal community composition within the plastisphere remains largely unchanged by nitrogen loading, bacterial diversity experiences a substantial boost, which is inversely correlated with fungal diversity. Furthermore, such conditions are associated with reduced intricate microbial interactions. Moreover, the plastisphere subjected to nitrogen loading shows an enrichment of genera and genes implicated in ammonium assimilation, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Metabolomics analysis highlighted the plastisphere's accumulation of L-glutathione oxidized (GSSG) in response to nitrogen loading. The research further highlighted a quartet of microbial phyla-Actinomycetota, Bacteroidota, Cyanobacteriota, and Pseudomonadota-that not only thrive but also constitute pivotal microbial resources within the plastisphere when confronted with strong nitrogen loading. In essence, this investigation illuminates the plastisphere's biodiversity dynamics and nitrogen metabolic adjustments during augmented nitrogen loading and offers novel perspectives on taking advantage of the plastisphere's untapped microbial potential.}, }
@article {pmid40554894, year = {2025}, author = {Zheng, SJ and Gao, XY and Diao, XH and Chen, ND}, title = {Dendrobium huoshanense improves atherosclerosis in high-fat-induced ApoE mice by regulating gut microbiota and serum metabolite profiles.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {145}, number = {}, pages = {156964}, doi = {10.1016/j.phymed.2025.156964}, pmid = {40554894}, issn = {1618-095X}, abstract = {BACKGROUND: Cardiovascular diseases, particularly atherosclerosis (AS), remain leading causes of mortality, with limited effective treatments available. Dendrobium huoshanense, a traditional medicinal herb, has shown promising anti-inflammatory and antioxidant effects, but its cardiovascular protective potential remains underexplored.<br><br>PURPOSE: This study aimed to explore the protective effects of Dendrobium huoshanense polysaccharides (DHP) against AS and elucidate the underlying mechanisms involved.<br><br>METHODS: An ApoE(-/-) mice model of AS was established, and DHP was administered at different concentrations via gavage. After 14 weeks, serum and fecal samples were collected. The effects of DHP on lipid profiles, aortic plaques, matrix metalloproteinases (MMP-2 and MMP-9), and the Nrf2/HO-1 pathway were assessed. Additionally, metagenomic sequencing of fecal samples and untargeted metabolomics of serum were conducted and correlations between these findings were explored.<br><br>RESULTS: DHP improved lipid profiles, reduced reactive oxygen species (ROS) and malondialdehyde (MDA) levels, and enhanced superoxide dismutase (SOD) activity. It stabilized aortic plaques, suppressed MMP-2 and MMP-9 overexpression, and activated the Nrf2/HO-1 pathway. DHP also promoted gut microbiota balance, increasing Mucispirillum, Bifidobacterium, and Faecalibaculum while decreasing Desulfovibrionaceae and Eubacterium. Metabolomics revealed alterations in metabolites, including taurochenodeoxycholic acid and ursocolic acid, influencing amino acid, glycerophospholipid, and bile acid metabolism.<br><br>CONCLUSIONS: DHP effectively lowers lipid levels, stabilizes aortic plaques, restores gut microbiota balance, and corrects metabolic disturbances, thereby inhibiting the progression of atherosclerosis. These findings provide a scientific basis for the clinical use of DHP in AS prevention and treatment.}, }
@article {pmid40554566, year = {2025}, author = {Calderón-Ezquerro, MC and Brunner-Mendoza, C and Guerrero-Guerra, C and Sanchez-Flores A, A and Salinas-Peralta, I and Toriello, C and Ponce-de León, A and Ortega-Rosas C I, CI}, title = {Genetic sequencing of the airborne fungal spectrum and air quality at a public hospital in Mexico City.}, journal = {PLOS global public health}, volume = {5}, number = {6}, pages = {e0004784}, pmid = {40554566}, issn = {2767-3375}, abstract = {Hospital bioaerosols represent significant risks for nosocomial infections, contributing to patient morbidity and mortality. Exposure to these particles, particularly airborne fungal spores or propagules, can trigger adverse effects on the immune system and cause respiratory diseases. This study evaluated the airborne fungal community in a public hospital in Mexico City using a metagenomic approach, two types of aerobiological samplers as well as temperature, humidity, and suspended particle analysis. Sampling was carried out in three areas within the hospital: and outside the hospital. Airborne sampling was performed for three consecutive days, except in the EU. The results showed that using two different samplers revealed fungal diversity and composition variations. Specifically, the Cμ-Sampler captured a higher abundance and diversity of fungi than the AVPS, with Total Taxonomy Annotations at a Genus level of 626 in F1, 632 in F2, 485 in EU and 617 in OH). In the analysis of fungal presence, Ascomycota and Basidiomycota were identified as dominant phyla. Using the AVPS sampler, Ascomycota showed an overwhelming presence of 90% to 100% inside and outside the hospital, while Basidiomycota was found in a range of 1% to 10%. Using the CμS-Sampler, Ascomycota was observed to vary between 39% and 72% in areas F1 and F2 of the hospital and from 73% to 82% outside it. On the other hand, Basidiomycota presented values between 54% and 61% in F1 and from 18% to 27% outside the hospital. The predominant genera were Aspergillus, Penicillium, Cladosporium and Alternaria. The identification of twenty-seven fungal species, including opportunistic pathogens such as Aspergillus fumigatus, Penicillium chrysogenum, P. expansum, Cladosporium and Alternaria alternata, is a significant result of this study. The results revealed the diversity of fungi in the hospital environment. The proposed complementary use of different samplers could significantly optimise current surveillance methods.}, }
@article {pmid40554279, year = {2025}, author = {Zhang, Z and Liu, C and Chen, T and Liu, F and Luo, S and Ye, J}, title = {Microorganisms and characteristic volatile flavor compounds in Luocheng fermented rice noodles.}, journal = {Food chemistry}, volume = {490}, number = {}, pages = {145133}, doi = {10.1016/j.foodchem.2025.145133}, pmid = {40554279}, issn = {1873-7072}, abstract = {The association between the appealing flavors of Luocheng fermented rice noodles (LCFN) and microbial succession during long-term fermentation is poorly understood. This study aims to elucidate the mechanism of flavor formation in LCFN during fermentation over a 30-day period. The electronic nose results showed that the LCFN underwent a flavor shift in 7-10 days with maturation in 15-30 days. This transformation was associated with the formation of characteristic flavors of (E)-2-decenal, 2-undecenal, (E, E)-2,4-decadienal, (E)-2-octenal, (E)-2-heptenal, hexanal, nonanal, and 2-pentyl furan, which had significant positive correlation with palmitic acid, oleic acid, and linoleic acid. Changes in lipase activity and the analysis of metagenomics, suggested that the characteristic flavors may be produced by Lactobacillaceae and Geotrichum via lipid metabolism. This study provides theoretical guidance for the screening of safe and efficient microorganisms for the production of flavorful rice noodles.}, }
@article {pmid40554148, year = {2025}, author = {Xiang, J and Zhou, Z and Liu, Z and Ren, C and Xu, Y}, title = {Constructing simplified microbial consortia that couple lactic acid and ethanol utilization to highly produce caproic acid from liquor-making wastewater.}, journal = {Water research}, volume = {284}, number = {}, pages = {123973}, doi = {10.1016/j.watres.2025.123973}, pmid = {40554148}, issn = {1879-2448}, abstract = {Converting biodegradable carbon in wastewater into medium-chain fatty acids (MCFAs) through stable microbiota is highly attractive. In this study, we utilized a top-down approach for constructing MCFA-producing microbial consortia. Specifically, an enrichment and plating-screening strategy employing lactic acid and ethanol as selective carbon sources was applied to isolate simplified caproic acid-producing microbial consortia from liquor-making pit mud. The representative microbial consortium SimpCom3 demonstrated high level of caproic acid production (14.62 ± 0.48 g/L) in a semi-synthetic medium, significantly outperforming consortium SimpCom1 (5.96 ± 0.11 g/L) and consortium SimpCom2 (9.63 ± 0.16 g/L). This performance of microbial consortium SimpCom3 was attributed to its ability to co-utilize lactic acid and ethanol, produce fewer odd-chain fatty acids byproducts, and maintain pH self-regulation between 6.45 and 8.29. Metagenomic analyses revealed the dominance of Clostridium kluyveri (30.69 %-50.46 %), C. butyricum (6.71 %-13.98 %) and C. tyrobutyricum (37.11 %-58.07 %) in consortium SimpCom3, which synergistically converted lactic acid and ethanol to caproic acid via reverse β-oxidation. Stable performance over 56 days of cyclic-batch fermentation processes confirmed the robustness of consortium SimpCom3. When applying consortium SimpCom3 to unsterilized liquor-making wastewater in a fermenter with a fed-batch approach, 22.13 g/L caproic acid was produced with 66.38 % selectivity, and microbial dynamics analysis demonstrated the consortium's high adaptability to real wastewater. Metabolic analysis based on high-quality assembly metagenomes (HQ-MAGs) revealed a novel cooperative metabolism: cross-feeding between Clostridium kluyveri (which utilizes ethanol and produces caproic acid) and lactate-utilizing butyrate producers maintained consortium stability and enhanced caproic acid production. Crucially, the decarboxylation of lactic acid counteracted acidification caused by ethanol-driven caproic acid synthesis, enabling self-regulated pH stability within the simplified microbiome system. Together, this study presents a simplified microbial consortium construction method for caproic acid production from liquor-making wastewater, overcoming the limitations of synthetic co-cultures and enhancing the viability of chain-elongation biorefineries in wastewater treatment.}, }
@article {pmid40554092, year = {2025}, author = {Choi, BS and Holm, JB and Brejnrod, A and Fjære, E and Xia, Z and Allingbjerg, ML and Larsen, IS and Kristensen, DM and Dall, M and Myrmel, LS and Koch, J and Danneskiold-Samsøe, NB and Kalliokoski, O and Treebak, JT and Xiao, L and Hansen, AK and Sørensen, H and Madsen, L and Arumugam, M and Kristiansen, K and Jensen, BAH}, title = {Housing matters: experimental variables shaping metabolism in obese mice.}, journal = {Molecular metabolism}, volume = {}, number = {}, pages = {102190}, doi = {10.1016/j.molmet.2025.102190}, pmid = {40554092}, issn = {2212-8778}, abstract = {Diet-induced obesity in mice is an important model for investigating host-diet interactions as well as dietary and pharmacological treatments of metabolic diseases. Experimental reproducibility is, however, a recurrent challenge. To determine key controllable experimental drivers of mouse metabolism, we distributed 338 C57BL/6JBomTac mice (males and females) into six research units across two countries, divided them into a variety of housing conditions (i.e., diets, cage types, temperatures, group-housing vs. single-housing) and kept 26 reference mice at the vendor. We applied linear mixed models to rank the influence of each variable on metabolic phenotype (i.e., body weight gain, glucose intolerance, liver, and visceral adipose tissue weight). Group-housing was the most potent driver of metabolic dysfunction apart from sex and diet. Accordingly, single-housed mice exhibited reduced weight gain (∼50%), increased energy expenditure, and diminished respiratory exchange ratio concomitant with improved glucose tolerance (∼20%) compared to their group-housed counterparts. Our results may aid in clarifying the impact of experimental design and promote rational, transparent reporting to increase reproducibility.}, }
@article {pmid40554085, year = {2025}, author = {Chen, H and Ruan, F and Wu, W and Liu, J and Wang, Z and Xu, X and Liu, Y and Wu, S and Zhou, J and Ma, J}, title = {Pulmonary fungal infection caused by Rhizopus microsporus in type II diabetic patient:A case report.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {2}, pages = {116953}, doi = {10.1016/j.diagmicrobio.2025.116953}, pmid = {40554085}, issn = {1879-0070}, abstract = {Pulmonary fungal infections are invasive fungal diseases with high mortality, particularly in immunocompromised patients. This case report describes a patient with type II diabetes mellitus who developed a pulmonary fungal infection. The patient presented with a one-week history of paroxysmal cough and expectoration of yellowish-white, purulent sputum following exposure to cold temperatures. Initial empirical antiviral therapy failed to yield any clinical improvement Subsequent chest computed tomography (CT) scans revealed irregular areas of increased density in the left lower lung, while metagenomic next-generation sequencing (mNGS) identified the infection as caused by Rhizopus microspores. The patient was treated with intravenous amphotericin B and showed clinical improvement without side effects during follow-up. This case highlighted the potential of mNGS as an adjunctive diagnostic tool for rare pathogen infections, especially in immunocompromised patients where conventional microbiological methods may be inconclusive.}, }
@article {pmid40554061, year = {2025}, author = {Yang, W and Zou, P and He, S and Cui, H and Yang, Z and An, H and Chen, Q and Huang, W and Guo, H and Liu, J and Ling, X and Cao, J and Ao, L}, title = {Perfluorooctane sulfonic acid impairs spermatogenesis via the liver-gut microbiota-testis axis: a central role of chenodeoxycholic acid metabolism.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.06.037}, pmid = {40554061}, issn = {2090-1224}, abstract = {INTRODUCTION: Perfluorooctane sulfonic acid (PFOS) as a global contaminant is ubiquitously presented in the environmental media and human body. The association between PFOS exposure and reduced male fertility has been recently discovered. However, the relevant mechanism remains unexplored.<br><br>OBJECTIVES: Our study aimed to investigate the effect and mechanism of PFOS exposure on male reproductive function.<br><br>METHODS: In a murine PFOS exposure model, single-nucleus transcriptome sequencing was performed to delineate the transcriptomic landscape of mouse testes at the single-cell resolution. We examined the serum metabolomic profile and conducted in-depth analysis of hepatic transcriptome datasets to explore the metabolic connections between liver and testis under PFOS exposure. Through integrating chenodeoxycholic acid intervention, fecal microbiota transplantation (FMT), metagenomic sequencing, testicular metabolome, Ligilactobacillus murinus (L. murinus) metabolome, and administration of L. murinus, we confirmed the role of the liver-gut microbiota-testis axis and screened the critical gut microbiota involved in PFOS-mediated spermatogenic disorders.<br><br>RESULTS: The results showed that PFOS exposure led to spermatogenic arrest and abnormal spermatogenic microenvironment in the mouse testis. The PFOS-repressed hepatic chenodeoxycholic acid (CDCA) synthesis contributed to the reduced serum/testicular levels of essential fatty acid (linoleic acid) and lipid-soluble vitamins (retinol, vitamin D3), which was responsible for the spermatogenic arrest. Beyond this, PFOS-mediated impaired CDCA production decreased the abundance of gut L. murinus, which affected spermatogenesis through the potential involvement of aspartic acid metabolism. For the first time to our knowledge, we comprehensively assessed the effects of PFOS exposure on the spermatogenic process and elucidated the unrecognized role of liver-gut microbiota-testis axis in PFOS-induced abnormal spermatogenesis.<br><br>CONCLUSIONS: The unveiled organ crosstalks provide new insights into the metabolism-disrupting properties, hepatotoxicity, and reproductive toxicity of PFOS, which may facilitate the development of molecule-, metabolite-, and microbe-based strategies for PFOS-induced metabolic diseases and reproductive disorders.}, }
@article {pmid40553742, year = {2025}, author = {Frutkoff, YA and Plotkin, L and Pollak, D and Livovsky, J and Focht, G and Lev-Tzion, R and Ledder, O and Assa, A and Yogev, D and Orlanski-Meyer, E and Broide, E and Kierkuś, J and Kang, B and Weiss, B and Aloi, M and Schwerd, T and Shouval, DS and Bramuzzo, M and Griffiths, AM and Yassour, M and Turner, D}, title = {Whole food diet induces remission in children and young adults with mild-moderate Crohn's disease and is more tolerable than exclusive enteral nutrition: a randomized controlled trial.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.06.011}, pmid = {40553742}, issn = {1528-0012}, abstract = {BACKGROUND: Tasty&amp;Healthy (T&amp;H) is a whole-food diet for Crohn's disease (CD), which excludes processed food, gluten, red meat, and dairy, without requiring formula or mandatory ingredients. TASTI-MM was a clinician-blinded, randomized-controlled trial comparing tolerability and effectiveness of T&amp;H vs. exclusive enteral nutrition (EEN).<br><br>METHODS: Patients with biologic-naive mild-moderate CD aged 6-25 years were randomized to either T&amp;H or EEN for 8 weeks, receiving weekly dietary support. Tolerability was evaluated by weekly interviews, questionnaires and intake diaries. Other outcomes included symptomatic remission, Mucosal-Inflammation Non-Invasive (MINI) index, calprotectin, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR). Fecal microbiome was analyzed by metagenomics at baseline, week-4 and week-8. Data were analyzed by the intention-to-treat approach unless specified otherwise.<br><br>RESULTS: Among 83 included patients (41 T&amp;H, 42 EEN; mean age 14.5&#xb1;3.7 years), 88% tolerated T&amp;H vs. 52% for EEN (aOR 7.7 [95%CI 2.4-25]; p<0.001). Calprotectin, CRP and ESR decreased significantly in both groups, with no between-group differences. Symptomatic remission was achieved in 56% of T&amp;H group vs. 38% of the EEN group (aOR 2.5 [0.98-6.3], p=0.1; per-protocol: 67% vs. 76%; p=0.47). Calprotectin <250&#x3bc;g/g was achieved in 34% vs. 33% (aOR 0.97 [0.37-2.6], p=0.84) and MINI<8 in 44% vs. 31% (aOR 1.8 [0.7-4.5]; p=0.33). Microbiome &#x3b1;-diversity improved in the T&amp;H arm and declined in the EEN arm, showing superior species richness at both week-4 and week-8. Species associated with bowel inflammation, such as Ruminococcus gnavus, decreased in T&amp;H and increased in EEN (q<0.001).<br><br>CONCLUSIONS: T&amp;H demonstrated better tolerability than EEN for inducing remission in mild-to-moderate CD, while positively affecting the microbiome (TASTI-MM, NCT#04239248).}, }
@article {pmid40553325, year = {2025}, author = {Mukhopadhyay, S and Ulaganathan, N and Dumpuri, P and Aich, P}, title = {Integrative AI-Based Approaches to Connect the Multiome to Use Microbiome-Metabolome Interactive Outcome as Precision Medicine.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2952}, number = {}, pages = {15-37}, pmid = {40553325}, issn = {1940-6029}, mesh = {Humans ; *Precision Medicine/methods ; *Metabolomics/methods ; *Metabolome ; Metagenomics/methods ; *Microbiota ; *Artificial Intelligence ; Computational Biology/methods ; Gastrointestinal Microbiome ; }, abstract = {In the era of Genome-Wide Association Studies (GWAS), biologists have unprecedented access to vast datasets, mirrored in the wealth of information from various omics studies, including genomics, transcriptomics, proteomics, metabolomics, and metagenomics. Integrating diverse data sources has emerged as crucial in unravelling the intricacies of biological processes. This chapter delves into our method for merging various omics methodologies, emphasizing metabolomics and metagenomics data. A powerful strategy addresses data processing challenges and opens new avenues for personalized microbiome-based interventions. The combined analysis of host and microbial metabolomics and metagenomics data has significantly advanced our understanding in diagnosing and treating conditions such as inflammatory bowel disease and irritable bowel syndrome. Metabolic signatures in biological fluids and their microbial counterparts serve as indicators, differentiating health from disease. The sheer volume of data demands sophisticated automated tools for processing and interpretation. Recognizing this need, integrating artificial intelligence (AI) and data science has become increasingly prominent. In this chapter, we combine microbiome and metabolome analyses through publicly available models to elucidate the correlations between microbial and metabolic profiles. By harnessing AI models across various omics data sources, this chapter bridges the gap between data acquisition and clinical applications, paving the way for personalized interventions and optimizing individual health.}, }
@article {pmid40552763, year = {2025}, author = {Claypool, J and Lindved, G and Myers, PN and Ward, T and Nielsen, HB and Blount, KF}, title = {Microbiome compositional changes and clonal engraftment in a phase 3 trial of fecal microbiota, live-jslm for recurrent Clostridioides difficile infection.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2520412}, doi = {10.1080/19490976.2025.2520412}, pmid = {40552763}, issn = {1949-0984}, mesh = {Humans ; *Clostridium Infections/therapy/microbiology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Male ; *Clostridioides difficile/physiology ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Recurrence ; Aged ; }, abstract = {Live microbiota therapies have shown promise in many gastrointestinal diseases, including in the prevention of recurrent Clostridioides difficile infections (rCDI); however, frameworks for their pharmacokinetic and pharmacodynamic analysis are not fully established. Fecal microbiota, live-jslm (RBL) is the first microbiota-based product approved by the US Food and Drug Administration for the prevention of rCDI and was superior to placebo in the PUNCH™ CD3 phase 3 clinical trial (NCT03244644). In this analysis, deep shotgun metagenomic sequencing was used to assess changes in gut microbiome compositions of participants and engraftment of bacterial clonal populations (i.e. strains) from RBL to recipients. Among RBL responders, gut microbiota shifted toward compositions that resembled healthy donors as early as 1 week after RBL administration; the resulting microbiota compositions included clonal populations that engrafted from RBL to recipients. Engraftment was higher in RBL responders compared with non-responders, and many clonally engrafted populations persisted for ≥ 6 months. Bacteroidia species were among the most effectively engrafted species from RBL. This study utilizes data from a large clinical trial to establish a method with high specificity for exploring clonal engraftment from microbiota-based treatments to facilitate future pharmacokinetic and pharmacodynamic analyses.Clinicaltrials Registration: NCT03244644.}, }
@article {pmid40552317, year = {2025}, author = {Jafari, E and Azizian, R and Tabasi, M and Banakar, M and Bagheri Lankarani, K}, title = {Human Gut Bacteriophageome: Insights Into Drug Resistance Mechanisms in Tuberculosis.}, journal = {Interdisciplinary perspectives on infectious diseases}, volume = {2025}, number = {}, pages = {8811027}, pmid = {40552317}, issn = {1687-708X}, abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major global health burden. The emergence of drug-resistant strains presents a critical challenge in TB management. The recent research has explored the interaction between TB and the human gut bacteriophage community (phageome). The gut phageome plays a crucial role in regulating microbial diversity and functionality, and its composition and function have been linked to various health conditions. Examining the gut phageome through metagenomic analysis provides insights into its composition, role in health, and interactions with the host immune system. Exploring the interaction between the gut phageome and M. tuberculosis may reveal how phages affect the bacterium's pathogenicity, survival, and mechanisms of drug resistance. Understanding the gut phageome's impact on TB drug resistance could inform novel therapeutic strategies, such as phage therapy, and highlight the importance of microbiome-based interventions in combating drug-resistant TB strains. This review explores the role of the gut phageome in influencing drug resistance in TB, focusing on interaction mechanisms and potential therapeutic implications, synthesizing current research findings, and identifying knowledge gaps in this emerging field. This review also synthesizes the current evidence on the gut phageome's role in TB drug resistance, focusing on phage-mediated horizontal gene transfer (e.g., rpoB, katG), immune modulation, and preclinical efficacy of mycobacteriophage therapies. Key findings highlight phage cocktails (e.g., DS6A, D29 LysB) as promising adjuncts to antibiotics, reducing M. tuberculosis burden in murine models. These insights advocate for phage therapy as a complementary strategy against drug-resistant TB, urging clinical validation to bridge the existing knowledge gaps.}, }
@article {pmid40551486, year = {2025}, author = {Yan, F and Wu, SM and Yuan, WQ and Yang, YH and Zhu, H and Cui, DJ}, title = {Thermophiles, Thick-Walled Bacteria, and Pseudomonads in High-Altitude Gut Microbiota.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.17032}, pmid = {40551486}, issn = {1440-1746}, support = {qiankehe2018-5764-11//Cultivation Fund of National Natural Science Foundation/ ; gzwkj2025-268//Science and Technology Fund of Guizhou provincial health committee/ ; }, abstract = {BACKGROUND AND AIM: High-altitude environments are characterized by low oxygen and reduced low pressure, which impose significant physiological challenges on organisms. Among various adaptive systems, the intestinal flora plays a crucial role in maintaining gut health and barrier integrity function under such conditions. This study aimed to elucidate the regulatory mechanisms of intestinal flora in high-altitude environments, focusing on downregulating intracellular Bone Morphogenetic Protein 4 (BMP4) to influence glycolysis metabolism, thereby affecting intercellular communication of the intestinal mucosal barrier and matrix remodeling.<br><br>METHODS: High-altitude mouse intestinal flora composition and function were analyzed using 16S rRNA and metagenomic sequencing. Additionally, single-cell sequencing was employed to examine cell population communication and gene expression differences between normal and high-altitude mouse intestinal tissues.<br><br>RESULTS: Single-cell sequencing showed significantly reduced interactions between intestinal fibroblasts and epithelial cells in high-altitude mice, accompanied by a marked increase in BMP4 expression. Overexpression of BMP4 was found to activate the glycolysis pathway. Gut microbiota metabolites, including secondary bile acids, lactic acid, and butyrate, exhibited protective effects on hypoxia-induced intestinal mucosal barrier injury, with butyrate showing the most prominent effect. Under hypoxic conditions, butyrate suppressed the BMP4/glycolysis pathway, thereby alleviating hypoxia-induced intestinal mucosal barrier damage.<br><br>CONCLUSION: This study uncovered a novel mechanism by which the gut microbiota in high-altitude environments modulate glycolysis metabolism through BMP4 downregulation, thereby affecting intercellular communication and matrix remodeling within the intestinal mucosal barrier.}, }
@article {pmid40551155, year = {2025}, author = {Mizsei, E and Sos, T and Móré, A and Wenner, B and Rák, G and Mebert, K}, title = {Restriction times on the rise: mechanistic modelling of activity time of grassland vipers (Vipera spp.) in the face of climate change.}, journal = {Frontiers in zoology}, volume = {22}, number = {1}, pages = {10}, pmid = {40551155}, issn = {1742-9994}, support = {LIFE18 NAT/HU/000799//LIFE programme/ ; }, abstract = {Climate change threatens species adapted to cool alpine environments, particularly ectotherms like reptiles. Small-sized grassland specialist vipers inhabit such environments in Eurasia and are highly susceptible to overheating and dehydration as global temperature rises. This study modelled activity restriction times, defined as hours when environmental temperatures exceed the thermal tolerance (i.e. not available for essential activities) of the species, for 20 grassland viper taxa to assess climate change impacts. Under future conditions, hours of activity restriction are projected to increase by 21% by the SSP1-2.6 scenario, and by 52.1% by the SSP5-8.5 scenario. Elevation and latitude significantly influenced restriction time changes, with high-altitude and northern populations predicted to be most affected. The taxa Vipera graeca and Vipera ursinii moldavica are expected to experience the greatest increase in restriction times. Despite warmer conditions potentially increasing hours within preferred thermal ranges, vipers are unlikely to exploit lower-elevation habitats due to competition and ecological constraints. These findings emphasise the urgent need for conservation strategies, including habitat preservation and connectivity, to mitigate the adverse effects of climate change on grassland vipers, particularly the most vulnerable populations.}, }
@article {pmid40550680, year = {2025}, author = {Lin, M and Hu, L and Hao, L and Wang, Z}, title = {[Microbiome and its genetic potential for carbon fixation in small urban wetlands].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {41}, number = {6}, pages = {2415-2431}, doi = {10.13345/j.cjb.240399}, pmid = {40550680}, issn = {1872-2075}, mesh = {*Wetlands ; *Microbiota/genetics ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; China ; Cities ; Geologic Sediments/microbiology ; Archaea/genetics/metabolism/classification ; Metagenomics ; Metagenome ; }, abstract = {Small urban wetlands are widely distributed and susceptible to human activities, serving as important sources and sinks of carbon. Microorganisms play a crucial role in carbon cycle, while limited studies have been conducted on the microbial diversity in small urban wetlands and the functions of microbiome in carbon fixation and metabolism. To probe into the microbiome-driven carbon cycling in small urban wetlands and dissect the composition and functional groups of microbiome, we analyzed the relationships between the microbiome structure, element metabolism pathways, and habitat physicochemical properties in sediment samples across three small wetlands in Huzhou City, and compared them with natural wetlands in the Zoige wetland. High-throughput sequencing of 16S rRNA gene amplicons and metagenomics was employed to determine the species and functional groups. Sixty medium to high-quality metagenome-assembled genomes (MAGs) were constructed, including 55 bacterial and 5 archaeal taxa, and their potential in driving elemental cycles were analyzed, with a focus on carbon fixation. Several bacterial species were found to encode a nearly complete carbon fixation pathway, including the Calvin cycle, the reductive tricarboxylic acid cycle, the Wood-Ljungdahl pathway, and the reductive glycine pathway. There were several potential novel carbon-fixing bacterial members, such as those belonging to Syntrophorhabdus (Desulfobacterota) and UBA4417 (Bacteroidetes), which had high relative abundance in the wetland microbiome. Unveiling the genetic potential of these functional groups to facilitate element cycling is of great scientific importance for enhancing the carbon sequestration capacity of small urban wetlands.}, }
@article {pmid40550672, year = {2025}, author = {Wang, X and Wang, S and Yang, K and Tang, Y and Xu, Y and Shen, Q and Wei, Z}, title = {[Methodological breakthroughs and challenges in research of soil phage microecology].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {41}, number = {6}, pages = {2310-2323}, doi = {10.13345/j.cjb.250258}, pmid = {40550672}, issn = {1872-2075}, mesh = {*Bacteriophages/genetics/isolation &amp; purification/physiology ; *Soil Microbiology ; Ecosystem ; Microbiota ; Metagenomics/methods ; }, abstract = {Phages, as obligate bacterial and archaeal parasites, constitute a virus group of paramount ecological significance due to their exceptional abundance and genetic diversity. These biological entities serve as critical regulators in Earth's ecosystems, driving biogeochemical cycles, energy fluxes, and ecosystem services across terrestrial and marine environments. Within soil microbiomes, phages function as microbial "dark matter," maintaining the soil-plant system balance through precise modulation of the microbial community structure and functional dynamics. Despite the growing research interests in soil phages in recent years, the proportion of such studies in environmental virology remains disproportionately low, which is primarily attributed to researchers' limited familiarity with the research methodologies for phage microecology, incomplete technical frameworks, and inherent challenges posed by soil environmental complexity. To address these challenges, this review synthesizes cutting-edge methodologies for soil phage investigation from four aspects: (1) tangential flow filtration (TFF)-based phage enrichment strategies; (2) integrated quantification approaches combining double-layer agar plating, epifluorescence microscopy, and flow cytometry; (3) multi-omics analytical pipelines leveraging metagenomics and viromics datasets; and (4) computational frameworks merging machine learning algorithms with eco-evolutionary theory for deciphering phage-host interaction networks. Through comparative analysis of methodological principles, technical merits, and application scopes, we establish a comprehensive workflow for soil phage research. Future research in this field should prioritize: (1) construction of soil phage resource libraries, (2) exploration of RNA phages based on transcriptomes, (3) functional characterization of unknown genes, and (4) deep integration and interaction validation of multi-omics data. This systematic methodological synthesis provides critical technical references for addressing fundamental challenges in characterizing soil phages regarding the community structure, functional potential, and interaction mechanisms with hosts.}, }
@article {pmid40550235, year = {2025}, author = {Howard-Jones, AR and Mahar, JE and Proudmore, K and Butel-Simoes, GI and Eden, JS and Neave, MJ and Mileto, P and Hueston, L and Freeman, K and Ellem, J and Caly, L and Sikazwe, C and Levy, A and Thomas, A and Taylor, C and Kurucz, N and Smyth, K and Jennison, A and Moore, P and Wright, R and Mee, PT and Brischetto, A and Feldman, R and Dwyer, DE and O'Sullivan, MV and Mahony, AA and Warner, MS and Papanicolas, LE and Schlebusch, S and Lim, CK and Baird, R and Speers, D and Williams, DT and Currie, BJ and Kok, J}, title = {Diagnostic and phylogenetic perspectives of the 2023 Murray Valley encephalitis virus outbreak in Australia: an observational study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101089}, doi = {10.1016/j.lanmic.2025.101089}, pmid = {40550235}, issn = {2666-5247}, abstract = {BACKGROUND: An outbreak of Murray Valley encephalitis virus (MVEV), the largest since 1974, was observed in Australia between Jan 1 and July 31, 2023. This study aims to characterise the utility of diagnostic platforms, testing algorithms, and genomic characteristics of MVEV to facilitate a comprehensive framework for MVEV testing and surveillance in the outbreak setting.<br><br>METHODS: In this observational study, we assessed flavivirus diagnostics for all patients with suspected Murray Valley encephalitis in Australia from Jan 1 to July 31, 2023. We included all patients with confirmed Murray Valley encephalitis, probable Murray Valley encephalitis, or acute unspecified flavivirus infection using the Communicable Diseases Network Australia case definition. Cases were excluded if an alternative diagnosis was identified. We collected blood, serum, cerebrospinal fluid, brain tissue, urine, or a combination of these samples, as appropriate and at the discretion of the treating clinician. We conducted multimodal diagnostic testing, which included flavivirus-specific serological and nucleic acid amplification testing. Metagenomic next-generation sequencing, including next-generation deep sequencing, target-enrichment, and targeted amplification, was conducted on human and representative mosquito-derived samples obtained from established mosquito population surveillance programmes for phylogenetic analysis.<br><br>FINDINGS: 27 patients with encephalitis were assessed for MVEV between Jan 1, 2023, and July 31, 2023, 23 (85%) of whom fulfilled national case definitions for confirmed Murray Valley encephalitis. Patient ages ranged from 6 weeks to 83 years (median 62&#xb7;0 years [IQR 31&#xb7;0-67&#xb7;5]) and patients were mostly male (21 [78%] male patients and six [22%] female patients). Incidence varied widely by geographical region and was highest in the Northern Territory (32&#xb7;0 per 1&#x2009;000&#x2009;000 population). Diagnostic specimen collection generally occurred promptly (median 6&#xb7;0 days [IQR 4&#xb7;0-14&#xb7;5] from symptom onset to diagnostic specimen collection). In seven patients, case assignation relied on convalescent serum samples to assess for seroconversion or an appropriate rise in antibody titre (to four times the initial value or greater), or both. MVEV-specific IgM was detectable in serum samples of 17 (81%) of 21 patients tested by day 7 and MVEV IgG or total antibody (TAb) were detected in 18 (100%) of 18 patients tested by day 30. MVEV-specific IgM (or TAb) and MVEV RNA were detected in cerebrospinal fluid collected within 14 days of symptom onset in nine (39%) of 23 patients and seven (28%) of 25 patients, respectively. Phylogenetic analysis revealed two circulating MVEV genotypes, G1A and G2, in mosquitoes and humans in 2023. In southeast Australia, only G1A was detected and probably introduced from enzootic foci in northern Australia.<br><br>INTERPRETATION: This study provides a comprehensive overview of the diagnostic workflows and phylogenetic evaluations used during the 2023 MVEV outbreak in Australia, emphasising the importance of a multimodal approach for accurate and timely confirmation of flavivirus infection. Further One Health surveillance for MVEV and other zoonotic flaviviruses is key, given potential expanded ecological niches in the context of episodic climatic events.<br><br>FUNDING: None.}, }
@article {pmid40549455, year = {2025}, author = {Goryanin, I and Sorokin, A and Seitov, M and Emilov, B and Iskakov, M and Goryanin, I and Osmonov, B}, title = {Metagenome and metabolome study on inhaled corticosteroids in asthma patients with side effects.}, journal = {Journal of integrative bioinformatics}, volume = {}, number = {}, pages = {}, pmid = {40549455}, issn = {1613-4516}, abstract = {This study investigates the gut microbiome and metabolome of asthma patients treated with inhaled corticosteroids (ICS), some of whom experience adverse side effects. We analyzed stool samples from 24 participants, divided into three cohorts: asthma patients with side effects, those without, and healthy controls. Using next-generation sequencing and LC-MS/MS metabolomics, we identified significant differences in bacterial species and metabolites. Multi-Omics Factor Analysis (MOFA) and Global Sensitivity Analysis-Partial Rank Correlation Coefficient (GSA-PRCC) provided insights into key contributors to side effects, such as tryptophan depletion and altered linolenate and glucose-1-phosphate levels. The study proposes dietary or probiotic interventions to mitigate side effects. Despite the limited sample size, these findings provide a basis for personalized asthma management approaches. Further studies are required to confirm initial fundings.}, }
@article {pmid40549420, year = {2025}, author = {Podowski, JC and Forrester, S and Yaqub, T and Aqel, A and Abu Lubad, M and Mukhtar, N and Waqar Aziz, M and Sardar, N and Bin Aslam, H and Pervaiz, H and Wolfe, AJ and Schabacker, DS}, title = {Genomic reconstruction of Bacillus anthracis from complex environmental samples enables high-throughput identification and lineage assignment in Pakistan.}, journal = {Microbial genomics}, volume = {11}, number = {6}, pages = {}, doi = {10.1099/mgen.0.001422}, pmid = {40549420}, issn = {2057-5858}, mesh = {*Bacillus anthracis/genetics/classification/isolation &amp; purification ; Pakistan ; *Anthrax/microbiology/epidemiology ; Animals ; *Genome, Bacterial ; Humans ; Genomics/methods ; Phylogeny ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {Bacillus anthracis, the causative agent of anthrax, is a highly virulent zoonotic pathogen primarily affecting domesticated and wild herbivores. Human exposure to B. anthracis is primarily through contact with infected animals or contaminated animal products. In Pakistan, where livestock vaccines are largely unavailable and infected carcasses are often disposed of improperly, the risk to humans, wildlife and livestock is significant. Currently, the diagnosis of anthrax infections and outbreak tracing necessitates the isolation and culturing of B. anthracis, a process that requires BSL-3 facilities. In this study, we show that positive identification, genome reconstruction and lineage assignment can be accomplished using bioinformatic analysis of DNA extracted directly from environmental samples that would otherwise provide the starting material for isolation and culturing. This approach does not require laboratory target enrichment as is necessary for other pathogens, due in part to the extremely high bacterial load in the bloodstream in the deceased animals. Using these methods, we greatly expand the knowledge of endemic B. anthracis in Pakistan. We provide the first reference B. anthracis genomes from Pakistan since the 1970s and identify A.Br.014 Aust94 as a minor circulating sublineage alongside the dominant A.Br.047 Vollum. Future work will focus on the limits of detection and will determine if this bioinformatic method can be expanded more broadly for B. anthracis or other pathogens to replace typical culture-based methods.}, }
@article {pmid40548737, year = {2025}, author = {Ren, G and Ma, L and Yan, C and Xue, Q and Zhang, H and Wang, W and Ren, X and Lei, Y and Li, S and Liu, Y and Zheng, Q and Wei, S and Zhang, Y and Wang, X}, title = {Application of targeted metagenomic next-generation sequencing in pneumonia patients.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0171324}, doi = {10.1128/spectrum.01713-24}, pmid = {40548737}, issn = {2165-0497}, abstract = {After the coronavirus disease 2019 (COVID-19) pandemic, the incidence rate of mixed infections, especially in critically ill patients with severe pneumonia, increases due to the immunity gap and has also been proven to be associated with mortality, increasing the difficulty in accurate and rapid diagnoses. Here, we evaluated the performance of targeted metagenomic next-generation sequencing (mNGS), including capture hybridization-based mNGS (chNGS) and multiplex PCR-based targeted mNGS (tNGS), in diagnosing pneumonia. Patients admitted to the Pulmonary and Critical Care Medicine, Beijing Aerospace General Hospital, and diagnosed as suspected pulmonary infections from April 2022 to March 2024 were retrospectively evaluated, and 110 patients were finally enrolled. According to the final comprehensive clinical diagnoses, there were 99 patients diagnosed with definite infectious diseases. Single infections accounted for 58.6% of these patients (58/99), while mixed infections occurred in about half of these patients (41.4%, 41/99) and were found in most of the death cases. Pseudomonas aeruginosa (n = 22), Pneumocystis jirovecii (n = 15), and severe acute respiratory syndrome coronavirus 2 (n = 13) were found to be the most common bacterial, fungal, and viral pathogens, respectively. Taking final comprehensive clinical diagnoses as the reference standard, the total coincidence rate (TCR) of chNGS can reach up to 64.1% (95% confidence interval [CI], 54.8%-73.3%), while the TCR of conventional methods was only 39.8% (95% CI, 30.4%-49.3%). The performance of tNGS was slightly superior to that of chNGS, while chNGS yielded more false-negative results, especially for viral detection. Additionally, chNGS combined with tNGS can improve the TCR to 81.3% (95% CI, 62.1%-100.0%).IMPORTANCEThis is the first report on evaluating the performance of capture hybridization-based metagenomicnext-generation sequencing (chNGS), multiplex PCR-based targeted mNGS (tNGS), and conventional methods in diagnosing pneumonia. Our findings emphasized the importance of chNGS and tNGS in diagnosing, managing, and ruling out infections, and an era of widespread application of regional tNGS in monitoring and diagnosing infections with high sensitivity and low economic burden on patients can be expected.}, }
@article {pmid40548531, year = {2025}, author = {Zhang, J and Li, Y and Zheng, J and Ding, X}, title = {Metagenomic Next-Generation Sequencing Provides a Reliable Method for Early Diagnosis of Pneumocystis jirovecii Pneumonia After Kidney Transplant: A Single-Center Retrospective Cohort Study.}, journal = {Experimental and clinical transplantation : official journal of the Middle East Society for Organ Transplantation}, volume = {23}, number = {5}, pages = {334-341}, doi = {10.6002/ect.2024.0250}, pmid = {40548531}, issn = {2146-8427}, mesh = {Humans ; Retrospective Studies ; *Pneumonia, Pneumocystis/diagnosis/microbiology/epidemiology/immunology ; *Pneumocystis carinii/genetics/pathogenicity/isolation &amp; purification ; Female ; Male ; *Kidney Transplantation/adverse effects ; Middle Aged ; Predictive Value of Tests ; Adult ; *High-Throughput Nucleotide Sequencing ; Early Diagnosis ; China/epidemiology ; *Metagenomics ; Time Factors ; Risk Factors ; Treatment Outcome ; Incidence ; }, abstract = {OBJECTIVES: Pneumocystis jirovecii pneumonia, a common pulmonary infection after kidney transplant, cannot be detected by conventional culture methods, and limitations have been shown with lung tissue biopsy, sputum collection, and sample smear staining. Early diagnosis is key as long-term survival is decreased in patients with Pneumocystis jirovecii pneumonia who are not treated in a timely and effective manner.<br><br>MATERIALS AND METHODS: From January 2018 to January 2023, our study enrolled 110 patients with pulmonary infection seen at the First Affiliated Hospital of Xi'an Jiaotong University (China). Of these patients, 46 had confirmed Pneumocystis jirovecii pneumonia per metagenomic next-generation sequencing or conventional detection methods. We compared percentages of positive tests, other pathogen species, and other factors between the 2 test methods. Clinical characteristics of patients with (n = 46) and without (n = 64) Pneumocystis jirovecii were analyzed retrospectively.<br><br>RESULTS: Overall incidence of PJP was 2.3% (46/1977). Among 46 patients diagnosed with Pneumocystis jirovecii pneumonia, average time of onset post-transplant was 7.21 &#xb1; 2.55 months; 42 patients were cured, and 4 patients died. Thirty-three patients had mixed pulmonary infections, with Pneumocystis jirovecii and human cytomegalovirus being the most common pathogen combination, and 13 patients had monotypic pulmonary infections. Sixteen patients were Pneumocystis jirovecii positive according to conventional pathogen detection, for a detection rate of 34.8% (16/46), with significant difference shown between detection methods (&#x3c7;2 = 92.0, P < .01). Patients who were treated with tacrolimus had insufficient use of sulfamethoxazole-trimethoprim and previous cytomegalovirus infection, and patients with acute rejection were more likely to develop Pneumocystis jirovecii pneumonia (P < .05).<br><br>CONCLUSIONS: Metagenomic next-generation sequencing showed more advantages in early diagnosis of Pneumocystis jirovecii pneumonia. Precision medicine can be adopted to reduce costs and improve cure rates based on results of metagenomic next-generation sequencing.}, }
@article {pmid40548332, year = {2025}, author = {Pita, L and Maldonado, M and Koutsouveli, V and Riesgo, A and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the kidney sponge, Chondrosia reniformis Nardo, 1847, and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {283}, pmid = {40548332}, issn = {2398-502X}, abstract = {We present a genome assembly from a specimen of Chondrosia reniformis (kidney sponge; Porifera; Demospongiae; Chondrillida; Chondrillidae). The genome sequence has a total length of 117.37 megabases. Most of the assembly (99.98%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs. Gene annotation of the host organism assembly on Ensembl identified 17,340 protein-coding genes. The metagenome of the specimen was also assembled and 53 binned bacterial genomes were identified, including 40 high-quality MAGs that were representative of a typical high microbial abundance sponge and included three candiate phyla (Poribacteria, Latescibacteria, Binatota).}, }
@article {pmid40548295, year = {2025}, author = {Diwan, A and Harke, S and Panche, AN}, title = {Exploration of novel bioactive compounds from the microbiome of fish and shellfish as an alternative to replace antibiotic drugs in aquaculture farming.}, journal = {Gut microbiome (Cambridge, England)}, volume = {6}, number = {}, pages = {e8}, pmid = {40548295}, issn = {2632-2897}, abstract = {The use of antibiotics in fish and shrimp aquaculture all over the world was found to be only partially successful in preventing infectious diseases. However, their overuse has resulted in the contamination of closed aquatic ecosystems, reduced antibiotic resistance in organisms that fight infectious diseases, and compromised the effectiveness of various antibiotic medications in controlling diseases. Excessive use of antibiotics damages aquaculture species and impacts human health, also rendering the most potent antibiotics increasingly ineffective, with limited alternatives. Therefore, intensive research efforts have been made to replace antibiotics with other protocols and methods like vaccines, phage therapy, quorum quenching technology, probiotics, prebiotics, chicken egg yolk antibody (IgY), and plant therapy," etc. Though all these methods have great potential, many of them are still in the experimental stage, except for fish vaccines. All these alternative technologies need to be carefully standardized and evaluated before implementation. In recent times, after realizing the importance of the gut microbiome community in maintaining the health of animals, efforts have been made to use the microbiome strains for the prevention of pathogenic bacterial and viral infections. Now it has been experimentally proven that animals should possess a healthy microbiome community in their gut tract to strengthen the immune system and prevent the entry of harmful pathogens. Investigations are now being carried out on the derivation of various bioactive compounds from the gut microbiome strains and their structural profile and functionality using the molecular tools of metagenomics and bioinformatics. Such newly discovered compounds from microbiomes can be used as potential alternatives to replace antibiotic drugs in the aquaculture industry. These alternatives are likely to emerge as breakthroughs in animal health management and farming, with effects on cost efficiency, species health, productivity, and yield enhancement. Therefore, introducing new micro-innovative technologies into an overall health management plan will be highly beneficial.}, }
@article {pmid40547922, year = {2025}, author = {Yuan, B and Jiang, T and Han, J and Wang, M}, title = {Neurobrucellosis with negative serological examination: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1583891}, pmid = {40547922}, issn = {2296-858X}, abstract = {Neurobrucellosis is an uncommon occurrence that can arise as a consequence of brucellosis. However, its clinical symptoms are severe and have the potential to be life-threatening. Timely detection, prompt diagnosis, and early treatment are crucial factors. Clinically, the gold standard for diagnosing pathogenic microorganisms is through culture. However, this method is hindered by its lengthy culture duration, low rate of positive results, and the absence of typical clinical signs of neurobrucellosis. Consequently, misdiagnosis and delayed treatment are common. Metagenomics next-generation sequencing (mNGS) technology is a novel approach in microbiological diagnosis that enables the simultaneous detection of all microorganisms present in a sample, including viruses, bacteria, fungus, and parasites. This method holds significant diagnostic significance for viral disorders affecting the central nervous system. This paper reports a case of neurobrucellosis detected by mNGS after a negative serological test, as well as a review of the relevant literature.}, }
@article {pmid40547485, year = {2025}, author = {Su, C and Zhu, M and Guo, Y and Sun, J and Liu, M and Ma, Y and Xu, Y and Bai, Y and Che, X and Zhang, N}, title = {DMAHDM@MPC nanoparticles in orthodontic adhesive inhibit cariogenic bacteria and sugar metabolism to prevent enamel demineralization.}, journal = {Materials today. Bio}, volume = {33}, number = {}, pages = {101969}, pmid = {40547485}, issn = {2590-0064}, abstract = {During orthodontic treatment, poor oral hygiene often facilitates the proliferation of cariogenic bacteria, particularly Streptococcus mutans, leading to lactic acid accumulation and subsequent enamel demineralization. To mitigate this issue, Dimethylaminohexadecyl methacrylate (DMAHDM) was incorporated onto the protein-repellent surface of 2-Methacryloyloxyethyl phosphorylcholine (MPC), resulting in the formation of a DMAHDM@MPC composite. This composite was then integrated into resin-modified glass ionomer cement (RMGIC) to develop an antimicrobial orthodontic adhesive, termed RMGIC + MPC + DMAHDM (RMD). This study demonstrated that DMAHDM@MPC nanoparticles self-assembled into a core-shell structure, thereby enhancing the antimicrobial activity. A six-month randomized controlled trial (RCT) involving 29 orthodontic patients, along with metagenomic and metabolomic analyses, revealed that RMD significantly reduced plaque accumulation by selectively inhibiting pathogenic bacteria while preserving beneficial microbiota. Additionally, MPC was shown to competitively bind to sucrose-6-phosphatase (SPP) in pathogenic bacteria, inhibiting sucrose synthesis and carbohydrate metabolism, thus reducing the production of organic acids. In conclusion, RMD effectively prevents enamel demineralization by selectively targeting cariogenic bacteria and their associated sugar metabolism pathways during orthodontic treatment.}, }
@article {pmid40546666, year = {2025}, author = {Jeyaraman, N and Jeyaraman, M and Dhanpal, P and Ramasubramanian, S and Nallakumarasamy, A and Muthu, S and Santos, GS and da Fonseca, LF and Lana, JF}, title = {Integrative review of the gut microbiome's role in pain management for orthopaedic conditions.}, journal = {World journal of experimental medicine}, volume = {15}, number = {2}, pages = {102969}, pmid = {40546666}, issn = {2220-315X}, abstract = {The gut microbiome, a complex ecosystem of microorganisms, has a significant role in modulating pain, particularly within orthopaedic conditions. Its impact on immune and neurological functions is underscored by the gut-brain axis, which influences inflammation, pain perception, and systemic immune responses. This integrative review examines current research on how gut dysbiosis is associated with various pain pathways, notably nociceptive and neuroinflammatory mechanisms linked to central sensitization. We highlight advancements in meta-omics technologies, such as metagenomics and metaproteomics, which deepen our understanding of microbiome-host interactions and their implications in pain. Recent studies emphasize that gut-derived short-chain fatty acids and microbial metabolites play roles in modulating neuroinflammation and nociception, contributing to pain management. Probiotics, prebiotics, synbiotics, and faecal microbiome transplants are explored as potential therapeutic strategies to alleviate pain through gut microbiome modulation, offering an adjunct or alternative to opioids. However, variability in individual microbiomes poses challenges to standardizing these treatments, necessitating further rigorous clinical trials. A multidisciplinary approach combining microbiology, immunology, neurology, and orthopaedics is essential to develop innovative, personalized pain management strategies rooted in gut health, with potential to transform orthopaedic pain care.}, }
@article {pmid40544959, year = {2025}, author = {Lin, T and Liu, X and Wu, L and Wu, Q and Zeng, H and Li, W and Tang, H and Zhao, J and Ding, Z}, title = {Clinical efficacy of metagenomic Next-Generation Sequencing for Pathogen Detection in Septic Patients based on Blood Samples in Intensive Care Units.}, journal = {Indian journal of medical microbiology}, volume = {}, number = {}, pages = {100897}, doi = {10.1016/j.ijmmb.2025.100897}, pmid = {40544959}, issn = {1998-3646}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is considered superior to traditional culture for pathogen detection. However, its utility in septic patients based on blood samples remains limited.<br><br>METHODS: This research aimed to compare mNGS and culture-based diagnostics in 78 septic patients, with 25 with sepsis and 53 with septic shock.<br><br>RESULTS: Among 68 cases with matching sample types, pathogens of 38 cases were solely identified through mNGS, and in contrast, 2 cases had their pathogens detected by microbiological culture only. Moreover, 17 of 63 cases (26.98%) were found to be positive by both mNGS and culture, and 6 of 63 cases (9.52%) came negative under both diagnostic methods. Regardless of prior antibiotic exposure, the positive rate of mNGS, which was 80.77%, was significantly higher than that of culture (37.18%). Significantly, among the 38 septic patients diagnosed solely by mNGS, 23 patients achieved a favorable outcome after physicians adjusted the treatment based on the mNGS findings.<br><br>CONCLUSION: In conclusion, mNGS offered a swift and accurate means for pathogen identification, and thus making this approach as a promising technology for detecting sepsis.}, }
@article {pmid40544684, year = {2025}, author = {Eckermann, C and Klein, CJ and Schäfer, F and Thiel, M and Weiss, AV and Motz, C and Lienkamp, K and Hannig, M and Schneider, M}, title = {Probiotics-embedded polymer films for oral health: Development, characterization, and therapeutic potential.}, journal = {Colloids and surfaces. B, Biointerfaces}, volume = {255}, number = {}, pages = {114886}, doi = {10.1016/j.colsurfb.2025.114886}, pmid = {40544684}, issn = {1873-4367}, abstract = {The oral microbiome plays a crucial role in maintaining homeostasis, and microbial imbalances contribute to diseases such as periodontitis. Probiotic strains such as Lactobacillus rhamnosus and Lactobacillus reuteri have shown potential in restoring microbial balance in the oral cavity. However, their application remains challenging due to limited survival and adherence under intraoral conditions. Thus, we aimed to develop and evaluate mucoadhesive polymer films for local probiotic delivery. L. rhamnosus and L. reuteri were microencapsulated via spray drying and embedded in films composed of hydroxypropyl methylcellulose-polyvinyl alcohol (HPMC-PVA) and foamed polyvinyl alcohol (PVA). The films were characterized in terms of bacterial viability, tensile strength, folding endurance, and mucoadhesive properties. A proof-of-concept in vivo study was conducted by intraorally exposing enamel samples to two volunteers for eight hours, followed by confocal imaging and morphological analysis of adherent bacteria. Microencapsulation preserved high bacterial viability. The resulting films exhibited suitable mechanical properties and strong mucoadhesion. Biological evaluation revealed clear effects: films containing microencapsulated bacteria led to a statistically significant increase in adherent rod-shaped lactobacilli and a consistent reduction in coccoid bacteria associated with dysbiosis. The foamed PVA formulation showed the most pronounced modulation of the enamel-associated microbiota. These findings demonstrate that probiotic films can enable both bacterial stabilization and effective oral delivery. The system enhances colonization by beneficial bacteria while reducing potentially pathogenic cocci. This approach presents a promising strategy for microbiome-based prevention of oral diseases and merits further clinical investigation.}, }
@article {pmid40544677, year = {2025}, author = {Bortoluzzi, C and Watson, M and Iuspa, MA and Lumpkins, B and Mathis, G and Jones, M and Hofacre, C}, title = {Precision biotics enhance growth performance in broiler chickens by selectively modifying their intestinal microbiome to better respond to enteric challenges.}, journal = {Poultry science}, volume = {104}, number = {9}, pages = {105454}, doi = {10.1016/j.psj.2025.105454}, pmid = {40544677}, issn = {1525-3171}, abstract = {Precision biotics (PB) are innovative feed additives designed to influence key metabolic pathways in the microbiome, particularly those involved in short-chain fatty acid (SCFA) production. These SCFAs are crucial for the healthy development and functionality of the gastrointestinal tract (GIT) in chickens. Our hypothesis was that adding a glycan-based PB to the diet would steer microbial metabolism towards increased SCFA production in the ceca, thereby reducing the adverse effects of necrotic enteritis (NE) in chickens. These studies evaluated the supplementation of PB on the cecal microbiome and growth performance in broiler chickens exposed to a necrotic enteritis (NE) challenge. Experiment 1: Day-old chicks were assigned to three treatment groups: a control, a challenged control, and a challenged group supplemented with PB. The birds were vaccinated for coccidiosis at day 0 and challenged with Clostridium perfringens. Cecal content was collected from one bird per pen on days 22 and 42 for microbiome analysis. Experiment 2: Day-old chicks were again assigned to three treatments: control, challenged control, and challenged with PB. All birds were vaccinated for coccidiosis and challenged with Eimeria maxima on day 14 and later with C. perfringens. On day 21, birds were euthanized for NE lesion scoring. In Exp. 1, the supplementation of PB significantly improved (P < 0.05) the growth performance of the challenged birds. An increased relative abundance of species related to SCFA production was observed on day 42, including several Faecalibacterium species (P < 0.05). This was paired with an increased relative abundance of both propionate (P<0.05) and butyrate pathways in birds with PB supplementation. In Exp. 2, on day 21, the challenge impaired growth performance, but the supplementation of PB counteracted this effect (P < 0.05). On day 42, the supplementation of PB improved BW by 10 % (P < 0.0001), and the FCR by 8.4 % (P < 0.0001) when compared to the challenged group. The supplementation of PB reduced NE associated mortality (5.5 vs 0.5 %; P = 0.002) and reduced the lesions characteristic of NE (P < 0.0001). Taken together, the microbiome metabolic shift observed with the supplementation of PB explains the improvement in growth performance, resilience to enteric stress and faster recovery of the intestine, which consequently improves welfare and the sustainability of poultry production.}, }
@article {pmid40544571, year = {2025}, author = {Cao, J and Xu, Y and Zhang, C and Li, X and Liu, R and Wang, X and Dai, X}, title = {Enhancing the participation of water in the anaerobic digestion of sewage sludge for highly efficient methanogenesis.}, journal = {Water research}, volume = {284}, number = {}, pages = {124047}, doi = {10.1016/j.watres.2025.124047}, pmid = {40544571}, issn = {1879-2448}, abstract = {Water is widely present in sewage sludge, in which it constitutes the largest proportion; however, its participation in the methanogenesis of sludge has been overlooked. Here we revealed the mechanisms enhancing the participation of water in methanogenesis of sludge. Through stable isotope tracing experiments, we observed that isoelectric point pretreatment significantly enhanced the participation of water in CO2-reduction methanogenesis. Experimental results show that solid-liquid non-covalent interactions and interfacial water ordering in sludge were significantly enhanced. The former outcome drove electron transfer, while the latter provided an efficient proton channel. Combined with hydrogen/deuterium kinetic isotope effect (KIE) tests, it demonstrated that the water-mediated proton-coupled electron transfer (PCET) in the sludge were enhanced, accompanied by possible quantum tunnelling effect (KIE >> 10). Variations in the concentrations of key enzymes indicated that enhancing water-mediated PCET promoted both intracellular and extracellular electron-proton flow and accelerated the efficiency of mutual conversion between NADH and NAD[+], strongly driving ATP synthesis. Further genome-centric metagenomic analysis and reaction thermodynamic calculations revealed that enhancing water-mediated PCET triggered enrichment of CO2-reduction methanogenic consortia and effectively bypassed the limitation of H2 partial pressure, providing a thermodynamic advantage to promote collaborative methanogenic metabolisms. These findings provide a theoretical basis for regulating the methanogenesis of perishable organic solid waste by water.}, }
@article {pmid40544520, year = {2025}, author = {Zhang, E and Gong, GA and Huang, S and Bao, Y and Ji, L and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Zhang, W}, title = {Viral Metagenomics of the Bharal (Pseudois nayaur) within the Qinghai-Tibet Plateau Revealed Diverse Viruses.}, journal = {Polish journal of microbiology}, volume = {74}, number = {2}, pages = {143-152}, doi = {10.33073/pjm-2025-012}, pmid = {40544520}, issn = {2544-4646}, mesh = {Animals ; *Metagenomics ; Phylogeny ; Genome, Viral ; Tibet ; Feces/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Genetic Variation ; }, abstract = {The Qinghai-Tibetan Plateau (QTP) provides a home to diverse flora and fauna, and its ecosystems are unique worldwide. The study focused on the bharal, an endemic species found in the QTP and adjacent regions. We applied viral metagenomics technology to extract samples from the feces of 10 wild bharal. Viral nucleic acids were isolated, enriched, and sequenced from these samples, revealing the presence of a novel strain of Astroviridae virus. Phylogenetic analysis and sequence comparison identified this virus as part of the Mamastro-virus, forming a cluster with other Mamastrovirus species. Recombination analysis confirmed a multiple recombination event, suggesting that the new strain may be a potential recombinant. Additionally, nearly complete genome sequences of viruses belonging to the family Circoviridae were characterized, and a phylogenetic tree was constructed based on genotyping and predicted amino acid sequence analysis of the rep protein. Overall, this study helps us better understand the viral communities in the gut microbiome of the rare bharal. Moreover, the new recombinant discovered in this study will provide insights into the origin, genetic diversity, and evolution of bharal from the QTP and play a crucial role in future research on its presence in the intestinal ecology of sheep.}, }
@article {pmid40544519, year = {2025}, author = {Yu, X and Liang, J and Yang, R and Gai, W and Zheng, Y}, title = {Clinical Features and Value of Tracheal Aspirate Metagenomic Next-Generation Sequencing for Severe Pneumonia in Children in Pediatric Intensive Care Unit.}, journal = {Polish journal of microbiology}, volume = {74}, number = {2}, pages = {192-205}, doi = {10.33073/pjm-2025-016}, pmid = {40544519}, issn = {2544-4646}, mesh = {Humans ; Infant ; *High-Throughput Nucleotide Sequencing ; Male ; Child, Preschool ; Female ; *Metagenomics/methods ; Child ; Intensive Care Units, Pediatric ; *Trachea/microbiology ; *Pneumonia/microbiology/diagnosis/virology ; Microbiota/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Coinfection/microbiology ; }, abstract = {Pneumonia is a leading cause of mortality in children. While metagenomic next-generation sequencing (mNGS) has the potential to detect all the microorganisms in pneumonia patients, the relationship between these microorganisms and the patients' clinical characteristics remains to be established. Fifty-five children, diagnosed with severe pneumonia and undergoing tracheal aspirate (TA) mNGS for pathogen detection at The Heilongjiang Hospital of Beijing Children's Hospital between July 2021 and November 2022, were included in this study. The clinical characteristics, pathogen distribution, and microbiome features of these children were analyzed. Results showed that the rate of mixed infections was notably high (80%, 44/55), with bacterial-viral infections being the most common. Streptococcus pneumoniae, Mycoplasma pneumoniae (MP), Candida albicans, and Respiratory syncytial virus (RSV) were the most common pathogens in this cohort. Furthermore, RSV and S. pneumoniae were the most prevalent pathogens in children younger than 12 months (infants), while MP and Haemophilus influenzae were more commonly identified in children between 12 and 144 months. Increased richness and diversity of the microbiota were observed in the TA of the older children. Linear discriminant analysis (LDA) effect size (LEfSe) analysis identified that RSV and Streptococcus mitis were the specific species associated with infants. In contrast, Human bocaparvovirus 1 and Prevotella histicola were significantly enriched in the older children. In addition, the top 20 most abundant species exhibited correlations with neutrophil count and C-reactive protein. This study emphasizes the significance of employing mNGS to understand better the clinical characteristics and microbial diversity in pediatric patients with severe pneumonia.}, }
@article {pmid40544513, year = {2025}, author = {Muccee, F and Mohiuddin, F and Shahab, A and Almajwal, A and Afsar, T and Amor, H and Razak, S}, title = {Whole Genome Shotgun Sequencing-Based Insights into the Benzene and Xylene Degrading Potentials of Bacteria.}, journal = {Polish journal of microbiology}, volume = {74}, number = {2}, pages = {244-261}, doi = {10.33073/pjm-2025-020}, pmid = {40544513}, issn = {2544-4646}, mesh = {*Xylenes/metabolism ; *Benzene/metabolism ; Biodegradation, Environmental ; Whole Genome Sequencing ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Genome, Bacterial ; Soil Microbiology ; Phylogeny ; Soil Pollutants/metabolism ; DNA, Bacterial/genetics ; Shotgun Sequencing ; }, abstract = {Due to their hazardous effects on human health and air quality, benzene and xylene constitute the primary pollutants. Coupling the physicochemical strategies with bacterial bioremediation is an emerging mode of decontamination. Considering the limited understanding of benzene and xylene degradation pathways in the genus Bacillus, failure of earlier documented bacteria to degrade these compounds due to poor optimization and complicated real-world contamination scenarios, we initiated the current project. It is an attempt to explore the gene repertoire and pathways associated with the bioremediation of benzene and xylene in new and efficient bacteria. Eleven bacteria were isolated from tannery industry soil in a previous study. Bacterial DNA was extracted by the organic method. To prepare a sample for whole genome sequencing (WGS) analysis, a mixture of genomic DNA was made by adding DNA from each isolate in equimolar concentration (100 ng). The sample was subjected to WGS. Results obtained as FASTq files were submitted to Sequence Read Archives (SRA), NCBI, to get the accession number assigned. Taxonomic profiling revealed that the sample was composed of phyla Proteobacteria (76%), Firmicutes (16%) and unclassified phyla (8%). Functional annotation unraveled the presence of benzoate, m-, p- and o-xylene isomers, benzene, aminobenzoate, 2-, 3- and 4-fluorobenzoate, toluene, chloroalkane and chloroalkene, naphthalene, polycyclic aromatic hydrocarbons (PAHs), dioxin, caprolactum, atrazine, styrene, and chlorobenzene and chlorocyclohexane degradation enzymes and pathways. It is the first ever study documenting the benzene degradation pathway similar to Gram-negative bacteria, in the genus Bacillus, inhabiting the tannery soil and coexistence of metabolic pathways for multiple organic pollutants.}, }
@article {pmid40544449, year = {2025}, author = {Yew, WC and Young, GR and Cheung, W and Nelson, A and Berrington, JE and Smith, DL}, title = {Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk.}, journal = {STAR protocols}, volume = {6}, number = {3}, pages = {103917}, doi = {10.1016/j.xpro.2025.103917}, pmid = {40544449}, issn = {2666-1667}, abstract = {Bacteriophages and lipids in human milk may benefit preterm infant health by modulating gut microbiomes. Here, we present a protocol for analyzing the phageome and lipidome in preterm milk using shotgun metagenomics and untargeted lipidomics approaches, respectively. We describe steps for extracting phages and lipids in low-volume milk, characterizing phageome using an in-house bioinformatic pipeline, and statistical analysis to correlate the phageome and lipidome. Finally, we detail an in vitro assay to examine the associations between fatty acid chain length and phage morphotype. For complete details on the use and execution of this protocol, please refer to Yew et al.[1].}, }
@article {pmid40544407, year = {2025}, author = {Matos, JSS and Demoliner, M and Gularte, JS and Filippi, M and de Abreu Góes Pereira, VM and de Barros, MP and Spilki, FR}, title = {SARS-CoV-2 Spillback in Opossums, Southern Brazil.}, journal = {EcoHealth}, volume = {}, number = {}, pages = {}, pmid = {40544407}, issn = {1612-9210}, abstract = {This study focuses on monitoring of SARS-CoV-2 in free-living animals in the Vale dos Sinos region, Rio Grande do Sul, Brazil, aiming to verify the presence of this emerging virus using next-generation sequencing (NGS) technique. Rectal and oral swab samples were collected from 52 white-eared opossums (Didelphis albiventris) and submitted to metagenomics and subsequently directed SARS-CoV-2 genome sequencing. Five positive samples were found to originate from these animals' contact with human waste or contaminated water bodies, indicating the spillover of SARS-CoV-2 to D. albiventris.}, }
@article {pmid40544290, year = {2025}, author = {Chege, MN and Ferretti, P and Webb, S and Macharia, RW and Obiero, G and Kamau, J and Alberts, SC and Tung, J and Akinyi, MY and Archie, EA}, title = {Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {70}, pmid = {40544290}, issn = {2524-4671}, support = {R01 AG071684/NH/NIH HHS/United States ; R01 AG071684/NH/NIH HHS/United States ; DEB 1840223//National Science Foundation/ ; }, abstract = {BACKGROUND: Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While high-throughput sequencing is commonly used to characterize bacterial communities in animal microbiota, these methods are less often applied to gut eukaryotic composition. Here we used shotgun metagenomic sequencing to characterize eukaryotic diversity in the microbiomes of wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, sequencing depth, and season of sample collection.<br><br>RESULTS: We analyzed a total of 75 fecal samples collected in 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of all samples, respectively (percentages indicate the percent of samples in which each kingdom was observed). Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effects of season, host age, or host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples).<br><br>CONCLUSIONS: Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is important for primate health monitoring and management strategies.}, }
@article {pmid40544256, year = {2025}, author = {Mannavola, CM and De Maio, F and Marra, J and Fiori, B and Santarelli, G and Posteraro, B and Sica, S and D'Inzeo, T and Sanguinetti, M}, title = {Bloodstream infection by Lactobacillus rhamnosus in a haematology patient: why metagenomics can make the difference.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {47}, pmid = {40544256}, issn = {1757-4749}, support = {PE00000007, INF-ACT//EU funding for the MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases/ ; }, abstract = {BACKGROUND: Bloodstream infections (BSIs) pose a persistent threat to hospitalized patients, particularly those who are immunocompromised and susceptible to infections caused by anaerobic or facultative anaerobic bacteria. Alterations in gut microbiota composition can predispose individuals to intestinal domination by one or more pathobionts, increasing the risk of bacterial translocation into the bloodstream and subsequent bacteremia.<br><br>CASE PRESENTATION: We report the case of a 20-year-old female with multiple relapsed/refractory Philadelphia-negative B-cell acute lymphoblastic leukemia, initially referred to our hematology center for CAR-T cell therapy. The patient ultimately underwent allogeneic hematopoietic stem cell transplantation, which was complicated by infections, moderate-to-severe graft-versus-host disease, hepatic sinusoidal obstruction syndrome, and transplant-associated thrombotic microangiopathy, all contributing to a fatal outcome. Blood cultures obtained in the final week before the patient succumbed to multi-organ toxicity grew Lactobacillus rhamnosus. A fecal sample collected concurrently for intestinal microbiota characterization revealed a marked predominance of Bacillota (98.5%), with Lacticaseibacillus dominating at 47.9%, followed by Pediococcus (18.59%) and Staphylococcus (3.5%) at the genus level. We performed genomic comparison between the L. rhamnosus isolated from blood cultures and the best-matched strain detected in the intestinal microbiota.<br><br>CONCLUSIONS: We report the isolation of L. rhamnosus from blood cultures in a patient post hematopoietic cell transplantation, with genomic similarity to a gut-dominant L. rhamnosus strain. This case highlights the potential link between intestinal domination and subsequent bloodstream infection, supporting the value of gut microbiota profiling as an adjunctive tool for monitoring high-risk patients, such as hematopoietic cell transplant recipients.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13099-025-00722-3.}, }
@article {pmid40543872, year = {2025}, author = {Yu, PF and Wang, D and Ma, XG and Fu, YB and Han, LY and Wang, A and Jiang, DL and Sun, HW and Li, DX and Jin, X and Yang, KD and Zhang, LC and Tang, YL}, title = {System characteristics of integrated continuous flow simultaneous partial Nitrification, Anammox and Denitrification (SNAD) for NH4[+]-rich wastewater: performance, sludge evolution, metagenomic sequencing analysis.}, journal = {Environmental research}, volume = {283}, number = {}, pages = {122175}, doi = {10.1016/j.envres.2025.122175}, pmid = {40543872}, issn = {1096-0953}, abstract = {The integrated process of simultaneous partial nitrification, anammox, and denitrification (SNAD) is designed to achieve efficient nitrogen removal and carbon reduction. This study details the design and successful implementation of an innovative, single-piece continuous flow SNAD system for treating high concentration NH4[+] wastewater. The system leverages simultaneous anammox and denitrification (SAD) granular sludge and employs a strategy of dosing partial nitrification sludge, alongside meticulous control of pH, dissolved oxygen (DO), free ammonia (FA), and free nitrous acid (FNA) was applied to initiate the SNAD process. The spectral analysis results suggest a marginal reduction in the stability and flocculation properties of the SNAD granular sludge. Molecular analysis via 16S rRNA gene sequencing revealed ammonia-oxidizing bacteria, anaerobic ammonia-oxidizing bacteria, and denitrifying bacteria as the predominant microbial populations within the SNAD system. A marked increase in the abundance of related functional genes was observed, alongside a reduction in quorum sensing (QS) and ATP-Binding Cassette (ABC) transporter proteins. These findings suggest a possible attenuation in the secretion of native signaling proteins within the SNAD system.}, }
@article {pmid40543557, year = {2025}, author = {Nunley, BE and Weixler, A and Kim, HG and Xie, H and Sereewit, J and Hajian, P and Ellis, S and Mills, MG and Pérez-Osorio, AC and Goya, S and Gov, J and Dewar, R and Fernandes, G and Templeton, KE and Maloney, DM and Greninger, AL and Roychoudhury, P}, title = {Clinical performance evaluation of a tiling amplicon panel for whole genome sequencing of respiratory syncytial virus.}, journal = {The Journal of molecular diagnostics : JMD}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmoldx.2025.05.005}, pmid = {40543557}, issn = {1943-7811}, abstract = {Accurate genomic characterization of respiratory syncytial virus (RSV) is crucial for studies of epidemiology and viral evolution, including monitoring potential escape from newly authorized vaccines and prophylactic monoclonal antibodies. We adapted a viral genome tiling amplicon panel (UW-ARTIC) and developed a custom bioinformatic pipeline for high-throughput, cost-effective sequencing of both RSV-A and RSV-B subgroups. We established genome acceptability criteria and determined the performance characteristics of the panel including assay sensitivity, specificity, breadth of genome recovery, accuracy, and precision using contrived and remnant clinical specimens. High-quality genomes (>95% genome completeness; >500X and >1000X average depth for whole genome and fusion gene respectively) were recovered from samples with Ct ≤ 30 (∼594 and 2,004 copies per reaction for RSV-A and RSV-B respectively). Minor variants were accurately identified at >5% allele frequency. The assay showed high accuracy when compared to Sanger, shotgun metagenomic, and hybridization capture-based sequencing, as well as high repeatability and reproducibility. The UW-ARTIC RSV panel has utility for cost-effective RSV genome recovery in public health, clinical, and research applications. It has been used to generate FDA-reportable data for clinical trials of RSV antiviral products, with robust performance in global samples from as recently as the 2023/24 season. Continued genomic surveillance and future updates to primers will be essential for continued recovery of genomes as RSV continues to evolve.}, }
@article {pmid40543442, year = {2025}, author = {Li, Y and Liu, J and Huang, G and Chen, Z and Ma, X and Huang, L}, title = {Metagenomic diagnosis of congenital tuberculosis with coinfections in an extremely preterm infant conceived via in vitro fertilization.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {2}, pages = {116960}, doi = {10.1016/j.diagmicrobio.2025.116960}, pmid = {40543442}, issn = {1879-0070}, abstract = {We describe a case of congenital tuberculosis in an extremely preterm infant (24 weeks' gestation, 800 g) conceived via in vitro fertilization, complicated by cytomegalovirus and Klebsiella pneumoniae coinfections. Diagnosis was confirmed by metagenomic next-generation sequencing after conventional tests were inconclusive. Management included anti-tuberculosis, antiviral, and antibacterial therapy, as well as surgical correction of a patent ductus arteriosus. The infant demonstrated significant clinical recovery, with resolution of pulmonary, splenic, and cardiac abnormalities. This case underscores the value of advanced molecular diagnostics and multidisciplinary care in managing life-threatening neonatal infections.}, }
@article {pmid40543441, year = {2025}, author = {Hong, WL and Yao, LY and Zhong, Z and Meng, FJ and Zhang, WY and Lu, K and She, ZY}, title = {Successful management of Nocardia farcinica brain abscess in an immunocompetent adult with trimethoprim/sulfamethoxazole hypersensitivity: A case report and review.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {2}, pages = {116954}, doi = {10.1016/j.diagmicrobio.2025.116954}, pmid = {40543441}, issn = {1879-0070}, abstract = {BACKGROUND: Nocardia farcinica brain abscesses are rare in immunocompetent individuals. Trimethoprim/sulfamethoxazole (TMP/SMX) is first-line therapy, but hypersensitivity reactions necessitate alternative regimens. This report details successful management in a TMP/SMX-allergic patient.<br><br>CASE REPORT: A 38-year-old immunocompetent male presented with recurrent seizures. MRI revealed expanding left frontal lobe lesions. Surgical excision and metagenomic next-generation sequencing (mNGS) confirmed N. farcinica. Due to hypersensitivity to TMP/SMX, an alternative antibiotic regimen consisting of intravenous imipenem/cilastatin for 18 days and amikacin for 7 days was administered, followed by oral amoxicillin for 435 days and minocycline for 252 days. This therapeutic approach resulted in effective infection control, as evidenced by sustained clinical improvement over a 28-month follow-up period.<br><br>CONCLUSION: N. farcinica brain abscess can occur in immunocompetent adults, posing therapeutic challenges with TMP/SMX intolerance. This case demonstrates that alternative regimens-imipenem/cilastatin, amikacin, amoxicillin, and minocycline-can achieve sustained remission. Individualized therapy based on drug susceptibility and patient factors is critical.}, }
@article {pmid40543402, year = {2025}, author = {Aziz, T and Shabbir, MA and Sarwar, A and Khan, AA and Zhao, L and Yang, Z and Shami, A and Alwethaynani, MS and Al-Asmari, F and Alghamdi, AM and Al-Joufi, FA}, title = {Exploring the multifaceted probiotic potential of Lactiplantibacillus plantarum NMGL2, investigating its antimicrobial resistance profiles and bacteriocin production.}, journal = {Journal of microbiological methods}, volume = {236}, number = {}, pages = {107178}, doi = {10.1016/j.mimet.2025.107178}, pmid = {40543402}, issn = {1872-8359}, abstract = {BACKGROUND: Lactiplantibacillus plantarum is widely recognized for its probiotic and antimicrobial properties, making it a valuable candidate for food and clinical applications. Genomic characterization provides deeper insight into its potential health benefits and safety profile.<br><br>AIM: This study aimed to sequence and analyze the genome of L. plantarum NMGL2 to evaluate its antimicrobial resistance, probiotic potential, and genetic suitability for biotechnological applications.<br><br>METHODS: The genomic DNA of L. plantarum NMGL2 was extracted and sequenced using Illumina technology. Genome assembly and annotation were performed, followed by gene prediction using Prokka and identification of antimicrobial resistance genes, virulence factors, and probiotic markers via BLAST. Metagenomic analysis of gut microbiota samples and phylogenetic analysis were conducted to assess strain relationships with other L. plantarum isolates.<br><br>RESULTS: The genome analysis revealed approximately 3000 protein-coding genes, including those encoding bile salt hydrolase, antimicrobial peptides, and antibiotic resistance determinants. Phylogenetic analysis showed that NMGL2 is closely related to other probiotic L. plantarum strains, supporting its probiotic characteristics and its potential role in combating pathogens.<br><br>CONCLUSION: L. plantarum NMGL2 demonstrates promising probiotic traits and carries genes that support its application in food safety and clinical contexts. Further, in vivo studies are needed to validate its health benefits and ensure safety, particularly in treating gastrointestinal disorders.}, }
@article {pmid40543345, year = {2025}, author = {Li, S and Jiang, Y and Wang, J and Bartlam, M and Wang, Y}, title = {Chiral naproxen enhances horizontal transfer of antibiotic resistance genes in biofilms: Molecular docking reveals stereoselective mechanisms.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {138980}, doi = {10.1016/j.jhazmat.2025.138980}, pmid = {40543345}, issn = {1873-3336}, abstract = {The dissemination of antibiotic resistance genes (ARGs) is a growing global health concern. This study investigates how the chiral enantiomers of the non-antibiotic drug naproxen (NAP) influence ARG dissemination in biofilms. Metagenomic sequencing and binning analyses revealed that NAP enantiomers selectively enriched ARGs and their bacterial hosts, enhancing resistance to specific antibiotics. Notably, the stereoselective effects of NAP enantiomers not only shaped microbial community composition but also affected the potential for ARG spread. Mechanistically, exposure to R-NAP, in comparison to S-NAP, resulted in a 1.53-fold increase in reactive oxygen species (ROS) production, an 18.20 % enhancement in cell membrane permeability, and a 1.93-fold rise in the abundance of genes associated with the type IV secretion system (T4SS). These physiological and genetic changes promoted microbial aggregation and DNA conjugation, particularly enhancing the transfer of the sul1 gene within the Aquabacter genus through the coordinated action of T4SS, two-component systems (TCS), and quorum sensing (QS). Molecular docking and qRT-PCR analyses further revealed that the stereoselectivity of NAP enantiomers stemmed from their distinct binding interactions with proteins involved in horizontal gene transfer, shedding light on the molecular mechanisms underlying ARG dissemination under chiral NAP exposure.}, }
@article {pmid40543204, year = {2025}, author = {Yang, J and Kim, JS and Jeon, HW and Lee, J and Seo, JH}, title = {Integrated culture-based and metagenomic profiling of airborne and surface-deposited bacterial communities in residential environments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {382}, number = {}, pages = {126703}, doi = {10.1016/j.envpol.2025.126703}, pmid = {40543204}, issn = {1873-6424}, abstract = {Indoor environments host diverse microbial communities, where airborne and surface-deposited bacteria contribute to human exposure and potential health risks. This study applies metagenomic analysis to examine bacterial diversity in residential apartments, focusing on four key indoor spaces: kitchens, living rooms, toilets, and bedrooms. Airborne bacteria were collected using a culture-based air sampler and surface-deposited bacteria were collected via swabbing of high-contact areas; both were analyzed through 16S rRNA gene sequencing and bioinformatics processing. Airborne bacterial communities were primarily composed of Staphylococcus, Bacillus, and Enhydrobacter, whereas surface-deposited bacteria varied by location, with Streptococcus and Staphylococcus being most common on high-contact surfaces. Overall, surface-deposited bacterial diversity was greater than that of airborne communities, highlighting their distinct but interconnected roles in indoor microbial ecosystems. Functional pathway analysis suggested that indoor bacterial communities may harbor metabolic functions, as well as antibiotic resistance and virulence-related pathways, pointing to potential health concerns. Principal component analysis (PCA) showed clear distinctions between airborne and surface-deposited bacterial communities. These findings highlight the need for space-specific microbial management strategies, such as improved ventilation and surface hygiene, to reduce exposure risks and promote healthier indoor environments.}, }
@article {pmid40542451, year = {2025}, author = {Ji, S and Ahmad, F and Peng, B and Yang, Y and Su, M and Zhao, X and Vatanen, T}, title = {Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {149}, pmid = {40542451}, issn = {2049-2618}, support = {U22A20365//Joint Funds of National Natural Science Foundation of China/ ; T2341019//National Natural Science Foundation of China/ ; 2023A1515012429//Natural Science Foundation of Guangdong Province/ ; 2024B03J1343//Guangzhou Science and Technology Plan Project/ ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is widely used to treat severe infections and investigated for the treatment of complex diseases. The therapeutic efficacy of FMT is related to the successful engraftment of bacteriophages from healthy donors to recipients. However, gut bacteriophage contributions to FMT engraftment and treatment outcomes remain unclear.<br><br>METHODS: The gut phageome from previously published metagenomes of donors and recipients across 23 FMT studies was assembled and functionally annotated for a meta-analysis.<br><br>RESULTS: Gut phageome profiles of FMT recipients, especially those with recurrent Clostridioides difficile infection (rCDI), shifted toward donor phageomes, accompanied by increased phageome alpha diversity. Engraftment of donor phages varied between recipient conditions with the highest engraftment rate, overrepresented by putative temperate phage, in patients with rCDI. Consistently, a higher proportion of auxiliary metabolic genes (AMGs), with the potential to support and modulate bacterial metabolism, were annotated on putative temperate phages.<br><br>CONCLUSIONS: FMT leads to significant taxonomic, functional, and lifestyle shifts in recipient phageome composition. Future FMT studies should include gut phageome characterization and consider it as a potential factor in microbial community shifts and treatment outcomes. Video Abstract.}, }
@article {pmid40542420, year = {2025}, author = {Yu, M and Chu, Y and Wang, Y and Mo, L and Tan, X and Guo, S and Yuan, S and Ma, Y}, title = {Metagenomic analysis reveals gut phage diversity across three mammalian models.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {146}, pmid = {40542420}, issn = {2049-2618}, support = {2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; B2302023//Shenzhen Medical Research Fund/ ; B2302023//Shenzhen Medical Research Fund/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; }, abstract = {BACKGROUND: The gut virome plays a pivotal role in shaping the host's microbiota. However, gut viruses across different mammalian models, and their connections with the human gut microbiota remain largely unknown.<br><br>RESULTS: We identified 977 high-confidence species-level viral operational taxonomic units (vOTUs) in mice (hcMGV), 12,896 in pigs (hcPGV), and 1480 in cynomolgus macaques (hcCMGV) from metagenomes, respectively. Clustering these vOTUs at approximately genus level uncovered novel clades with high prevalence across animal guts (>&#x2009;=&#x2009;60%). In particular, crAss-like phages and cas-harboring jumbophages were characterized. Comparative analysis revealed that hcCMGV had a closer relationship with hcPGV than hcMGV, despite the animal-specific characteristics, and that 55.88% hcCMGV had connections with the human microbiota.<br><br>CONCLUSIONS: Our findings shed light on the diversity of gut viruses across these three animals, contributing to future gut microbial studies using model animals. Video Abstract.}, }
@article {pmid40542368, year = {2025}, author = {Liu, F and Zhuang, Y and Huang, X and Papazian, L and Cai, H and Shao, H and Chen, Q and Xie, C and Tang, K and Li, K and Wang, M and Xu, Y and Shen, P and Wang, Q and He, X and Wang, N and Wang, H and Dai, M and Xiong, Y and Zhong, L and Pan, Y and Chu, L and Yang, B and Zhang, G and Zhou, H and Xu, J and Jiang, C and Huang, L}, title = {The Landscape of lower respiratory tract herpesviruses in severe pneumonia patients: a multicenter, retrospective study with prospective validation.}, journal = {Critical care (London, England)}, volume = {29}, number = {1}, pages = {254}, pmid = {40542368}, issn = {1466-609X}, support = {82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; LTGY24H190001//Zhejiang Provincial Natural Science Fund/ ; 2025C02090//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; }, abstract = {OBJECTIVE: Herpesviruses are widely distributed in the lower respiratory tract, yet no study has comprehensively characterized their clinical features and prognostic impact in severe pneumonia.<br><br>METHOD: In this multicenter, retrospective study, we included severe pneumonia patients who underwent bronchoalveolar lavage fluid (BALF) metagenomic testing in intensive care units across 17 medical centers from January 2019 to June 2023. Based on metagenomic results, patients were categorized into herpesvirus-negative, HSV-1, EBV, CMV, HHV-6B, and HHV-7 groups. Propensity score matching and multivariable Cox regression were used to compare mortality between herpesvirus-positive and -negative patients. Interaction analyses were conducted to assess the impact of co-detection of different herpesviruses. Besides, main findings were validated using data from a prospective multicenter cohort.<br><br>RESULTS: Among 1,737 enrolled patients, the 28-day mortality rate was 41.3% (718/1,737). Herpesviruses were detected in 828 patients. Detection frequencies were: HSV-1 (26.8%), CMV (17.8%), EBV (16.6%), HHV-7 (5.3%), HHV-6B (2.2%), and VZV (0.5%). Clinical characteristics varied across herpesvirus groups. No single herpesvirus was independently associated with increased mortality compared to the negative group. However, co-detection of HSV-1 and CMV was significantly associated with higher 28-day mortality (vs. both negative: adj-HR&#x2009;=&#x2009;1.439, 95% CI: 1.093-1.894, P&#x2009;=&#x2009;0.009). This finding was validated in a prospective cohort (adj-HR&#x2009;=&#x2009;1.656, 95% CI: 1.061-2.585, P&#x2009;=&#x2009;0.026).<br><br>CONCLUSIONS: Herpesviruses are frequently detected in the lower respiratory tract of patients with severe pneumonia, with distinct clinical features across virus types. Co-detection of HSV-1 and CMV was associated with increased 28-day mortality.}, }
@article {pmid40542287, year = {2025}, author = {Fierer, N and Leung, PM and Lappan, R and Eisenhofer, R and Ricci, F and Holland, SI and Dragone, N and Blackall, LL and Dong, X and Dorador, C and Ferrari, BC and Goordial, J and Holmes, SP and Inagaki, F and Korem, T and Li, SS and Makhalanyane, TP and Metcalf, JL and Nagarajan, N and Orsi, WD and Shanahan, ER and Walker, AW and Weyrich, LS and Gilbert, JA and Willis, AD and Callahan, BJ and Shade, A and Parkhill, J and Banfield, JF and Greening, C}, title = {Guidelines for preventing and reporting contamination in low-biomass microbiome studies.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40542287}, issn = {2058-5276}, support = {SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; }, abstract = {Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.}, }
@article {pmid40541587, year = {2025}, author = {Pletsch, EA and Smith, AD and Ragonese, JS and Narrowe, AB and Cheung, L and Chen, CT and Wang, TTY and Dawson, HD}, title = {Broccoli consumption alters microbial diversity, metatranscriptome and host transcriptome in mice fed a Total Western Diet.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2025.05.041}, pmid = {40541587}, issn = {1541-6100}, abstract = {BACKGROUND: Cruciferous vegetables (CV) are a source of dietary fiber and phytochemicals that alter the microbiome in animals and humans. Constituent CV compounds, such as glucosinolates, have demonstrated anti-inflammatory properties in animal models, though often using doses and basal diets that are not relevant to humans. The mechanism(s) are unclear, but the gut microbiota may metabolize these compounds into bioactive molecules that influence immune pathways.<br><br>OBJECTIVE: We investigated the effects of a broccoli powder-supplemented Total Western Diet (TWD) on changes in the gut microbiome, the host transcriptome and the metatranscriptome at levels relevant to the human diet to understand how these changes affect metabolic and immune functions.<br><br>METHODS: C57BL/6 male mice (n = 40) were fed a TWD control diet for six weeks followed by supplementation with 0, 0.5, 1 or 2.5% broccoli powder (BP) (reflecting a human intake from &#xbc; -1 cup per day) for three weeks. Microbial communities from cecal contents were taxonomically profiled using 16S rRNA amplicon and shotgun metagenomic sequencing, and metatranscriptomics was used to assess functionality of the microbial communities. The host cecal transcriptome was also assessed.<br><br>RESULTS: Beta diversity was significantly higher (p = 1.20E-03) for mice fed the 2.5% BP diet compared to the control group at the species level. Lachnospiraceae MD335 was significantly more abundant in mice fed higher levels of broccoli, and analysis of bacterial RNA transcripts indicated a dose-dependent increase in transcription of genes associated with butyrate and acetate production, plant cell wall degradation and carbohydrate utilization. Activation of the aryl hydrocarbon receptor pathway in the cecum was evident.<br><br>CONCLUSIONS: Consumption of a broccoli-supplemented TWD induces changes in the gut microbiome, host and microbial gene expression that affect immune health and inflammation in the gut at levels that are achievable in the human diet.}, }
@article {pmid40541578, year = {2025}, author = {Tian, J and Hu, J and Xiong, Y and Deng, X and Fang, Y and Wang, G and Chi, R and Xiao, C}, title = {Metagenomic and metabolomic insights into microalgal-bacterial symbiosis under low carbon-to-nitrogen ratios.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132849}, doi = {10.1016/j.biortech.2025.132849}, pmid = {40541578}, issn = {1873-2976}, abstract = {Microalgal-bacterial symbiotic system (MBSS) is expected to efficiently treat ammonia nitrogen (NH4[+]-N) wastewater at low carbon-to-nitrogen ratio (CNR). In this study, MBSS was constructed and operated at CNRs of 0, 2, and 4 for 36 days, named as L (low CNR), M (medium CNR), and H (high CNR). Microbial interaction mechanisms were explored through metagenomics and non-targeted metabolomics. The average NH4[+]-N removal efficiencies of L, M, and H were 9.2 ± 4.3 %, 33.6 ± 10.9 %, and 51.6 ± 14.1 %, respectively. CNR significantly influenced NH4[+]-N removal. Metagenomics and metabolomics showed that bacteria dominate MBSS, with phylum Pseudomonadota having a large advantage. Addition of simple organic carbon sources may inhibit the generation of complex organic compounds by microalgae, consequently leading to bacteria utilizing simple carbon sources. Certain key microorganisms, genes, and metabolites respond to different CNRs to regulate MBSS performance. This study provides new insights into MBSS nitrogen removal at low CNR.}, }
@article {pmid40541123, year = {2025}, author = {Jiao, Y and Xiao, D and Li, X and Jiang, M and Li, H}, title = {Integrative fMRI and multiomics reveal neuroprotective mechanisms of Astragalus membranaceus in sleep deprivation-induced depression.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {145}, number = {}, pages = {156959}, doi = {10.1016/j.phymed.2025.156959}, pmid = {40541123}, issn = {1618-095X}, abstract = {BACKGROUND: Sleep deprivation (SD) is a significant public health concern and a risk factor for neuropsychiatric disorders, including depression. SD disrupts the gut-brain axis, causing dysbiosis and neuroinflammation. Astragalus membranaceus (AST) exhibits antidepressant and anti-inflammatory properties, including modulation of the gut microbiota; however, its neuroprotective effects on SD-induced neuropsychiatric disturbances remain largely unexplored. This study investigates the potential of AST using an innovative integrative multiomics approach.<br><br>PURPOSE: This study was conducted to investigate the neuroprotective effects of AST against SD-induced depression-like behavior and to explore the mechanism underlying its regulatory effects on the gut-brain axis.<br><br>METHODS: We established a chronic SD mouse model that was subjected to AST intervention and employed a pioneering integrative multiomics approach-combining resting-state functional magnetic resonance imaging for brain function, metagenomics for microbiota profiling, metabolomics for metabolic alterations, and transcriptomics for gene expression in key brain regions. Behavioral tests and cytokine assays complemented these analyses to comprehensively evaluate the therapeutic effects of AST.<br><br>RESULTS: SD induced depression-like behavior, neuroinflammation (IL-1&#x3b2;, IL-6, and TNF-&#x3b1; secretion), gut dysbiosis (Proteobacteria expansion, loss of beneficial microbes), and disrupted metabolic pathways. AST alleviated behavioral deficits, normalized brain connectivity, and reduced the levels of proinflammatory cytokines. It also reshaped microbiota, enriching Muribaculum and Butyricicoccus, and restored metabolic profiles, increasing the levels of short-chain fatty acids and promoting bile acid pathways. Integrated analysis linked microbiota restoration to reduced neuroinflammation and improved neuroprotection.<br><br>CONCLUSION: AST modulates the gut-brain axis to counteract SD-induced dysbiosis, neuroinflammation, and metabolic imbalance, alleviating depression-like symptoms. These findings offer novel mechanistic insights into the therapeutic potential of AST for SD-related neuropsychiatric conditions.}, }
@article {pmid40540838, year = {2025}, author = {Conti Taguali, S and Pöter, R and Aloi, F and Fernández-Trujillo, C and Acedo, A and La Spada, F and Li Destri Nicosia, MG and Pane, A and Schena, L and Cacciola, SO}, title = {Influence of environmental and agronomic variables on soil microbiome in citrus orchards: A comparative analysis of organic and conventional farming system.}, journal = {Microbiological research}, volume = {299}, number = {}, pages = {128260}, doi = {10.1016/j.micres.2025.128260}, pmid = {40540838}, issn = {1618-0623}, abstract = {Crop health and productivity depend on the structure and functionality of soil microbiota associated with the root system of plants. The agricultural policy of the European Union promotes organic farming systems to ensure environmental sustainability and food safety. The objective of this study was to investigate the impact of organic farming on soil microbiome in citrus orchards. The soil microbiota of eight conventionally and seven organically managed commercial citrus orchards across eastern Sicily was characterised using Illumina sequencing and BeCrop® primers for PCR amplification. The structure (diversity and relative abundance) and functionality of soil bacterial and fungal communities depended primarily on the sampling site. Other variables influencing the soil microbiome included soil total carbon content, seasonality, rootstock genotype, soil tillage and irrigation system. The latter three exerted differential effects on either bacterial or fungal communities. Conversely, age and visible health status of the tree had negligible influence on both communities. The differences between organically and conventionally managed citrus orchards accounted for a significant proportion of the variability, indicating a relevant effect of the farming system on soil microbiome. Organically managed orchards compared to those managed conventionally exhibited higher microbial diversity and a unique composition of nutrient-cycling microbes. In particular, organic farming promoted beneficial microbial functions, such as nitrogen fixation and phosphorus solubilization. Findings provide insights into the dynamic and complex interactions between environmental variables and soil microbial communities in citrus orchards, confirming the potential of microbial diversity as an indicator of sustainability in agricultural systems.}, }
@article {pmid40540566, year = {2025}, author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ}, title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.}, journal = {Science advances}, volume = {11}, number = {25}, pages = {eadq5232}, pmid = {40540566}, issn = {2375-2548}, abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.}, }
@article {pmid40540222, year = {2025}, author = {Xiao, YY and Lu, AL and Mo, HY and He, ZD and Wen, JL and Yin, X}, title = {Clinical value of metagenomic next-generation sequencing in patients with connective tissue diseases co-infections: a single-center study from southern hospital in China.}, journal = {Clinical rheumatology}, volume = {}, number = {}, pages = {}, pmid = {40540222}, issn = {1434-9949}, support = {81760298//National Natural Science Foundation of China/ ; 2021JJA140699//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; (Grant No. YYZS2023005).//the First Afliated Hospital of Guangxi Medical University/ ; }, abstract = {OBJECTIVES: This study aimed to assess the clinical value of metagenomic next-generation sequencing (mNGS) in patients with connective tissue diseases (CTDs) co-infections, thereby establishing a foundation for early infection identification and the development of anti-infective regimens.<br><br>METHODS: This retrospective study analyzed 304 CTD patients with suspected infections at the First Affiliated Hospital of Guangxi Medical University between October 2020 and April 2024. The study compared the diagnostic efficacy between mNGS and conventional microbiological testing (CMT), examined pathogen detection rates across different periods and pathogen types, and evaluated the clinical outcomes of mNGS-guided antimicrobial regimen adjustments.<br><br>RESULTS: Among the 180 confirmed infections (Group I), mNGS demonstrated superior diagnostic performance compared to conventional microbiological testing (CMT). mNGS exhibited significantly higher sensitivity (89.6% vs. 57.0%; OR&#x2009;=&#x2009;6.5, 95% CI: 3.7-11.0, p&#x2009;<&#x2009;0.001), with a specificity of 81.5%, positive predictive value (PPV) of 97.2%, and negative predictive value (NPV) of 52.4%. mNGS outperformed CMT in detecting bacterial and viral pathogens (p&#x2009;<&#x2009;0.05). Viral infections were the most common. Compared to prior studies, mNGS exhibited improved pathogen detection rates. mNGS-guided treatment optimization significantly enhanced clinical outcomes, with higher cure rates, lower mortality, and shorter hospital stays.<br><br>CONCLUSION: Current evidence suggests that while mNGS demonstrates superior diagnostic performance over CMT for detecting infections in CTD patients, their combined use provides optimal pathogen identification accuracy and enhanced clinical management. Key Points &#x2022; This is the larger-scale retrospective study of mNGS application in patients with CTDs co-infections following the Coronavirus Disease 2019 (COVID-19). &#x2022; We found that the distribution of pathogens and positivity rates have changed in recent years, especially after the COVID-19. &#x2022; The clinical value of mNGS was further demonstrated through its impact of mNGS results on antibiotic regimens and the analysis of negative samples.}, }
@article {pmid40539808, year = {2025}, author = {Sun, H and Chen, Q and Zhang, D and Hu, L and Li, S and Lu, M and Wang, Y and Su, H and Gao, Y and Guo, J and Zhao, Y and Du, J and Liu, C and Xia, H and Xu, Y and Ge, X and Yang, Q}, title = {Integrative study of pulmonary microbiome and clinical diagnosis in pulmonary tuberculosis patients.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0156324}, doi = {10.1128/spectrum.01563-24}, pmid = {40539808}, issn = {2165-0497}, abstract = {UNLABELLED: This study investigated the diagnostic potential of mNGS for detecting MTB in pulmonary tuberculosis patients. We analyzed pulmonary microbiome data to assess its impact on mNGS diagnostic accuracy and explored the association between microbiome profiles and clinical diagnosis. Bronchoalveolar lavage fluid samples were collected from 236 patients with pulmonary infections, and the diagnostic performance of mNGS was compared with traditional methods in detecting MTB. Furthermore, the incidence of false negatives and false positives, as well as the characteristics of the lung microbiota in TB patients, was analyzed to improve the diagnostic precision of mNGS. We observed that among all detection methods, mNGS showed the highest sensitivity (73.33%), followed by X-pert (60.00%), culture (53.33%), RT-PCR (53.33%), and sputum smear (23.33%). Notably, mNGS produced 3 false positive results in 236 samples, yielding a specificity of 98.54%. Analysis of the pulmonary microbiome revealed significant differences in both α-diversity and β-diversity between patients with TB and uninfected controls (P<0.05). Shannon index and Chao1 index were identified as significant predictors associated with MTB infection. ROC curve analysis demonstrated an AUC of 0.765, indicating good discriminatory performance. This study suggested that integrating wet-laboratory techniques with bioinformatics analysis can further enhance the diagnostic accuracy of mNGS for TB. Furthermore, microbiome analysis holds significant potential for the diagnosis of MTB infection.<br><br>IMPORTANCE: This study focuses on the application of next-generation sequencing (NGS) technology in detecting Mycobacterium tuberculosis in bronchoalveolar lavage fluid and explores the impact of M. tuberculosis infection on the pulmonary microbiome. By optimizing the methods and conducting microbial analyses, the accuracy of metagenomic NGS for detecting M. tuberculosis has been improved.}, }
@article {pmid40539782, year = {2025}, author = {Qi, Y-H and Ye, Z-X and Feng, K-H and Ma, X-W and Zhang, C-X and Hu, M-H and Shi, M and Chen, J-P and Li, J-M}, title = {Diversity and evolutionary history of RNA viruses among different horseshoe crab species.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0016425}, doi = {10.1128/jvi.00164-25}, pmid = {40539782}, issn = {1098-5514}, abstract = {Horseshoe crabs (Xiphosura: Limulidae) are the sole surviving species of the class Merostomata, with only four extant species remaining today. Recent advances in metagenomic next-generation sequencing have unveiled a vast diversity of RNA viruses and non-retroviral endogenous RNA viral elements (nrEVEs) in invertebrates. This raises intriguing questions about the RNA virome and nrEVEs in horseshoe crabs as "living fossils," potentially offering insights into the evolutionary relationships between RNA viruses and these ancient organisms. In this study, 22 novel RNA viruses were identified across the four horseshoe crab species by screening 117 data sets, including picornaviruses, totiviruses, a flavivirus, a rhabdovirus, as well as a plant-associated tombusvirus and a fungi-associated narnavirus. Additionally, 20 nrEVEs were identified in the genomes of the four horseshoe crab species (hcEVEs), with most sharing homology with the viral family Chuviridae (N = 11), supporting the hypothesis that modern negative-sense RNA viruses may trace their origins to ancient oceanic chuviruses. A time-scaled phylogenetic tree based on hcEVEs suggests that at least two independent ancient chuvirus infections and genome integration events occurred in the common ancestor of horseshoe crab species. Interestingly, transcriptional analyses indicated that hcEVE-containing transcripts display typical exon-intron structures in the three Asian horseshoe crab species, suggesting that these hcEVEs may have been co-opted by horseshoe crabs during coevolution. These findings advance our understanding of the RNA viruses associated with horseshoe crabs and shed light on the potential role of RNA viruses in shaping the evolutionary history of this "living fossil" arthropod host.IMPORTANCERecent studies have discovered abundant RNA viruses in invertebrates, revealing that viral genomes may integrate into host genomes, creating a genetic record of past infections. In this study, we explored the evolutionary relationship between RNA viruses and the four extant horseshoe crab species-the last representatives of the class Merostomata, often termed "living fossils"-by analyzing viral sequences embedded in their genomes. The presence of chuvirus-like sequences in the genomes of these horseshoe crabs suggests that modern negative-sense RNA viruses may trace their origins back to ancient chuviruses from the ocean. Furthermore, we identified at least two independent ancient integrations of chuviruses in the evolutionary history of horseshoe crabs, with one orthologous gene containing a chuvirus-derived G protein gene/coding sequence potentially inherited from a common ancestor of the three Asian species before their divergence. Our findings contribute to a deeper understanding of the long-term coevolution between RNA viruses and their arthropod hosts.}, }
@article {pmid40539777, year = {2025}, author = {Olmsted, CN and Gahler, M and Roden, E and Peterson, B and Lazarcik, J and Tran, PQ and Berg, M and Bryant, DA and Goudeau, D and Malmstrom, RR and Qin, M and McMahon, KD}, title = {Cryptic cycling by electroactive bacterioplankton in Trout Bog Lake.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0178924}, doi = {10.1128/aem.01789-24}, pmid = {40539777}, issn = {1098-5336}, abstract = {The potential for extracellular electron transfer (EET) is a prevailing genomic feature of humic lake bacterioplankton. However, there has been little evidence for the substantial ecological contribution predicted by genetics. We hypothesized that anoxygenic phototrophic electrotrophs and accompanying heterotrophic electrogens cycle dissolved organic matter (DOM) between oxidized and reduced states. We predicted that such bacterioplankton would exhibit diel-scale oscillations due to the light dependency of photosynthesis. Using Trout Bog Lake in Wisconsin, USA, as our model ecosystem, we profiled the water column with depth-discrete metagenomic, physiochemical, and electrochemical analyses. We observed variation in oxidation reduction potential (ORP) in response to sunlight, initiating at depths populated by anoxygenic phototrophs with EET genes. We developed an automated buoy to measure electric current flow between many pairs of electrodes simultaneously, observing correlation in electron consumption to sunlight. Our results, combined with published metatranscriptomic analysis, indicate the occurrence of electron cycling between phototrophic oxidation (electrotrophic metabolism) by Chlorobium and anaerobic respiration (electrogenic metabolism) by Geothrix, involving DOM. We also repeatedly observed gradual seasonal increases in hypolimnion ORP throughout summer. These diel and seasonal patterns imply that electroactive DOM mediates the ecology of electroactive bacteria in lakes, controlling humic lake methane emissions.IMPORTANCEWe investigated the physical, chemical, and redox characteristics of a bog lake and electrodes hung therein to test the hypothesis that dissolved organic matter is being cycled between oxidized and reduced states by electroactive bacterioplankton powered by phototrophy. To do so, we performed field-based analyses on multiple timescales using both established and novel instrumentation. We paired these analyses with recently developed bioinformatics pipelines for metagenomics data to investigate genes that enable electroactive metabolism and accompanying metabolisms. Our results are consistent with our hypothesis and yet upend some of our other expectations. Our findings have implications for understanding greenhouse gas emissions from lakes, including electroactivity as an integral part of lake metabolism throughout more of the anoxic parts of lakes and for a longer portion of the summer than expected. Our results also give a sense of what electroactivity occurs at given depths and provide a strong basis for future studies.}, }
@article {pmid40539111, year = {2025}, author = {Ma, Y and Wu, Q and Wang, X and Sui, W and Zhang, X}, title = {Carbon components in organic amendments drive nitrogen metabolism in one-year-long anaerobic soil microcosms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1588169}, pmid = {40539111}, issn = {1664-302X}, abstract = {INTRODUCTION: Long-term studies on the dynamic changes in nitrogen metabolism and functional microbial communities under anaerobic conditions, particularly those driven by organic amendments, remain scarce.<br><br>METHODS: We conducted a year-long anaerobic microcosm experiment using three organic amendments-aerobically fermented pig-manure digestate (ACM), compost (ACP) and straw powder (ACS)-alongside an inorganic fertilizer-only control (ACN).<br><br>RESULTS: Temporal shifts revealed that organic amendments drove distinct nitrogen metabolism pathways. Amendments of digestate and compost promoted the proliferation of nitrogen-mineralizing bacteria such as Ramlibacter and Lysobacter, leading to significant ammonium accumulation. After 12-month incubation, the ACM treatment caused a 75.6-fold increase in ammonium, a 43.4% rise in total nitrogen (TN), and a 27.0% increase in total organic carbon (TOC). In contrast, the ACS treatment exhibited superior nitrogen fixation, with an average of 1.69-fold higher rate than ACM and 5.30 fold higher than ACP The ACS treatment enriched cellulolytic nitrogen-fixing bacteria, including Clostridium, and nitrogen-fixing archaea.<br><br>DISCUSSION: This study provides profound insights in to the unique nitrogen metabolism pathways influenced by organic amendments under anoxic conditions, ultimately offering valuable insights into improved soil fertility and sustainable nitrogen management practices in agricultural systems.}, }
@article {pmid40539103, year = {2025}, author = {Lin, ZY and He, SS and Mo, ZT and Liao, XT and Feng, ZS and Kong, J and Zhu, L and Li, Y and Tan, HY and Su, ZW and Jia, CH and Wu, F}, title = {Integrated analysis of serum metabolomics and fecal microbiome in infants with necrotizing enterocolitis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1584041}, pmid = {40539103}, issn = {1664-302X}, abstract = {BACKGROUND: Necrotizing enterocolitis (NEC), a lethal gastrointestinal disorder in preterm infants, remains poorly understood in its pathology, and early diagnosis are critically limited. Multi-omics approaches present unprecedented opportunities to elucidate NEC pathogenesis and identify clinically translatable biomarkers.<br><br>METHODS: Infants with Bell stage II-III NEC and gestational age-matched controls were enrolled. Serum/stool samples from NEC patients at acute (NEC-D) and recovery (NEC-R) phases, and controls (non-NEC) were collected. Fecal metagenomic sequencing and serum untargeted metabolomic profiling were performed. Clinical parameters were compared.<br><br>RESULTS: The study comprised seven NEC and seven non-NEC infants. Baseline neonatal characteristics and maternal perinatal parameters showed no significant differences between NEC-D and non-NEC except for markedly lower leukocyte counts in NEC infants. Fecal metagenomics revealed severely diminished alpha diversity in NEC-D versus both non-NEC controls and NEC-R, characterized with lower Chao1 index. NEC-D exhibited elevated Escherichia coli relative abundance alongside reduced Staphylococcus haemolyticus, Staphylococcus aureus, Staphylococcus epidermidis, and Lactobacillus paracasei. Correspondingly, KEGG functional gene analysis demonstrated impaired metabolism in NEC-D. Serum metabolomics identified significantly decreased ornithine, DL-arginine, L-threonine, leucine, and D-proline in NEC-D versus non-NEC. NEC-D also showed lower taurodeoxycholic acid, glycocholic acid, and chenodeoxycholic acid compared to NEC-R. Integrative analysis revealed a positive correlation between the metabolites D-proline and ornithine and the Lactobacillus paracasei, Staphylococcus epidermidis, and Staphylococcus aureus abundance.<br><br>CONCLUSION: NEC is characterized by gut microbiota dysbiosis with reduced diversity, altered functional gene expression, and disrupted host-microbiota metabolic crosstalk. The identified serum metabolite-microbiome correlations provide mechanistic insights into NEC pathogenesis and potential diagnostic biomarkers.}, }
@article {pmid40538825, year = {2025}, author = {Hofman, J and Brenerova, P and Borilova Linhartova, P}, title = {State-of-the-art approaches in the investigation of human seminal bacteriome using metagenomic methods.}, journal = {Frontiers in reproductive health}, volume = {7}, number = {}, pages = {1557912}, pmid = {40538825}, issn = {2673-3153}, abstract = {Although the understanding of the causes of infertility is the key to its successful treatment, recent studies have shown that as many as 50% of male-caused infertility cases are considered idiopathic. The microbial colonization of the male reproductive system was shown to be associated with reduced male reproductive fitness. Investigation of the seminal microbiome, however, remains challenging. This article aimed to improve this situation by creating the first comprehensive review of literature on the metagenomic methods (including the pre-analytical and analytical approaches) used in the research on human seminal bacteriome (total bacterial DNA in the matrix), published in 2018-2024. A total of 29 studies addressing the analysis of the human seminal bacteriome were identified. The analysis typically involved DNA extraction from the supernatant using commercial kits, amplification of the gene for 16S rRNA, and sequencing of amplicons. Where the separation of seminal plasma was performed, centrifugation was the dominant method used for this purpose. The significant heterogeneity in individual steps of methodological approaches in the analysis of the human seminal bacteriome complicates the comparison of results among studies and the establishment of standard procedures, hindering clinical advancements. For this reason, a protocol for the analysis of the human seminal plasma bacteriome is proposed here, which could lead to improved comparability of results among studies and make future research more efficient. This protocol is founded on rigorous quality control measures, compliance with the WHO laboratory manual for sample collection, extensive pretreatment involving mechanical and enzymatic lysis, DNA extraction using the QIAamp DNA Mini Kit (Qiagen), and short-read sequencing conducted on the MiSeq platform (Illumina).}, }
@article {pmid40538739, year = {2025}, author = {Zou, ZL and Shen, ZH}, title = {Amoebic liver abscess co-infected with bacterial liver abscess: A rare case in an immunocompromised patient.}, journal = {IDCases}, volume = {41}, number = {}, pages = {e02279}, pmid = {40538739}, issn = {2214-2509}, abstract = {We present a complex case of a 43-year-old HIV-positive Chinese male with co-infection of amoebic liver abscess (ALA) and bacterial liver abscess caused by Salmonella enterica subsp. enterica serotype Typhi (abbreviated as Salmonella Typhi). The patient presented with fever and abdominal pain. Initial bacterial cultures identified Salmonella Typhi, but targeted antibiotic therapy failed to resolve his symptoms, prompting to further investigation. Metagenomic next-generation sequencing (mNGS) of pleural and liver abscess drainage fluids revealed sequences of Entamoeba histolytica, confirming a dual infection. The patient was treated with combination therapy, resulting in clinical improvement. This case highlights diagnostic challenges in immunocompromised patients and underscores the critical role of mNGS in identifying co-infections and guiding treatment. Early recognition and timely intervention are essential for achieving optimal outcomes in such complex cases.}, }
@article {pmid40538403, year = {2025}, author = {Chengsupanimit, T and Mahajan, A and Farhadian, S and Machiavello Roman, F}, title = {Case Report: Spinal cord abscess due to Nocardia farcinica presenting as longitudinally extensive transverse myelitis.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1613770}, pmid = {40538403}, issn = {2296-858X}, abstract = {A middle-aged man, renal transplant recipient, was admitted with lower extremity paralysis, loss of sensation and urinary retention. The initial diagnostic workup revealed extensive inflammatory spinal changes on imaging, consistent with longitudinally extensive transverse myelitis. Cerebrospinal fluid testing demonstrated neutrophilic pleocytosis; routine tests for bacterial and viral pathogens were negative. The patient received high-dose steroids for presumed autoimmune myelitis, but his condition worsened. Repeat spinal imaging revealed an intramedullary spinal cord abscess and a loculated collection in the cauda equina. Nocardia farcinica was isolated from spinal biopsy tissue cultures and metagenomic sequencing of cerebrospinal fluid. He received treatment with trimethoprim-sulfamethoxazole and linezolid, with subsequent improvement of the radiological abnormalities. At outpatient follow-up two months after initiating antimicrobials, the patient endorsed improved upper extremity strength, though remained paraplegic. This case report highlights the protean manifestations of central nervous system nocardiosis and the benefits of using metagenomic sequencing to diagnose complex central nervous system infections.}, }
@article {pmid40537892, year = {2025}, author = {Kang, J and Choi, Y and Keum, GB and Doo, H and Kwak, J and Kim, H and Chae, Y and Lee, S and Yang, H and Kim, S and Sun, X and Kim, HB and Yoo, SJ}, title = {Effect of Diet and Lifestyle Changes on Gut Microbial Diversity in Healthy Adolescents.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2503018}, doi = {10.4014/jmb.2503.03018}, pmid = {40537892}, issn = {1738-8872}, abstract = {The human gut microbiome is a complex ecosystem shaped by both intrinsic and extrinsic factors, with external elements such as diet and exercise significantly influencing its diversity and composition. In this study, we evaluated gut microbiome shifts in adolescents participating in a four-week camp with controlled diets, lifestyle, and a healthy living environment. Stool samples were collected before and after the camp period and analyzed through 16S rRNA gene sequencing to assess changes in microbial composition and diversity. Post-intervention, gut microbiome diversity increased significantly, with notable changes in the relative abundance of taxa such as Lachnospira, Alistipes, and Barnesiella, which are associated with enhanced immune function and gut health. Additionally, functional prediction using PICRUSt indicated an increase in genes associated with energy production and metabolism, suggesting a broader functional impact of lifestyle modifications on gut microbial functionalities. These findings revealed the potential causal relationships between lifestyle modifications and gut microbiome shifts, providing valuable insights into the interactions between environment, diet, and the gut microbiota.}, }
@article {pmid40537881, year = {2025}, author = {Linghu, Y and Hu, RS and Tang, XM and Li, RT and Li, WY and Wu, JH}, title = {Unveiling viral diversity and dynamics in mosquitoes through metagenomic analysis in Guizhou Province, China.}, journal = {Infectious diseases of poverty}, volume = {14}, number = {1}, pages = {51}, pmid = {40537881}, issn = {2049-9957}, support = {Qian Ke He Platform Talent-GCC [2022] 033-1//The Training Project for High-Level Innovative talents in Guizhou Province, China/ ; Qian Ke He Platform Talent-CXTD [2022] 004//The Science and Technology Innovation Talent team of Guizhou Province, China/ ; Project Contract Number: Xiao Bo He J Zi [2023] 44//The Scientific Research Foundation for Advanced Talents, Guizhou Medical University/ ; NO. 2024GCC16Z//The High-level Talent Research Start-up Project of Sichuan University of Arts and Science/ ; }, abstract = {BACKGROUND: Poverty, disease, and vector ecology intersect to present ongoing health threats, particularly in ecologically sensitive regions. Guizhou Province in China, with its complex karst topography and rich biodiversity, offers a unique environment to study mosquito-borne viral transmission. Despite over 5000 reported cases of Japanese encephalitis in the past two decades and the detection of Zika virus in 2016, the virological landscape of this region remains poorly understood. This study aims to characterize the mosquito-associated virome, assess viral diversity, and identify factors influencing transmission dynamics in Guizhou Province.<br><br>METHODS: Between 2021 and 2022, we conducted a 2-year mosquito surveillance across eight ecologically distinct regions in Guizhou Province. Adult mosquitoes were collected using a variety of methods, including BG Mosquitaire CO2 traps, mosquito-killing lamps, manual collection, human bait traps, and oviposition traps. To investigate the virome diversity and dynamics within mosquito populations, we performed metagenomic sequencing and bioinformatics analysis on pooled mosquito samples collected from geographically diverse sampling sites.<br><br>RESULTS: We collected more than 40,000 adult mosquitoes, primarily belonging to four genera: Aedes, Anopheles, Armigeres, and Culex. Dominant species included Aedes albopictus, Anopheles sinensis, Armigeres subalbatus, and Culex tritaeniorhynchus. Notably, we report the first provincial record of the Anopheles baileyi complex, expanding the known distribution of mosquito vector in this region. Viral metagenomic sequencing, coupled with bioinformatic analysis, identified 162 viral contigs, including 140 known and 22 previously uncharacterized viruses. We experimentally confirmed the genotypes of three medically important zoonotic viruses: Japanese encephalitis virus (JEV-GI), Getah virus (GETV-GIII) and Banna virus (BAV-A2). Comparative analysis of viral abundance across mosquito species revealed that Aedes albopictus populations in Guizhou harbor a distinct virome composition, diverging from those reported in other geographic regions.<br><br>CONCLUSIONS: This study presents the comprehensive characterization of the mosquito-associated virome in Guizhou Province, providing critical insights into viral diversity, vector competence, and transmission dynamics within karst ecosystems. The detection of multiple zoonotic viruses highlights the need for strengthened surveillance and targeted public health interventions in this region.}, }
@article {pmid40537478, year = {2025}, author = {Sommer, AJ and Skarlupka, JH and Teseo, S and Otani, S and Suen, G and Coon, KL and Sapountzis, P}, title = {Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {111}, pmid = {40537478}, issn = {2055-5008}, support = {WIS04039//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; }, abstract = {Dairy farms are major reservoirs of zoonotic bacterial pathogens, which harbor antimicrobial resistance genes (ARGs), and raise critical questions about their dissemination on and off the farm environment. Here, we investigated the role of coprophagous muscid flies (Diptera: Muscidae) as carriers of zoonotic pathogens and antimicrobial resistance. We collected cow manure and flies on a dairy farm and used shotgun metagenomics to identify the presence of clinically relevant bacteria, virulence factors, and ARGs in both environments. Our results reveal that, although the fly microbiome is largely composed of manure-associated taxa, they also harbor specific insect-associated bacteria, which may be involved in nutrient provisioning to the host. Furthermore, we identifed shared ARGs, virulence factors, and zoonotic pathogens enriched within the fly gastrointestinal tract (GIT). Our study illustrates the potential flow of pathogenic microorganisms from manure to coprophagous flies, suggesting that flies may pose an important zoonotic threat on dairy farms.}, }
@article {pmid40537448, year = {2025}, author = {Rudi, K and Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Philip, M and Martin, J and Sundt, M&#xd8; and Snipen, LG}, title = {The Coastal Seafloor Microbiota Is Structured by Local Selection of Cosmopolitan Taxa.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70123}, doi = {10.1111/1758-2229.70123}, pmid = {40537448}, issn = {1758-2229}, support = {320076//Norges Forskningsr&#xe5;d/ ; }, abstract = {Understanding the assembly processes of the coastal seafloor microbiota is crucial for gaining insights into how ocean ecosystems work. In our study, we addressed the question about how local selection affects the global distribution of coastal seafloor microorganisms. We identified two main clusters of samples by examining the geographical distribution of 356 high-quality prokaryote metagenome-assembled genomes (MAGs) from 94 coastal samples collected along the Norwegian and Icelandic coasts. There was no identifiable correlation between the abundance of MAGs and the geographic distance between them central to the identified clusters (no distance decay). In contrast, noncentral MAGs demonstrate a pronounced distance decay. We also observed significant functional differences between the two sample clusters. One cluster showed enrichment in functions such as dissimilatory nitrate reduction to ammonium (DNRA), acetoclastic methanogenesis, thiosulphate conversion and acetate and butyrate metabolism. The other cluster was enriched in propionate metabolism, nitrite oxidation to nitrate and cobalamin-dependent carbon fixation. These results suggest that localised environmental selection acts on cosmopolitan taxa to shape seafloor microbiota. Our findings therefore profoundly impact the understanding of seafloor ecological processes and their management.}, }
@article {pmid40536635, year = {2025}, author = {Zhang, X and Feng, Y and Shi, X and Zhang, Y and Wang, W}, title = {Degradable plastic of high-density polyethylene (HDPE)-CaCO3 reduced the abundance of antibiotic resistance genes in soil.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {7}, pages = {773}, pmid = {40536635}, issn = {1573-2959}, support = {20170031//Henan Normal University Outstanding Youth Science Fund/ ; 20170031//Henan Normal University Outstanding Youth Science Fund/ ; 20170031//Henan Normal University Outstanding Youth Science Fund/ ; 41907121//National Natural Science Foundation of China/ ; }, mesh = {*Polyethylene/chemistry ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Calcium Carbonate/chemistry ; *Biodegradable Plastics ; *Soil Pollutants/analysis ; Soil/chemistry ; Biodegradation, Environmental ; Plastics ; }, abstract = {A large number of degradable plastics have entered the market because traditional plastics are not easy to degrade. However, degradable plastics have problems such as inability to be completely degraded in time. Therefore, evaluating whether degradable plastics pose environmental harm is both urgent and crucial. High-density polyethylene (HDPE) disposable degradable plastic bags which were filled with CaCO3 have been widely circulated in the market. But there has been no reported research on whether HDPE/CaCO3 degradable plastics are harmful to the environment. Therefore, in this study, HDPE-CaCO3 degradable plastics circulated in the market were taken as the research objects, and the antibiotic resistance genes (ARG), a new type of environmental pollution indicator, were used as the evaluation indicators. The HDPE/CaCO3 degradable plastics were made into plastic pieces less than 10 mm in size and then evenly mixed with soil. After 30 days, metagenomic sequencing was performed on the soil microorganisms, and the soil microbial community structure and the abundance of ARGs in the soil were analyzed to evaluate the potential environmental risks of HDPE/CaCO3 degradable plastics. The results showed that comparing with HDPE, the HDPE/CaCO3 degradable plastics could reduce the abundance of soil ARGs and change the soil microbial community structure. Our results indicated that HDPE/CaCO3 degradable plastics imposed a reduced environmental impact compared to conventional HDPE plastics.}, }
@article {pmid40535544, year = {2025}, author = {Wang, X and Cao, D and Chen, W and Sun, J and Hu, H}, title = {Metagenomics reveals unique gut mycobiome biomarkers in major depressive disorder - a non-invasive method.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1582522}, pmid = {40535544}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Depressive Disorder, Major/microbiology/diagnosis ; *Mycobiome ; Biomarkers/analysis ; Male ; Female ; Adult ; *Metagenomics/methods ; *Fungi/classification/genetics/isolation &amp; purification ; Middle Aged ; Machine Learning ; Support Vector Machine ; Case-Control Studies ; Feces/microbiology ; }, abstract = {BACKGROUND: An increasing amount of evidence suggests a potential link between alterations in the intestinal microbiota and the onset of various psychiatric disorders, including depression. Nevertheless, the precise nature of the link between depression and the intestinal microbiota remains largely unknown. A significant proportion of previous research has concentrated on the study of gut bacterial communities, with relatively little attention paid to the link between gut mycobiome and depression.<br><br>METHODS: In this research, we analyzed the composition and differences of intestinal fungal communities between major depressive disorder (MDD) and healthy controls. Subsequently, we constructed a machine learning model using support vector machine-recursive feature elimination to search for potential fungal markers for MDD.<br><br>RESULTS: Our findings indicated that the composition and beta diversity of intestinal fungal communities were significantly changed in MDD compared to the healthy controls. A total of 22 specific fungal community markers were screened out by machine learning, and the predictive model had promising performance in the prediction of MDD (area under the curve, AUC = 1.000). Additionally, the intestinal fungal communities demonstrated satisfactory performance in the validation cohort, with an AUC of 0.884 (95% CI: 0.7871-0.9476) in the Russian validation cohort, which consisted of 36 patients with MDD and 36 healthy individuals. The AUC for the Wuhan validation cohort was 0.838 (95% CI: 0.7403-0.9102), which included 40 patients with MDD and 42 healthy individuals.<br><br>CONCLUSION: To summarize, our research revealed the characterization of intestinal fungal communities in MDD and developed a prediction model based on specific intestinal fungal communities. Although MDD has well-established diagnostic criteria, the strategy based on the model of gut fungal communities may offer predictive biomarkers for MDD.}, }
@article {pmid40535541, year = {2025}, author = {Kato-Kogoe, N and Tsuda, K and Kudo, A and Sakaguchi, S and Omori, M and Komori, E and Ohmichi, M and Hamada, W and Nakamura, S and Nakano, T and Tamaki, J and Ueno, T}, title = {Salivary microbiota and IgA responses are different in pre-diabetic individuals compared to normoglycemic controls.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1591285}, pmid = {40535541}, issn = {2235-2988}, mesh = {Humans ; *Saliva/microbiology/immunology ; Female ; Male ; *Immunoglobulin A/analysis/immunology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Microbiota/immunology ; *Prediabetic State/immunology/microbiology ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Diabetes Mellitus, Type 2/immunology/microbiology ; Aged ; Metagenomics ; DNA, Bacterial/genetics/chemistry ; }, abstract = {INTRODUCTION: In recent years, changes in the oral microbiota of patients with type 2 diabetes mellitus (T2DM) have been increasingly recognized. The salivary microbiota may also be altered in pre-diabetes, which is the earliest stage of abnormal blood glucose regulation and a reversible stage preceding T2DM; however, its characteristics are poorly understood. Salivary immunoglobulin A (IgA) is a host defense factor central to the oral immune system and may play an important role in regulating the salivary microbiota. Given that alterations in immunoreactivity are observed in pre-diabetes, we hypothesized that the salivary IgA response may also be altered; however, limited knowledge exists regarding this. Therefore, in the present study, we aimed to evaluate the characteristics of salivary microbiota and IgA responses against salivary microbiota in individuals with pre-diabetes, comparing them to those in individuals with normoglycemia.<br><br>METHODS: Saliva samples were collected from 101 pre-diabetic individuals (PreDM group) and 101 age- and sex-matched normoglycemic controls (Normal group). Further, 16S rRNA metagenomic analysis was performed to compare bacterial microbiota composition. For each of the 19 saliva samples from the PreDM and Normal groups, IgA-enriched and IgA-nonenriched fractions were separated via magnetic-activated cell sorting, followed by 16S rRNA metagenomic analysis. The IgA index was calculated to evaluate the difference in the IgA response to each bacterium between the PreDM and Normal groups.<br><br>RESULTS: Bacterial species richness was significantly lower in the PreDM group than in the Normal group (observed operational taxonomic unit index, p = 0.042), and a difference between these groups was noted in the overall salivary microbiota structure (unweighted UniFrac distances, p = 0.009). Salivary IgA responses against several bacterial genera differed between the PreDM and Normal groups. Significantly higher IgA responses were noted against Haemophilus in the PreDM group, with lower responses against Capnocytophaga, Corynebacterium, and Streptococcus relative to those in the Normal group.<br><br>CONCLUSIONS: Salivary microbiota and IgA responses differ between pre-diabetic individuals and normoglycemic controls. The current findings advance our understanding of the interaction between oral bacteria and host immune responses in patients with a poor glycemic status.}, }
@article {pmid40535168, year = {2025}, author = {Huang, J and Ren, W and Hu, W and Ni, J}, title = {Diagnosis of secondary tuberculosis infection in an asymptomatic elderly with cancer using next-generation sequencing: Case report.}, journal = {Open life sciences}, volume = {20}, number = {1}, pages = {20251123}, pmid = {40535168}, issn = {2391-5412}, abstract = {In recent years, there has been a notable increase in the prevalence of tumors and tuberculosis (TB), particularly among elderly and immunocompromised populations. Early diagnosis and treatment are crucial for significantly improving patient outcomes. However, traditional diagnostic methods exhibit certain limitations. The rapid advancement of metagenomic next-generation sequencing (mNGS) has shown promising applications in the field of infectious diseases. We describe an 88-year-old male with multiple comorbidities, including newly diagnosed localized prostate cancer, who presented asymptomatically. Routine mNGS screening unexpectedly identified Mycobacterium tuberculosis, suggesting that malignancy may foster immune conditions favoring latent TB reactivation. This case emphasizes mNGS's role as a rapid, sensitive diagnostic adjunct for occult infections in high-risk populations.}, }
@article {pmid40535082, year = {2025}, author = {Wang, C and Hu, B and Liang, Q and Jiang, H and Yuan, L and Li, S}, title = {Oral microbiome and risk of lung cancer: results from a two-sample mendelian randomization analysis.}, journal = {Translational lung cancer research}, volume = {14}, number = {5}, pages = {1715-1723}, pmid = {40535082}, issn = {2218-6751}, abstract = {BACKGROUND: Numerous studies have suggested that the oral microbiome may function as a biomarker for lung cancer screening. However, the relationship between oral microbiome and lung cancer has not been thoroughly investigated. Consequently, investigating the causal relationship between oral microbiome and lung cancer was the primary goal of this study.<br><br>METHODS: We conducted a two-sample Mendelian randomization (MR) analysis to investigate the causal relationship between the oral microbiome and lung cancer. Summary statistics for the oral microbiomes were obtained from large-scale metagenome-genome-wide association studies (mgGWAS), while genome-wide association study (GWAS) summary statistics for lung cancer were sourced from the IEU-OpenGWAS online platform. We employed inverse variance weighted (IVW) analysis and Wald ratio methods to evaluate the causal associations between the oral microbiome and lung cancer. Finally, we performed MR Steiger's test to strengthen the validity of the causal associations.<br><br>RESULTS: Three oral microbiomes were causally associated with lung cancer. Gemella haemolysans (pheno.388) from saliva and an unclassified species (pheno.844) of Clostridia from saliva were protective factors for lung cancer, and an unclassified species (pheno.1354) of Prevotella from tongue was a risk factor for lung cancer. And there is no bidirectional association of causality between oral microbiomes and lung cancer.<br><br>CONCLUSIONS: The oral microbiomes, Gemella haemolysans (pheno.388) from saliva, an unclassified species (pheno.844) of Clostridia from saliva and an unclassified species (pheno.1354) of Prevotella from tongue, were causally associated with lung cancer. Oral microbiology holds significant potential for clinical applications in etiologic exploration, early screening, prevention, and enhancing survival in lung cancer. Regarding treatment, personalized therapy based on oral flora may provide novel therapeutic strategies for lung cancer.}, }
@article {pmid40535022, year = {2025}, author = {Blaustein, RA and Smith, JE and Toro, M and Pachepsky, Y and Stocker, MD}, title = {Water metagenomes reflect physicochemical water quality throughout a model agricultural pond.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1535096}, pmid = {40535022}, issn = {1664-302X}, abstract = {Agricultural ponds are essential irrigation resources, though may also serve as reservoirs for pathogens and antimicrobial resistance (AMR) genes. While monitoring microbiological water quality is critical for food safety, the influence of sampling factors (e.g., when and where to collect samples) in making risk assessments and potential applications for using environmental covariates as indicators remain unclear. Here, we explored the hypothesis that metagenomes of agricultural waters change with spatiotemporal shifts in physicochemical water quality, i.e., across water depths over time. Water samples and underlying sediments were collected at a model pond at the surface and within the water column (0, 1, 2 m depths) throughout one day (i.e., 9:00, 12:00, 15:00). All samples were processed for shotgun metagenomic sequencing analysis and enumeration of various water quality parameters (e.g., temperature, nutrient concentrations, turbidity, pH, culturable Escherichia coli). At the pond surface, Microcystis aeruginosa and members of Cyanobacteria, along with genes encoding pathways related to photosynthesis and nucleotide biosynthesis, were enriched throughout the day. In contrast, within the water column (1-2 m depths) and sediments, diverse members of Proteobacteria and Actinobacteria were more dominant, along with encoded pathways related to respiration and amino acid biosynthesis. Various aspects of water quality (i.e., chlorophyll dissolved organic matter, ammonia, E. coli concentrations) correlated with water metagenome diversity, albeit not with any specific AMR genes or virulence factors. Nevertheless, de novo assembly of sequenced reads uncovered 22 unique strains encoding several AMR, virulence, or stress response genetic elements, thus linking metagenome functional potential to key taxa. Overall, our findings highlight distinctions in agricultural pond water metagenomes at the surface and in the water column and demonstrate the potential for metagenomic surveillance in water quality monitoring to support food safety.}, }
@article {pmid40535021, year = {2025}, author = {Chen, Z and Li, Q and Li, F and Yin, L and Wang, L and Ye, T and Wang, Y and Fu, S and Wang, W and Huang, X}, title = {Evolution in a plant matrix: adaptive reshaping of kefir grains microbiota and function during long-term soymilk culture.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1614639}, pmid = {40535021}, issn = {1664-302X}, abstract = {To explore the adaptability of kefir grains in long-term subculture in soymilk, this study tracked the succession and functional changes of its microbial community over 4 months. High-throughput sequencing results showed that the microbial community structure was drastically reshaped, mainly manifested in the relative abundance of Lacticaseibacillus kefiranofaciens decreasing from 95.00 to 15.70%, while Lacticaseibacillus paracasei increased from 0.32 to 76.94%, becoming the dominant bacteria. Metagenomic analysis indicated that L. paracasei possesses key enzymes for metabolizing raffinose, stachyose and sucrose, which is the basis for its efficient utilization of soymilk oligosaccharides and its competitive advantage. The decrease in the abundance of L. kefiranofaciens was associated with a decrease in the synthesis of extracellular polysaccharides (EPS), which in turn caused a reduction in the diameter of kefir grains, an increase in surface viscosity and a partial collapse of the gel matrix structure. The pH and free amino acid content of fermented soymilk did not fluctuate much during the passage process, but the sensory acceptance, antioxidant capacity and angiotensin converting enzyme (ACE) inhibitory activity all showed a downward trend. This work reveals the adaptive evolution mechanism of kefir grains in a plant matrix environment and provides a theoretical basis for the optimization of soymilk fermentation based on limited strains.}, }
@article {pmid40535015, year = {2025}, author = {Chen, Y and Jiang, X and Zhao, J and Yang, M and Chen, Y and Ling, H and Liu, Y and Deng, F and Wang, Z}, title = {Microbial response under sulfate stress in a sulfur-based autotrophic denitrification system.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1615317}, pmid = {40535015}, issn = {1664-302X}, abstract = {This study investigated the responses of the bacterial community structure and metabolic pathways in a sulfur-based autotrophic denitrification filter (SADF) system to fast elevated sulfate salinity, from 0.04 to 1.2% in 30 days. Results showed that the SADF system exhibited robust sulfate salinity stress tolerance at low nitrate concentrations. In the context of sulfate scenarios, the genus Thiobacillus significantly proliferated and was identified as the dominant sulfur-oxidizing player in the SADF system, achieving a relative abundance of 63.79% under 1.2% sulfate salinity. Cooperative and competitive interactions were found in the SADF-related microorganisms, promoting stable denitrification performance under high salinity. Surprisingly, with a low hydraulic retention time (HRT) of 60 min, metagenomic sequencing revealed a upregulated abundance of functional genes encoding for enzymes associated with nitrogen and sulfur metabolism, while positive correlations were observed between these two pathways in response to sulfate salinity. Furthermore, global wastewater treatment plants were thoroughly explored for the distribution of the SADF-related microorganisms identified in this study. Interestingly, one-way ANOVA analysis showed that the SADF-related microorganisms were widely distributed globally, demonstrating their universality in potential engineering applications worldwide.}, }
@article {pmid40535009, year = {2025}, author = {He, S and Qi, Y}, title = {The microbiota, the malarial parasite, and the mice-a three-sided relationship.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1615846}, pmid = {40535009}, issn = {1664-302X}, abstract = {In recent years, the role of gut microbiota in modulating malaria susceptibility and infection progression has emerged as a pivotal focus in interdisciplinary research. While existing reviews have delineated mechanisms by which mosquito-associated gut microbiota regulate Plasmodium development, a systematic synthesis of the tripartite interplay among host gut microbiota, Plasmodium and host immunometabolic networks remains absent. Compared with previous studies predominantly focusing on single species or unitary mechanisms, this review fills the gap in cross-species integrated analysis of host-microbiota-pathogen interactions. By consolidating metagenomic, metabolomic, and immunological data, this review transitions from unitary mechanistic explanations to multi-omics-driven systematic analyses, demonstrating that murine microbiota suppresses Plasmodium proliferation through adaptive immune activation and metabolic product regulation. Meanwhile, Plasmodium infection induces decreased microbial diversity and functional pathway deviation in murine microbiota, exacerbating host immunometabolic imbalance. These advancements not only elucidate core biological principles governing "microbiota-host-pathogen" interactions but also transcend traditional pathogen-centric perspectives by pioneering precise intervention strategies based on microbiota homeostasis restoration. This provides theoretical foundation for developing microbiome-targeted precision prevention approaches, which will continue to make substantial contributions to malaria research.}, }
@article {pmid40535002, year = {2025}, author = {Xamxidin, M and Zhang, X and Zheng, G and Chen, C and Wu, M}, title = {Metagenomics-assembled genomes reveal microbial metabolic adaptation to athalassohaline environment, the case Lake Barkol, China.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1550346}, pmid = {40535002}, issn = {1664-302X}, abstract = {Salt-tolerant and halophilic microorganisms are critical drivers of ecosystem stability and biogeochemical cycling in athalassohaline environments. Lake Barkol, a high-altitude inland saline lake, provides a valuable natural setting for investigating microbial community dynamics and adaptation mechanisms under extreme salinity. In this study, we employed high-throughput metagenomic sequencing to characterize the taxonomic composition, metabolic potential, and ecological functions of microbial communities in both water and sediment samples from Lake Barkol. We reconstructed 309 metagenome-assembled genomes (MAGs), comprising 279 bacterial and 30 archaeal genomes. Notably, approximately 97% of the MAGs could not be classified at the species level, indicating substantial taxonomic novelty in this ecosystem. Dominant bacterial phyla included Pseudomonadota, Bacteroidota, Desulfobacterota, Planctomycetota, and Verrucomicrobiota, while archaeal communities were primarily composed of Halobacteriota, Thermoplasmatota, and Nanoarchaeota. Metabolic reconstruction revealed the presence of diverse carbon fixation pathways, including the Calvin-Benson-Bassham (CBB) cycle, the Arnon-Buchanan reductive tricarboxylic acid (rTCA) cycle, and the Wood-Ljungdahl pathway. Autotrophic sulfur-oxidizing bacteria, alongside members of Cyanobacteria and Desulfobacterota, were implicated in primary production and carbon assimilation. Nitrogen metabolism was predominantly mediated by Gammaproteobacteria, with evidence for both nitrogen fixation and denitrification processes. Sulfur cycling was largely driven by Desulfobacterota and Pseudomonadota, contributing to sulfate reduction and sulfur oxidation pathways. Microbial communities exhibited distinct osmoadaptation strategies. The "salt-in" strategy was characterized by ion transport systems such as Trk/Ktr potassium uptake and Na[+]/H[+] antiporters, enabling active intracellular ion homeostasis. In contrast, the "salt-out" strategy involved the biosynthesis and uptake of compatible solutes including ectoine, trehalose, and glycine betaine. These strategies were differentially enriched between water and sediment habitats, suggesting spatially distinct adaptive responses to local salinity gradients and nutrient regimes. Additionally, genes encoding microbial rhodopsins were widely distributed, suggesting that rhodopsin-based phototrophy may contribute to supplemental energy acquisition under osmotic stress conditions. The integration of functional and taxonomic data highlights the metabolic versatility and ecological roles of microbial taxa in sustaining biogeochemical processes under hypersaline conditions. Overall, this study reveals extensive taxonomic novelty and functional plasticity among microbial communities in Lake Barkol and underscores the influence of salinity in structuring microbial assemblages and metabolic pathways in athalassohaline ecosystems.}, }
@article {pmid40533851, year = {2025}, author = {Rahman, N and McCullough, T and Orozco, DF and Walkowiak, S and Farzan, A and Shekarriz, S and Surette, MG and Cicek, N and Derakhshani, H}, title = {Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {66}, pmid = {40533851}, issn = {2524-4671}, support = {(RGPIN-2023-04359)//NSERC Discovery Grant/ ; }, abstract = {INTRODUCTION: The widespread use of antimicrobials in the livestock industry has raised global concerns regarding the emergence and spread of antimicrobial resistance genes (ARGs). Comprehensive databases of ARGs specific to different farm animal species can greatly improve the surveillance of ARGs within the agri-food sector and beyond. In particular, defining the association of ARGs with mobile genetic elements (MGEs)-the primary agents responsible for the spread and acquisition of resistant phenotypes among bacterial populations-could help assess the transmissibility potential of clinically relevant ARGs. Recognizing the gut microbiota as a vast reservoir of ARGs, we aimed to generate a representative isolate collection and genome database of the swine gut microbiome, enabling high-resolution characterization of ARGs in relation to bacterial host range and their association with MGEs.<br><br>RESULTS: We generated a biobank of bacteria from different sections of the gastrointestinal tracts of four clinically healthy pigs housed at a research farm in Ontario, Canada. The culturing was performed under anaerobic conditions using both selective and general enrichment media to ensure the capture of a diverse range of bacterial families within the swine gut microbiota. We sequenced the genomes of 129 unique isolates encompassing 44 genera and 25 distinct families of the swine gut microbiome. Approximately 85.3% (110 isolates) contained one or more ARGs, with a total of 246 ARGs identified across 38 resistance gene families. Tetracycline and macrolide resistance genes were the most prevalent across different lineages of the swine gut microbiota. Additionally, we observed a wide range of MGEs, including integrative conjugative elements, plasmids, and phages, frequently associated with ARGs, indicating that the swine gut ecosystem is conducive to the horizontal transfer of ARGs. High-throughput alignment of the identified ARG-MGE complexes to large-scale metagenomics datasets of the swine gut microbiome suggests the presence of highly prevalent and conserved resistome sequences across diverse pig populations.<br><br>CONCLUSION: Our findings reveal a highly diverse and relatively conserved reservoir of ARGs and MGEs within the gut microbiome of pigs. A deeper understanding of the microbial host range and potential transmissibility of prevalent ARGs in the swine microbiome can inform development of targeted antimicrobial resistance surveillance and disease control programs.}, }
@article {pmid40533761, year = {2025}, author = {Hosch, S and Hamelin, B and Haslbauer, JD and Field, CM and Heim, A and Boeck, L and Savic Prince, S and Gradistanac, TA and Gander, AE and Keller, PM and Leuzinger, K and Mertz, KD}, title = {Human mastadenovirus pneumonia in two immunocompetent patients.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {198}, pmid = {40533761}, issn = {1743-422X}, mesh = {Humans ; Female ; Lung/pathology/virology/diagnostic imaging ; *Mastadenovirus/isolation &amp; purification/genetics/classification ; *Pneumonia, Viral/pathology/virology/diagnosis ; Middle Aged ; Switzerland ; Tomography, X-Ray Computed ; *Adenovirus Infections, Human/pathology/virology/diagnosis ; Immunocompetence ; Histocytochemistry ; Whole Genome Sequencing ; Aged ; }, abstract = {BACKGROUND: Human adenoviruses (hAdV) are common pathogens associated with acute respiratory tract infections. Mastadenovirus blackbeardi (hAdV-B) has been linked to severe pneumonia and disseminated disease, primarily in immunocompromised patients. The histopathological and clinical features of adenoviral pneumonia remain poorly characterized.<br><br>CASE PRESENTATION: We report two cases of hAdV-B pneumonia in immunocompetent female patients with a history of smoking. Both patients are of Caucasian origin and reside in Switzerland. They presented with persistent respiratory symptoms, pulmonary infiltrates on CT scans, and necrotizing granulomatous inflammation in lung tissue. After excluding other pathogens, metagenomic whole-genome sequencing identified hAdV-B in both cases. Both patients recovered fully following wedge resection of the affected lung tissue, without the need for additional therapy.<br><br>CONCLUSIONS: These two cases demonstrated a remarkably similar clinical and histopathological profile, characterized by chronic granulomatous lung inflammation. The findings suggest a prolonged inflammatory response leading to persistent tissue damage. Our observations highlight the potential of hAdV-B to cause chronic pneumonia even in otherwise healthy individuals.}, }
@article {pmid40533170, year = {2025}, author = {Kumari Nawarathna, TNT and Fujii, N and Yamamoto, K and Kuroda, K and Narihiro, T and Ozaki, N and Ohashi, A and Kindaichi, T}, title = {Metagenomic Insights into Candidatus Scalindua in a Long-term Cultivated Marine Anammox Consortium: The Important Role of Tetrahydrofolate-mediated Carbon Fixation.}, journal = {Microbes and environments}, volume = {40}, number = {2}, pages = {}, doi = {10.1264/jsme2.ME25007}, pmid = {40533170}, issn = {1347-4405}, mesh = {*Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Carbon Cycle ; Metagenomics ; *Microbial Consortia/genetics ; *Ammonia/metabolism ; Folic Acid/metabolism/biosynthesis ; *Seawater/microbiology ; Metagenome ; Bioreactors/microbiology ; Metabolic Networks and Pathways ; Phylogeny ; Genome, Bacterial ; Wastewater/microbiology ; Carbon/metabolism ; }, abstract = {Marine anammox bacteria have been an exciting research area in recent years due to their high effectiveness in treating ammonia-containing saline wastewater. However, their direct implementation in the wastewater industry faces challenges due to slow growth, difficulty obtaining pure cultures, and their tendency to exist as part of an anammox consortium, interacting symbiotically with other bacteria. In the present study, 91 draft genome metagenome-assembled genomes (MAGs) from a long-term-operated reactor were recovered to clarify detailed symbiotic interactions within an anammox consortium. One marine anammox bacterial MAG, identified as Candidatus Scalindua, was successfully recovered and was abundant within the sampled microbial community. A comprehensive metabolic pathway ana-lysis revealed that Ca. Scalindua exhibited the complete anammox pathway and the Wood-Ljungdahl pathway for carbon fixation. The folate biosynthesis pathway in Ca. Scalindua was incomplete, lacking dihydrofolate reductase, a key enzyme for tetrahydrofolate (THF) production. The folate biopterin transporter, essential for transporting folate-related metabolites among coexisting bacteria, was identified exclusively in Ca. Scalindua. In addition, the impact of exogenously supplied THF on microbial activity and carbon uptake rates was investigated in batch experiments using [14]C-labeled bicarbonate. The results obtained revealed that 2‍ ‍mg L[-1] of exogenous THF resulted in a 43% increase in the carbon uptake rate, while anammox activity remained unaffected. The present results suggest that THF is a key intermediate for carbon fixation in Ca. Scalindua and may be essential for their growth.}, }
@article {pmid40532861, year = {2025}, author = {Biswas, I and Mitra, D and Mallik, C and Das Mohapatra, PK}, title = {Characterization and toxicity assessment of metabiotic produced through natural tannin fermentation by newly isolated probiotic Lactiplantibacillus plantarum PKI15 and study of its effect on gut microbiome through metagenomics approach.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107815}, doi = {10.1016/j.micpath.2025.107815}, pmid = {40532861}, issn = {1096-1208}, abstract = {Metabiotic fabrication has been done by mixed plant fermentation of Terminalia bellirica and Phyllanthus emblica fruit extract with probiotic bacteria Lactiplantibacillus plantarum PKI15 and showed considerable tannase (0.36 U/ml), gallic caid and pyrogallol production. Fermentative end-product analysis through FTIR, LC-MS and GC-MS analysis result indicates the presence of several bioactive compounds confirming the presence of gallic acid and pyrogallol respectively. Molecular docking analysis of the identified bioactive compounds with the protein myeloperoxidase denotes quercetin-3β-D-glucoside as the best ligand showing a binding score of -9.5 Kcal/mol. The formulated metabiotic revealed potential antibacterial and antioxidant properties activities. In-vivo toxicity assessment was done on the laboratory rats. Results revealed reduced body weight, urea content and creatinine level. Increase in superoxide dismutase, catalase activity and reduced content of conjugated diene, glutamate pyruvate transaminase and glutamic-oxaloacetic transaminase further supports the antioxidative potential of the metabiotic. Further study through histological sectioning of liver, kidney and spleen showed no structural abnormalities. Finally, metagenomics analysis of the gut microbiome of the experimental rats was done to check the influence of the formulated metabiotic on the gut commensals and it was found that species of Bifidobacterium and Pseudomonas are the most prevalent members of the examined groups, while, the relative proportion of other bacterial genera, such as Lactobacillus, Lactococcus, and Bacillus, were found to vary among the groups. Thus, both the in vivo and in silico studies proved that the formulated metabiotic is non-toxic and safe in use.}, }
@article {pmid40532815, year = {2025}, author = {Pan, D and Sun, H and Liu, Y and Wang, J and Kuang, Y and Shi, T and Zhang, H}, title = {Mobilome dominates fomesafen-responsive dissemination of antibiotic resistome in manure-amended agricultural soils.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126686}, doi = {10.1016/j.envpol.2025.126686}, pmid = {40532815}, issn = {1873-6424}, abstract = {Pesticides are increasingly perceived as emerging drivers in the spread of antibiotic resistance genes (ARGs) within agroecosystems. Pesticides with longer half-lives tend to impose persistent stresses on soil microbiomes, yet the selection for ARG dissemination remains overlooked. Focusing on a widely used long residual herbicide fomesafen, we examined recommended dose-based selection on the dissemination of ARGs in agricultural soils with or without manure amendment. The degradation half-lives of fomesafen in the blank soils and manure-amended soils were 35.77-124.00 and 20.00-73.27 d, respectively. After 42d exposure, the total abundances of ARGs in the fomesafen-treated manure-amended soils at exposure concentrations of 1 and 5 mg/kg were 1.20- and 1.36-fold higher than that in the controls, with the changes of mobile genetic elements (MGEs) reaching 1.24-2.22 folds; while no significant changes were observed in the blank soils. Furthermore, no significant changes were observed in either bacterial communities or ARG-carrying metagenome-assembled genomes in both manure-amended soils and blank soils under fomesafen selection. Variation partition analysis suggested that 24.42%-25.41% of the variations in ARGs could be individually explained by MGEs, while only 13.47%-13.75% by bacterial communities. Overall, these findings demonstrate that MGE-mediated horizontal transfer predominates fomesafen-responsive dissemination of ARGs in manure-amended agriculture soils and underscores the urgency of re-evaluating agricultural practices involving co-application of manures and long residual herbicides.}, }
@article {pmid40532696, year = {2025}, author = {Er, YX and Lee, SC and Aneke, C and Conlan, S and Muslim, A and Deming, C and Che, Y and Yap, NJ and Tee, MZ and Abdull-Majid, N and Shahrizal, S and Leong, KF and Han, J and Shen, Z and Than, LTL and Park, M and Mohd Sayed, I and ,  and Seyedmousavi, A and Kong, HH and Loke, P and Segre, JA and Lim, YAL}, title = {Trichophyton concentricum fungal infections and skin microbiomes of Indigenous Peninsular Malaysians.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.05.034}, pmid = {40532696}, issn = {1097-4172}, abstract = {Recent outbreaks of multidrug-resistant fungi infecting human skin emphasize the importance of understanding fungal pathophysiology and spread. In efforts to address health concerns with various Indigenous Peninsular Malaysians (Orang Asli [OA]), tinea imbricata-a Trichophyton concentricum fungal skin infection-emerged as a particular concern. We investigated the etiology and transmission of tinea imbricata by culturing, testing antifungal sensitivities, and sequencing T. concentricum isolates in remote OA villages. Among regionally conserved isolates, we identified the emergence of terbinafine-resistant T. concentricum microbiologically and genomically. Investigating the skin microbiomes of 82 Indigenous OA, we found unique microbiota and lower relative abundances of bacterial commensals (Cutibacterium acnes, Staphylococcus epidermidis) among OA versus Malaysian and US urban populations, emphasizing how understudied populations provide unprecedented knowledge on host-microbiome co-evolution. These findings provide valuable insights into clinical, microbiological, and genomic features of chronic fungal skin infections, offering the potential to inform strategies to address drug resistance and effective therapy.}, }
@article {pmid40532535, year = {2025}, author = {Wang, Z and He, Y and Luo, M and Liu, S and Hou, J and Cao, B and An, X}, title = {Transfer toxicity of polystyrene microplastics in vivo: Multi-organ crosstalk.}, journal = {Environment international}, volume = {202}, number = {}, pages = {109604}, doi = {10.1016/j.envint.2025.109604}, pmid = {40532535}, issn = {1873-6750}, abstract = {The accumulation of microplastics (MPs) within the environment caused serious ecological and health problems. Nevertheless, its systemic toxicity to organisms and its mechanisms lack effective evidence. This study established a model of MP exposure through the gavage of polystyrene (PS)-MPs particles to maternal mice on days 1 to 21 of lactation. The results demonstrated that PS-MPs were distributed widely in maternal mice, occurring mainly in the feces, colon, liver and mammary glands. Further experiments revealed that the gut and blood-milk barriers were disrupted, and pathological injury and inflammatory reactions were observed in the liver, gut, and mammary glands. Metabolomic and metagenome analysis indicated abnormalities in hepatic bile acid metabolism and significant alterations in the gut microbiota after exposure to PS-MPs. These alterations led to increased disruption of the intestine-liver axis. Notably, with fecal microbiota transplantation and antibiotic experiments, we observed that elimination of the intestinal microbiota reduced tissue inflammation and improved gut and blood-milk barrier leakage. These findings demonstrated that PS-MPs exaggerated intestine-liver axis disorders by inducing colonic injury, intestinal ecological dysregulation and abnormal hepatic bile acid metabolism. Furthermore, PS-MPs translocated via the intestine-liver axis and exerted broader toxic effects on mammary tissue. Overall, our study uncovered the transfer toxicity of PS-MPs in mice, proposing the possibility of a gut-liver-mammary axis.}, }
@article {pmid40532529, year = {2025}, author = {Parab, AS and Ghose, M and Manohar, CS}, title = {Metagenomic reconstruction of microbial genomes and biogeochemical pathways: insights into carbon and nitrogen flux dynamics in the eastern Arabian Sea.}, journal = {Marine environmental research}, volume = {210}, number = {}, pages = {107292}, doi = {10.1016/j.marenvres.2025.107292}, pmid = {40532529}, issn = {1879-0291}, abstract = {The eastern Arabian Sea (EAS) experiences seasonal nutrient availability and productivity shifts driven by the Indian monsoon, influencing microbial contributions to biogeochemical cycles. This study explores carbon, nitrogen and sulfur cycling using metagenome-assembled genomes (MAGs) from water samples collected at chlorophyll maxima (C-Max) depths during non-monsoon and monsoon seasons. A total of 49 high-quality MAGs were reconstructed from 12 metagenomic samples, including four novel lineages from the phyla Pseudomonadota and Bacteroidota. These MAGs revealed distinct seasonal shifts in microbial composition and function. During the non-monsoon season, microbial communities dominated by Idiomarina and Marinobacter showed increased gene abundance for C1 compound metabolism, nitrogen cycling and sulfur oxidation, processes essential for managing climate-active gases such as carbon dioxide (CO2) and nitrous oxide (N2O), while also preventing toxic sulfide accumulation. In contrast, monsoon conditions enhanced organic matter influx, promoting nitrogen retention pathways driven by Sinimarinibacterium and Oleibacter, raising concerns about potential nutrient buildup and localized hypoxia. Despite seasonal variations, functional redundancy ensured the stability of nutrient cycling processes. PERMANOVA analysis (p < 0.001) confirmed that microbial functional gene distribution was primarily shaped by taxonomic structure, with genus-level composition playing a dominant role. The study highlights microbial adaptability and resilience, ensuring ecosystem stability in the dynamic EAS environment. Understanding microbial processes at C-Max depths has enhanced our understanding of biogeochemical cycling in the EAS. Although focused on oxygenated depths, these findings offer insights relevant to microbial functions in the OMZ, reflecting the distinct environmental conditions of EASs.}, }
@article {pmid40532377, year = {2025}, author = {Deng, Y and Li, J and Taherzadeh, MJ and Lu, H and Kong, D and Ma, B and Hu, Y and Chen, G and Ruan, Y}, title = {Metagenomics reveal the mechanisms of integrated heterotrophic and sulfur autotrophic denitrification (HSAD) using PBAT/starch as carbon source.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {138943}, doi = {10.1016/j.jhazmat.2025.138943}, pmid = {40532377}, issn = {1873-3336}, abstract = {The accumulation of nitrate in recirculating aquaculture system constrains the sustainable development of aquaculture industry. This study evaluated the performance of two heterotrophic sulfur autotrophic denitrification (HSAD) reactors packed with PBAT/starch granules and supplemented with thiosulfate in the influent, operating at salinities of 0 ‰ (Reactor I) and 25 ‰ (Reactor II) over a 163-day period. Reactor I achieved an average nitrate removal rate of 0.17 kg/m[3]/d with minimal accumulation of nitrite, total ammonia nitrogen (TAN) and dissolved organic carbon (DOC). In contrast, Reactor II exhibited a slower start-up, a lower denitrification rate of 0.08 kg/m[3]/d, and higher fluctuations in water quality parameters. Over time, both reactors transitioned from heterotrophic to sulfur autotrophic denitrification, as evidenced by increased effluent sulfate concentration, acidification and a decline in microbial biomass. Metagenomics and metatranscriptomics analyses revealed the coexistence of autotropic and heterotrophic denitrifying bacteria, with salinity inhibiting the abundance of denitrifying bacteria and expression of functional genes associated with nitrogen and sulfur metabolism. Network analysis further identified positive correlations among microorganisms involved in carbon, nitrogen and sulfur cycling. This study provides insights into the microbial mechanisms in HSAD process and offers a promising approach for the treatment of nitrate-rich aquaculture wastewater.}, }
@article {pmid40531665, year = {2025}, author = {Phithakrotchanakoon, C and Kitikhun, S and Siriarchawatana, P and Charoenyingcharoen, P and Jeennor, S and Nilsakha, T and Chanpet, A and Vorajinda, T and Mayteeworakoon, S and Yukphan, P and Ingsriswang, S}, title = {Flavobacterium mekongense sp. nov., isolated from the Mekong River in Thailand.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {6}, pages = {}, doi = {10.1099/ijsem.0.006815}, pmid = {40531665}, issn = {1466-5034}, mesh = {Thailand ; *Flavobacterium/classification/genetics/isolation &amp; purification ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rivers/microbiology ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Vitamin K 2/analogs &amp; derivatives/chemistry/analysis ; Nucleic Acid Hybridization ; Genome, Bacterial ; Phospholipids/analysis/chemistry ; *Water Microbiology ; }, abstract = {Two Gram-stain-negative, aerobic, non-motile, non-gliding, rod-shaped bacterial strains, designated as TBRC 19031[T] and TBRC 19032, were isolated from water samples collected from the Mekong River, Thailand. Strain TBRC 19031[T] was obtained from Chiang Saen in the upstream section near the borders with China and Myanmar, while TBRC 19032 originated from Khong Chiam, in the downstream section where the river exits Thailand. Colonies of both strains were circular, smooth and deep yellow on Reasoner's 2A agar and did not produce flexirubin-type pigments. Phylogenetic analysis with 16S rRNA gene sequences placed both strains within the genus Flavobacterium, showing the highest sequence similarity to Flavobacterium cheonhonense ARSA-15[T] (98.29% for TBRC 19031[T] and 98.22% for TBRC 19032). However, whole-genome comparisons between the strains and F. cheonhonense ARSA-15[T] revealed average nt identity (89.39% and 89.29%), average aa identity (92.84% and 92.95%) and digital DNA-DNA hybridization (35.00% and 34.70%). The predominant fatty acids were iso-C15:1, iso-C15:0 and iso-C15:0 3-OH, and menaquinone MK-6 was the major respiratory quinone. The major polar lipids of both strains included phosphatidylethanolamine, steryl ester and diacylglycerol. The genome sizes were 3.02 and 3.04 Mbp, with G+C contents of 38.3% and 38.2% for TBRC 19031[T] and TBRC 19032, respectively. Comparative genomic analyses revealed the absence of genes involved in sulphate reduction and denitrification pathways and the presence of a gene encoding phosphatidylinositol synthase, distinguishing them from other Flavobacterium within the clade. Ecological profiling using public metagenomic datasets showed that both strains were associated with lotic freshwater environments. This study not only introduces Flavobacterium mekongense sp. nov. as a new species but also provides broader insights into the ecology, metabolism and environmental distribution of freshwater Flavobacterium. The genomic features identified here offer promising leads for future studies in microbial ecology, comparative genomics and functional gene mining in aquatic ecosystems. The type strain is TBRC 19031[T] (TBRC 19031[T]=NBRC 117006[T]).}, }
@article {pmid40530883, year = {2025}, author = {Ganote, CL and Caesar, L and Rice, DW and Whitaker, RJ and Newton, ILG}, title = {Evolutionary trends in Bombella apis CRISPR-Cas systems.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0016625}, doi = {10.1128/msystems.00166-25}, pmid = {40530883}, issn = {2379-5077}, abstract = {UNLABELLED: Bacteria and archaea employ a rudimentary immune system, CRISPR-Cas, to protect against foreign genetic elements such as bacteriophage. CRISPR-Cas systems are found in Bombella apis. B. apis is an important honey bee symbiont, found primarily in larvae, queens, and hive compartments. B. apis is found in the worker bee gut but is not considered a core member of the bee microbiome and has therefore been understudied with regard to its importance in the honey bee colony. However, B. apis appears to play beneficial roles in the colony, by protecting developing brood from fungal pathogens and by bolstering their development under nutritional stress. Previously, we identified CRISPR-Cas systems as being acquired by B. apis in its transition to bee association, as they are absent in a sister clade. Here, we assess the variation and distribution of CRISPR-Cas types across B. apis strains. We found multiple CRISPR-Cas types, some of which have multiple arrays, within the same B. apis genomes and also in the honey bee queen gut metagenomes. We analyzed the spacers between strains to identify the history of mobile element interaction for each B. apis strain. Finally, we predict interactions between viral sequences and CRISPR systems from different honey bee microbiome members. Our analyses show that the B. apis CRISPR-Cas systems are dynamic; that microbes in the same niche have unique spacers, which supports the functionality of these CRISPR-Cas systems; and that acquisition of new spacers may be occurring in multiple locations in the genome, allowing for a flexible antiviral arsenal for the microbe.<br><br>IMPORTANCE: Honey bee worker gut microbes have been implicated in everything from protection from pathogens to breakdown of complex polysaccharides in the diet. However, there are multiple niches within a honey bee colony that host different groups of microbes, including the acetic acid bacterium Bombella apis. B. apis is found in the colony food stores, in association with brood, in worker hypopharyngeal glands, and in the queen's digestive tract. The roles that B. apis may serve in these environments are just beginning to be discovered and include the production of a potent antifungal that protects developing bees and supplementation of dietary lysine to young larvae, bolstering their nutrition. Niche specificity in B. apis may be affected by the pressures of bacteriophage and other mobile elements, which may target different strains in each specific bee environment. Studying the interplay between B. apis and its mobile genetic elements (MGEs) may help us better understand microbial community dynamics within the colony and the potential ramifications for the honey bee host.}, }
@article {pmid40530822, year = {2025}, author = {Wu, H and Sun, B and Li, J}, title = {Metagenomics research on PAH biodegradation in the lower reaches of the Shiwuli River in Chaohu, China.}, journal = {Environmental science. Processes &amp; impacts}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5em00025d}, pmid = {40530822}, issn = {2050-7895}, abstract = {Metagenomics is a powerful tool for investigating functional microorganisms, molecular mechanisms and genes involved in the degradation of polycyclic aromatic hydrocarbons (PAHs) in situ complex environments. In this study, we selected three land use types in the lower reaches of the Shiwuli River in Chaohu and applied metagenomics technology. The results revealed that Rhodoplanes and Bradyrhizobium were the abundant PAH-degrading microorganisms across the three land use types. Based on the functional annotation and PAH degradation pathway, it was found that the in situ microbial communities of the three land use types shared common metabolic pathways for phenanthrene degradation. In addition, a unique metabolic pathway for PAH degradation was identified in the agricultural land. Only Patulibacter contributed to flnE (KO14604) in the agricultural land, which was involved in the metabolic pathway of fluorene degradation. Results of this study suggested that the in situ degradation of PAHs was not completed by a single genus, and it involved the synergy effects of different PAH-degrading microorganisms. There was no significant difference between the compositions and relative abundances of PAH-degrading microorganisms in the three land use types and those presented in the Kyoto Encyclopedia of Genes and Genomes Orthology (KO). However, the same microorganism contributed to different functional genes in different samples. Genes encoding protocatechuic acid 4,5-dioxygenase were widely distributed and relatively abundant. Therefore, this gene may serve as an indicator of PAH degradation potential. Among all the factors, the total organic carbon and nitrate nitrogen contents exhibited significant influences on the functional genes (KO) related to PAH degradation (p < 0.05).}, }
@article {pmid40530648, year = {2025}, author = {Alam, I and Najar, F and Fathepure, B}, title = {Metagenome-assembled genomes of two salt-tolerant methylotrophs enriched from a sulfur-rich Zodletone spring in Oklahoma, USA.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0046125}, doi = {10.1128/mra.00461-25}, pmid = {40530648}, issn = {2576-098X}, abstract = {We obtained metagenome-assembled genomes (MAGs) of two salt-tolerant methylotrophic bacteria, Methylohalobius sp. strain ZOD2 and Methyloligella sp. strain ZOD6, from an enrichment culture derived from sediment collected at a sulfur-rich spring in Oklahoma, USA. These MAGs offer insights into the methane oxidation capabilities of these bacteria under high-salinity conditions.}, }
@article {pmid40530272, year = {2025}, author = {Jia, Y and Wang, J and Lin, X and Liang, T and Dai, H and Wu, B and Yang, M and Zhang, Y and Li, R}, title = {Integrated metabolomics and metagenomics reveal plant-microbe interactions driving aroma differentiation in flue-cured tobacco leaves.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1588888}, pmid = {40530272}, issn = {1664-462X}, abstract = {Current research on tobacco aroma predominantly focuses on single-omics approaches. In this study, we conducted a comprehensive investigation of the relationships between tobacco metabolite profiles, microbial communities, and aroma characteristics. Untargeted metabolomics and metagenomic analyses were performed on flue-cured upper tobacco leaves to compare light aromatic tobacco (LAT) and strong aromatic tobacco (SAT). The results showed that sugar metabolite levels in LAT were significantly higher than those in SAT, whereas levels of specific acids and amino acid metabolites in SAT exceeded those in LAT. Redundancy analysis (RDA) and metabolomic correlation analyses indicated that the genera Methylorubrum and Pseudomonas may promote sugar metabolite accumulation, while Pseudokineococcus potentially regulates both sugar and acid metabolites. In contrast, Methylobacterium and Sphingomonas were associated with acid and amino acid metabolism, with Methylobacterium additionally exhibiting inhibitory effects on sugar metabolism. Metagenomic analysis revealed that Methylorubrum, Pseudomonas, and Pseudokineococcus were abundant in LAT, whereas Methylobacterium and Sphingomonas dominated in SAT. Notably, the bidirectional regulation of aromatic metabolites by microbial genera such as Pseudokineococcus highlights the universality of plant-microbe interactions in shaping metabolic networks-a mechanism potentially applicable to other crop systems. These findings reveal conserved microbial functional traits (e.g., metabolic pathway modulation) that may drive plant phenotypic differentiation beyond tobacco, offering insights into microbiome-mediated crop quality improvement. The results provide theoretical guidance for tobacco aging and aroma regulation and underscore the broader significance of microbial community engineering in agriculture for manipulating plant metabolic outputs.}, }
@article {pmid40529498, year = {2025}, author = {Zhu, L and Han, R and He, L and Pan, B and Zhong, W and Li, Y and Liu, X}, title = {Innovative strategies for post-stroke depression: integrating traditional Chinese medicine with neurobiological insights, including the gut-brain axis.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1539357}, pmid = {40529498}, issn = {1663-9812}, abstract = {Post-stroke depression (PSD) is a debilitating condition affecting more than one-third of stroke survivors, leading to significant impairments in mood, cognitive function, and overall quality of life. While conventional treatments like selective serotonin reuptake inhibitors (SSRIs) are commonly used, their efficacy is often limited, and they are associated with adverse side effects. Emerging research underscores the critical roles of neuroinflammation, neurotransmitter imbalances, and disruptions in the gut-brain axis in the development and progression of PSD, suggesting that targeting these pathways could lead to more effective therapeutic outcomes. Traditional Chinese Medicine (TCM) presents a promising multi-faceted approach, addressing these complex biological mechanisms by regulating neurotransmitter systems, modulating immune responses, and restoring gut microbiota balance. Key herbs such as Salvia miltiorrhiza Bunge (Lamiaceae; Dan Shen) and Bupleurum chinense DC. (Apiaceae; Chai Hu) have shown significant potential in modulating neurotransmitter levels, reducing neuroinflammation, and providing neuroprotection. Additionally, TCM formulations like Chaihu Shugan Powder (CSP) and Shugan Jieyu Capsules (SG) further enhance these effects by promoting gut microbiota homeostasis and restoring metabolic balance. This review delves into the biological mechanisms underlying PSD, with a particular focus on neuroinflammation, neurotransmitter dysregulation, and gut-brain axis dysfunction. It also explores the potential of integrating TCM with advanced multi-omics technologies-such as metabolomics, metagenomics, and transcriptomics-to develop personalized treatment strategies for PSD. By combining the holistic principles of TCM with modern Western medicine and cutting-edge omics technologies, this integrative approach offers a comprehensive framework for managing PSD, with the potential to significantly improve recovery outcomes and enhance the quality of life for stroke survivors.}, }
@article {pmid40529430, year = {2025}, author = {Chen, R and Li, R and Jiang, J and Zhou, L and Zhao, S and Zhang, Y and Xia, Q and Yang, Z}, title = {Coconut oil derived medium-chain triglycerides ameliorated memory deficits via promoting neurite outgrowth and maintaining gut homeostasis in 5×FAD mice.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1585640}, pmid = {40529430}, issn = {2296-861X}, abstract = {Alzheimer's disease (AD) is a prevalent neurodegenerative disorder characterized by neurite atrophy, neuronal loss, and memory impairment. Medium-chain triglycerides (MCT), a type of fatty acid predominantly found in coconut oil, have been shown to improve metabolic syndrome as well as cognitive performance via ketone production in humans. Here, we investigated the protective effects of MCT on neurite atrophy and memory deficits in 5×FAD mice and elucidated the underlying mechanisms. First, virgin coconut oil (VCO), refined, bleached, and deodorized coconut oil (RBDCO), and MCT were orally administered to 6-8 months old 5×FAD mice for 9 consecutive weeks, the effects on cognition were then evaluated. MCT demonstrated superior effects compared to RBDCO and VCO in reducing Aβ levels, inhibiting hyperactivated microglia and astroglia, protecting neurons, and mitigating memory decline. Further, metagenomic analysis and RT-qPCR results revealed that MCT intervention increased the relative abundance of Akkermansia, reduced intestinal permeability, and elevated the concentration of short-chain fatty acids in the brain. Additionally, MCT treatment significantly protected primary cortical neurons against Aβ25-35-induced apoptosis and promoted neurite regeneration. Transcriptome and RT-qPCR data suggested that Ucp1 and Flor1 may be potential targets through which MCT exerts its neuroprotective effects. Our findings suggest that MCT may help prevent the progression of AD by promoting neurite outgrowth and maintaining gut homeostasis in 5×FAD mice, offering a theoretical foundation for the development of dietary therapies for AD.}, }
@article {pmid40528946, year = {2025}, author = {Miao, Y and Sun, M and Huo, R and Chen, Y and Xie, J and Dong, T and Zhang, M}, title = {Metagenomics and volatile metabolomics reveal microbial succession and flavor formation mechanisms during fermentation of Novel Pasture-style Laozao.}, journal = {Food chemistry: X}, volume = {28}, number = {}, pages = {102598}, pmid = {40528946}, issn = {2590-1575}, abstract = {Novel Pasture-style Laozao (NPLZ) is a local specialty fermented food with unique flavor and mouthfeel. This study investigated the dynamic changes of physicochemical properties, volatile flavor substances and microbial community succession during the fermentation of NPLZ and revealed their interactions through the joint analysis of metagenomics and volatile metabolomics. Differences in the contents of 52 characteristic flavor substances were the main reasons for the changes in aroma. Saccharomyces cerevisiae, Pseudomonas oryzihabitans, and Pantoea vagans were the dominant microbial communities during fermentation. Under symbiotic conditions, five species including Paenibacillus piri and Methyloversatilis thermotolerans were found to be crucial in influencing microbial community succession. The accumulation of organic acids was identified as the primary environmental factor driving changes in microbial community structure. Through correlation analysis, eight microbial species were identified as core microorganisms affecting flavor differences, and the metabolic networks of key flavor metabolites were reconstructed in conjunction with the KEGG database.}, }
@article {pmid40528807, year = {2025}, author = {Ding, X and Wang, J and Zhu, W}, title = {The hydrogenation metabolism process of rosmarinic acid by microbial enzymes in chickens.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70000}, pmid = {40528807}, issn = {1097-0010}, support = {2017YFE0135200//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: The gut microbiota plays a critical role in the metabolism of rosmarinic acid (RA) through converting RA to caffeic acid (CA), danshensu (DSS), and m-coumaric acid. However, the gut environment and microbiota may have complicated metabolic converting RA processes. This study aimed to investigate the metabolism of RA in gastrointestinal tract of chickens through liquid chromatography-tandem mass spectrometry (LC-MS/MS) and metagenomic analysis.<br><br>RESULTS: Through in vivo and in vitro studies, RA was found to be hydrogenated into dihydrorosmarinic acid, then hydrolyzed into DSS and dihydrocaffeic acid (DHCA). DSS and DHCA could be further converted to 3-hydroxyphenylpropionic acid. But RA remained stable in the stomach, duodenum, jejunum, and ileum, as well as in the cecum of antibiotic-treated chickens. This indicated that the degradation of RA was mainly mediated by cecal microbiota. Furthermore, the metagenomic analysis of cecal microbiota revealed that reductases and hydrolases from Clostridium spp., Alistipes spp., and other microbiota were involved in these processes. NADH:flavin oxidoreductase and 3-oxoacyl-[acyl-carrier-protein] reductase participated in the hydrogenation reaction of RA, and BaiCD involved in dehydroxylation reaction of RA.<br><br>CONCLUSION: The hydrogenation process by microbial enzymes was an important metabolic pathway of RA. These hydrogenation products contribute to improving the biological function of RA. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid40528698, year = {2025}, author = {Bonilla-Espadas, M and Lifante-Martínez, I and Camacho, M and Orgilés-Calpena, E and Arán-Aís, F and Bertazzo, M and Bonete, MJ}, title = {Chromium-Tanned Leather and Microbial Consortia: Identification of Taxa With Biodegradation Potential and Chromium Tolerance.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70134}, doi = {10.1111/1758-2229.70134}, pmid = {40528698}, issn = {1758-2229}, support = {IMDEEA/2021/11//European Union through the European Regional Development Fund within the Operational Programme of the Valencian Community 2014-2020/ ; UAIND21-02B//Universidad de Alicante/ ; }, mesh = {*Chromium/metabolism/toxicity ; *Microbial Consortia ; Biodegradation, Environmental ; Biofilms/growth &amp; development ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Microscopy, Electron, Scanning ; Tanning ; }, abstract = {Chromium-tanned leather waste poses significant environmental challenges due to its resistance to degradation and heavy metal content. This study investigates the potential of naturally selected microbial consortia to initiate the degradation of chromium-tanned leather and identifies key bacterial genera capable of tolerating chromium and producing enzymes relevant to collagen breakdown. A novel multidisciplinary approach combining gravimetric assays, metagenomic sequencing, and scanning electron microscopy (SEM) was applied to characterise both microbial composition and degradation dynamics. Dominant genera such as Bacillus, Microbacterium, and Acinetobacter were associated with collagen degradation and metal tolerance, with Bacillus-rich communities showing the most pronounced mass loss (up to 3%). SEM analysis revealed the formation of robust biofilms and extensive matrix disruption, indicating enzymatic activity and structural breakdown of the leather. The formation of exopolysaccharide-rich biofilms was found to be critical for microbial adhesion and biodegradation efficacy. These findings provide initial insights into microbial mechanisms involved in the degradation of chromium-tanned leather and suggest potential applications for microbial consortia in future sustainable leather waste management strategies.}, }
@article {pmid40528272, year = {2025}, author = {Guitart-Matas, J and Vera-Ponce de León, A and Pope, PB and Hvidsten, TR and Fraile, L and Ballester, M and Ramayo-Caldas, Y and Migura-Garcia, L}, title = {Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {65}, pmid = {40528272}, issn = {2524-4671}, support = {10385//European Molecular Biology Organization/ ; RYC2019-027244-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RTI2018-095586-B-C22//Ministerio de Econom&#xed;a y Competitividad/ ; }, abstract = {BACKGROUND: High-throughput sequencing technologies play an increasingly active role in the surveillance of major global health challenges, such as the emergence of antimicrobial resistance. The post-weaning period is of critical importance for the swine industry and antimicrobials are still required when infection occurs during this period. Here, two sequencing approaches, shotgun metagenomics and metatranscriptomics, have been applied to decipher the effect of different treatments used in post-weaning diarrhea on the transcriptome and resistome of pig gut microbiome. With this objective, a metagenome-assembled genome (MAG) catalogue was generated to use as a reference database for transcript mapping obtained from a total of 140 pig fecal samples in a cross-sectional and longitudinal design to study differential gene expression. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, gentamicin, and amoxicillin, and an oral commercial vaccine, a control with water acidification, and an untreated control. For metatranscriptomics, fecal samples from pigs were selected before weaning, three days and four weeks post-treatment.<br><br>RESULTS: The final non-redundant MAGs collection comprised a total of 1396 genomes obtained from single assemblies and co-assemblies per treatment group and sampling time from the metagenomics data. Analysis of antimicrobial resistance genes (ARGs) at this assembly level considerably reduced the total number of ARGs identified in comparison to those found at the reads level. Besides, from the metatranscriptomics data, half of those ARGs were detected transcriptionally active in all treatment groups. Differential gene expression between sampling times after treatment found major number of differential expressed genes (DEGs) against the group treated continuously with amoxicillin, with DEGs being correlated with antimicrobial resistance. Moreover, at three days post-treatment, a high number of significantly downregulated genes was detected in the group treated with gentamicin. At this sampling time, this group showed an altered expression of ribosomal-related genes, demonstrating the rapid effect of gentamicin to inhibit bacterial protein synthesis.<br><br>CONCLUSIONS: Different antimicrobial treatments can impact differently the transcriptome and resistome of microbial communities, highlighting the relevance of novel sequencing approaches to monitor the resistome and contribute to a more efficient antimicrobial stewardship.}, }
@article {pmid40528256, year = {2025}, author = {Viver, T and Knittel, K and Amann, R and Orellana, LH}, title = {Comparative metagenomics indicates metabolic niche differentiation of benthic and planktonic Woeseiaceae.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {74}, pmid = {40528256}, issn = {2524-6372}, abstract = {BACKGROUND: Benthic microbiomes exhibit remarkable temporal stability, contrasting with the dynamic, substrate-driven successions of bacterioplankton. Nonetheless, understanding their role in carbon cycling and interactions between these two microbial communities is limited due to the complexity of benthic microbiomes.<br><br>RESULTS: Here, we used a long-reads (LRs) metagenomic approach to examine benthic microbiomes and compared them to the microbiomes in the overlaying water column and on particles, sampled at the same site and time off the island Heligoland in the North Sea. Although the diversity is vast in marine sediments, we recovered high quality metagenome assembled genomes (MAGs). Based on taxonomy and metabolic annotation of predicted proteins, benthic microbiomes are distinctly different from pelagic microbiomes. When comparing the 270 MAGs from free living and particle attached microbes from the water column to 115 MAGs from sediments only 2 MAGs affiliated to Acidimicrobiia and Desulfocapsaceae were shared at species level. Although, we recovered MAGs with the same taxonomic annotation in pelagic and benthic microbiomes, their metabolic potentials were different. A prominent example was the family Woeseiaceae that was among the most abundant taxa in the sediments. In benthic Woeseiaceae MAGs, we found polysaccharide utilization loci (PULs), predicted to target laminarin, alginate, and &#x3b1;-glucan. In contrast, pelagic Woeseiaceae MAGs were only recovered in the particle attached but not in the free-living fraction, and lacked PULs. They encoded a significantly more sulfatases and peptidases genes. Additionally, while genes involved in iron acquisition, gene regulation, and iron storage were widespread in Woeseiaceae MAGs, genes linked to dissimilatory iron reduction were mostly restricted to benthic Woeseiaceae, suggesting niche-specific adaptations to sediment redox conditions. Both, benthic and pelagic particle-attached Woeseiaceae MAGs encoded pilus TadA genes, which are essential for adhesion, colonization, and biofilm formation.<br><br>CONCLUSIONS: LR sequencing is currently the most valuable tool for analyzing highly diverse benthic microbiomes. The small overlap of MAGs from water column and sediments indicated a limited bentho-pelagic coupling. The data suggest that Woeseiaceae have habitat-specific metabolic specialization: while benthic Woeseiaceae possess the metabolic capabilities to utilize fresh organic compounds like laminarin derived from algae blooms, and to perform dissimilatory nitrate, nitrite and iron reduction for gain energy, particle attached Woeseiaceae from the water column may be specialized in degrading protein-rich and sulfated organic matter likely reflecting adaptation to the different types of organic matter and redox conditions in sediments vs. the water column.}, }
@article {pmid40528221, year = {2025}, author = {Gao, L and Liao, H and Chen, Y and Ye, C and Huang, L and Xu, M and Du, J and Zhang, J and Huang, D and Cai, S and Dong, H}, title = {Airway microbiota associated D-phenylalanine promotes non-small cell lung cancer metastasis through epithelial mesenchymal transition.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {673}, pmid = {40528221}, issn = {1479-5876}, support = {82170032//National Natural Science Foundation of China/ ; 82470058//National Natural Science Foundation of China/ ; 82270024//National Natural Science Foundation of China/ ; YZ2022ZX04//President Foundation of The Fifth Affiliated Hospital, Southern Medical University/ ; 2023A1515110216//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023M731546//China Postdoctoral Science Foundation/ ; }, mesh = {*Epithelial-Mesenchymal Transition/drug effects ; Humans ; *Carcinoma, Non-Small-Cell Lung/pathology/microbiology ; *Lung Neoplasms/pathology/microbiology ; Animals ; Male ; Neoplasm Metastasis ; Female ; *Microbiota ; *Phenylalanine/metabolism/pharmacology/administration &amp; dosage ; Middle Aged ; Bronchoalveolar Lavage Fluid/chemistry ; Cell Line, Tumor ; Mice ; Aged ; *Respiratory System/microbiology ; }, abstract = {BACKGROUND: Lung cancer is the leading cause of cancer-related death worldwide, and patients with distant metastasis have a poor prognosis. Various studies have reported that microbiota and metabolites significantly differ between healthy individuals and lung cancer patients. However, the effects of metabolites on tumor formation and metastasis are unclear. Therefore, our study aimed to determine the correlation between airway metabolites and microbiota, along with their respective roles in lung cancer metastasis.<br><br>METHODS: Bronchoalveolar lavage fluid (BALF) samples were collected from 30 non-small cell lung cancer (NSCLC) patients, including 11 patients without metastasis (M0) and 19 patients with metastasis (M1). Integrated pathogenic metagenomic and Liquid chromatography-mass spectrometry (LC&#x2012;MS) analyses were employed to explore differences between two groups. The omics data were analyzed and integrated via Spearman's correlation coefficient. Specific metabolites were subsequently used to intervene in lung cancer cells and animal models to assess their influence on tumor metastasis.<br><br>RESULTS: A total of 801 metabolites were identified in the BALF of all patients. Compared with those in the M0 group, 48 metabolites in the M1 group were significantly different. D-phenylalanine was notably upregulated in M1 and was positively related to Metamycoplasma salivarium. Intranasal administration of D-phenylalanine promoted tumor intrapulmonary metastasis and induced epithelial mesenchymal transition (EMT) process in NSCLC mouse models. Moreover, D-phenylalanine promotes the proliferation of non-small cell lung cancer cells and facilitates their migration and invasion via EMT.<br><br>CONCLUSION: The airway microbiota associated D-phenylalanine could promote lung cancer metastasis via EMT, which could be a new predictor for the diagnosis of tumor metastasis in NSCLC patients.}, }
@article {pmid40528214, year = {2025}, author = {Zhang, Y and Luo, J and Chen, K and Li, N and Luo, C and Di, S and Qin, J and Zhang, F and Chen, H and Dai, M}, title = {Cross-cohort analysis identifies shared gut microbial signatures and validates microbial risk scores for colorectal cancer.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {676}, pmid = {40528214}, issn = {1479-5876}, support = {2022-I2M-1-0031//Institute of Chinese Materia Medica, China Academy of Chinese Medical Science/ ; 82173606//National Natural Science Foundation of China/ ; 82273726//National Natural Science Foundation of China/ ; 20230484397//Beijing Nova Program of Science and Technology/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Risk Factors ; Risk Assessment ; Reproducibility of Results ; Male ; Female ; Middle Aged ; Metagenomics ; Case-Control Studies ; }, abstract = {BACKGROUND: Microbiome-wide association studies showed links between colorectal cancer (CRC) and gut microbiota. However, the clinical application of gut microbiota in CRC prevention has been hindered by the diversity of study populations and technical variations. We aimed to determine CRC-related gut microbial signatures based on cross-regional, cross-population, and cross-cohort metagenomic datasets, and elucidate its application value in CRC risk assessment.<br><br>METHODS: We used the MMUPHin tool to perform a meta-analysis of our own cohort and seven publicly available metagenomics datasets to identify gut microbial species associated with CRC across different cohorts, comprising of 570 CRC cases and 557 controls. Based on differential species sets, we constructed the microbial risk score (MRS) using &#x3b1;-diversity of the sub-community (MRS&#x3b1;), weighted/unweighted summation methods and machine learning algorithms. Cohort-to-cohort training and validation were performed to demonstrate the transferability.<br><br>RESULTS: We found that MRS&#x3b1; of core species was better validated and more interpretable than those constructed with summation methods or machine learning algorithms. Six species, including Parvimonas micra, Clostridium symbiosum, Peptostreptococcus stomatis, Bacteroides fragilis, Gemella morbillorum, and Fusobacterium nucleatum, were included in MRS&#x3b1; constructed by half or more of the cohorts. The AUC of MRS&#x3b1;, calculated based on the sub-community of six species, varied between 0.619 and 0.824 across the eight cohorts.<br><br>CONCLUSION: We identified six CRC-related species across regions, populations, and cohorts. The constructed MRS&#x3b1; could contribute to the risk prediction of CRC in different populations.}, }
@article {pmid40527424, year = {2025}, author = {Liu, Z and Tang, S and Ren, Y and Chen, P and Ma, D and Si, B and Jiang, W and Lu, H and Zhang, Y}, title = {Biohydrogen production from food waste using a novel rotational drum reactor integrated with milli-magnetite.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132822}, doi = {10.1016/j.biortech.2025.132822}, pmid = {40527424}, issn = {1873-2976}, abstract = {Dark fermentation, regarded as a promising path for sustainable hydrogen production from food waste, is hindered by slow hydrolysis and low hydrogen yield. This study presented a novel rotational drum reactor integrated with milli-magnetite (RD-M) to enhance hydrogen production, using potato peel as feedstock. The RD-M designed to simultaneously achieve grinding and biochemical stimulation. To verify the promoting performance and elucidate the underlying mechanisms, a drum reactor with sand (RD-S) and one without additives (RD-C) were used as controls. Enhanced hydrolysis in RD-M was confirmed from a smaller dominant particle size distribution (100-500 µm), accelerated production of organic acids (e.g., acetate, butyrate), and increased volatile solids degradation (by 23.6 %) compared to RD-C. Notably, hydrogen production in RD-M increased by 97.04 %. The RD-M system induced a shift in fermentation to an acetate-butyrate pathway, associated with an enrichment of butyrate-producing Clostridium. Metagenomic analysis further revealed that milli-magnetite established an efficient electron transfer chain that improved electron utilization and hydrogen yield. Additives were shown to promote direct interspecies electron transfer by upregulating genes encoding flagella and cytochrome-c synthesis. Furthermore, intracellular electron bifurcation at pyruvate ferredoxin directed electrons into the butyrate pathway, while enhanced iron metabolism explained the fermentation shift observed in RD-M. This study highlights the combined mechanical and biochemical benefits of RD-M, offering a promising solution for sustainable biohydrogen production from solid waste.}, }
@article {pmid40527400, year = {2025}, author = {Clodfelter, EB and Doña, J and Walden, KKO and Johnson, KP}, title = {Metagenomic analyses reveal three supergroups of Wolbachia in a single genus of feather-feeding lice (Penenirmus).}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {108387}, doi = {10.1016/j.ympev.2025.108387}, pmid = {40527400}, issn = {1095-9513}, abstract = {Insects with nutritionally limited diets often harbor bacterial endosymbionts that supplement their nutritional requirements. However, not all interactions between bacteria and insects are mutually beneficial. Wolbachia is a genus of bacteria that frequently causes cytoplasmic incompatibility and other reproductive parasitic effects on many of its arthropod hosts. In nematodes and some insects, however, Wolbachia is a nutritional mutualist. A lineage of Wolbachia closely related to mutualist strains has previously been identified in parasitic lice, including the louse genus Penenirmus (Ischnocera), which specializes in feeding on feathers. In this study, we used genome-resolved metagenomics to examine the diversity of Wolbachia across the genus Penenirmus, with a focus on evidence of long term associations with their hosts, which could indicate a mutualistic relationship. Phylogenomic analysis of over 100 genes from Wolbachia provided a well-resolved phylogeny of this bacterial genus. Across diverse species of the louse genus Penenirmus, genome-resolved metagenomic assemblies of Wolbachia from these insects revealed the presence of three different supergroups (B, F, and V). Supergroup V had not previously been known from lice. Cophylogenetic analysis revealed significant congruence between the Wolbachia and louse trees, although some branches showed incongruence. The Wolbachia in Penenirmus species from supergroups F and B showed evidence of potential mutualism by having long branches, cophylogenetic congruence with their louse hosts, and comparatively smaller genome sizes. Long branch attraction may be affecting the phylogenetic position of two lineages of Wolbachia, but the relative position of all other samples was comparatively stable.}, }
@article {pmid40527211, year = {2025}, author = {Ghosh, S and Nath, S and Chakraborty, A and Bhowmick, S and Majumdar, KK and Mukherjee, S and Pramanik, S}, title = {Long-term arsenic exposure perturbs gut microbial diversity, composition and predicts metabolic dysregulation.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {138836}, doi = {10.1016/j.jhazmat.2025.138836}, pmid = {40527211}, issn = {1873-3336}, abstract = {The present study documents significant alterations in human gut microbial composition in arsenic exposed populations of West Bengal, India through amplicon sequencing of human stool metagenomic DNA. A notable reduction in α-diversity underscored a reduced species richness and an altered predominance. β- diversity analysis revealed prominent inter-individual differences. Among the 26 phyla detected, significant perturbation was noted in Bacteroidetes, Actinobacteria, Proteobacteria, and Firmicutes. Species analysis identified significant increase in Bifidobacterium adolescentis, B.longum, Blautia luti, B.wexlerae, Clostridium saudiense, Romboutsia timonensis and Streptococcus salivarius whereas members of Faecalibacterium prausnitzii, Megasphaera elsdenii, Prevotella copri and P. stercorea were found to be highly diminished due to As stress. PICRUSt analysis predicted significant upregulation (pT-test< 0.05) in gene families associated with carbohydrate, amino acid, nucleotide and lipid metabolism along with fermentation and secondary metabolite/ vitamin synthesis pathways in exposed group confirmed through Linear Discriminant Analysis. B.longum, B.luti and S.salivarius were found to be associated with obesity and ulcerative colitis. Network interactions were also characterized with major disruptions in keystone species interaction. The major findings of this study shall drive future studies like community-based metagenomics, metabolomics and in-vitro microbial verifications for designing of microbial therapeutics targeting gut health to combat the harmful impact of As exposure.}, }
@article {pmid40527192, year = {2025}, author = {Yin, Y and Xiao, K and Wang, YF and Cao, JM and Dong, JP and Zhu, D and Zhu, YG}, title = {Nanoplastics released from textile washing enrich antibiotic resistance and virulence genes in sewage sludge microbiomes.}, journal = {Environment international}, volume = {202}, number = {}, pages = {109611}, doi = {10.1016/j.envint.2025.109611}, pmid = {40527192}, issn = {1873-6750}, abstract = {The washing of synthetic textiles is a major source of microplastic pollution, contributing to the widespread presence of nanoplastics (NPs) in wastewater treatment plants (WWTPs). However, the role of laundry-released NPs in shaping microbial communities and facilitating the spread of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in sludge remains unclear. Here, we quantified the concentration and size distribution of NPs released during the washing of polyamide (PA), polypropylene (PP), and polyethylene terephthalate (PET) textiles using nanoparticle tracking analysis. Substantial NP release was observed, with concentrations ranging from 3.4 × 10[7] to 1.7 × 10[8] particles mL[-1], and sizes between 130 and 240 nm. We then evaluated their impact on ARG and VFG profiles, as well as bacterial communities in anaerobic sludge through metagenomic and 16S rRNA gene sequencing. Laundry-released NPs significantly increased the abundance of ARGs, VFGs, and mobile genetic elements (MGEs) in sludge, with D8A-2 and Halomonas identified as potential ARG and VFG hosts. Notably, the mechanisms driving ARG enrichment varied by NP type. PA-released NPs elevated reactive oxygen species levels in bacterial communities, facilitating horizontal gene transfer via MGEs, while PP- and PET-released NPs enhanced ARG enrichment through both horizontal gene transfer and shifts in bacterial community composition. These findings highlight the risks posed by laundry-released NPs accumulating in WWTPs, emphasizing the urgent need for improved wastewater management strategies to mitigate their environmental and public health impacts.}, }
@article {pmid40526465, year = {2025}, author = {Zhang, J and Yuan, B and Peng, R and Zhang, P and Liu, X and Qu, Y and Xiao, G and Li, Y and Zhang, X and Hong, J}, title = {Etiology of Iridocorneal Endothelial Syndrome: Viral Infection and Immune Suppression.}, journal = {Cornea}, volume = {}, number = {}, pages = {}, doi = {10.1097/ICO.0000000000003911}, pmid = {40526465}, issn = {1536-4798}, support = {82371027//National Natural Science Foundation of China/ ; }, abstract = {PURPOSE: Iridocorneal endothelial (ICE) syndrome is a rare ocular disease affecting the anterior segment, leading to cornea edema and glaucoma. Its unclear etiology limits clinical management to symptomatic interventions. This study uses diverse methodologies to explore potential viral sequences in patients' samples and to elucidate the transcriptomic profiles of ICE cells.<br><br>METHODS: We used a convenience sampling method, including all eligible patients for analysis. We reviewed polymerase chain reaction (PCR) results for herpes viruses across all samples obtained from ICE syndrome patients at our institution. To further delve into potential pathogenic involvement, we used metagenomic sequencing and whole-genome sequencing techniques on samples. We used smart-seq2 RNA sequencing to explore the transcriptomic features of ICE cells compared with normal cells.<br><br>RESULTS: In our PCR tests involving 141 samples, only two positive results were detected in the aqueous humor. Furthermore, the application of metagenomic sequencing on three aqueous humor samples and three corneal endothelium samples, along with whole-genome sequencing on one corneal endothelium sample, yielded no evidence of viral sequences. RNA sequencing revealed upregulated cell growth and neuronal death in ICE cells, alongside downregulated expression in extracellular matrix composition, cell adhesion, and immune response functions.<br><br>CONCLUSIONS: Our findings from multiple sequencing assays consistently indicate the absence of compelling evidence supporting viral infection in patients with ICE syndrome. Furthermore, the transcriptional analysis of ICE cells reveals a distinct profile characterized by upregulated cell growth and suppressed immune response. Future studies are necessary to validate these findings and improve the generalizability of the results.}, }
@article {pmid40525868, year = {2025}, author = {Wang, H and Xue, W and Cheng, J and He, Y and Song, Y and Hu, D and Peng, A and Li, C and Bao, H}, title = {Altered fecal microbial and metabolic profiles reveal potential mechanisms underlying anemia in patients with chronic renal failure.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0316624}, doi = {10.1128/spectrum.03166-24}, pmid = {40525868}, issn = {2165-0497}, abstract = {The gut microbiomes communicate with the kidney and may play a crucial role in the development of anemia in patients with chronic renal failure (CRF). However, the alterations in microbiota and their association with functional metabolites remain unclear. We performed metagenomics and untargeted metabolomics in a cohort of 30 patients with anemia of CRF and 20 healthy controls (HCs) to identify the characteristics of the gut microbiome and explore its potential interactions with the host. Decreased microbiota diversity and significant compositional differences were observed in the patients with anemia of CRF. We identified six gut microbiotas significantly changed in the patients with anemia of CRF, particularly Faecalibacterium prausnitzii, Prevotella copri, and Escherichia coli, which were closely correlated with hemoglobin (Hb) levels and estimated glomerular filtration rate (eGFR). These changes were accompanied by functional alterations in distinctive microbial pathways. Further fecal and serum metabolomics revealed fecal 12-KETE-LTB4 in arachidonic acid metabolism, uracil and L-aspartic acid in beta-alanine metabolism, gulonic acid in ascorbate and aldarate metabolism, accompanied by the top 15 differential serum metabolites that were closely correlated with Hb levels. Furthermore, we observed a complex co-occurrence between anemia of CRF-related gut microbiota species and the characterized metabolites. Moreover, a non-invasive model incorporating Faecalibacterium prausnitzii and Prevotella copri, combined with fecal 12-KETE-LTB4, uracil, L-aspartic acid, and gulonic acid, distinguished the patients with anemia of CRF from HCs (area under the curve: 0.879). Collectively, our results suggest that a disordered gut microbiome associated with functional metabolites may be a non-invasive diagnostic and therapeutic target for anemia of CRF.IMPORTANCEAnemia is a prevalent complication in patients with chronic renal failure (CRF), which is associated with a high burden of morbidity and adverse clinical outcomes. Various evidence suggests that gut microbiota dysbiosis may contribute to the pathogenesis of anemia in CRF, although the mechanism is still obscure. This work provides substantial evidence identifying the specific characteristics of the gut microbiomes accompanied by functional alterations in anemia of CRF. We highlight the intricate interactions among the anemia of CRF-related gut microbiome and the functional metabolites, which may regulate toxic accumulation, oxidative stress, and immune-inflammatory responses to induce and exacerbate anemia in patients with CRF. Furthermore, we found that evaluating the gut microbiota and fecal metabolites in combination might be a non-invasive prognostic indicator of CRF-induced anemia. These findings provide important insights into the role of gut microbiota in the mechanism of anemia in CRF.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05543291.}, }
@article {pmid40525692, year = {2025}, author = {Jarrett, ZS and Xia, H and O'Neil, ER and Lonergan, TP and Gonzales, M and Sobieszczyk, M and Gibbons, TF and Marcus, JE}, title = {Characterizing Microbiome Changes in Veno-Venous Extracorporeal Membrane Oxygenation: A Case Report of Multidrug-Resistant Bacteremia.}, journal = {ASAIO journal (American Society for Artificial Internal Organs : 1992)}, volume = {}, number = {}, pages = {}, doi = {10.1097/MAT.0000000000002479}, pmid = {40525692}, issn = {1538-943X}, support = {//Clinical Investigations &amp; Research Support (CIRS)/ ; }, abstract = {Microbiome analysis using metagenomics next-generation sequencing (mNGS) is rarely performed in patients receiving extracorporeal membrane oxygenation (ECMO). Patient body sites were swabbed within 72 hours of ECMO cannulation and weekly during ECMO course. Specimens underwent 16S sequencing to identify the microbiome along with mNGS to determine antimicrobial resistance genes. Fifty-two year old male who suffered polytraumatic injuries and developed acute respiratory syndrome was placed on veno-venous (VV) ECMO to treat severe respiratory failure. On ECMO day 1, the patient was undergoing treatment for urinary tract infection due to susceptible Pseudomonas aeruginosa (PsA). On ECMO day 22, the patient developed fulminant septic shock and tracheal aspirate and blood cultures both grew MDR PsA and Enterobacter cloacae complex (ECC) and ultimately died on day 23. There were significant microbiome and antimicrobial resistance changes that preceded sepsis on day 22, as evidenced by the increase in oral PsA colonization and expansion of resistance genes, such as KPC and OXA-50, which suggest several possible reservoirs for infection outside of the circuit. Further application of these methods is needed to understand microbiome changes in ECMO and ultimately guide infection prevention efforts.}, }
@article {pmid40525681, year = {2025}, author = {Reinhardt, CR and Kastner, DW and Kulik, HJ}, title = {Role of Active Site Residues and Weak Noncovalent Interactions in Substrate Positioning in N,N-Dimethylformamidase.}, journal = {Biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.biochem.5c00207}, pmid = {40525681}, issn = {1520-4995}, abstract = {N,N-Dimethylformamide (DMF) is a solvent that can be metabolized naturally by DMF-utilizing microorganisms via a nonheme iron enzyme N,N-dimethylformamidase (DMFase). DMF is a small molecule with very few hydrogen bond donors or acceptors, and thus must be bound in the active site through other noncovalent interactions. We investigated the unusual protein fold, role of active site residues, and substrate positioning by performing molecular dynamics (MD) simulations and studying DMF binding. Our docking studies support idea that the DMF substrate directly coordinates the iron center through its carbonyl group, with Fe-DMF distances consistent with structures of inorganic complexes. DMF binding is predominantly stabilized by weak noncovalent interactions with nearby phenylalanine residues, which also serve to control access of solvent to the active site according to cavity analysis of crystal structures and MD snapshots. Based on noncovalent interactions sampled in our simulations and on sequence conservation, we ascribe roles to active site residues E657β, H519β, N547β, F611β, and F693β'. We perform sequence and structural alignments to identify putative DMFases and active site geometries in protein structures predicted from metagenomic DNA. These analyses suggest common conserved residues among putative DMFases and relate them to catalytic function, providing guidance for future experimental studies or characterization of new DMFases for DMF bioremediation.}, }
@article {pmid40524271, year = {2025}, author = {Serrano-Gómez, G and Yañez, F and Soler, Z and Pons-Tarin, M and Mayorga, L and Herrera-deGuise, C and Borruel, N and Rodriguez-Sinovas, A and Consegal, M and Manjón, I and Vega-Abellaneda, S and Manichanh, C}, title = {Microbiome multi-omics analysis reveals novel biomarkers and mechanisms linked with CD etiopathology.}, journal = {Biomarker research}, volume = {13}, number = {1}, pages = {85}, pmid = {40524271}, issn = {2050-7771}, support = {72190278//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FI21/00262//Instituto de Salud Carlos III/ ; PI20/00130//Instituto de Salud Carlos III/ ; 2021 SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; 2021 SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; 2021 SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, abstract = {BACKGROUND: The gut microbiome plays a key role in the development of inflammatory bowel disease (IBD), as imbalances in microbial composition are associated with immune dysfunction. However, the specific mechanisms by which certain microorganisms contribute to this process remain unclear.<br><br>METHODS: Here, we employed a multi-omics approach on fecal samples to identify novel microbiome markers and elucidate mechanisms underlying IBD. Shotgun metagenomics was applied to 212 samples (850 in total with validation cohort), shotgun metatranscriptomics to 103 samples and metabolomics to 105 samples. Machine learning techniques were used to predict disease and the three omics data were integrated to propose a mechanistic role of the microbiota.<br><br>RESULTS: Metagenomic analysis identified Crohn's disease (CD)-specific microbiome signatures, including a panel of 20 species that achieved a high diagnostic performance, with an area under the ROC curve (AUC) of 0.94 in an external validation set. Metatranscriptomic analysis revealed significant alterations in microbial fermentation pathways in CD, but not in ulcerative colitis (UC), highlighting disruptions that explain the depletion of butyrate-a key anti-inflammatory metabolite-observed in metabolomics analysis. Integrative multi-omics analyses further identified active virulence factor genes in CD, predominantly originating from the adherent-invasive Escherichia coli (AIEC). Notably, these findings unveiled novel mechanisms, including E. coli-mediated aspartate depletion and the utilization of propionate, which drives the expression of the ompA virulence gene, critical for bacterial adherence and invasion of the host's macrophages. Interestingly, these microbiome alterations were absent in UC, underscoring distinct mechanisms of disease development between the two IBD subtypes.<br><br>CONCLUSIONS: In conclusion, our study not only identifies promising novel biomarkers with strong diagnostic potential, which could be valuable in challenging clinical scenarios, but also offers an integrated multi-omics perspective on the microbial mechanisms underlying inflammation and virulence in Crohn's disease.}, }
@article {pmid40524224, year = {2025}, author = {Jaffe, AL and Salcedo, RSR and Dekas, AE}, title = {Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {167}, pmid = {40524224}, issn = {1474-760X}, support = {Postdoctoral Research Fellowship//Division of Ocean Sciences/ ; OCE-1634297//Division of Ocean Sciences/ ; }, mesh = {*Ribulose-Bisphosphate Carboxylase/metabolism/genetics ; *Carbon Cycle/genetics ; Metagenome ; *Seawater/microbiology ; *Bacteria/genetics/metabolism/classification/enzymology ; Oceans and Seas ; Phylogeny ; }, abstract = {BACKGROUND: Rubisco is among the most abundant enzymes on Earth and is a critical conduit for inorganic carbon into the biosphere. Despite this, the full extent of rubisco diversity and the biology of organisms that employ it for carbon fixation are still emerging, particularly in unlit ecosystems like the deep sea.<br><br>RESULTS: We generate fifteen metagenomes along a spatially resolved transect off the California coast and combine them with globally distributed public data to examine the diversity, distribution, and metabolic features of rubisco-encoding organisms from the dark water column. Organisms with the form I and/or form II rubisco are detected in the vast majority of all samples and comprise up to around 20% of the binned microbial community. At 150&#xa0;m and below, the potential for autotrophic carbon fixation via rubisco is dominated by just two orders of gammaproteobacteria and SAR324, encoding either the form I or II rubisco. Many of these organisms also possess genes for the oxidation of reduced sulfur compounds, which may energetically support carbon fixation. Transcriptomic profiling in the epi- and mesopelagic suggests that all major forms of rubisco (I, II, and III) can be highly expressed in the deep water column but are not done so constitutively, consistent with metabolic flexibility.<br><br>CONCLUSIONS: Our results demonstrate that the genetic potential to fix carbon via rubisco is significant and spatially widespread in the dark ocean. We identify several rubisco-encoding species that are particularly abundant and cosmopolitan, highlighting the key role they may play in deep-sea chemoautotrophy and the global marine carbon cycle.}, }
@article {pmid40523923, year = {2025}, author = {Zhang, M and Liang, C and Li, B and Jiang, F and Song, P and Gu, H and Gao, H and Cai, Z and Zhang, T}, title = {Gut microbiome and diet contribute to ecological niche differentiation between argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) on the Qinghai-Tibet Plateau.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {930}, pmid = {40523923}, issn = {2399-3642}, mesh = {Animals ; *Gastrointestinal Microbiome ; Tibet ; *Diet/veterinary ; Sheep/microbiology ; Ecosystem ; Herbivory ; }, abstract = {The gut microbiota plays a critical role in plant digestion, nutrient absorption, and ecological adaptation in herbivores. However, how gut microbiota and diet jointly influence ecological niche differentiation in sympatric species remains unclear. Here, we use metagenomic sequencing and plant trnL (UAA) fragment sequencing to examine the gut microbiota and dietary composition of sympatric Tibetan argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) in the Kunlun Mountains of the Qinghai-Tibet Plateau. Despite inhabiting similar environments, the two species harbor distinct microbial compositions and functional profiles. Interestingly, higher dietary diversity does not correspond to higher microbial diversity. Tibetan argali, despite having a simpler diet, possesses a more diverse and flexible gut microbiome. In contrast, blue sheep show broader dietary preferences and stronger microbial metabolic adaptation to glycan biosynthesis and metabolism. These findings reveal significant associations between gut microbiota composition, function, and diet, supporting a microbial contribution to trophic niche differentiation. Our results highlight distinct microbial-dietary strategies in sympatric herbivores and underscore the role of the gut microbiome in ecological adaptation and species coexistence.}, }
@article {pmid40523587, year = {2025}, author = {Valadez-Cano, C and Reyes-Prieto, A and Johnston, L and Huang, Y and Morris, H and Zamlynny, L and Comeau, AM and Beach, DG and Jamieson, RC and Lawrence, J}, title = {The co-existence of Microcoleus strains with gene variations in the anatoxin-a biosynthesis cluster can explain the different toxin profiles observed in freshwater benthic mats.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {}, number = {}, pages = {108461}, doi = {10.1016/j.toxicon.2025.108461}, pmid = {40523587}, issn = {1879-3150}, abstract = {Distinct anatoxin profiles can occur in Microcoleus-dominated benthic mats. Metagenomic data from a dihydrohomoanatoxin-a-producing mat revealed two co-occurring Microcoleus strains with variations in the anatoxin biosynthesis gene cluster. One cluster contained an anaK (F420-dependent oxidoreductase) similar to homologs from dihydroanatoxin-a-producing strains. The second contained the long anaG (polyketide-synthase) previously associated with homoanatoxin-a. Neither strain alone explained the observed toxin profile, suggesting that strain interaction contributes to the production of dihydrohomoanatoxin-a within benthic mats.}, }
@article {pmid40523415, year = {2025}, author = {Xu, Y and Ontita, NC and Zeng, W and Huang, J and Jiang, L and Huang, X and Li, Q and Hu, P}, title = {High-efficiency nitrogen removal by cold-tolerant bacteria consortium at low temperatures.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132816}, doi = {10.1016/j.biortech.2025.132816}, pmid = {40523415}, issn = {1873-2976}, abstract = {A cold-tolerant bacteria consortium (M2) was developed to enhance nitrogen removal efficiency in wastewater treatment processes operating at low temperatures (below 15 ℃). Bacteria consortium M2 demonstrated high removal efficiencies for nitrogen (NH4[+]-N, 97.34 %; NO3[-]-N, 97.13 %; NO2[-]-N, 59.92 %). Dominated by genera including Comamonas, Pseudomonas, and Acinetobacter, M2 produced substantial extracellular polymeric substances (EPS) and unsaturated fatty acids, which mitigated cold-induced stress. Metagenomic analysis revealed the presence of cold-shock responsive genes, including unsaturated fatty acid synthase, and cpsA, which contribute to its resilience under low-temperature conditions. Moreover, M2 enhanced both nitrogen assimilation and nitrate reduction under cold stress. These findings highlight the potential of M2 as an effective and practical strategy for improving nitrogen removal in wastewater treatment facilities during winter, thereby addressing a critical operational limitation in cold-climate regions.}, }
@article {pmid40523412, year = {2025}, author = {Li, D and Zhou, A and Mei, J and Liu, Z and Duan, H and Luo, J and He, Z and Liu, W and Ni, BJ and Yue, X}, title = {Synergy among multiple electron donors in electro-fermentation chain elongation: Accelerated directional electron transfer and enhanced microbial functions.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132817}, doi = {10.1016/j.biortech.2025.132817}, pmid = {40523412}, issn = {1873-2976}, abstract = {Electro-fermentation assisted chain elongation (EF_CE) effectively converts organic waste into medium-chain fatty acids (MCFAs), yet the regulatory mechanisms involving multiple electron donors (EDs) require elucidation. This study systematically explored the synergistic effects of ethanol and lactate as EDs on MCFA biosynthesis in EF_CE systems. The cross-niche microbial associations shaped by multiple EDs coupled with inoculation with caproate-synthesizing bacteria led to a 2.9-3.9-fold increase in caproate synthesis. Metagenomic analysis revealed that multiple EDs decreased the relative abundances of genes encoding Mut in the acrylate pathway, while increasing the relative abundances of genes encoding ascB in the Wood-Ljungdahl pathway, and ADH, kor and cdhA in ethanol and lactate oxidation pathways. These findings highlight the dual role of ED synergy in directing MCFAs production and reshaping microbial networks, offering insights for improving organic waste/wastewater recycling.}, }
@article {pmid40523310, year = {2025}, author = {Johnson, LA and Smith, DDN and Subasinghe, R and Raap, M and Richter, R and Huyben, D and Lau, C and Brown, L and Chu, J and Khomenko, O and Manning, A and Johnson, S and Hamoutene, D}, title = {Influence of aquaculture and genomic surveillance techniques on antimicrobial resistance gene profiles and microbiota detected in marine and freshwater sediments.}, journal = {Canadian journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1139/cjm-2024-0206}, pmid = {40523310}, issn = {1480-3275}, abstract = {Surveillance methods for antimicrobial resistance genes (ARGs) are needed to assess potential risk of antimicrobial resistance (AMR), especially in complex environmental samples with limited data on ARG distribution. This study employed target-enrichment metagenomics (bait-capture) and a Resistomap qPCR assay to assess the resistome in marine and freshwater sediments associated with active Canadian finfish aquaculture operations. Differences in resistome profiles were considered with distance to the net-pens, concentrations of three aquaculture-associated chemical residues, and microbial communities as detected with 16S rRNA gene amplicon sequencing. With bait-capture, a total of 194 ARGs and 41 replicon types were detected across the sediment samples. Differences due to aquaculture proximity were noted in the composition of the resistome, which was dominated by tetracycline resistance genes. With qPCR, 37 out of 51 ARGs targets were detected, and proximity to net-pens or region did not show changes in resistome composition. Co-occurrence networks revealed significant correlations among genera and the resistome detected with bait-capture, highlighting a potential influence of aquaculture on ARGs in the environment. This study demonstrates the utility of bait-capture and qPCR assays in detection of ARGs in both freshwater and marine sediments from aquaculture sites that will assist further ARG surveillance.}, }
@article {pmid40523202, year = {2025}, author = {Dal Bó, B and Guo, Y and Mayr, MJ and Pereira, OS and Levin, LA and Orphan, VJ and Goffredi, SK}, title = {Methane-powered sea spiders: Diverse, epibiotic methanotrophs serve as a source of nutrition for deep-sea methane seep Sericosura.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {26}, pages = {e2501422122}, doi = {10.1073/pnas.2501422122}, pmid = {40523202}, issn = {1091-6490}, support = {OCE-2048481//NSF (NSF)/ ; OCE-2048720//NSF (NSF)/ ; OCE-2048666//NSF (NSF)/ ; }, mesh = {Animals ; *Methane/metabolism ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Male ; *Spiders/microbiology/physiology ; Bacteria/metabolism/genetics ; Female ; Methanol/metabolism ; Pacific Ocean ; }, abstract = {Methane seeps harbor uncharacterized animal-microbe symbioses with unique nutritional strategies. Three undescribed sea spider species (family Ammotheidae; genus Sericosura) endemic to methane seeps were found along the eastern Pacific margin, from California to Alaska, hosting diverse methane- and methanol-oxidizing bacteria on their exoskeleton. δ[13]C tissue isotope values of in situ specimens corroborated methane assimilation (-45‰, on average). Live animal incubations with [13]C-labeled methane and methanol, followed by nanoscale secondary ion mass spectrometry, confirmed that carbon derived from both compounds was actively incorporated into the tissues within five days. Methano- and methylotrophs of the bacterial families Methylomonadaceae, Methylophagaceae and Methylophilaceae were abundant, based on environmental metagenomics and 16S rRNA sequencing, and fluorescence and electron microscopy confirmed dense epibiont aggregations on the sea spider exoskeleton. Egg sacs carried by the males hosted identical microbes suggesting vertical transmission. We propose that these sea spiders farm and feed on methanotrophic and methylotrophic bacteria, expanding the realm of animals known to harness C1 compounds as a carbon source. These findings advance our understanding of the biology of an understudied animal lineage, unlocking some of the unique nutritional links between the microbial and faunal food webs in the oceans.}, }
@article {pmid40522529, year = {2025}, author = {Singh, S and Kumar, M and Sarma, DK and Kumawat, M and Verma, V and Kriti, M and Tiwari, R}, title = {Advancing AMR Surveillance: Confluence of One Health and Big Data Integration : Converging One Health and Big Data for AMR.}, journal = {EcoHealth}, volume = {}, number = {}, pages = {}, pmid = {40522529}, issn = {1612-9210}, abstract = {Antibiotic resistance poses a critical global health threat, demanding robust surveillance systems to monitor its prevalence, patterns, and trends. The One Health approach has emerged as a comprehensive framework, emphasizing the interconnectedness of human health, animal health, and the environment in addressing this complex issue. This article explores the potential of One Health-based antibiotic resistance surveillance, integrating big data analytics and interdisciplinary collaboration. Challenges and opportunities in harmonizing surveillance efforts across sectors are discussed, underscoring the importance of data sharing and standardization. Advanced technologies like genomics and metagenomics are examined for understanding the genetic basis of antibiotic resistance and tracking its spread. The article also highlights the potential of real-time monitoring and early warning systems to inform evidence-based policies and antimicrobial stewardship programs. By analyzing the state-of-the-art in antibiotic resistance surveillance, this article sheds light on the transformative potential of One Health approaches, leveraging big data and interdisciplinary collaboration to combat antibiotic resistance effectively. The urgency of adopting a united global effort to safeguard the efficacy of antibiotics for future generations is emphasized.}, }
@article {pmid40521483, year = {2025}, author = {Wang, Y and Yang, J and Hu, X and Wang, Y and Qin, S and Fan, J and He, M}, title = {Metagenomic Analysis and Core Flooding Reveals the Indigenous Bacterial Community Information and MEOR Potential of the Main Water-Drive Low-Permeability Reservoir in the Ordos Basin.}, journal = {ACS omega}, volume = {10}, number = {22}, pages = {23272-23280}, pmid = {40521483}, issn = {2470-1343}, abstract = {Oil recovery decreased with prolonged waterflood development in the main reservoirs in the Ordos Basin, and the extraction of the remaining oil was gradually difficult. To exploit oil-producing potential through microbial enhanced oil recovery (MEOR), bacterial communities of 26 samples from Yan 9, 10 layers, and 15 samples from Chang 6 layers were analyzed based on high-throughput sequencing. 1578 and 3581 amplicon sequence variants were obtained from Jurassic and Triassic samples, and α diversity analysis showed that dominant bacterial genera existed distinctly in both study areas. The distribution of the Jurassic bacteria community differed from that of the Triassic, revealed by a principal coordinate analysis. Pseudomonas (15.74%) and Sulfurospirillum (9.94%) were identified as the dominant bacteria in the Jurassic study areas, as well as Pseudomonas (33.54%) and Acinetobacter (11.41%) were the main bacteria in the Triassic reservoirs. Co-occurrence network analysis indicated that the Jurassic and Triassic study areas had both complex and unstable bacterial consortiums, which were closely connected with Proteobacteria and Firmicutes, respectively. The different development strategies and reservoir properties led to the discrepancy in indigenous bacteria distribution between the Jurassic and Triassic study areas. However, some bacteria that have been reported to have oil-displacing ability, such as Pseudomonas, Halomonas, Acinetobacter, Marinobacterium, and Marinobacter, were found in both regions, suggesting that these bacteria had extensive adaptability. Among them, the utilization of functional bacteria of Proteobacteria and Firmicutes might be conducive to enhancing oil recovery stably. Based on this, Pseudomonas aeruginosa PA2 was isolated from study areas and enhanced oil recovery by 17.85 and 11.89% during Jurassic and Triassic core flooding tests, respectively.}, }
@article {pmid40520796, year = {2025}, author = {Chen, M and Wu, H and Xie, L and Wu, M and Lan, P}, title = {Successful management of severe pulmonary form of leptospirosis with VV-ECMO, prone ventilation, and bronchoalveolar lavage: two case reports.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1598589}, pmid = {40520796}, issn = {2296-858X}, abstract = {BACKGROUND: Leptospirosis is a globally prevalent zoonotic acute infectious disease that can rapidly progress to severe pulmonary form of leptospirosis (SPFL), leading to multiple organ failure with a high mortality rate. It is estimated that approximately 58,900 deaths occur annually due to leptospirosis, with critically ill patients admitted to intensive care units facing extremely high fatality rates. Therefore, timely and effective treatment strategies are crucial.<br><br>CASE PRESENTATION: Two patients developed fever after farm work exposure, followed by progressive dyspnea and hemoptysis, leading to hospitalization. They rapidly developed acute respiratory distress syndrome (ARDS) and diffuse alveolar hemorrhage (DAH) with severe thrombocytopenia, accompanied by a continuous decline in the ratio of the partial pressure of arterial oxygen to the fraction of inspired oxygen (PaO&#x2082;/FiO&#x2082; [P/F]). Despite endotracheal intubation and mechanical ventilation, hypoxemia persisted. Venovenous extracorporeal membrane oxygenation (VV-ECMO) was initiated to provide oxygenation support, heparin anticoagulation was not used in the early stage. Meanwhile, prone ventilation and bronchoscopy alveolar lavage were performed to promote the clearance of pulmonary hemorrhage, along with anti-infection treatment. The diagnosis of leptospirosis was confirmed through Metagenomic Next-Generation Sequencing (mNGS). Both patients ultimately recovered, were successfully weaned from life support, discharged in stable condition, and returned to normal life.<br><br>CONCLUSION: Early VV-ECMO support, combined with prone ventilation and bronchoalveolar lavage, can improve the prognosis of patients with SPFL. mNGS testing aids in the definitive diagnosis of leptospirosis and provides a reliable basis for antibiotic selection.}, }
@article {pmid40520638, year = {2025}, author = {Zakaria, D and Sandri, C and Modesto, M and Spiezio, C and Scarafile, D and Cedras, A and Borruso, L and Manghi, P and Trevisi, P and Segata, N and Mattarelli, P and Arita, M}, title = {Disentangling the gut microbiota of Aldabra giant tortoises of different ages and environments.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19566}, pmid = {40520638}, issn = {2167-8359}, mesh = {Animals ; *Turtles/microbiology ; *Gastrointestinal Microbiome/genetics ; Italy ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Age Factors ; Seychelles ; Environment ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: The gut microbiota plays a pivotal role in regulating the physiological functions of its host, including immunity, metabolism, and digestion. The impact of environment and age on microbiota can be assessed by observing long-lived animals across different age groups and environments. The Aldabra giant tortoise (Aldabrachelys gigantea) is an ideal species for this study due to its exceptionally long lifespan of over 100 years.<br><br>METHODS: Using 16S rRNA gene amplicon analysis, we analyzed 52 fecal samples from giant tortoises in Seychelles (Curieuse and Mah&#xe9; islands) and in a zoological park in Italy, from very young individuals to those of >100 years old. We performed Alpha and Beta diversity analysis, relative abundance analysis, and complex upset plot analysis, comparing the results of tortoises from different environments and age groups.<br><br>RESULTS: The diversity and overall composition of the gut microbiota of tortoises were impacted mainly by geolocation rather than their age. The greater diversity of microbiota in wild tortoises was attributed to their food variance such as wild leaves and branches, compared to captive or domesticated conditions. Beta diversity analysis also revealed the contribution of both environment and age to the variation between samples, with environments accounting for a larger proportion of this contribution. Certain bacterial families, such as Spirochaetota and Fibrobacterota, were more prevalent in environments with higher fiber intake, reflecting dietary differences. Additionally, a range of host-independent environmental bacteria was found to be specific to individuals in Curieuse and not in other geolocations. On the other hand, there were no bacterial taxa specific to centenarians, whose microbial complexity was reduced compared to adult or elderly tortoises.<br><br>CONCLUSIONS: Our records showed that environment is the primary influence in the overall composition and diversity of the gut microbiota of Aldabra giant tortoises. As giant tortoises are amongst the longest-lived vertebrate animals, these findings can be utilized to monitor their health according to their ages, and enhance their conservation efforts.}, }
@article {pmid40520380, year = {2025}, author = {Muzami, EM and Kitundu, G and Muriithi, OM and Kavoo, AM and Gichuru, VG and Mbinda, WM}, title = {Metagenomic insights to bacterial communities, functional traits, and soil health in banana smallholder agroecosystems of Kenya.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1582271}, pmid = {40520380}, issn = {1664-302X}, abstract = {Microbes inhabiting the banana rhizosphere are varied and mediate essential functions that enhance plant growth and increase crop productivity. Their abundance in soil habitats is a potential indicator of soil health and quality. Despite the well-known benefits of rhizosphere microorganisms in banana cultivation, their genomic and functional diversity remains largely unexplored within smallholder agroecosystems. In this study, we characterized the community composition and functional potential of bacteria in banana rhizospheric soils from Gituamba, Mangu and Ngenda constituencies in Kiambu County, Kenya. Using Illumina Novaseq sequencing, we analyzed 16S rRNA gene amplicons and shotgun metagenomic profiles to explore these microbial communities. Variations of soil physicochemical parameters across the study sites were assessed. The parameters varied across the sites, with soils in Gituamba and Ngenda depicting better soil fertility characteristics than Mangu. Amplicon sequencing profiles revealed higher bacterial diversity in Gituamba compared to Mangu, while the single sample from Ngenda exhibited moderate diversity. The dominant phyla across the study sites were Proteobacteria, Actinobacteria, and Cyanobacteria. Functional profiling of 16S rRNA gene amplicons showed a higher enrichment in Gituamba compared to Mangu. Overall, the functional profiling indicated that predicted metabolic pathways across the study sites were linked to genes encoded by the members of the most abundant bacterial phyla in the soil environments, majorly contributing to beneficial roles for soil health and crop yield. This study offers methods to reveal the banana rhizosphere as a rich reservoir for potential microbes of agricultural and biotechnological significance, which can promote sustainable agriculture.}, }
@article {pmid40520307, year = {2025}, author = {Ye, S and Peng, S and Wang, X and Fan, J and Zhu, C and Huang, L and Huang, Y and Cheng, K and Ni, T and Qian, Y and Wu, X and Xu, Y}, title = {Microbial community structure and resistome dynamics on elevator buttons in response to surface disinfection practices.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1593114}, pmid = {40520307}, issn = {2296-2565}, mesh = {*Disinfection/methods ; *Disinfectants/pharmacology ; Humans ; COVID-19/prevention &amp; control ; China ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Microbiota/drug effects ; SARS-CoV-2 ; }, abstract = {BACKGROUND: Disinfectants have been extensively used in public environments since the COVID-19 outbreak to help control the spread of the virus. This study aims to investigate whether disinfectant use influences the structure of bacterial communities and contributes to bacterial resistance to disinfectants and antibiotics.<br><br>METHODS: Using molecular biology techniques-including metagenomic sequencing and quantitative PCR (qPCR)-we analyzed the bacterial communities on elevator button surfaces from two tertiary hospitals, one infectious disease hospital, two quarantine hotels (designated for COVID-19 control), and five general hotels in Nanjing, Jiangsu Province, during the COVID-19 pandemic. We focused on detecting disinfectant resistance genes (DRGs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs).<br><br>RESULTS: Significant differences were observed in the bacterial community structures on elevator button surfaces across the four types of environments. Quarantine hotels, which implemented the most frequent disinfection protocols, exhibited distinct bacterial profiles at the phylum, genus, and species levels. Both &#x3b1;-diversity (within-sample diversity) and &#x3b2;-diversity (between-sample diversity) were lower and more distinct in quarantine hotels compared to the other environments. The abundance of DRGs, ARGs, and MGEs was also significantly higher on elevator button surfaces in quarantine hotels. Notably, antibiotic-resistant bacteria (ARBs), including Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa, were detected in all four settings.<br><br>CONCLUSION: The structure of bacterial communities on elevator button surfaces varies across different environments, likely influenced by the frequency of disinfectant use. Increased resistance gene abundance in quarantine hotels suggests that disinfection practices may contribute to the selection and spread of resistant bacteria. Enhanced monitoring of disinfection effectiveness and refinement of protocols in high-risk environments such as hospitals and hotels are essential to limit the spread of resistant pathogens.}, }
@article {pmid40379209, year = {2025}, author = {Xie, D and Liu, Y and Cong, W and Qi, G and Mu, C}, title = {Pathogen Diagnostic Value of Nanopore Sequencing in Postoperative Central Nervous System Infections.}, journal = {World neurosurgery}, volume = {199}, number = {}, pages = {124090}, doi = {10.1016/j.wneu.2025.124090}, pmid = {40379209}, issn = {1878-8769}, abstract = {OBJECTIVE: To evaluate the diagnostic performance of nanopore sequencing in postoperative central nervous system infections (PCNSIs).<br><br>METHODS: A total of 34 patients with suspected PCNSIs after craniocerebral surgery were included from the Aviation General Hospital between June 2022 and October 2023. Cerebrospinal fluid samples were collected immediately. Clinical information was gathered for all patients, and tests including blood routine examination, biochemical analysis, microbial culture, metagenomic next-generation sequencing (mNGS), and nanopore sequencing were performed. Relevant data were compiled.<br><br>RESULTS: Among 34 patients suspected of PCNSIs, nanopore sequencing identified specific pathogenic sequences in 27 (79.41% positivity), surpassing both mNGS (73.53%) and microbial culture (55.88%). Compared to microbial culture and mNGS, nanopore sequencing demonstrated superior sensitivity (79.41%) and diagnostic performance, thereby minimizing the missed diagnosis rate of microbial culture (36.67% vs. 11.76%). Nanopore sequencing combined with microbial culture shows significant consistency with the final clinical diagnosis (K = 0.717, P < 0.05). In contrast, the consistency of using microbial culture alone with the final clinical diagnosis is lower (K = 0.289, P < 0.05), suggesting that microbial culture may have limitations in certain situations.<br><br>CONCLUSIONS: Compared to microbial culture and mNGS, nanopore sequencing has a higher pathogen detection rate and a lower missed diagnosis rate. In clinical practice, using nanopore sequencing as a supplement to microbial culture can aid in the diagnosis of PCNSIs.}, }
@article {pmid40520149, year = {2025}, author = {Maldonado, M and Pita, L and Hentschel, U and Erpenbeck, D and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the sponge Crambe crambe (Schmidt, 1862) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {275}, pmid = {40520149}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Crambe crambe (Porifera; Demospongiae; Poecilosclerida; Crambeidae). The host genome sequence is 143.20 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.53 kilobases in length. Several symbiotic prokaryotic genomes were assembled as MAGs, including two relevant sponge symbionts, the Candidatus Beroebacter blanensis/ AqS2 clade (Tethybacterales, Gammaproteobacteria) of LMA sponges, and the widely distributed archaeal Nitrosopumilus sp. clade.}, }
@article {pmid40519722, year = {2025}, author = {Kong, Y and Zhang, T and Ye, X and Wu, J}, title = {Alterations of gut microbiota and metabolites in children with Crohn's disease and their correlation with disease activity.}, journal = {Translational pediatrics}, volume = {14}, number = {5}, pages = {960-971}, pmid = {40519722}, issn = {2224-4344}, abstract = {BACKGROUND: The disruption of the gut microbiota is a prominent feature seen in children with Crohn's disease (CD), impacting metabolic processes. These factors collectively contribute significantly to the onset and progression of CD. The aim of this study was to assess the variations in gut microbiota and metabolites in children with newly diagnosed CD and those in remission, and to investigate their potential correlation with clinical indexes.<br><br>METHODS: This was a retrospective study. From June 2018 and March 2024, 57 children with CD admitted to Beijing Children's Hospital were included, and 22 healthy children during the same period were selected as the control group. Their peripheral blood and fecal samples were obtained, and clinical data were collected. Analysis of the fecal microbiota and serum metabolites was conducted using metagenomic sequencing and non-targeted mass spectrometry, respectively, to compare the alteration in children with CD and healthy controls (HCs), and their correlation with clinical indexes.<br><br>RESULTS: Analysis of fecal metagenomic sequencing data revealed that the alpha diversity was significantly lower in the newly diagnosed CD group compared to the HC group, whereas it was ameliorated in the CD remission group. The beta diversity showed that the microbial structures of the three groups were obviously separated. Firmicutes was identified as the primary altered bacteria in the microbiota. Specifically, the abundance of Ruminococcus, Faecalimonas, Blautia, and Faecalibacterium were correlated with clinical indexes such as pediatric Crohn's disease activity index (PCDAI). Metabolomic analysis highlighted differences in lipid metabolism, bile acid (BA) metabolism, amino acid metabolism and energy homeostasis between the CD remission and newly diagnosed CD groups. Notably, the levels of citric acid were correlated with clinical indexes such as PCDAI, which was also potential indicator for identifying clinical activity of pediatric CD patients [area under the curve (AUC) =0.77, specificity =0.64, sensitivity =0.83].<br><br>CONCLUSIONS: The microbial diversity of children with newly diagnosed CD decreased, but then ameliorated in the remission stage. Some short-chain fatty acids (SCFAs)-producing bacteria, lipid metabolites, and energy homeostasis products were associated with clinical indexes. In particular, citric acid demonstrated specific effectiveness in identify clinical activity of pediatric CD patients, which was a potential biomarker. Further exploring the mechanism of energy homeostasis in CD is beneficial to find new therapeutic targets.}, }
@article {pmid40519668, year = {2025}, author = {Miller, SJ and Zhang, F and Taylor, SL and Shoubridge, AP and Flynn, E and Vasil, E and Woodman, RJ and Papanicolas, LE and Rogers, GB}, title = {Oropharyngeal detection of specific gut-derived Enterobacterales is associated with increased respiratory infection risk in older adults.}, journal = {Frontiers in aging}, volume = {6}, number = {}, pages = {1566034}, pmid = {40519668}, issn = {2673-6217}, abstract = {Respiratory tract infections (RTI) are a major contributor to morbidity and mortality in later life. RTI risk factors in older populations, including declining general health, altered airway physiology, and increased pharmaceutical exposures, also contribute to changes in the oropharyngeal (OP) microbiota. We sought to investigate whether such changes predict future incidence of RTI. OP microbiota characteristics were measured in 190 residents of long-term aged care. Fifty-four participants (28.4%) experienced one or more study-defined RTIs during the 12-month follow-up period, of which 28 (14.7%) occurred within 90 days of sample collection. OP microbiota composition was significantly associated with days to RTI event (F = 1.74, R[2] = 1.02%, p = 0.04). Detection of Enterobacterales species (Enterobacter cloacae, Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae, Klebsiella variicola, and Proteus mirabilis) were independently associated with RTI risk after covariate adjustment (subdistribution HR: 4.84; 95% CI: 1.65-14.19; p = 0.002). Strain-level analysis performed on metagenomes from contemporaneous OP and stool samples identified co-carriage of indistinguishable Enterobacterales strains in those with Enterobacterales-positive OP samples, suggesting intra-participant strain acquisition. We report OP carriage of Enterobacterales species to be a marker of future RTI risk in long-term aged care residents, reflecting the independent influence of common ageing-associated risk exposures.}, }
@article {pmid40519351, year = {2025}, author = {Plazola, CE and Rehman, A and Morel, M and Vu, C and Castro, JG and Ayoade, F}, title = {Aspergillus fumigatus endocarditis in an immunocompetent host aided by metagenomic next-generation sequencing assay: case report and literature review.}, journal = {Le infezioni in medicina}, volume = {33}, number = {2}, pages = {226-232}, pmid = {40519351}, issn = {2532-8689}, abstract = {Aspergillus fumigatus endocarditis is a rare but severe infection associated with high mortality, typically affecting immunocompromised individuals. Diagnosing fungal endocarditis can be challenging due to the often negative blood cultures and nonspecific symptoms. We present a case of Aspergillus fumigatus infective endocarditis in a 59-year-old immunocompetent man with no typical risk factors, diagnosed with the assistance of metagenomic microbial plasma cell-free DNA next-generation sequencing assay (Karius test). The patient presented with ocular symptoms and was found to have a heart murmur and a hypodense liver lesion, leading to suspicion of infective endocarditis. Blood cultures failed to reveal a pathogen, but elevated fungal biomarkers and the Karius test supported Aspergillus fumigatus as the causal agent. The patient received antifungal therapy with voriconazole and liposomal amphotericin B followed by surgical intervention for mitral valve replacement. The case exemplifies the difficulty in diagnosing Aspergillus endocarditis, as blood cultures are often negative and histological confirmation may be delayed. Molecular diagnostics, such as metagenomic microbial plasma cell-free DNA next-generation sequencing assay, significantly enhance pathogen detection in culture-negative cases. However, although treatment with antifungal therapy and surgery can improve outcomes, the high mortality associated with Aspergillus endocarditis remains a critical concern, highlighting the need for further research and advancements in both diagnostic and therapeutic approaches.}, }
@article {pmid40518950, year = {2025}, author = {Chen, C and Xu, Y and Ouyang, J and Xiong, X and Łabaj, PP and Chmielarczyk, A and Różańska, A and Zhang, H and Liu, K and Shi, T and Wu, J}, title = {VirulentHunter: deep learning-based virulence factor predictor illuminates pathogenicity in diverse microbial contexts.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {3}, pages = {}, doi = {10.1093/bib/bbaf271}, pmid = {40518950}, issn = {1477-4054}, support = {32370720//National Natural Science Foundation of China/ ; 2023YFC2706503//National Key Research and Development Program of China/ ; }, mesh = {*Deep Learning ; *Virulence Factors/genetics/metabolism ; Humans ; *Mycobacterium tuberculosis/pathogenicity/genetics ; *Computational Biology/methods ; *Software ; Bacterial Proteins/genetics ; *Mycobacterium avium/pathogenicity/genetics ; }, abstract = {Virulence factors (VFs) are critical determinants of bacterial pathogenicity, but current homology-based identification methods often miss novel or divergent VFs, and many machine learning approaches neglect functional classification. Here, we present VirulentHunter, a novel deep learning framework that enable simultaneous VF identification and classification directly from protein sequences by leveraging the crucial step of fine-tuning pretrained protein language model. We curate a comprehensive VF database by integrating diverse public resources and expanding VF category annotations. Our benchmarking results demonstrate that VirulentHunter outperforms existing methods, particularly in identifying VFs lacking detectable homologs. Additionally, strain-level analysis using VirulentHunter highlights distinct pathogenicity profiles between Mycobacterium tuberculosis and Mycobacterium avium, revealing enrichment in VFs related to adherence, effector delivery systems, and immune modulation in M. tuberculosis, compared to biofilm formation and motility in M. avium. Furthermore, metagenomic profiling of gut microbiota from inflammatory bowel disease patient reveals a depletion of VFs associated with immune homeostasis. These results underscore the versatility of VirulentHunter as a powerful tool for VF analysis across diverse applications. To facilitate broader accessibility, we provide a freely accessible web service for VF prediction (http://www.unimd.org/VirulentHunter), accommodating protein sequences, genomes, and metagenomic data.}, }
@article {pmid40518036, year = {2025}, author = {Salgado, O and Martínez, O and Rivas, Y and Loyola, F}, title = {Highly Specific Virus-Host Linkages in Mesothermophilic and Circumneutral Hot Springs Microbial Communities.}, journal = {Research in microbiology}, volume = {}, number = {}, pages = {104300}, doi = {10.1016/j.resmic.2025.104300}, pmid = {40518036}, issn = {1769-7123}, abstract = {Microbial communities in hot springs are distributed globally and have been extensively characterized regarding their diversity and composition. However, most studies have focused on cellular microbes, with relatively few addressing viruses, and even fewer examining virus-host ecology. Furthermore, research on viral communities and virus-host interactions has predominantly targeted extremely thermophilic environments, leaving mesothermophilic (40-80°C) and circumneutral (pH 6-8) hot spring less explored. Here, we describe virus-host linkages using 37 metagenomic datasets obtained from 14 mesothermophilic and circumneutral hot springs. A parallel analysis of hot spring habitats-sediment, microbial mat, and water-employing diversity metrics, network analyses, and machine learning for virus-host pair identification revealed that viral communities appear to be more endemic than their hosts. Additionally, certain host taxa were identified as differentially abundant across habitats, some corresponding to specific hubs in the network analyses. Most viruses were linked to hosts within the same metagenome, with only a small fraction classified as cosmopolitan. Furthermore, nearly all virus-host pairs were exclusive to a single habitat type-sediment, microbial mat, or water. These findings suggests that virus-host linkages in mesothermophilic and circumneutral hot springs are highly specific, reflecting ecological adaptation within habitat niches.}, }
@article {pmid40517714, year = {2025}, author = {Huang, H and Xiao, K and Shen, T and Chu, D and Xie, Z and Bi, Y and Ning, K and Yan, Y}, title = {The impact of enclosure management on the conservation and restoration of microbial community in a typical urban lake.}, journal = {The Science of the total environment}, volume = {989}, number = {}, pages = {179827}, doi = {10.1016/j.scitotenv.2025.179827}, pmid = {40517714}, issn = {1879-1026}, abstract = {Urban lake freshwater ecosystems, as vital lifelines intricately connected to human well-being, hosted microbes vital for biosynthetic and global biochemical cycles. Despite their ecological importance, current research has yet to fully elucidate how urban lake restoration efforts influence microbial diversity, community structure, and functional dynamics, leaving a significant gap in our understanding of the ecological outcomes of such interventions. Donghu Lake's ongoing restoration project employs enclosure management as a conservation strategy. To evaluate the impact of enclosure management on protecting and restoring microbial communities, we analyzed 72 metagenomic samples from the restoration waterbody. It was found that enclosure management profoundly reshaped microbial communities, making them more stable and similar to natural conditions, and boosting their biosynthetic gene encoding potential. Furthermore, research revealed antibiotic resistance genes (ARGs) tended to be preferentially hosted by specific microbes, identifying Gammaproteobacteria as a critical target for managing ARGs proliferation. These findings provide not only a fresh perspective for the understanding, but also a robust foundation for the management of urban lake freshwater ecosystems. Our findings highlight that enclosure management promotes microbial community stability and functional resilience, which are critical for restoring ecosystem services in urban lakes. This study provides actionable insights for designing targeted conservation strategies to enhance the sustainability of freshwater ecosystems under anthropogenic pressure.}, }
@article {pmid40517504, year = {2025}, author = {Tang, X and Liu, Y and Yang, W and Wu, Y and Yong, T and Liu, W and Lv, F and Hussain, K and Wang, Y and Gao, X and Zhang, Y}, title = {Macroplastics in soybean cultivation: Neutral on plant growth but disruptive to nitrogen-fixing microbiome.}, journal = {Ecotoxicology and environmental safety}, volume = {301}, number = {}, pages = {118499}, doi = {10.1016/j.ecoenv.2025.118499}, pmid = {40517504}, issn = {1090-2414}, abstract = {Macroplastics are an emerging yet underexplored pollutant in agricultural soils, with the potential to disrupt nitrogen (N) cycling through physical interference and microbial community shifts. While extensive studies have focused on microplastics, the effects of larger plastic debris (>2 cm) on soil-plant systems in legume cropping systems remain poorly understood. We conducted a 71-d mesocosm study utilizing [15]N isotopic tracing and metagenomic sequencing to demonstrate how macroplastics influence soybean growth and soil-soybean continuum N cycling. Soybean growth was not affected under macroplastics exposure (up to 200 kg ha[-][1]). However, macroplastics increased soil NO3[-] and NH4[+] concentrations, and elevated urease and ammonia monooxygenase activities, suggesting enhanced N availability. Paradoxically, macroplastics significantly disrupted the N-fixing microbial community, reducing the abundance of key bacteria such as Azorhizobium and Bradyrhizobium. Nitrogen fixation pathways (in log10-transformed TPM+1) were markedly suppressed in soils treated with 200 kg ha[-1] macroplastics compared to untreated soils (p < 0.001). Our findings highlight the potential risks of macroplastics posing to N cycling and microbial health in agricultural soils. This study addresses a critical knowledge gap by shifting the focus from micro- to macroplastic impacts on biogeochemical cycling.}, }
@article {pmid40517474, year = {2025}, author = {Yu, X and Li, J and Zhou, Y and Chen, Y and Zou, L and Luo, C and Shen, C and Liu, F and Xu, J and Tang, X}, title = {Identification of the microorganisms for methane-dependent arsenate reduction in wetland using DNA-stable isotope probing and metagenomics.}, journal = {Water research}, volume = {284}, number = {}, pages = {123934}, doi = {10.1016/j.watres.2025.123934}, pmid = {40517474}, issn = {1879-2448}, abstract = {The methane-dependent arsenate reduction (M-AsR) process is recently demonstrated to enhance the release of mobile and toxic arsenite [As(III)], with critical implications for ecosystem safety in wetland ecosystem. However, the key functional microorganisms and the underlying metabolic mechanisms of M-AsR in wetland remain unclear. In this study, [13]C-labeled methane (CH4) was used as the sole carbon source to track the active microorganisms responsible for M-AsR. DNA-stable isotope probing (DNA-SIP) combined with amplicon and metagenomic sequencing was further employed to identify the microorganisms involved in M-AsR. The results showed that arsenate [As(V)] reduction occurred exclusively in the treatment amended with both CH4 and As(V). After a 50-day incubation, significant shifts in the relative abundance of functional genes (pmoA, ANME-2d mcrA and arrA) were observed in the heavy DNA fractions from the treatment amended with [13]CH4 and As(V), indicating the incorporation of [13]C into M-AsR microorganisms. Furthermore, the Methanobacterium, Methylobacter and arsenate-reducing bacteria (Chryseobacterium and Hydrogenophaga) were the predominant genera in [13]CH4-As heavy fractions and identified as the potential microorganisms responsible for M-AsR in wetland. Metagenomic analysis further confirmed that most of these microorganisms contained genes for CH4 oxidation and As(V) reduction. This multi-omics approach provides mechanistic insights into microbial mediated As(V) reduction in methane-rich wetland area.}, }
@article {pmid40517085, year = {2025}, author = {Schoenle, A and Francis, O and Archibald, JM and Burki, F and de Vries, J and Dumack, K and Eme, L and Florent, I and Hehenberger, E and Hoffmeyer, TT and Irisarri, I and Lara, E and Leger, MM and Lukeš, J and Massana, R and Mathur, V and Nitsche, F and Strassert, JFH and Worden, AZ and Yurchenko, V and Del Campo, J and Waldvogel, AM}, title = {Protist genomics: key to understanding eukaryotic evolution.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2025.05.004}, pmid = {40517085}, issn = {0168-9525}, abstract = {All eukaryotes other than animals, plants, and fungi are protists. Protists are highly diverse and found in nearly all environments, with key roles in planetary health and biogeochemical cycles. They represent the majority of eukaryotic diversity, making them essential for understanding eukaryotic evolution. However, these mainly unicellular, microscopic organisms are understudied and the generation of protist genomes lags far behind most multicellular lineages. Current genomic methods, which are primarily designed for animals and plants, are poorly suited for protists. Advancing protist genome research requires reevaluating plant- and animal-centric genomic standards. Future efforts must leverage emerging technologies and bioinformatics tools, ultimately enhancing our understanding of eukaryotic molecular and cell biology, ecology, and evolution.}, }
@article {pmid40516682, year = {2025}, author = {Sadah Al Azzawi, DH and Jalali, A and Rezaei, M}, title = {Metagenomic Insights into Bacterial Communities and Antibiotic Resistance Genes in Landfill-Impacted Waters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126663}, doi = {10.1016/j.envpol.2025.126663}, pmid = {40516682}, issn = {1873-6424}, abstract = {Municipal landfills are significant sources of environmental and microbial pollution, impacting groundwater and surface water quality. This study investigated the microbial community composition and antibiotic resistance genes (ARGs) in water downstream of landfills of Gilan, Mazandaran, and Golestan provinces, Iran. Water samples were collected from seven sites, and shotgun metagenomic sequencing was used to analyze microbial diversity and ARGs. Heavy metals and BTEX (benzene, toluene, ethylbenzene, and xylene) compounds were measured using inductively coupled plasma (ICP), and gas chromatography-mass spectrometry (GC-MS) methods, respectively. Pseudomonadaceae and Enterobacteriaceae were the most abundant bacterial families, with efflux pump ARGs being the most prevalent. Concentrations of arsenic and cadmium exceeded WHO and US-EPA standards at all sites. Significant positive correlations were observed between Pseudomonadaceae abundance and lead concentration (r =0.998, p = 0.031, CI [0.966, 0.999]), and between Enterobacteriaceae abundance and chromium concentration (r =0.999, p = 0.0078, CI [0.993, 1.000]). A significant negative correlation was found between the abundance of the two-component system (TCS) gene class and BTEX concentration (r = -0.457, p = 0.014, CI [-0.72, -0.09]). Additionally, aluminum concentration negatively correlated with antibiotic inactivation (r =0.999, p = 0.018, CI [-1.000, -0.997]) and antibiotic target protection classes (r = -0.997, p = 0.048, CI [-0.999, -0.990]). These findings indicate that landfill sites significantly influence bacterial communities, promoting resistance to heavy metals and pollutants. The abundance of ARGs near landfills suggests microbial adaptation to pollution, highlighting the need for improved waste management to mitigate the spread of antibiotic resistance.}, }
@article {pmid40516493, year = {2025}, author = {Semwal, P and Shivhare, R and Majhi, B and Mishra, SK and Misra, S and Misra, A and Srivastava, S and Chauhan, PS}, title = {Endophytic bacterial's phenylalanine and trans-cinnamic acid as exogenous precursors involved in the modulating colchicine biosynthesis pathway in Gloriosa superba.}, journal = {Plant physiology and biochemistry : PPB}, volume = {227}, number = {}, pages = {110151}, doi = {10.1016/j.plaphy.2025.110151}, pmid = {40516493}, issn = {1873-2690}, abstract = {Unlocking the hidden power of endophytes reveals a novel pathway for boosting colchicine biosynthesis in Gloriosa superba. Metabolite analysis of endophyte culture filtrates identifies essential precursors i.e., phenyl ethyl alcohol, phenylalanine, trans-cinnamic acid, and benzoic acid participating in colchicine biosynthesis. Bacilli-treated Gloriosa superba plants demonstrated a remarkable increase in plant growth and colchicine content over untreated plants. Moreover, enhanced nutrient uptake (Fe, Zn, Cu, Mn) further induced the enzymatic activities critical for colchicine biosynthesis genes such as PAL, NMT, CYP450, and OMT. The metagenomic analysis associated with Bacilli-treated G. superba plants further revealed a shift in Bacillus species, and the functional pathway confirmed the upregulation of precursors in colchicine biosynthesis. Our study highlights the significant role of endophytic Bacilli on plant growth, enhanced nutrient uptake, and shifts in the endophytic microbiome to induce colchicine biosynthesis in G. Superba. It offers a detailed understanding of the endophyte's potential for deciphering its role in enhancing growth and active metabolite composition. It provides valuable insights for sustainable agriculture and unlocking new possibilities for pharmaceutical applications.}, }
@article {pmid40516400, year = {2025}, author = {Ju, X and Sun, H and Ruan, C and Wang, H and Shi, B and Alvarez, PJJ and Yu, P}, title = {Prophage induction and quorum sensing enhance biofilm stability and resistance under ammonia-oxidizing bacteria-mediated oxidative stress.}, journal = {Water research}, volume = {284}, number = {}, pages = {124010}, doi = {10.1016/j.watres.2025.124010}, pmid = {40516400}, issn = {1879-2448}, abstract = {Ammonia-oxidizing bacteria (AOB) and prophage-carrying bacteria are prevalent in water treatment and reuse systems, yet their interactions and implications for biofilm formation and microbial risks remain insufficiently understood. Here, we demonstrate that oxidative stress arising from the metabolism of the AOB Nitrosomonas europaea induces prophage activation in lysogenized Escherichia coli (λ+). This activation triggers cellular lysis, leading to the release of intracellular components (e.g., protein and DNA) and upregulated quorum sensing (QS) followed by biosynthesis and excretion of extracellular polymeric substance (EPS). Integrated transcriptomic and proteomic analysis revealed that the presence of N. europaea significantly upregulated QS- and EPS-related genes by 2.14-2.93 and 2.81-3.11 folds in E. coli (λ+), respectively. Surviving E. coli (λ+) exhibited enhanced prophage-bacterium symbiosis and activated toxin-antitoxin systems, enhancing their resilience to environmental stress. These microbial adaptations markedly increased EPS production, fostering biofilm development and conferring enhanced biofilm resilience to disinfectants and bacterial antibiotic tolerance. Furthermore, metagenomic analysis at the microbial community wide level demonstrated that ammonia addition-driven AOB enrichment stimulated multi-species biofilm formation, promoted bacterium-phage interactions, and increased bacterial antibiotic resistance. Overall, our findings reveal that oxidative stress driven by AOB accelerates biofilm development, an overlooked phenomenon with potential to exacerbate microbial risks.}, }
@article {pmid40516324, year = {2025}, author = {Xu, R and Li, T and Wang, Z and Wang, H and Sun, M and Xie, J and Tong, L and Peng, W and Wang, Y}, title = {Association among lean mass, gut microbiome alterations and bone mineral density in high-altitude.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {51}, number = {}, pages = {18-27}, doi = {10.1016/j.clnu.2025.05.018}, pmid = {40516324}, issn = {1532-1983}, abstract = {BACKGROUND: Body composition, particularly lean body mass, plays a pivotal role in skeletal health and has been increasingly linked to the gut microbiota (GM). However, evidence from vulnerable high-altitude populations remains scarce.<br><br>OBJECTIVE: This study aimed to evaluate the association between body composition and bone mineral density (BMD) at high altitudes and explore the potential role of GM.<br><br>METHODS: A total of 820 Tibetan participants were recruited. BMD at the lumbar spine (L1-L4) and total hip was measured using dual-energy X-ray absorptiometry (DXA). Multivariate linear regression was applied to evaluate the associations between body composition indices and BMD. Participants were stratified into low lean mass index (LLMI) and high lean mass index (HLMI) subgroups using restricted cubic splines (RCS) and body mass index. Stool samples from a subset of participants (n = 383) were analyzed to determine the relative abundances of KEGG Orthology groups.<br><br>RESULTS: LMI was positively associated with hip BMD at high altitude [&#x3b2; (95 % CI) = 0.005 (0.003,0.007), P < 0.05], whereas no significant association was observed with spine BMD. This correlation varied significantly by altitude (Pinter< 0.05). A similar positive relationship was observed between microbial diversity (Shannon index) and hip_BMD [hip: &#x3b2; (95 % CI) = 0.605 (0.165, 1.044), P < 0.05]. Compared to the HLMI group, LLMI participants exhibited greater microbial diversity (P < 0.05), higher Faecalibacteriums abundance, and lower levels of Prevotella copri (P< 0.05). Functional metagenomic analysis identified differential enrichment of microbial pathways, including riboflavin metabolism, terpenoid backbone biosynthesis, alanine, aspartate, and glutamate metabolism (P < 0.05).<br><br>CONCLUSION: These findings highlight the correlation between LMI and hip BMD among high-altitude Tibetan adults, offering a potential mechanism for the interplay between GM profiles and bone health in high-altitude populations.}, }
@article {pmid40516282, year = {2025}, author = {Victor, MP and Radisic, V and Grevskott, DH and Marathe, NP}, title = {Hospital effluent in a low-resistance setting is responsible for dissemination of novel antibiotic resistance genes into the marine environment.}, journal = {Ecotoxicology and environmental safety}, volume = {301}, number = {}, pages = {118390}, doi = {10.1016/j.ecoenv.2025.118390}, pmid = {40516282}, issn = {1090-2414}, abstract = {Norway has low prevalence of resistance in the clinics, the contribution of hospital effluent to the spread of antimicrobial resistance (AMR) in the environment is largely unknown. The aim of our study was to determine the role of hospital sewage in dissemination of AMR by defining resistome of hospital effluent, and influent and treated-effluent from the receiving sewage treatment plant (STP) using culture-based methods and metagenomics. Around 94 % E. coli strains (n = 66) were multidrug-resistant (MDR), while 92.3 % of the Klebsiella spp. strains (n = 55) showed MDR phenotype, with some strains carrying carbapenemases, such as NDM-5 (n = 3) and KPC-3 (n = 3). Identical clones of Klebsiella michiganensis were detected in hospital effluent, influent and STP treated effluent. From approximately 238 Gigabases of sequence data, we assembled 1205 antibiotic resistance genes (ARGs) using fARGene method, of which 349 genes represented novel ARGs (< 90 % amino acid identity against known ARGs). Both known and novel ARGs (n = 54) were shared between hospital effluent and the treated effluent of the receiving STP. We assembled 523 metagenome assembled genomes (MAGs) with several representing novel taxa, of which 138 (26 %) MAGs carried 429 ARGs with > 83 % representing putative novel ARGs. Potential pathogens accounted for 60 % of the detected ARGs. Around 15.4 % MAGs were shared between hospital effluent and STP treated effluent. We demonstrate that hospital effluent in Norway has a high diversity of both known and novel ARGs. We show that hospital effluent contributes to the dissemination of not only clinically relevant pathogens but also known and novel ARGs into the receiving marine environment in Norway.}, }
@article {pmid40516202, year = {2025}, author = {Botero, J and Basler, N and Cnockaert, M and Peeters, C and Schreiber, M and Marz, M and de Graaf, DC and Matthijnssens, J and Vandamme, P}, title = {Identification and functional genomic analyses of Bartonella isolates from honey bees, and reassessment of the taxonomy of the genus Bartonella.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {4}, pages = {126625}, doi = {10.1016/j.syapm.2025.126625}, pmid = {40516202}, issn = {1618-0984}, abstract = {We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and whole-genome sequence analyses to identify 90 Bartonella isolates from honey bee gut samples in Belgium. While the identification of 62 isolates as Bartonella apihabitans and three as Bartonella choladocola was straightforward, the identification of 25 Bartonella apis-like isolates was challenging. A taxonomic and functional analysis of four B. apis-like genomes and of publicly available B. apis genomes demonstrated that neither OrthoANIu and digital DNA-DNA hybridization analyses, nor functional annotation supported a clear separation of B. apis and B. apis-like genomes. Different phylogenomic analyses showed that B. apis and B. apis-like strains formed a monophyletic clade with an inconsistent internal structure. We therefore considered the remaining 25 isolates identified as B. apis. We subsequently re-addressed an earlier phylogenetic and functional divergence between three major clades of Bartonella species which differed not only in phylogenomic position and ecology, but also in genome size and genomic percentage G + C content, and in many metabolic capabilities. We propose to reclassify the single species of the Bartonella tamiae clade into the novel genus Attibartonella gen. nov., with Attibartonella tamiae comb. nov. as the type species. Similarly, we propose to reclassify species of the honey bee-associated Bartonella clade into the novel genus Ditibartonella gen. nov., with Ditibartonella apis comb. nov. as the type species. The phylogenomic analyses of publicly available genome and metagenome sequences revealed additional Ditibartonella species in honey bee samples, highlighted an evolutionary adaptation of Ditibartonella bacteria to bee hosts and suggested shared transmission routes.}, }
@article {pmid40515809, year = {2025}, author = {Zhang, Z and Yang, Z and Lin, S and Jiang, S and Zhou, X and Li, J and Lu, W and Zhang, J}, title = {Probiotic-induced enrichment of Adlercreutzia equolifaciens increases gut microbiome wellness index and maps to lower host blood glucose levels.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2520407}, doi = {10.1080/19490976.2025.2520407}, pmid = {40515809}, issn = {1949-0984}, mesh = {Humans ; *Probiotics/administration &amp; dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Blood Glucose/analysis/metabolism ; Adult ; Middle Aged ; Metagenomics ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Young Adult ; }, abstract = {The gut microbiome is essential for maintaining host health, influencing gut function and metabolic regulation. While probiotics are widely used to manage gut health, evidence of their specific effects in healthy individuals remains limited. Most studies focus on diseased populations, with little attention to early interventions in individuals without major diseases. In this study, we investigated the effects of probiotics on gut health in participants free from significant health conditions. Fifty-four participants were randomly assigned to receive either a placebo or composite probiotics for 60 d. Shotgun metagenomics revealed that individuals with lower baseline Gut Microbiome Wellness Index 2 (GMWI) exhibited more decisive responses to probiotic intervention, characterized by an increased abundance of beneficial commensal bacteria, including Adlercreutzia equolifaciens. Probiotic intake significantly improved the function of the gut microbiome, reducing antibiotic resistance genes and virulence factors while enhancing carbohydrate-active enzymes. Notably, A. equolifaciens promoted the production of palmitoyl serinol, a metabolite associated with improved GMWI and preventive benefits in blood glucose. In a population-based experiment, these findings were validated in a follow-up single-strain probiotic intervention with Lacticaseibacillus casei Zhang. Our study highlights the potential of probiotics as an early intervention strategy for maintaining gut health in individuals without significant health conditions.}, }
@article {pmid40514168, year = {2025}, author = {Ebrahimi, F and Maleki, H and Ebrahimi, M and Beiki, AH}, title = {A novel approach to finding the compositional differences and biomarkers in gut microbiota in type 2 diabetic patients via meta-analysis, data-mining, and multivariate analysis.}, journal = {Endocrinologia, diabetes y nutricion}, volume = {72}, number = {6}, pages = {501561}, doi = {10.1016/j.endien.2025.501561}, pmid = {40514168}, issn = {2530-0180}, mesh = {*Diabetes Mellitus, Type 2/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Data Mining ; Biomarkers/analysis ; Multivariate Analysis ; Male ; Middle Aged ; Female ; }, abstract = {Type 2 diabetes mellitus (T2DM)-one of the fastest globally spreading diseases-is a chronic metabolic disorder characterized by elevated blood glucose levels. It has been suggested that the composition of gut microbiota plays key roles in the prevalence of T2DM. In this study, a novel approach of large-scale data mining and multivariate analysis of the gut microbiome of T2DM patients and healthy controls was conducted to find the key compositional differences in their microbiota and potential biomarkers of the disease.<br><br>METHODS: First, suitable datasets were identified (9 in total with 946 samples), analyzed, and their operational taxonomic units (OTUs) were computed by identical parameters to increase accuracy. The following OTUs were merged and compared based on their health status, and compositional differences detected. For biomarker identification, the OTUs were subjected to 9 different attribute weighting models. Additionally, OTUs were independently analyzed by multivariate algorithms (LEfSe test) to verify the realized biomarkers.<br><br>RESULTS: Overall, 23 genera and 4 phyla were identified as possible biomarkers. At genus level, the decrease of Bacteroides, Methanobrevibacter, Paraprevotella, and [Eubacterium] hallii group in T2DM and the increase of Prevotella, Megamonas, Megasphaera, Ligilactobacillus, and Lachnoclostridium were selected as biomarkers; and at phylum level, the increase of Synergistota and the decrease of Euryarchaeota, Desulfobacterota (Thermodesulfobacteriota), and Ptescibacteria.<br><br>CONCLUSION: This is the first study ever conducted to find the microbial compositional differences and biomarkers in T2DM using data mining models applied on a widespread metagenome dataset and verified by multivariate analysis.}, }
@article {pmid40513522, year = {2025}, author = {Zhao, W and Wang, Z}, title = {The unforeseen presence of Bordetella pertussis in animal hosts beyond humans: Assessing reliability amidst metagenomic species-resolution challenges.}, journal = {Veterinary microbiology}, volume = {307}, number = {}, pages = {110599}, doi = {10.1016/j.vetmic.2025.110599}, pmid = {40513522}, issn = {1873-2542}, }
@article {pmid40513457, year = {2025}, author = {Zhang, B and Zhang, L and Liu, J and Cai, C and Zhou, Y}, title = {Community succession and protein enhancement in a mixed methanotroph-microalgae system with stepwise increase of ammonium loading - Inhibition and adaptation.}, journal = {Water research}, volume = {284}, number = {}, pages = {123995}, doi = {10.1016/j.watres.2025.123995}, pmid = {40513457}, issn = {1879-2448}, abstract = {The integration of methanotrophs and microalgae in coculture systems presents a promising approach for sustainable biogas valorization and single-cell protein (SCP) production, offering dual benefits of greenhouse gas mitigation and nutrient recovery from waste streams. However, the resilience and metabolic interplay of these consortia under ammonium stress, common in industrial wastewater, remain poorly understood, limiting their scalability. This study systematically investigated the performance of a microalgae-methanotroph consortium under stepwise ammonium concentrations (130, 200 and 260 mg NH4[+]-N/L). The system demonstrated remarkable acclimation, achieving stable biogas conversion with 95.8 ± 5.3 mg CO2-C/(L·day) and 109.0 ± 11.4 mg CH4-C/(L·day) even at highest ammonium concentration. The SCP content increased from 32 % to over 52 % of cell dry weight with yield peaking at 90 mg/(L·day) under 200 mg N/L. A microbial community shift from Methylosinus to ammonia-tolerant Methylococcus dominance underpinned functional stability. Metagenomic analyses revealed ammonium-driven metabolic adaptations: extracellular substance secretion reprograms under stress, nitrogen assimilation was enhanced via glutamine synthetase, and antioxidant defenses were activated. Network analysis highlighted intensified competition (31 % negative correlations) under stress, yet key synergies within coculture system sustained carbon and nitrogen metabolism. These findings resolve knowledge gaps in ammonium-stressed consortia dynamics and provide insights for engineering systems to advancing the circular bioeconomy.}, }
@article {pmid40513456, year = {2025}, author = {Wu, D and Zhang, M and Hu, S and Liu, Y and Zhen, F and Liu, H and Sun, Y}, title = {Multidimensional insights into efficiency-stability trade-off in anaerobic digestion from organic overloading stress: Kinetic behavior, energy harvesting, and genome-centric metagenomics microbial self-adaptation.}, journal = {Water research}, volume = {284}, number = {}, pages = {123990}, doi = {10.1016/j.watres.2025.123990}, pmid = {40513456}, issn = {1879-2448}, abstract = {Despite its potential environmental and financial benefits, organic overloading poses a critical challenge to the stability of anaerobic digestion (AD). Currently, the trade-off between operational efficiency and process stability of AD has not been addressed, leaving opportunities for optimization to support sustainable and resilient energy self-sufficiency. This study systematically investigated how organic overloading affected the efficiency-stability trade-off of AD treating lignocellulosic biomass in batch-operated digesters, with a focus on kinetic behavior, energy harvesting, and microbial interactions. A novel quantitative stability coefficient (hydrolysis-to-methanogenesis, H/M) was proposed for batch-operated digesters, and a substantial drop in H/M from 1.68 to 0.40 corresponded to a 5-fold increase in organic loading with only a 13% decrease in methane yield, revealing a non-linear kinetic relationship between the stability and organic loading stress (R[2] > 0.999). The dynamic energy distribution during intermediate degradation failed to balance the energy demands for efficient methane generation under stress, with acetate and propionate metabolism identified as critical bottlenecks. Genome-centric metagenomic analysis suggested that the organic overloading induced the reassembly of the microbial community, re-evolution of functional traits, and remodeling of microbial interactions to adapt to the stress. Metabolic reconstruction further highlighted that metagenome-assembled genomes (MAGs) encoding active transporters (MctC), energy-converting reductase (e.g., Fix and Rnf), and energy-converting hydrogenases (e.g., Eha/b and mvh) gained a competitive advantage by utilizing intermediates and conserving energy. The adaptability of these MAGs allowed them to dominate ecological niches and maintain microbial energy balance under elevated organic loadings, trading operational efficiency for process stability. This study provides multidimensional insights into microbial adaptation mechanisms, emphasizing the importance of a flexible paradigm that prioritizes acceptable resilience and treatment capacity enhancements over solely efficiency maximization.}, }
@article {pmid40513160, year = {2025}, author = {Shi, J and Zhao, L and Fan, M and Yao, J and Wang, J and Xu, D and Ma, Q}, title = {Deciphering the intricate microbial responses and potential degraders of p-chloro-m-xylenol in marine sediments.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {138785}, doi = {10.1016/j.jhazmat.2025.138785}, pmid = {40513160}, issn = {1873-3336}, abstract = {The widespread use of p-chloro-m-xylenol (PCMX) as a broad-spectrum antimicrobial agent raises concerns about its ecological risks in ecosystems. While prior studies focused on activated sludge systems, the impacts of PCMX on marine systems remain unknown. Here, we systematically investigated the responses of marine sediment communities to PCMX (0.005-50 mg/L) exposure through integrated enzymatic assays, multi-omics, and enrichment culture approaches. High PCMX exposure (50 mg/L) significantly suppressed dehydrogenase (63.8 %) and protease (53.8 %) activity, reduced microbial diversity, and inhibited nutrient cycling and ATP production. Meanwhile, antibiotic resistance genes associated with efflux pumps were enriched. Metagenomic analysis revealed upregulated aromatic degradation pathways and stress-response mechanisms (e.g., chemotaxis and biofilm formation) under PCMX stress. A halotolerant marine consortium enriched from high-PCMX sediments demonstrated efficient PCMX degradation (50 mg/L, 72 h) across broad salinity (1.5-5.5 % NaCl) and temperature (25-40°C) ranges, with metabolite profiling suggesting ortho-cleavage pathways. This work underscores the need for regulatory measures to mitigate the ecological risks posed by PCMX in marine ecosystems, while simultaneously demonstrating the remediation potential of a halotolerant microbial consortium for remediating contaminated environments.}, }
@article {pmid40513136, year = {2025}, author = {Boualam, MA and Provost, EL and Drancourt, M and Hama, HO}, title = {Diagnosing past infections: A review.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {2}, pages = {116933}, doi = {10.1016/j.diagmicrobio.2025.116933}, pmid = {40513136}, issn = {1879-0070}, abstract = {Diagnosis of ancient infectious diseases has seen remarkable advances, contributing significantly to understanding historical health challenges and shaping medical research. This review explores the evolution of diagnostic methods and features emerging diagnostic techniques. The early detection of ancient infectious diseases primarily relied on observational evidence, skeletal remains, and historical records. Notable outbreaks such as the Black Death in the 14th century and smallpox epidemics, have left historical imprints. Pioneering diagnostic methods included the paleopathological analysis of the remains of bones and tissue lesions. Later, microbiology methods were adapted to ancient materials, including molecular and serological techniques such as PCR, serology and immunodetection, which were employed to detect DNA or antibodies from ancient pathogens under the name of the paleomicrobiology approach. This emerged as a distinct field, making it possible to isolate and identify ancient pathogens from preserved samples. Advances in next generation sequencing are now revolutionising the diagnosis of ancient diseases, enabling the retrieval of ancient pathogen genomes from well-preserved samples such as dental pulp, tartar, bone and mummified tissues, helping understand disease evolution and transmission patterns. Ongoing improvements in DNA sequencing and metagenomics will enhance the accuracy and scope of the diagnosis of ancient diseases. Collaboration between archaeologists, historians, paleomicrobiologists, geneticists and epidemiologists will drive further breakthroughs. Advances in paleocytology, metagenomic analysis, including non-invasive techniques, such as mass spectrometry, may offer new avenues for identifying ancient pathogens. Current technologies and interdisciplinary collaboration hold promise for uncovering even more insights from the past and potentially informing future disease prevention strategies.}, }
@article {pmid40512990, year = {2025}, author = {Madrigal-Trejo, D and Baldes, MJ and Tamura, N and Klepac-Ceraj, V and Bosak, T}, title = {Arsenic Accumulation in Microbial Biomass and the Interpretation of Signals of Early Arsenic-Based Metabolisms.}, journal = {Geobiology}, volume = {23}, number = {3}, pages = {e70024}, pmid = {40512990}, issn = {1472-4669}, mesh = {*Arsenic/metabolism/analysis ; *Biofilms/growth &amp; development ; *Biomass ; *Cyanobacteria/metabolism/genetics ; }, abstract = {Carbonaceous particles that concentrate arsenic in microbialites as old as ~3.5 Ga are similar to As-rich organic globules in modern microbialites. The former particles have been interpreted as tracers of As cycling by early microbial metabolisms. However, it is unclear if arsenic accumulation is a consequence of biological activity or passive postmortem binding of arsenic by organic matter during diagenesis in volcanically influenced, As-rich environments. Here, we address this uncertainty by evaluating the concentrations, speciation, and detectability of As in active or heat-killed biofilms formed by cyanobacteria or anoxygenic photosynthetic microbes exposed to environmentally relevant concentrations of As(III) or As(V) (50 μM to 3 mM). The genomes or metagenomes of these biofilms contain genes involved in detoxifying or energy-yielding As metabolisms. Biomass accumulates As from the solution in a concentration-dependent manner and with a preference for oxidized As(V) over As(III). Autoclaved biomass accumulates As even more strongly than active biomass, likely because living biofilms actively detoxify As. Active biofilms oxidize and reduce As and accumulate both As(III) and As(V), whereas a small fraction of As(V) can be reduced in inactive biofilms that bind As during diagenesis. Arsenic enrichments in the biomass are detectable by X-ray based spectroscopy techniques (XRF, EPMA-WDS) that are commonly used to analyze geological materials. These findings enable the reconstruction of past active and passive interactions of microbial biomass with arsenic in fossilized microbial biofilms and microbialites from the early Earth.}, }
@article {pmid40512544, year = {2025}, author = {Pan, J and Mabuchi, M and Kneller, DW and Fuchs, RT and Curcuru, JL and Tamanaha, E and Tanner, NA and Robb, GB and Corrêa, IR}, title = {Kinetic analysis and engineering of thermostable Cas12a for nucleic acid detection.}, journal = {Nucleic acids research}, volume = {53}, number = {11}, pages = {}, pmid = {40512544}, issn = {1362-4962}, support = {//New England Biolabs, Inc./ ; }, mesh = {Kinetics ; *CRISPR-Associated Proteins/genetics/chemistry/metabolism ; *Nucleic Acid Amplification Techniques/methods ; *Endodeoxyribonucleases/genetics/chemistry/metabolism ; Protein Engineering ; *Bacterial Proteins/genetics/chemistry/metabolism ; *Nucleic Acids/analysis ; Enzyme Stability ; Temperature ; }, abstract = {Cas12a trans nuclease activity has been leveraged for nucleic acid detection, often coupled with isothermal amplification to increase sensitivity. However, due to the lack of highly efficient thermostable Cas12a orthologs, use of Cas12a in one-pot combination with high temperature (55-65°C) amplification, such as loop-mediated isothermal amplification (LAMP), has remained challenging. Here, we attempt to address this challenge by comparative study of the thermostable, but poorly trans-active YmeCas12a (from Yellowstone metagenome) with the mesophilic, highly trans-active LbaCas12a (from Lachnospiraceae bacterium ND 2006). Kinetic characterizations identified that poor trans substrate affinity (high Km) is the key limiting factor in YmeCas12a trans activity. We engineered YmeCas12a by structure-guided mutagenesis and fusion to DNA-binding domains to increase its affinity to the trans substrate. The most successful combinatorial variant showed 5-50-fold higher catalytic efficiency with the trans substrate depending on the target site. With the improved variant, we demonstrate efficient nucleic acid detection in combination with LAMP in a single reaction workflow, setting the basis for development of point-of-care tests.}, }
@article {pmid40512497, year = {2025}, author = {Qi, W and Kong, M and Meng, X and Sun, Z and Mei, Z and Pu, Y and Zhou, X and Wang, Q and Qiu, JG and Jiang, BH and Shen, J and Yuan, C and Ji, JS and Wang, X and Kan, H and Zheng, Y}, title = {The Role of Gut Microbiota in the Association Between Air Pollution and Cognitive Function in Older Adults.}, journal = {Environmental health perspectives}, volume = {}, number = {}, pages = {}, doi = {10.1289/EHP16515}, pmid = {40512497}, issn = {1552-9924}, abstract = {BACKGROUND: Growing evidence links air pollution to cognitive dysfunction in older adults. The gut microbiome and circulating metabolites present an important yet unexplored pathway, given their crucial role in the gut-brain axis.<br><br>OBJECTIVES: We aimed to explore the potential roles of gut bacteria, fungi, microbial functional potentials, and circuiting metabolites in the association of residential PM2.5 and O3 exposures with cognitive dysfunction.<br><br>METHODS: We analyzed gut microbiome data from 1,027 older adults using metagenome and internal transcribed spacer sequencing to profile bacterial and fungal taxa, functional pathways, and enzyme abundances. Targeted metabolomics quantified 195 circulating metabolites, such as amino acids and organic acids. Annual average ambient PM2.5 and O3 exposures were estimated using satellite-based models. Cognitive outcomes, including mild cognitive impairment and cognitive decline, were assessed using the Mini-mental State Examination and Hasegawa dementia scale. Statistical analyses included Microbiome Multivariable Association with Linear Models (with a false discovery rate threshold of 0.25) for microbial associations and multivariate regression for metabolites and cognitive outcomes.<br><br>RESULTS: Higher PM2.5 and O3 exposures were associated with disturbances in microbial composition, altered taxonomic profiles (e.g., decreased abundances of Blautia obeum and Gordonibacter pamelaeae), and disrupted functional pathways, particularly those regulating 2-oxoglutarate. These findings were partially replicated in an independent population. Higher air pollution levels were associated with increased circulating levels of 2-oxoglutarate and L-glutamine (key metabolites in neurodegenerative progression), which were further linked to higher odds of concurrent mild cognitive impairment (OR: 1.39-1.56) and an increased 2-year risk of cognitive decline (OR: 1.26-1.37). These associations were partially mediated by air pollution-related changes in microbial anaerobic energy metabolism pathways, especially involving 2-oxoglutarate metabolism and the enzyme aspartate transaminase.<br><br>CONCLUSIONS: Our findings highlight the role of the gut microbiome and microbial metabolites in mediating the detrimental impact of air pollution on cognitive health in older adults, providing new insights into the underlying etiology for future hypothesis generation. https://doi.org/10.1289/EHP16515.}, }
@article {pmid40511850, year = {2025}, author = {Coelho, JT and Teubner, L and Henson, MW and Lanclos, VC and Kojima, CY and Thrash, JC}, title = {Culture-supported ecophysiology of the SAR116 clade demonstrates metabolic and spatial niche partitioning.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf124}, pmid = {40511850}, issn = {1751-7370}, abstract = {Marine SAR116 bacterioplankton are ubiquitous in surface waters across global oceans and form their own order, Puniceispirillales, within the Alphaproteobacteria. To date no comparative physiology among diverse SAR116 isolates has been performed to capture the functional diversity within the clade, and further, diversity through the lens of metabolic potential and environmental preferences via clade-wide pangenomics continues to evolve with the addition of new genomes. Using high-throughput dilution-to-extinction cultivation, we isolated and genome sequenced five new and diverse SAR116 isolates from the northern Gulf of Mexico. Here we present a comparative physiological analysis of these SAR116 isolates, along with a pangenomic investigation of the SAR116 clade using a combination of metagenome-assembled genomes (MAGs, n = 258), single-amplified genomes (SAGs, n = 84), previously existing (n = 2), and new isolate genomes (n = 5), totaling 349 SAR116 genomes. Phylogenomic investigation supported the division of SAR116 into three distinct subclades, each with additional structure totaling 15 monophyletic groups. Our SAR116 isolates belonged to three groups within subclade I representing distinct genera with different morphologies and varied phenotypic responses to salinity and temperature. Overall, SAR116 genomes encoded differences in vitamin and amino acid synthesis, trace metal transport, and osmolyte synthesis and transport. They also had genetic potential for diverse sulfur oxidation metabolisms, placing SAR116 at the confluence of the organic and inorganic sulfur pools. SAR116 subclades showed distinct patterns in habitat preferences across open ocean, coastal, and estuarine environments, and three of our isolates represented the most abundant coastal and estuarine subclade. This investigation provides the most comprehensive exploration of SAR116 to date anchored by new culture genomes and physiology.}, }
@article {pmid40510855, year = {2025}, author = {Yang, M and Wang, Y and Luo, LL and Qiao, LN}, title = {Recurrent acute appendicitis after recovery from scrub typhus that was associated with hemophagocytic lymphohistiocytosis and other severe complications in children: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1528903}, pmid = {40510855}, issn = {2296-858X}, abstract = {BACKGROUND: With the advancement of diagnostic technology, diagnosing and treating scrub typhus (ST) has become easier, and ST is currently commonly associated with various complications. At present, there is no report of a recurrent acute appendicitis requiring surgical resection after the successful treatment of ST with severe complications, such as hemophagocytic lymphohistiocytosis (HLH), in children during follow-up.<br><br>CASE PRESENTATION: We report the case of a 10-year-old girl from Sichuan, China, who had fever, abdominal pain, and lethargy. Abdominal computed tomography (CT) scans indicated appendicitis, and the surgeons indicated that surgery was unnecessary. She was then admitted to the Pediatric Intensive Care Unit (PICU) and rapidly developed severe complications (HLH, septic shock, acute kidney injury, acute respiratory distress syndrome, and disseminated intravascular coagulation) within 24&#x202f;h after admission. She was diagnosed with ST by metagenomics next-generation sequencing (mNGS). After treatment with doxycycline, dexamethasone (DEX), and etoposide, as well as advanced life support, she recovered after 25&#x202f;days of hospitalization and was discharged. However, she underwent a laparoscopic appendectomy due to abdominal pain a month after a reduction in the dose of DEX. The appendix was 6&#x202f;cm long and 1.0&#x202f;cm in diameter, and the pathological report suggested simple acute appendicitis. After 11&#x202f;months of follow-up, that is, 10&#x202f;months after the appendectomy, all indicators were normal and no similar abdominal pain recurred.<br><br>CONCLUSION: Pediatricians should be vigilant and should initiate HLH treatment protocols when ST-associated HLH occurs with other severe complications. Acute appendicitis may not only occur during the course of ST, but may also occur after successful treatment for ST.}, }
@article {pmid40510676, year = {2025}, author = {Bruins-van Sonsbeek, LGR and Verschuren, MCM and Kaal, S and Lindenburg, PW and Rodenburg, KCW and Clauss, M and Speksnijder, AGCL and Rutten, VPMG and Bonnet, BFJ and Wittink, F}, title = {Rhinoceromics: a multi-amplicon study with clinical markers to transferrin saturation levels in ex-situ black rhinoceros (Diceros bicornis michaeli).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1515939}, pmid = {40510676}, issn = {1664-302X}, abstract = {Iron overload disorder (IOD) is a common condition in ex-situ black rhinoceroses (Diceros bicornis), although it has not been reported in the wild. This study aimed to gain a deeper understanding of the relationship between 25-hydroxy vitamin D [25(OH)D], inflammatory markers, insulin levels, the gut microbiome, dietary components, and transferrin saturation (TS) in ex-situ black rhinoceroses. Blood and fecal samples from 11 black rhinoceroses at five different European zoological institutions were monitored over a 1-year period. Inflammatory markers such as interleukin 6 (IL-6), serum amyloid A (SAA), interferon γ (IFN-γ), and tumor necrosis factor α (TNF-α) were analyzed. Our study corroborates the findings of previous research, which demonstrated that insulin, inflammatory markers, and TS% are higher in ex-situ black rhinoceroses compared to published wild ranges. Our data show no correlations between insulin, 25(OH)D, TS%, inflammatory markers, or short-chain fatty acids (SFCAs). Serum 25(OH)D exhibited significantly higher levels in summer than in winter. Transferrin saturation was influenced by age, which is consistent with previous studies. The microbiome did not differ significantly among individuals, institutions, sex, or season, unlike the mycobiome, which exhibited significant differences across institutions. The impact of the mycobiome differences on the physiology of the animals could not be determined from this study.}, }
@article {pmid40510672, year = {2025}, author = {Yang, M and Wang, J and Qi, Y and Gao, P and Li, L and Guo, J and Zhao, Y and Liu, J and Chen, Z and Zhao, J and Yu, L}, title = {Plant developmental stage drives the assembly and functional adaptability of endophytic microbial communities.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1492141}, pmid = {40510672}, issn = {1664-302X}, abstract = {INTRODUCTION: The seeds of Amorphophallus muelleri represent a unique category of herbaceous seeds that arise from triploid apomixis. They necessitate an exceptionally protracted maturation phase of 8 months, followed by a dormancy period of 4 months, before they can germinate and give rise to fully formed new plants. Currently, the connection between endophytic microbial communities in A. muelleri seeds and the host plant's development is largely unexplored.<br><br>METHODS: Herein, we analyzed the temporal dynamics of the endophytic bacterial and fungal communities from seed germination to seedling establishment (seven stages) through amplicon sequencing.<br><br>RESULTS AND DISCUSSION: The results showed that plant developmental stage explained the large variation in endophytic bacterial and fungal communities in A. muelleri and that multiple microbial attributes (e.g., &#x3b1;, &#x3b2;-diversity, community composition, and bacterial and fungal ecological networks) are driven by the developmental state of A. muelleri. Metagenomic analyses further indicated that the four stages after rooting have higher microbial functional diversity. Microbial functional genes involved in cell wall/membrane/envelope biogenesis, inorganic ion transport and metabolism, and carbon degradation were abundant in A. muelleri seeds from Stage 1 to Stage 3 (before rooting). From Stage 4 to Stage 7 (after rooting), microbial functional genes involved in the carbon, nitrogen and phosphorus cycles, starch and sucrose metabolism, and energy production and conversion were more abundant. Coincidentally, more abundant Proteobacteria, and Basidiomycota taxa related to carbon degradation were found in stages 1-3, while more Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Stenotrophomonas taxa associated with nitrogen cycling and plant growth promotion were observed in stages 4-7. These findings have greatly improved our basic understanding of the assembly and functional adaptability of the endophytic microbiome during A. muelleri plant development and are helpful for the mining, development and utilization of functional microbial resources.}, }
@article {pmid40510640, year = {2025}, author = {Chigwada, AD and Ogola, HJO and Tekere, M}, title = {Metagenomic assembled dataset of potentially polyethylene terephthalate-degrading microcosms enriched from seawater, cow dung, and landfill soil.}, journal = {Data in brief}, volume = {60}, number = {}, pages = {111671}, pmid = {40510640}, issn = {2352-3409}, abstract = {We present a dataset of 99 prokaryotic metagenome-assembled genomes (MAGs) derived from 180-day culture-enrichment microcosms of seawater, landfill soil, and cow dung, with polyethylene terephthalate (PET) as the sole carbon source. The recovered MAGs met the medium-to-high quality standards of the Minimum Information for Metagenome-Assembled Genomes (MIMAG) criteria with completeness ranging from 76.5% to 100% and low contamination levels (<10%). The majority of the MAGs were obtained from seawater (52), followed by cow dung (28), and landfill soil (19). Additionally, the dataset includes detailed DRAM (Distilled and Refined Annotation of Metabolism) functional profiles of the MAGs, which highlight the potential role of these microorganisms in the biodegradation of PET polymers. This genomic data provides valuable reference information on bacteria and archaea with the potential capacity to biodegrade plastic, contributing to our understanding of microbial plastic biodegradation.}, }
@article {pmid40510172, year = {2025}, author = {Jáuregui, I and Ancín, M and García-Mina, JM and Zamarreño, AM and Iglesias-Sanchez, A and Florez-Sarasa, I and Aranjuelo, I}, title = {Permanent crop cover as a strategy for drought-resistant viticulture: insights on how rhizosphere metagenomics influences leaf-level -omics for an enhanced overall plant response.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1543171}, pmid = {40510172}, issn = {1664-462X}, abstract = {The viticulture sector is currently threatened by climate change, impacting grape quality and yield through altered weather patterns and reduced soil health. The incorporation of cover crops can significantly bolster sustainability by enhancing soil moisture retention and structural integrity, both of which are essential for the enduring viability of vineyards in the long term. Cover cropping presents numerous advantages, such as the enhancement of soil health, mitigation of erosion, and facilitation of nutrient cycling; however, it may also pose certain short-term risks, including competition for vital resources like water. In spite of the progress made in comprehending the advantages of cover crops in vineyard settings, the intricate dynamics between plant-microbe interactions and the leaf-level metabolic responses of grapevines at the leaf level to drought conditions remain unexplored. This study examines the impact of water availability and green cover (comprising perennial ryegrass and Trifolium repens) on grapevine photosynthetic and metabolism efficiency, positing that crop cover fosters a microhabitat that bolsters microbial communities and drought resilience. Through comprehensive examinations of gas exchange, isotopic analysis, metabolomics, transcriptomics, and soil metagenomics, this study clarifies the relationships among irrigation methodologies, photosynthesis, and soil health, ultimately aiding in the fortification of agricultural resilience in the face of climate change. Our investigation demonstrates that the adoption of cover crops yields unexpected immediate benefits in bolstering drought resilience for vineyards. Despite an observed increase in overall evapotranspiration during drought conditions, the use of cover crops facilitated carbon accumulation and enhanced osmolyte-acting metabolites (including sugars and sugar alcohols) and abscisic acid (ABA) concentrations, alongside a comprehensive molecular adaptation to drought stress. Moreover, cover cropping was shown to promote the expression of defense-related pathways, while vineyards devoid of cover crops exhibited minimal transcriptional responses; certain taxa exhibited responses contingent upon the treatment, with Tistrellales and Gaiellales being linked to crop cover under favorable conditions, whereas Rhizoctonia demonstrated a strong association with rhizospheric soil during drought conditions when crop cover was present. Our study is the first to show that cover cropping can boost cash crop resilience to drought through intricate plant-soil-microbe interactions, providing benefits from the outset.}, }
@article {pmid40510115, year = {2025}, author = {Dang, Y and Xu, X and Ma, J and Zhou, M and Xu, C and Huang, X and Xu, F and Wang, Z and Shi, H and Zhang, S}, title = {Gut microbiome signatures predict 5-ASA efficacy in ulcerative colitis.}, journal = {iScience}, volume = {28}, number = {6}, pages = {112568}, pmid = {40510115}, issn = {2589-0042}, abstract = {Ulcerative colitis (UC) prevalence is rising globally, yet fewer than 50% of patients achieve mucosal healing (MH) with first-line 5-aminosalicylic acid (5-ASA) therapy. We aimed to identify microbial signatures that could predict the treatment efficacy of 5-ASA. Active UC patients on standardized 5-ASA treatment were prospectively enrolled. Shotgun metagenomic sequencing was performed to identify the taxonomic and functional profiles before and after treatment. Six species were enriched in the effective group and 3 species in the ineffective group at baseline. Faecalibacterium prausnitzii, Blautia massiliensis, and Phascolarctobacterium faecium were consistently depleted in the ineffective group at both time points. A random forest model based on these three species predicted ineffective 5-ASA treatment with area under the curve (AUC) = 0.80 (validation in the Inflammatory Bowel Disease Multi'omics Database [IBDMDB]: AUC = 0.82, specificity = 0.88, negative predictive value [NPV] = 0.70, and positive predictive value [PPV] = 0.80). Gut microbiome signatures have potential to serve as non-invasive predictors for ineffective 5-ASA treatment in UC.}, }
@article {pmid40509365, year = {2025}, author = {Sai-Ut, S and Indriani, S and Srisakultiew, N and Kingwascharapong, P and Suriyarak, S and Issara, U and Phongthai, S and Rawdkuen, S and Pongsetkul, J}, title = {The Role of CO2 Levels in High-Oxygen Modified Atmosphere Packaging on Microbial Communities of Chilled Goat Meat During Storage and Their Relationship with Quality Attributes.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/foods14111837}, pmid = {40509365}, issn = {2304-8158}, support = {FF3-303-68-24-27//(i) Suranaree University of Technology (SUT), (ii) Thailand 592 Science Research and Innovation (TSRI), and (iii) National Science, Research and Innovation Fund 593 (NSRF)/ ; F01-683R-04-594 045//the Reinventing University Program Fund/ ; FtR.66/41/2567//SUT for the Full-time Doctoral Researcher/ ; }, abstract = {This study investigated the influence of CO2 levels (20-40%: M20, M30, and M40) in high-oxygen modified atmosphere packaging (Hi-O2 MAP) on microbial communities and quality attributes of chilled goat meat stored at 4 °C for 12 days. Alpha diversity indices (Chao1, ACE, Simpson, and Shannon) revealed a significant decline in microbial diversity over time, with storage duration exerting a greater impact than packaging conditions. Nonetheless, MAP played a crucial role in shaping microbial profiles, with air packaging (AP) showing the most distinct community, while M40 differed notably from M20 and M30, particularly by day 12, as shown by beta diversity analysis using principal coordinates analysis (PCoA). Proteobacteria and Firmicutes dominated microbial composition, with Pseudomonas and Brochothrix linked to spoilage in AP, while MAP, especially M40, favored the growth of Lactococcus, Acinetobacter, and Vagococcus, enhancing microbial stability. Despite pathogen levels remaining within safe limits, AP exceeded the spoilage threshold (TVC > 7.00 log colony-forming unit (CFU)/g), whereas all MAPs extended shelf life, with M40 most effectively suppressing microbial growth (p < 0.05). Interestingly, metagenomic functional profiling revealed that elevated CO2 levels (>30%) altered metabolic pathways, shifting spoilage mechanisms from protein degradation in AP to carbohydrate metabolism in MAP, potentially influencing odor and texture attributes. MAP, particularly M40, also reduced protein and lipid degradation and oxidation, as indicated by lower total volatile base nitrogen (TVB-N), thiobarbituric acid reactive substances (TBARSs), and shear force, suggesting better prevention of increased meat hardness and the development of undesirable odors and flavors, although high CO2 negatively affected redness. Overall, M40 provided the greatest microbial stability and shelf life extension, highlighting the potential of optimized CO2 levels in Hi-O2 MAP to preserve goat meat quality and regulate spoilage dynamics.}, }
@article {pmid40509083, year = {2025}, author = {Florit-Ruiz, A and Rago, L and Rojas, A and Guzelkhanova, B and Pont-Beltran, A and Lamelas, A and Solaz-Fuster, MC and Martinez-Blanch, JF and López, ME and García-Lainez, G and Rosier, BT and Day, R and Rubio, T and Batchelor, R and Nixon, SL}, title = {Postbiotic Lactiplantibacillus plantarum CECT 9161 Influences the Canine Oral Metagenome and Reduces Plaque Biofilm Formation.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/ani15111615}, pmid = {40509083}, issn = {2076-2615}, support = {N/A//Archer Daniels Midland (United States)/ ; }, abstract = {Periodontal diseases are highly prevalent in dogs and intricately interconnected with the composition and functional attributes of the oral microbiota. The demand for non-invasive interventions to support oral health presents an opportunity for functional ingredients. The novel postbiotic heat-treated (HT) Lactiplantibacillus plantarum CECT 9161 inhibited growth and biofilm formation of oral microorganisms in vitro. The in vitro growth of saliva-derived biofilms was also inhibited and revealed microbiome modulation. Two doses of the postbiotic (LOW: 5 mg dog/day, HIGH: 25 mg/dog/day) were assessed in a placebo-controlled, double-blinded, 57-day clinical trial involving 60 dogs. Associations were found between the postbiotic, reduced plaque formation, and modulation of the oral microbiome, including increased abundance of genes involved in denitrification, heme and catechol biosynthesis, and oxidative stress reduction. The results suggest that HT Lactiplantibacillus plantarum CECT 9161 may support oral health in dogs by modifying the microbiome of supragingival plaque and reducing plaque formation.}, }
@article {pmid40509014, year = {2025}, author = {Omar, AH and Pellegrini, F and Catella, C and Diakoudi, G and Salvaggiulo, A and Casalino, G and Circella, E and D'Amico, F and Schiavitto, M and Camarda, A and Camero, M and Bányai, K and Matthijnssens, J and Ciarlet, M and Martella, V and Lanave, G}, title = {Complete Genome Sequencing of a G3P[14] Rabbit Rotavirus.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/ani15111548}, pmid = {40509014}, issn = {2076-2615}, support = {PE00000007, INF-ACT//Ministero dell'Universit&#xe0; e della ricercar (Rome, Italy) Piano Nazionale di Ripresa e Resilienza MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases/ ; RRF-2.3.1-21-2022-00001 and RRF-2.3.1-21-2022-00010//National Research, Development and Innovation Office, Hungary/ ; }, abstract = {Group A rotaviruses (RVAs) are a major cause of acute dehydrating diarrhea in infants and young animals worldwide. In rabbits, RVAs are associated with enteric disease, likely in combination with other pathogens. We report the identification and characterization of a lapine RVA strain in an Italian rabbit breeding farm. Increased mortality rates associated with enteric symptoms were reported in the facility in post-weaning rabbits around 40 days of age. By quantitative RT-PCR, an RVA strain was identified in the intestinal contents of deceased rabbits. A PCR-based enrichment protocol coupled with Nanopore sequencing allowed the reconstruction of the nearly complete genome of a rabbit RVA strain, Rabbit-wt/ITA/36-9/2022/G3P[14], with a genotype constellation (G3-P[14]-I2-R2-C2-M3-A9-N2-T6-E5-H3) conserved among lapine RVAs. Each of the 11 gene segments displayed high nucleotide identity and phylogenetic clustering with lapine rotavirus strains, as well as two Belgian human G3P[14] strains, which had been shown to have a zoonotic (lapine) origin. However, the NSP2 gene of strain 36-9 clustered closer with a group of rare human G3P[9] strains, suggesting a common path during their evolution. Gathering sequence data on animal RVAs is pivotal to reconstructing the history of homologous and heterologous RVAs in various mammals, including humans.}, }
@article {pmid40508035, year = {2025}, author = {Toto, F and Scanu, M and Gramegna, M and Putignani, L and Del Chierico, F}, title = {Impact of DNA Extraction and 16S rRNA Gene Amplification Strategy on Microbiota Profiling of Faecal Samples.}, journal = {International journal of molecular sciences}, volume = {26}, number = {11}, pages = {}, doi = {10.3390/ijms26115226}, pmid = {40508035}, issn = {1422-0067}, support = {Current Research funds//Italian Ministry of Health/ ; n.a.//Technogenetics S.p.A./ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Humans ; *DNA, Bacterial/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Bacteria/genetics/classification ; Metagenome ; }, abstract = {High-throughput 16S rRNA metagenomic sequencing has advanced our understanding of the gut microbiome, but its reliability depends on upstream processes such as DNA extraction and bacterial library preparation. In this study, we evaluated the impact of three different DNA extraction methods (a manual method with an ad hoc-designed pre-extraction phase (PE-QIA), and two automated magnetic bead-based methods (T180H and TAT132H)) and two bacterial library preparation protocols (home brew and VeriFi) on the 16S rRNA-based metagenomic profiling of faecal samples. T180H and TAT132H produced significantly higher DNA concentrations than PE-QIA, whereas TAT132H yielded DNA of lower purity compared to the others. In the taxonomic analysis, PE-QIA provided a balanced recovery of Gram-positive and Gram-negative bacteria, TAT132H was enriched in Gram-positive taxa, and T180H was enriched in Gram-negative taxa. An analysis of Microbial Community Standard (MOCK) samples showed that PE-QIA and T180H were more accurate than TAT132H. Finally, the VeriFi method yielded higher amplicon concentrations and sequence counts than the home brew protocol, despite the high level of chimeras. In conclusion, a robust performance in terms of DNA yield, purity, and taxonomic representation was obtained by PE-QIA and T180H. Furthermore, it was found that the impact of PCR-based steps on gut microbiota profiling can be minimized by an accurate bioinformatic pipeline.}, }
@article {pmid40507096, year = {2025}, author = {Lutsiv, T and Fitzgerald, VK and Neil, ES and McGinley, JN and Hussan, H and Thompson, HJ}, title = {Cooked Bean (Phaseolus vulgaris L.) Consumption Alters Bile Acid Metabolism in a Mouse Model of Diet-Induced Metabolic Dysfunction: Proof-of-Concept Investigation.}, journal = {Nutrients}, volume = {17}, number = {11}, pages = {}, doi = {10.3390/nu17111827}, pmid = {40507096}, issn = {2072-6643}, support = {58-3060-8-031//USDA ARS/ ; 2020-05206//National Institute for Food and Agriculture:/ ; }, mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice, Inbred C57BL ; *Phaseolus ; Mice ; Male ; Liver/metabolism ; Disease Models, Animal ; Feces/chemistry ; Cecum/microbiology/metabolism ; Gastrointestinal Microbiome ; Cooking ; Obesity/metabolism ; Metabolomics ; *Diet ; *Metabolic Diseases/etiology/metabolism ; Diet, High-Fat/adverse effects ; }, abstract = {Background/Objectives: Metabolic dysregulation underlies a myriad of chronic diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD) and obesity, and bile acids emerge as an important mediator in their etiology. Weight control by improving diet quality is the standard of care in prevention and control of these metabolic diseases. Inclusion of pulses, such as common bean, is an affordable yet neglected approach to improving diet quality and metabolic outcomes. Thus, this study evaluated the possibility that common bean alters bile acid metabolism in a health-beneficial manner. Methods: Using biospecimens from several similarly designed studies, cecal content, feces, liver tissue, and plasma samples from C57BL/6 mice fed an obesogenic diet lacking (control) or containing cooked common bean were subjected to total bile acid analysis and untargeted metabolomics. RNA-seq, qPCR, and Western blot assays of liver tissue complemented the bile acid analyses. Microbial composition and predicted function in the cecal contents were evaluated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Results: Bean-fed mice had increased cecal bile acid content and excreted more bile acids per gram of feces. Consistent with these effects, increased synthesis of bile acids in the liver was observed. Microbial composition and capacity to metabolize bile acids were markedly altered by bean, with greater prominence of secondary bile acid metabolites in bean-fed mice, i.e., microbial metabolites of chenodeoxycholate/lithocholate increased while metabolites of hyocholate were reduced. Conclusions: In rendering mice resistant to obesogenic diet-induced MASLD and obesity, cooked bean consumption sequesters bile acids, increasing their hepatic synthesis and enhancing their diversity through microbial metabolism. Bean-induced changes in bile acid metabolism have potential to improve dyslipidemia.}, }
@article {pmid40507017, year = {2025}, author = {Ying, J and Xu, X and Zhou, R and Chung, ACK and Ng, SK and Fan, X and Subramaniam, M and Wong, SH}, title = {The Gut Microbiota in Young Adults with High-Functioning Autism Spectrum Disorder and Its Performance as Diagnostic Biomarkers.}, journal = {Nutrients}, volume = {17}, number = {11}, pages = {}, doi = {10.3390/nu17111748}, pmid = {40507017}, issn = {2072-6643}, support = {Nil//NHG-LKCMedicine Clinician-Scientist Preparatory Programme Plus/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Autism Spectrum Disorder/microbiology/diagnosis ; Male ; Female ; Biomarkers ; Young Adult ; Adult ; Case-Control Studies ; Feces/microbiology ; Metagenomics ; Machine Learning ; ROC Curve ; Adolescent ; }, abstract = {Background/Objectives: Diagnosing ASD in adults presents unique challenges, and there are currently no specific biomarkers for this condition. Most existing studies on the gut microbiota in ASD are conducted in children; however, the composition of the gut microbiota in children differs significantly from that of adults. This study aimed to study the gut microbiota of young adults with high-functioning ASD. Methods: Using metagenomic sequencing, we evaluated the gut microbiota in 45 adults with high-functioning ASD and 45 matched healthy controls. Results: Adjusting for sociodemographic information, dietary habits, and clinical data, we observed a distinct microbiota profile of adults with ASD in comparison to controls, with the intensity of autistic traits strongly correlating to microbial diversity (correlation coefficient = -0.351, p-value < 0.001). Despite a similar dietary pattern, the ASD group exhibited more gastrointestinal symptoms than the healthy controls. An internally validated machine-learning predictive model that combines the Autism Spectrum Quotient questionnaire score of individuals with their microbial features could achieve an area under the receiver operating characteristic curve (AUC) of 0.955 in diagnosing ASD in adults. Conclusions: This study evaluates the gut microbiota in adult ASD and highlights its potential as a non-invasive biomarker to enhance the diagnosis of ASD in this population group.}, }
@article {pmid40506735, year = {2025}, author = {Kampouris, ID and Kuhl-Nagel, T and Behr, JH and Sommermann, L and Babin, D and Francioli, D and Zrenner, R and Kublik, S and Schloter, M and Ludewig, U and Smalla, K and Neumann, G and Grosch, R and Geistlinger, J}, title = {Selective recruitment of beneficial microbes in the rhizosphere of maize affected by microbial inoculants, farming practice, and seasonal variations.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {69}, pmid = {40506735}, issn = {2524-6372}, abstract = {BACKGROUND: Plant beneficial microorganisms as inoculants can improve crop performance, but factors affecting their impact on plant performance under field conditions remain unclear, thereby limiting their use in farming. Here, we investigated how farming practices (e.g., tillage and N-fertilization intensity) and growing seasons influenced the impact of a beneficial microorganism consortium (BMc: Trichoderma, Bacillus, and Pseudomonas strains) in maize and affected the rhizosphere competence of each BMc strain. In addition, we tested whether the consortium affects the resident rhizosphere microbiome and crop performance. In two growing seasons (2020 and 2021), we assessed how BMc inoculation affects maize growth, nutritional status, gene expression, and rhizosphere microbiome under different farming practices at the flowering stage.<br><br>RESULTS: Inoculated strains successfully colonized the maize rhizosphere independently of farming practice. BMc inoculation improved plant growth and iron uptake in 2020, regardless of farming practice. These effects co-occurred with lower precipitation levels in 2020 compared to 2021. BMc inoculation reduced the expression of several stress-related genes in maize in 2020 under drought. An increased iron uptake by the BMc-inoculated plants was observed in 2020 and was associated with the upregulation of the gene ZmNAS3, which is linked to iron uptake. Therefore, BMc inoculation mitigated the drought impact on maize. The microbial rhizosphere communities were altered by BMc inoculation in both years, but patterns of responder taxa differed between seasons. Metagenome analysis revealed that more genes (e.g., genes encoding biosurfactants and siderophores) were enriched in the rhizosphere of BMc-inoculated plants in 2020 than in 2021. Moreover, we identified bacterial and fungal taxa positively associated with maize iron uptake. The relative abundance of these iron uptake-associated bacterial and fungal taxa significantly increased due to BMc inoculation in 2020, while they showed overall higher relative abundances in 2021, independently of BMc inoculation. We mapped the sequences of these iron-associated taxa to publicly available genomes and verified the occurrence of various plant beneficial traits in several mapped genomes.<br><br>CONCLUSIONS: Overall, we show that the growing season determined the effect of BMc inoculation on maize plants by shaping microbiome composition and function in the maize rhizosphere more than farming practice. These findings highlight the importance of the complex interplay between microbial inoculants and the resident rhizosphere microorganisms under abiotic stress conditions.}, }
@article {pmid40506497, year = {2025}, author = {Jung, DR and Choi, Y and Jeong, M and Singh, V and Jeon, SY and Seo, I and Park, NJ and Lee, YH and Park, JY and Han, HS and Shin, JH and Chong, GO}, title = {Metagenomic insight into the vaginal microbiome in women infected with HPV 16 and 18.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {105}, pmid = {40506497}, issn = {2055-5008}, mesh = {Female ; Humans ; *Vagina/microbiology/virology ; *Human papillomavirus 16/genetics/isolation &amp; purification ; *Papillomavirus Infections/virology/microbiology ; *Microbiota/genetics ; Metagenomics ; *Human papillomavirus 18/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; Uterine Cervical Neoplasms/virology/microbiology ; Metagenome ; Adult ; Middle Aged ; }, abstract = {Human papillomavirus (HPV) 16 and 18 (HPV 16/18) account for over 70% of cervical cancer (CC) cases, yet their interaction with the vaginal microbiome (VM) remains unclear. This study explored the association between high-risk HPV types (HR-HPVs), VM composition and bacterial function using shotgun metagenomic sequencing. In early-stage cervical lesions, the HPV 16/18 group showed reduced Lactobacillus-dominant community state types compared to other HR-HPVs, while invasive CC exhibited increased pathogenic bacteria, including Streptococcus agalactiae, Fannyhessea vaginae, and Sneathia vaginalis. The VM associated with HPV 16/18 was enriched in immune response and inflammation pathways, whereas other HR-HPVs were linked to cellular metabolism and hormonal signaling. Notably, HPV 16/18 exhibited stronger bacterial-fungal correlations, indicating shifts in the microbial community. Furthermore, 137 metagenome-assembled genomes provided insights into unique microbial genomic signatures. Our study links VM differences with HPV 16/18 oncogenic potential across cervical lesion stages, urging further research for better diagnostics and treatments.}, }
@article {pmid40506443, year = {2025}, author = {Bredon, M and Hausfater, P and Khalki, L and Tijani, Y and Cheikh, A and Brot, L and Creusot, L and Rolhion, N and Trottein, F and Lambeau, G and Georgin-Lavialle, S and Bleibtreu, A and Baudel, JL and Lefèvre, A and Emond, P and Tubach, F and Simon-Tillaux, N and Simon, T and Gorochov, G and Zaid, Y and Sokol, H}, title = {Gut microbiota alterations are linked to COVID-19 severity in North African and European populations.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {106}, pmid = {40506443}, issn = {2055-5008}, support = {ANR-23-CE15-0014-01, GUTSY//AAP g&#xe9;n&#xe9;rique 2022/ ; ANR-23-CE15-0014-01, GUTSY//AAP g&#xe9;n&#xe9;rique 2022/ ; PR-BLV-20220527//Balvi Filantropic Fund/ ; RPH20003DDP//DIM One Health 2020/ ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification/genetics/isolation &amp; purification ; *COVID-19/microbiology/pathology ; *Dysbiosis/microbiology ; Feces/microbiology ; France/epidemiology ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Morocco/epidemiology ; North African People ; Severity of Illness Index ; }, abstract = {Although COVID-19 primarily affects the respiratory system, many patients experience gastrointestinal symptoms, suggesting a role for the gut microbiota in disease pathogenesis. To explore this, we performed shotgun metagenomic sequencing on stool samples from 200 COVID-19 patients and 102 healthy controls in Morocco and France. Despite geographic differences in microbiota composition, patients with COVID-19 in both continents exhibited significant gut microbiota alterations, which were more pronounced in severe cases, with similar features compared with controls. Functional pathways, including L-Tryptophan biosynthesis, were disrupted, particularly in patients with severe disease. Machine learning models accurately predicted disease severity based on gut microbial profiles in the Moroccan cohort, though not in the French cohort. These results highlight consistent microbiota changes associated with COVID-19 and support a potential link between gut dysbiosis and disease severity.}, }
@article {pmid40506318, year = {2025}, author = {Xu, CH and Zhang, LN and Liu, T and Zhu, GQ and Fan, YP and Chen, X and Shen, YY and Yu, YT and Shi, YY and Jiang, EL and Feng, SZ}, title = {Performance of Galactomannan, Aspergillus-PCR, and Metagenomic sequencing for the diagnosis of invasive pulmonary aspergillosis in hematological patients.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2025.06.001}, pmid = {40506318}, issn = {1995-9133}, abstract = {BACKGROUND/PURPOSE(S): Invasive pulmonary aspergillosis (IPA) is a serious fungal infection, and its diagnosis is diverse, especially in patients with hematological disorders. This study aims to determine the optimal diagnostic strategy for IPA in such patients by comparing various microbiological tests.<br><br>METHODS: A total of 490 blood and 138 bronchoalveolar lavage fluid (BALF) samples collected from 182 IPA and 407 no-IPA patients (based on EORTC/MSGERC criteria) were retrospectively analyzed by metagenomic next-generation sequencing (mNGS), Aspergillus-PCR, and galactomannan (GM) (enzyme immunoassay [EIA] and lateral flow assay [LFA]).<br><br>RESULTS: In BALF samples, GM-EIA, GM-LFA, Aspergillus-PCR, and mNGS showed sensitivities of 68.1&#xa0;%, 53.2&#xa0;%, 83.0&#xa0;%, and 59.6&#xa0;%-all higher than in blood (43.7&#xa0;%, 34.4&#xa0;%, 51.7&#xa0;%, 55.0&#xa0;%). In blood samples, mNGS had the highest sensitivity (71.9&#xa0;%) in neutropenic patients, which was further improved when combined with GM-EIA (77.1&#xa0;%). In non-neutropenic patients, Aspergillus-PCR was the most sensitive assay (47.3&#xa0;%), with sensitivity improving to 56.4&#xa0;% when combined with GM-EIA. Blood test sensitivities were lower in patients with prolonged antifungal therapy (&#x2265;7 days) vs. <7 days (Aspergillus-PCR: 38.6&#xa0;% vs. 57.0&#xa0;%; mNGS: 31.8&#xa0;% vs. 64.5&#xa0;%; GM-EIA: 27.3&#xa0;% vs. 50.5&#xa0;%; all P&#xa0;<&#xa0;0.05), with no impact on BALF results.<br><br>CONCLUSION: BALF is critical for accurate IPA diagnosis, particularly in patients with prior antifungal therapy. BALF Aspergillus-PCR offers optimal sensitivity, while blood-based mNGS and PCR are recommended for neutropenic and non-neutropenic patients, respectively. Combining molecular methods with GM testing enhances diagnostic performances. Tailored strategies are essential to improve early detection and clinical outcomes in high-risk hematologic populations.}, }
@article {pmid40506034, year = {2025}, author = {Cho, J}, title = {Multiple Inositol Polyphosphate Phosphatase ; A Hidden Phytate Digester with Bioactive Function Potential in Animal husbandry - A review.}, journal = {Animal bioscience}, volume = {}, number = {}, pages = {}, doi = {10.5713/ab.25.0122}, pmid = {40506034}, issn = {2765-0189}, abstract = {The objective of this review was to describe the enzymatic properties of multiple inositol polyphosphate phosphatase (MINPP1/MIPP) as an unusual member of histidine acid phosphatase, distinct from conventional microbial phytases and their additional physiological functions besides degrading phytate. Considering parameters such as pH activity profile, substrate specificity, catalytic efficiency, and stability, MINPP1 is of merit as a novel phytase source for developing an ideal feed additive supported by functional metagenomics fused with recombinant DNA technology and classical protein engineering. In addition, MINPP1 appears to be involved in some biological activities such as cell survival, stress, lipopolysaccharide (LPS) and inorganic polyphosphate-induced inflammatory response, milk fatty acid composition-related metabolism and bone-related growth and pathophysiology, which can be important for the production performance of farm animals. Future directions need profound studies revealing the direct effects of MINPP1 on these physiological events.}, }
@article {pmid40505965, year = {2025}, author = {Guo, Q and Wang, L and Han, B and Mu, X and Wu, W and Bi, Q and Chen, J}, title = {Diagnosis of Tropheryma Whipplei pneumonia in an immunnocompromised Lymphoma patient Using Metagenomic Next Generation Sequencing: A Case Report.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {}, number = {}, pages = {102752}, doi = {10.1016/j.jiac.2025.102752}, pmid = {40505965}, issn = {1437-7780}, abstract = {Whipple's disease (WD) is a rare chronic infectious illness caused by Tropheryma whipplei (T.whipplei), primarily affecting the gastrointestinal tract and joints, with rare lung involvement. Diagnosis can be challenging due to nonspecific symptoms and the difficulty in isolating the bacterium. This report describes a patient with pneumonia resulting from T.whipplei and Streptococcus pneumoniae infections during lymphoma treatment with chemotherapy and glucocorticoids. Imaging revealed pulmonary infections characterized by diffuse ground glass opacities and small nodules. Metagenomic sequencing of bronchoalveolar lavage fluid confirmed the mixed infection. The patient was treated with moxifloxacin and ceftriaxone, leading to improved inflammation within eight days. After completing chemotherapy, the patient was discharged with significant remission. This case highlights the susceptibility of immunocompromised patients to T.whipplei infection, emphasizing the need for early diagnosis and treatment.}, }
@article {pmid40505473, year = {2025}, author = {Song, RH and Zhu, D and Yang, ZQ and Li, JL and Yang, ZF and Lv, ZH and Xie, KQ and Yang, LQ and Zhou-Cun, A and Sang, P and Yin, YR}, title = {Characterization of a GH10 family thermophilic, alkali- and salt-tolerant xylanase from Xinjiang salt lake.}, journal = {Enzyme and microbial technology}, volume = {190}, number = {}, pages = {110693}, doi = {10.1016/j.enzmictec.2025.110693}, pmid = {40505473}, issn = {1879-0909}, abstract = {Xylanase is extensively employed in the food, feed, and paper sectors, with those derived from extreme environments offering distinct advantages. This study identified a novel xylanase gene (designated xynaes) through metagenomic analysis of samples from Aiting Lake, Xinjiang, China. Cloned and expressed in Escherichia coli after PCR amplification. The recombinant protein was purified using Ni-NTA affinity chromatography XynAES demonstrated optimal activity at pH 8.0 and 65 °C, its half-life (T1/2) was 120 min. XynAES preserved over 80 % residual activity after 12 h in pH 6.0-9.0 buffer. Its activity was enhanced to 132 % and 135 % in the presence of 1 mM Mg[2][+] and Zn[2+], respectively. Additionally, XynAES maintained over 60 % relative activity in 0-3.0 M NaCl and its Km and Vmax of XynAES were determined to be 3.23 mg/mL and 72.46 μmol/min/mg, respectively. It is worth noting that the main products of XynAES enzymatic hydrolysis of xylan are xylose disaccharides and xylose tetrasaccharides, and XynAES shows obvious activity against the pre-treated wheat bran. In summary, XynAES is a thermophilic, alkali-tolerant, and salt-resistant xylanase, signifying its potential applications in the feed, food baking, paper manufacturing, and prebiotic production industries.}, }
@article {pmid40505375, year = {2025}, author = {Shen, R and Li, Q and Lu, Q and He, Z and He, X and Wang, S}, title = {Nationwide screening of landfill-derived organohalide-respiring bacteria elucidates a unique cross-feeding interaction for microbial reductive dehalogenation.}, journal = {Water research}, volume = {284}, number = {}, pages = {123964}, doi = {10.1016/j.watres.2025.123964}, pmid = {40505375}, issn = {1879-2448}, abstract = {Landfill as a major reservoir of organohalide pollutants provides a unique niche for selective enrichment of organohalide-respiring bacteria (OHRB), playing a critical role in cycling of anthropogenic organohalides in natural environments. Nonetheless, information on the landfill-derived OHRB and associated microbial interactions for microbial reductive dehalogenation remains unknown. In this study, dehalogenation microcosms were established with nationwide landfill leachate samples collected from 45 cities in China, which dechlorinated a common anthropogenic organohalide - tetrachloroethene - to chloroethenes in varied extent. Both the 16S rRNA gene amplicon-sequencing and metagenomics analyses suggested critical roles of unknown Dehalococcoidia and phylogenetically-diverse facultative OHRB in microbial reductive dehalogenation in landfills. Further culture-based interaction examination showed a complicated metabolic network among OHRB, sulfate-reducing bacteria, fermenting bacteria and methanogenic archaea. Particularly, the acetate competition between obligate/facultative OHRB and methanogens were shown to have a threshold concentration of 0.06/0.20 mM, above which the methanogenic Methanosarcina became more competitive, in contrast to the dominance of acetotrophy of obligate/facultative OHRB under the threshold concentration. Accordingly, the Methanosarcina and OHRB preferred acetate transfer from fermenting Clostridium and sulfate-reducing Desulfovibrio, respectively, which was determined by the "Maximum Power Principle" to maximize ecological fitness through optimizing energy utilization efficiency. This study provided the first insight into landfill-derived OHRB and their metabolic interactions with associated functional microorganisms, which could support future bioremediation of organohalide-contaminated landfills.}, }
@article {pmid40505372, year = {2025}, author = {Xu, P and Sun, L and Chen, Y and Guo, Z and Ding, L and Wu, Z}, title = {Bioelectrochemical modulation of sulfur oxidation enhances arsenic sequestration from sediments in Vallisneria natans through root iron plaque formation and arsenic oxidation: Processes and mechanisms.}, journal = {Water research}, volume = {284}, number = {}, pages = {123975}, doi = {10.1016/j.watres.2025.123975}, pmid = {40505372}, issn = {1879-2448}, abstract = {This study investigated the potential of bioelectrochemical systems (BESs) in enhancing arsenic (As) sequestration in sulfur-rich sediments through submerged aquatic plant Vallisneria natans (V. natans). A mechanism entailing bioelectrogenesis-driven sulfur oxidation, which facilitated root iron plaque (IP) formation and As oxidation, was proposed. A 125-day microcosm study was conducted using coupled plant-BES configurations, comprising: a microbial fuel cell (MFC), microbial electrolysis cells (MECs) with voltage gradients, and V. natans. Results showed that As accumulation and enrichment efficiency in IPs increased proportionally with applied voltage. Electrogenesis enhanced IP development, with MECs outperforming the MFC. Rhizospheric phosphorus deficiency in MFC stimulated radial oxygen loss (ROL) and microbial Fe[2+] oxidation for IP formation. In MECs, enhanced endogenous Fe[2+] availability and reduction in ΣH2S concentrations collectively facilitated IP development. As oxidation in MFC was significantly amplified within the rhizosphere by As-oxidizing microorganisms. Sulfite (SO3[2-]), a metabolite of sulfur oxidation, was electrochemically activated in MECs to generate sulfite radicals (SO3[•-]), demonstrating superior As oxidation efficacy compared to MFC. Metagenomic analysis revealed extracellular electron transfer (EET) efficiency dictated the sulfur oxidation pathway. MFC exhibited FeS2-dominated oxidation with terminal S[0] and intermediate S2O3[2-] formation, suppressing ΣH2S elimination. MECs displayed insufficient EET, driving ΣH2S oxidation, FeS consumption, and SO3[2-] accumulation. Intracellular sulfur oxidation pathways differed between systems: the rDsr pathway dominated in MFC, while Hdr process prevailed in MECs. Anode-associated keystone genera responsible for sulfur oxidation were Thiobacillus and Pseudomonas in MFC and MECs, respectively. Iron-oxidizing Collimonas and As oxidizing Halomonas/Acinetobacter were crucial for mediating IP formation and As oxidization, respectively in MFC. These findings demonstrate that BESs are effective tools for augmenting As sequestration by submerged aquatic plants. This investigation establishes foundational insights for practical implementation of integrated plant-BESs in As-contaminated sediment remediation strategies.}, }
@article {pmid40505265, year = {2025}, author = {Chen, M and Wang, G and Ma, B and Musat, N and Shen, P and Wei, Z and Wei, Y and Richnow, HH and Zhang, J}, title = {Deciphering the transfer of antimicrobial resistance genes in the urban water cycle from water source to reuse: a review.}, journal = {Environment international}, volume = {201}, number = {}, pages = {109584}, doi = {10.1016/j.envint.2025.109584}, pmid = {40505265}, issn = {1873-6750}, abstract = {Antimicrobial resistance genes (ARGs) threaten ecosystems and human health, impacting United Nations Sustainable Development Goal 3 (Good Health and Well-being). This review examines ARG occurrence and transfer within the urban water cycle (UWC) from drinking water source to wastewater reuse, highlighting molecular mechanisms and research gaps. Quantitative and metagenomic data reveal that UWC amplifies ARG spread, with plasmid-mediated ARGs rising from ∼ 2.23 % to ∼ 49.51 % and high-risk ARGs increasing from ∼ 0.25 % to ∼ 5.07 %, enhancing horizontal gene transfer in receiving waters. The primary sources of ARGs in UWC are wastewater treatment plants and combined sewage overflows. Multidrug-resistant Pseudomonas aeruginosa in drinking water treatment plant and multidrug-resistant fecal coliforms in wastewater treatment plants should be emphasized. These pose significant risks to both the environment and human health and underscore the urgent need for targeted monitoring and mitigation strategies within the UWC to safeguard public health and aquatic ecosystems. Future research should: (1) map ARG dynamics across the entire UWC, (2) identify hosts of high-risk ARGs and key pathogens, (3) elucidate HGT mechanisms and risk transmission, and (4) develop targeted control technologies for high-risk ARGs at critical UWC points. These insights will inform strategies to ensure water security and curb ARG proliferation in aquatic environments.}, }
@article {pmid40504819, year = {2025}, author = {Kaboré, DPA and Exbrayat, A and Charriat, F and Soma, DD and Sawadogo, SP and Ouédraogo, GA and Tuaillon, E and Van de Perre, P and Baldet, T and Morel, C and Dabiré, RK and Gil, P and Gutierrez, S}, title = {A metagenomics survey of viral diversity in mosquito vectors allows the first detection of Sindbis virus in Burkina Faso.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0323767}, pmid = {40504819}, issn = {1932-6203}, mesh = {Animals ; Burkina Faso/epidemiology ; *Mosquito Vectors/virology ; *Metagenomics/methods ; *Sindbis Virus/genetics/isolation &amp; purification/classification ; *Aedes/virology ; Phylogeny ; *Culex/virology ; Humans ; Genome, Viral ; }, abstract = {Arboviruses (i.e., Arthropod-borne viruses) pose a threat to human health worldwide. This taxonomically-diverse group includes numerous viruses that recurrently spread into new regions. Therefore, periodic surveys of the arboviral diversity in a given region can help optimize the diagnosis of arboviral infections. However, such surveys are infrequent, especially in low-income countries. Consequently, case investigation is often limited to a fraction of the arboviral diversity. This situation is likely to result in undiagnosed cases. Here, we investigated the diversity of mosquito-borne arboviruses in two regions of Burkina Faso. To this end, we used untargeted metagenomics to screen mosquitoes collected over three years in six urban and rural areas. The analysis focused on two mosquito species, Aedes aegypti and Culex quinquefasciatus, considered to be among the most important vectors of arboviruses worldwide. The screening detected Sindbis virus (SINV, Togaviridae) for the first time in Burkina Faso. This zoonotic arbovirus has spread from Africa to Europe. SINV causes periodic outbreaks in Europe but its distribution and epidemiology in Africa remains largely unstudied. SINV was detected in one of the six areas, and at a single year. Detection was validated with isolation in cell culture. SINV was only detected in Cx. quinquefasciatus, adding to the list of potential vectors of SINV in nature. The SINV infection rate in mosquitoes was similar to those observed in European regions experiencing SINV outbreaks. Phylogenetic analysis placed the nearly-full genome within a cluster of Central African strains of lineage I. This cluster is thought to be at the origin of the SINV strains introduced into Europe. Our results call for studies on the prevalence of SINV infections in the region to estimate the disease burden and the interest of SINV diagnostic in case investigation.}, }
@article {pmid40504464, year = {2025}, author = {Chen, YR and Chen, LD and Zheng, LJ}, title = {Exploring the trimethylamine-degrading genes in the human gut microbiome.}, journal = {AMB Express}, volume = {15}, number = {1}, pages = {91}, pmid = {40504464}, issn = {2191-0855}, support = {32100082//National Natural Science Foundation of China/ ; 2023A03J0696//Science and Technology Program of Guangzhou/ ; }, abstract = {Trimethylamine (TMA), produced by gut microbes, is a precursor to a risk factor for cardiovascular diseases. Currently, TMA-degrading bacteria in the human gut have rarely been studied. This study combined TMA-enriched cultures (from 104 young male stool samples) with metagenomic profiling to identify key microbial players of TMA degradation. The results showed that the contribution of Enterococcus to methane metabolism was significantly higher in TMA-enriched culture samples. The 68.58% up-regulation of dmd-tmd (dimethylamine/trimethylamine dehydrogenase) in the TMA-enriched group indicated that the anaerobic dehydrogenase pathway participated in TMA metabolism. Notably, we first identified that taxa containing dmd-tmd belonged to Christensenella timonensis. The up-regulation of genes involved in methanogenesis (M00563) as well as the significant enrichment of M00563 (Reporter Score = 2.223) indicated that the methanogenesis pathway may play a role. We constructed gene databases for genes involved in the anaerobic dehydrogenase pathway (1526 sequences for dmd-tmd, 1319 sequences for mauA, and 326 sequences for mauB, respectively) and the aerobic oxidation pathway (2146 sequences for tmm, 1445 sequences for tdm, and 1519 sequences for dmm, respectively) based on genomes from the Integrated Microbial Genome (IMG) database, most of which belong to Pseudomonadota. Screening gut metagenomes with these databases revealed low sequence identity (< 70%), possibly because of the underrepresentation of gut-specific genomes from IMG. This study links Christensenella timonensis to TMA degradation, providing potential targets for microbiota modulation and a gene-centric framework to advance the characterization of gut microbial TMA metabolism.}, }
@article {pmid40503898, year = {2025}, author = {Han, H and Ji, M and Li, Y and Gong, X and Song, W and Zhou, J and Ma, K and Zhou, Y and Liu, X and Wang, M and Li, Y and Tu, Q}, title = {Tracing non-fungal eukaryotic diversity via shotgun metagenomes in the complex mudflat intertidal zones.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0041325}, doi = {10.1128/msystems.00413-25}, pmid = {40503898}, issn = {2379-5077}, abstract = {Eukaryotes, both micro- and macro-, constitute the dominant component of Earth's biosphere visible to the naked eye. Although relatively big in organismal size, tracing eukaryotic diversity in complex environments is not easy. For example, they may actively escape from sampling and be physically absent from the collected samples. In this study, we strived to recover non-fungal eukaryotic DNA sequences from typical shotgun metagenomes in the complex mudflat intertidal zones. Multiple recently developed approaches for identifying eukaryotic sequences from shotgun metagenomes were comparatively assessed. Considering the low overlap among different approaches, an integrative workflow was proposed. The integrative workflow was then used to recover the eukaryotic communities in complex intertidal sediments. The temporal dynamics of intertidal eukaryotic communities were investigated through a time-series sampling effort. Thirty-four non-fungal eukaryotic phyla were detected from 36 shotgun metagenomes. Clear temporal variation in relative abundance was observed for eukaryotic genera such as Timema and Navicula. Strong temporal turnover of intertidal eukaryotic communities was observed. By comparing to 18S rRNA gene amplicon sequencing, dramatically different community profiles were observed between these two approaches. However, the temporal patterns for intertidal eukaryotic communities recovered by both approaches were generally comparable. This study provides valuable technical insights into the recovery of non-fungal eukaryotic information from complex environments and demonstrates an alternative route for reusing the massive metagenomic data sets generated in the past and future.IMPORTANCEEukaryotes represent the dominant component visible to the naked eye and contribute to the primary biomass in the Earth's biosphere. Yet, tracing the eukaryotic diversity in complex environments remains difficult, as they can actively move around and escape from sampling. Here, using the intertidal sediments as an example, we strived to retrieve non-fungal eukaryotic sequences from typical shotgun metagenomes. Compared to 18S rRNA gene amplicon sequencing, the shotgun metagenome-based approach resolved dramatically different eukaryotic community profiles, though comparable ecological patterns could be observed. This study paves an alternative way for utilizing shotgun metagenomic data to recover non-fungal eukaryotic information in complex environments, demonstrating significant potential for environmental monitoring and biodiversity investigations.}, }
@article {pmid40503893, year = {2025}, author = {Pan, F and Han, P and Wu, Q and Hou, W and Rao, G and Ma, Z and Weng, W and Zhang, H}, title = {Rapid prediction of antibiotic resistance in Enterobacter cloacae complex using whole-genome and metagenomic sequencing.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0058425}, doi = {10.1128/msystems.00584-25}, pmid = {40503893}, issn = {2379-5077}, abstract = {Clinical management and surveillance of the Enterobacter cloacae complex (ECC) face significant challenges due to inaccurate species identification and prolonged turnaround time for culture-based antimicrobial susceptibility testing (AST). To date, no studies have leveraged whole-genome sequencing (WGS) and metagenomic next-generation sequencing (mNGS) to develop a rapid AST prediction model for ECC. Here, a total of 1,054 ECC strain genomes with AST data were collected from a public database and a local hospital. The results of species identification between the average nucleotide identity (ANI)-based method on culture were compared, and machine learning was employed to identify resistance features for imipenem (IPM), meropenem (MEM), ciprofloxacin (CIP), levofloxacin (LEV), and trimethoprim-sulfamethoxazole (SXT). By referring to ANI-based species classification, culture-based methods showed a 74% misidentification rate for 1,054 ECC isolates. The antimicrobial resistance prediction model demonstrated good performance, with the area under the curve values of 91.25% (IPM), 89.69%, 88.17% (CIP), 91.01% (LEV), and 90.93% (SXT) respectively. Moreover, a combined WGS and mNGS approach was utilized and validated using 104 pediatric sputum specimens. Compared to culture-based AST, the overall accuracy of models exceeded 95%, especially achieving 100% for IPM and 98.80% for MEM, and the detection turnaround time was shortened by 69.64 h. Furthermore, it would enable early escalated therapy in 20.83% of cases, significantly improving patient management. This established WGS and mNGS-based AST prediction model addresses the limitations of traditional methods, offering a rapid, accurate, and clinically applicable tool for managing multidrug-resistant ECC infections.IMPORTANCEThe Enterobacter cloacae complex (ECC) poses a major challenge to clinical management due to difficulties in accurate species identification and the slow turnaround times of conventional culture-based antimicrobial susceptibility testing (AST). Current methods are often inefficient and prone to misidentification, leading to delayed or inappropriate treatment. This study introduces a novel approach that combines whole-genome sequencing (WGS) and metagenomic next-generation sequencing (mNGS) to develop a rapid and accurate AST prediction model for ECC. By leveraging machine learning to analyze WGS data from over 1,000 ECC isolates and validating the model with pediatric clinical specimens. The model achieved over 88% area under the curve accuracy for all antibiotics, demonstrated >95% accuracy in clinical validation, and reduced detection turnaround time by 69.64 h compared to traditional methods. The model has the potential to revolutionize ECC management by facilitating timely, targeted therapies and enhancing patient outcomes, especially in the context of multidrug-resistant infections.}, }
@article {pmid40503892, year = {2025}, author = {He, B and Wang, Y and Xu, M and Hutchins, DA and Fu, F-X and Xia, X and Duan, R and Lin, T-H and Jiao, N and Zheng, Q}, title = {Distinct survival strategies in oligotrophic and eutrophic ecotype Synechococcus-bacteria co-cultures under iron limitation and warming conditions.}, journal = {mBio}, volume = {}, number = {}, pages = {e0109825}, doi = {10.1128/mbio.01098-25}, pmid = {40503892}, issn = {2150-7511}, abstract = {Phytoplankton-bacteria interactions underpin primary production and nutrient cycling in both oligotrophic and eutrophic aquatic environments, profoundly influencing marine biogeochemical cycles. Despite their importance, how these interactions vary under simultaneous environmental stressors such as warming and iron (Fe) limitation remains largely unexplored, especially across differing ecotypes. Here, we compared the responses of oligotrophic (strain YX04-1) and eutrophic (strain XM-24) ecotype Synechococcus-heterotrophic bacteria interactions to concurrent warming and Fe limitation, using the 16S rRNA gene amplicon sequencing alongside metagenomic and metatranscriptomic analyses. Our results revealed that community composition and gene expression in the oceanic Synechococcus sp. YX04-1 co-culture were more sensitive to warming, whereas the coastal Synechococcus sp. XM-24 co-culture responded more strongly to Fe limitation. The resilience of oligotrophic YX04-1 and its bacterial partners to iron deficiency may result from potential mutualistic triangular dynamics, involving complex carbohydrate decomposition, low-molecular-weight organic substrate transfer, and feedback of public goods. In contrast, the eutrophic XM-24 co-culture experienced intensified competition and opportunistic exploitation of organic resources by dominant mixotrophic bacteria under concurrent warming and Fe limitation conditions. These findings reveal contrasting survival strategies of oligotrophic and eutrophic Synechococcus-bacteria co-cultures, highlighting the tighter and mutually beneficial interactions in the oligotrophic co-culture that may assist oligotrophic species in adapting to changing ocean conditions.IMPORTANCEPhytoplankton-bacteria interactions serve as a crucial biological network linking primary production and nutrient cycling in marine ecosystems. In the context of global change, the upper ocean inevitably faces increased warming and iron limitation, which will shift primary producer composition toward Synechococcus and impact its nutrient exchanges with co-existing bacteria. The changes in this fundamental and widespread microbial interaction may affect the stability of nutrient cycling, yet its universal response under warming and iron limitation remains poorly understood. Our research reveals contrasting responses of oligotrophic and eutrophic Synechococcus-bacteria interactions under the same stress, driven by stronger metabolic dependencies in the oligotrophic co-culture but greater individual competitiveness in the eutrophic one. These findings emphasize the importance of cooperative heterotrophic bacteria for host survival and imply a non-uniform co-evolution of in situ microbial interactions across different marine ecosystems in the future.}, }
@article {pmid40503882, year = {2025}, author = {Jonas, L and Lee, Y-Y and Bachvaroff, T and Hill, RT and Li, Y}, title = {Two novel Patescibacteria: Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov., both associated with microalgae optimized for carbon dioxide sequestration from flue gas.}, journal = {mBio}, volume = {}, number = {}, pages = {e0123125}, doi = {10.1128/mbio.01231-25}, pmid = {40503882}, issn = {2150-7511}, abstract = {The functional roles of bacterial symbionts associated with microalgae remain understudied despite the importance of microalgae in biotechnology and environmental microbiology. 16S rRNA gene sequencing was conducted to analyze bacterial communities associated with two microalgae optimized for growth with flue gas containing 5%-10% CO2. Two dominant bacteria with no taxonomic classification beyond the class level (Paceibacteria) were discovered repeatedly in the most productive algal cultures. Long-read metagenomic sequencing was conducted to yield high-quality metagenomes, from which two novel species were discovered under the Seqcode (seqco.de/r:ywe1blo2), Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov. The genus Phycocordibacter gen. nov. was proposed as the nomenclatural type of the family Phycocordibacteraceae fam. nov. and the order Phycocordibacterales ord. nov. Both bacteria possessed features typical of Patescibacteria such as reduced genomes (<800 kbp), lack of complete glycolysis and tricarboxylic acid (TCA) cycle pathways, and inability to synthesize amino acids. Instead, they rely on the reductive pentose phosphate pathway (Calvin cycle) for essential biosynthesis and redox balance. P. aenigmaticus may also rely on elemental sulfur oxidation (sdo), partial nitrite reduction (nirK), and sulfur-related amino acid metabolism (SAMe → SAH). Both bacteria were found in high relative abundance in cultures of Tetradesmus obliquus HTB1 (freshwater) and Nannochloropsis oceanica IMET1 (marine), suggesting a tight association with microalgae in various environments. The absence of full metabolic pathways for energy production suggests extreme metabolic limitations and obligate symbiosis, most likely with other bacteria associated with the microalgae.IMPORTANCETo our knowledge, this is the first report of Patescibacteria as dominant bacteria associated with microalgae or within a biologically mediated carbon capture system. Two novel Patescibacteria were found in two ecologically distinct microalgal cultures (one freshwater strain and one marine) regardless of whether the cultures were bubbled with air, 5% CO2, or 10% CO2. This unexpected and unprecedented dominance led to long-read sequencing and the assembly of high-quality metagenomes for both Patescibacteria, as well as five other bacteria in the system. The discovery of two novel species belonging to two novel genera, one novel family, and one novel order has enabled us to fill in gaps of a major, uncharacterized branch within the bacterial tree of life. Additionally, the extreme gene loss found in both Patescibacteria, Phycocordibacter aenigmaticus and Minusculum obligatum, contributes knowledge to a rapidly advancing body of research on the scavenging metabolic nature of this enigmatic and largely unclassified phylum.}, }
@article {pmid40503829, year = {2025}, author = {Zhao, J and Zhuge, R and Guo, K and Tang, J and Sun, Y and Zhang, Y and Yuan, L and Qiu, C and Yan, Y and Wang, K and Jiang, Q and Chen, J and Hua, Z and Qiu, L and Fang, H and Zhuge, J}, title = {The clinical utility of bronchoalveolar lavage fluid metagenomic next-generation sequencing in immunocompromised critically ill patients with invasive pulmonary aspergillosis: a multicenter retrospective study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0058425}, doi = {10.1128/spectrum.00584-25}, pmid = {40503829}, issn = {2165-0497}, abstract = {UNLABELLED: The clinical utility of metagenomic next-generation sequencing (mNGS) in immunocompromised critically ill patients with invasive pulmonary aspergillosis (IPA) remains poorly studied. Given the diagnostic challenges and high mortality associated with IPA in this population, further research on the use of mNGS for early diagnosis and targeted therapy is urgently needed. This multicenter, retrospective, observational study enrolled immunocompromised patients admitted to the intensive care units of six tertiary hospitals in China from April 2021 to November 2024. Comprehensive clinical data were systematically collected, including demographic information, underlying conditions, and detailed records of specimen types and microbiological examination methods. The primary objective was to evaluate the diagnostic and prognostic values of mNGS in comparison to conventional microbiological tests (CMTs) for IPA in this high-risk population. Kappa analysis results indicated a significant agreement between the results of mNGS and CMTs in both groups (Kappa value = 0.638, P < 0.001). The receiver operating curve demonstrated that mNGS exhibited comparable sensitivity (94.03% vs. 95.52%) and higher specificity (96.20% vs. 78.85%), as well as a higher area under the curve (AUC) (0.951 vs. 0.872) in diagnosing IPA compared to CMTs. Moreover, mNGS was significantly superior to other single methods, including cultures (AUC: 0.620, sensitivity: 27.88%, specificity: 96.15%), galactomannan test (AUC: 0.711, sensitivity: 53.73%, specificity: 88.46%), and PCR (AUC: 0.770, sensitivity: 62.69%, specificity: 91.35%). The clinical application of mNGS-guided antibiotic adjustments significantly decreased the 28-day mortality rate (46.51% vs. 66.67%, P < 0.05). mNGS is a feasible and highly sensitive diagnostic tool for detecting Aspergillus infections in immunocompromised critically ill patients compared to CMTs and other single conventional methods. It also performs well in identifying mixed infections, facilitating appropriate antibiotic regimen adjustments and improving patient prognosis.<br><br>IMPORTANCE: mNGS demonstrated significantly higher specificity and area under the curve for diagnosing IPA in immunocompromised critically ill patients compared to CMTs. mNGS showed superior diagnostic performance over single methods, such as cultures, galactomannan test, and PCR, with higher sensitivity and specificity for Aspergillus detection. The use of mNGS-guided antibiotic adjustments led to a significant reduction in 28-day mortality (46.51% vs. 66.67%) among immunocompromised patients. mNGS demonstrated utility in identifying mixed infections, supporting targeted therapy and better patient outcomes. The application of mNGS in diagnosing IPA and guiding treatment in ICU patients helped optimize antibiotic regimens, ultimately improving clinical prognosis.}, }
@article {pmid40503491, year = {2025}, author = {Dong, J and Xu, C and Jin, S and Xie, T and Xu, Z and Hao, D and Dong, L}, title = {Gut Microbiota and Tryptophan Metabolism as Therapeutic Targets for Spinal Cord Injury: Insights From Probiotic Treatment.}, journal = {Journal of inflammation research}, volume = {18}, number = {}, pages = {7337-7355}, pmid = {40503491}, issn = {1178-7031}, abstract = {BACKGROUND: Probiotics have been demonstrated to repair spinal cord injuries (SCI) by improving gut microbiota dysbiosis; however, the specific mechanisms underlying their therapeutic effects on SCI remain incompletely elucidated.<br><br>OBJECTIVE: This study aims to investigate the therapeutic effects of probiotics and analyze the mechanisms of probiotic treatment for SCI through the gut-spinal cord axis.<br><br>METHODS: A rat model of SCI was established to evaluate the therapeutic effects of probiotics. Fecal samples were analyzed to assess gut microbiota composition and metabolite profiles, while differential gene expression in spinal cord tissue was examined.<br><br>RESULTS: Pathological assessments demonstrated that probiotic treatment facilitated structural restoration of the spinal cord tissue. Behavioral evaluations via the Basso Mouse Scale (BMS) and inclined plane tests revealed significant improvements in locomotor recovery after SCI. Metagenomic sequencing showed that probiotics enhanced gut microbiota diversity, particularly enriching the relative abundance of Bacillota (formerly Firmicutes) and Clostridia. Metabolite profiling identified an enrichment of key tryptophan metabolites, including 3-Indoleacetonitrile, Xanthoxic acid, Serotonin, and Tryptophanol. Transcriptomic analysis identified 468 upregulated and 173 downregulated genes in spinal cord tissues. Furthermore, gut microbiota, microbial metabolites and spinal cord gene expression were integrated to construct a "gut microbiota-tryptophan metabolites-signaling pathway network" using Cytoscape v.3.10.2. This network linked 19 microbial species (17 belonging to Bacillota and Clostridia, including seven Lactobacillus species) with tryptophan metabolites and downstream signaling pathways. Among these, tryptophan metabolites activated 17 genes predominantly involved in anti-inflammatory and neuroregenerative processes. Protein-level validation confirmed the neuroprotective and anti-inflammatory effects of probiotics.<br><br>CONCLUSION: The "Gut microbiota-tryptophan metabolites-signaling pathway network" offers novel therapeutic targets for SCI injury treatment. Probiotics exert their effects by modulating gut microbiota and enhancing tryptophan metabolism, thereby influencing multiple signaling pathways in the spinal cord that can lead to anti-inflammatory and neuroprotective outcomes.}, }
@article {pmid40503301, year = {2025}, author = {Tang, K and Li, S and Luo, Y and Feng, W and Zhang, Z and Wang, L and Zhao, H and Chen, X and Li, X and Wu, Z}, title = {Integrating metagenomics and untargeted metabolomics to analyze the relationship between microbial dynamics and non-volatile metabolomic profiles in plant-derived microbial fuel cells (MFCs).}, journal = {RSC advances}, volume = {15}, number = {25}, pages = {19582-19597}, pmid = {40503301}, issn = {2046-2069}, abstract = {Microbial Fuel Cells (MFC) are an emerging biomass energy technology that harnesses the power of electroactive bacteria living on a bacterial biofilm to convert biomass energy within waste materials into usable electricity. A pivotal aspect of MFC research involves understanding the behavior and underlying mechanisms of electroactive bacteria during extracellular electron transfer to the anode, which plays a crucial role in energy conversion. In this paper, four MFCs were operated at external resistances of 500 and 1000 ohms, and the changes in the biofilm's electroactive bacterial composition due to altered external resistances were indicated by the voltage and power differences. After stable power generation, total DNA was extracted from the biofilm for sequencing, and metabolites were tested. The expression trends of genes and the differences in final metabolites from the whole period indicate that electron transfer gene families are associated with Shewanella, Pseudomonas, Trichococcus, and Enterococcus, while tyrosine and purine metabolism showed significant differences in effective metabolite accumulation among communities with varying energy output efficiency. Omics techniques revealed, to some extent, the coordination mechanisms and bacterial interactions within biofilms during microbial community succession.}, }
@article {pmid40503221, year = {2025}, author = {Fehér, E and Kemenesi, G and Görföl, T and Wazzani, Y and Bodó, K and Lanszki, J and Máté, D and Kaszab, E and Domán, M and Zádori, Z and Lanszki, Z}, title = {Occurrence of Recombinant Canine Coronavirus, Picodicistrovirus, and Circovirus in Red Foxes (Vulpes vulpes) Implies Frequent Virus Transmission Events Among Carnivores.}, journal = {Transboundary and emerging diseases}, volume = {2025}, number = {}, pages = {6681119}, pmid = {40503221}, issn = {1865-1682}, mesh = {Animals ; *Foxes/virology ; *Coronavirus, Canine/genetics/isolation &amp; purification ; *Circovirus/genetics/isolation &amp; purification ; Phylogeny ; *Coronavirus Infections/veterinary/virology/epidemiology/transmission ; Hungary/epidemiology ; Genome, Viral ; *Circoviridae Infections/veterinary/virology/epidemiology/transmission ; Carnivora/virology ; Recombination, Genetic ; }, abstract = {Although their pathogenicity is most often unclear, some canine viruses have been found to infect carnivores other than dogs. This study relies on the surveillance of coronaviruses in 206 saliva and fecal samples of huntable, sympatric canid and mustelid species captured in Hungary, such as the native red fox (Vulpes vulpes), European badger (Meles meles), golden jackal (Canis aureus), and stone marten (Martes foina), as well as the recently settled alien raccoon dog (Nyctereutes procyonoides). Metagenomics-based and direct sequence analysis were deployed to determine the genome sequence of coronaviruses identified in two specimens collected from red foxes. Near-complete genome sequences of two canine coronaviruses (CCoVs) were obtained, together with the complete genome sequence of a canine circovirus (CanineCV) and the near-complete genome sequence of a canine picodicistrovirus (CPDV) from one of the samples. These provided the first fox origin CCoV and CPDV sequence data, and the first recorded appearance of the CPDV in Europe. The results suggested that recombination is of great importance in the evolution of CCoV, CanineCV, and CPDV infecting dogs and wild-living carnivores, including the red fox and golden jackal. These are widespread in Central and Southeast Europe, and have large ranges, facilitating transmission of the multihost canine pathogens.}, }
@article {pmid40502641, year = {2025}, author = {Lu, L and Li, Y and Su, H and Ren, S and Liu, Y and Shao, G and Liu, W and Ji, G and Xu, H}, title = {Huangqin decoction inhibits colorectal inflammatory cancer transformation by improving gut microbiome-mediated metabolic dysfunction.}, journal = {Journal of pharmaceutical analysis}, volume = {15}, number = {5}, pages = {101138}, pmid = {40502641}, issn = {2214-0883}, abstract = {Colorectal inflammatory cancer transformation poses a major risk to patients with colitis. Patients with chronic intestinal inflammation have an approximately 2-3 folds increased risk of developing colorectal cancer (CRC). Unfortunately, there is currently no effective intervention available. Huangqin decoction (HQD), a well-known traditional Chinese medicine (TCM) formula, is frequently clinically prescribed for treating patients with colitis, and its active ingredients have effective antitumour efficacy. Nonetheless, the mechanism of HQD-mediated prevention of colorectal inflammatory cancer transformation remains unclear. A strategy integrating metagenomic, lipidomic, and messenger RNA (mRNA) sequencing analysis was used to investigate the regulatory effects of HQD on the gut microbiome, metabolism and potential mechanisms involved in colorectal inflammatory cancer transformation. Our study revealed that HQD suppressed colorectal inflammatory cancer transformation, which was associated with enhanced intestinal barrier function, decreased the inflammatory response, and regulation of the gut microbiome. Notably, cohousing experiments revealed that the transfer of the gut microbiome from HQD-treated mice largely inhibited the pathological transformation of colitis. Moreover, gut microbiome transfer from HQD-treated mice primarily resulted in the altered regulation of fatty acid metabolism, especially the remodeling of arachidonic acid metabolism, which was associated with the amelioration of pathological transformation. Arachidonic acid metabolism and the key metabolic enzyme arachidonic acid 12-lipoxygenase (ALOX12) were affected by HQD treatment, and no obvious protective effect of HQD was observed in Alox 12 [-/-] mice, which revealed that ALOX12 was a critical mediator of HQD protection against colorectal inflammatory cancer transformation. In summary, multiple omics analyses were applied to produce valuable data and theoretical support for the application of HQD as a promising intervention for the transformation of inflammatory CRC.}, }
@article {pmid40502184, year = {2025}, author = {Verna, G and De Santis, S and Islam, B and Sommella, EM and Licastro, D and Zhang, L and De Almeida Celio, F and Merciai, F and Caponigro, V and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F}, title = {A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.05.31.657160}, pmid = {40502184}, issn = {2692-8205}, abstract = {UNLABELLED: Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors, including the gut microbiome. Since ulcerative colitis (UC), a significant risk factor for CAC, is rising in prevalence worldwide, an integrative approach is essential to identify potential triggers linking inflammation to cancer. In the present study, we investigated the role of the gut microbiome using Winnie mice, a UC-like model with a relevant missense mutation in the Muc2 gene. Upon transfer from a conventional (CONV) to a specific-pathogen-free (SPF) facility, Winnie mice exhibited a more severe colitis phenotype, and notably, spontaneous CAC as early as four weeks of age, which progressively worsened over time. In contrast, CONV Winnie developed only mild colitis but with no overt signs of tumorigenesis. Notably, when rederived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis or colon tumor development, indicating an essential role for the gut microbiome in the initiation and progression of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct pro-inflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Fecal microbiota transplantation (FMT), using either SPF Winnie or WT (Bl/6) donors into GF Winnie recipients, demonstrated that while colitis developed regardless of donor, only FMT from SPF Winnie donors resulted in CAC, revealing a microbiota-driven, host-specific susceptibility to tumorigenesis in Winnie mice. Our studies present a novel and relevant model of CAC, providing further evidence that the microbiome plays a key role in the pathogenesis of CAC, thereby challenging the concept of colon cancer as a strictly non-transmissible disease.<br><br>LAY SUMMARY: This study reveals a distinct metagenomic, metabolomic, and lipidomic profile associated with tumorigenesis in a murine model of ulcerative colitis, highlighting the risks of specific intestinal dysbiosis in genetically predisposed subjects.<br><br>WHAT YOU NEED TO KNOW: Background and context: Colitis-associated colorectal cancer arises from complex host-environment interactions, including gut microbiome influences, driving chronic inflammation, with the intestinal lumen environment remaining a largely unexplored potential risk factor in cancer development.New findings: Winnie mice in specific pathogen-free conditions developed severe colitis, and a novel juvenile colon dysplasia and cancer, with gut microbiome changes driving colitis-associated cancer initiation and progression.Limitations: We identified a pro-inflammatory microbial/metabolic signature promoting colitis-to-CAC transition in Winnie mice, with FMT confirming microbiota-driven tumor susceptibility. However, further research is needed to pinpoint the key bacteria-metabolite-lipid combination driving CAC.Clinical research relevance: This newly characterized microbiota-metabolome-based model of CAC, challenges the dogma of cancer as a non-transmittable disease, providing a foundation for developing microbiota-based strategies for CAC prevention and treatment.Basic research relevance: Unlike genetic or chemically induced models, the Winnie mouse model uniquely serves as a dual model for spontaneous colitis and juvenile CAC, offering a fast, 100% penetrant phenotype that enhances reliability, accelerates research, and provides valuable insights into IBD and CAC.}, }
@article {pmid40502000, year = {2025}, author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG}, title = {The Spinal Cord-Gut Axis Regulates Gut Microbial Homeostasis: Insights from a New Murine Metagenomic Catalog.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.05.27.656368}, pmid = {40502000}, issn = {2692-8205}, abstract = {The spinal cord, a nexus for brain-body crosstalk, controls gut physiology and microbial homeostasis. Here, >6,500 microbial metagenome-assembled genomes were recovered de novo , from male and female C57BL/6 mice gut metagenomes before and up to 6 months after disrupting the "spinal cord-gut axis". This "Mouse B6 Gut Catalog" improved or doubled species- and strain-level representation in other published catalogs. Analyses showed that breaking the spinal cord-gut axis caused persistent microbial changes that varied by sex, spinal lesion level, and time. A key bacterium, Lactobacillus johnsonii , was consistently reduced, and feeding this to mice with a clinically relevant spinal cord injury improved host health. Genome-resolved, community-contextualized metabolic profiling showed that spinal-dependent effects on microbe-encoded carbohydrate metabolism explain the reduction of L. johnsonii . These data improve murine microbiome catalogs and emphasize that mammalian health and gut ecosystem function depend on a functional spinal cord-gut axis.}, }
@article {pmid40501659, year = {2025}, author = {Vemuganti, V and Kang, JW and Zhang, Q and Aquino-Martinez, R and Harding, S and Harpt, JL and Deming, Y and Johnson, S and Asthana, S and Zetterberg, H and Blennow, K and Engelman, CD and Ulland, TK and Bäckhed, F and Bendlin, BB and Rey, FE}, title = {Gut bacterial metabolite imidazole propionate potentiates Alzheimer's disease pathology.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.06.08.657719}, pmid = {40501659}, issn = {2692-8205}, abstract = {UNLABELLED: The gut microbiome modulates metabolic, immune, and neurological functions and has been implicated in Alzheimer's disease (AD), though the specific mechanisms remain poorly defined. The bacterial metabolite imidazole propionate (ImP) has been previously associated with several AD comorbidities, such as type 2 diabetes and cardiovascular disease. Here, we show that elevated plasma ImP levels are associated with lower cognitive scores and AD biomarkers in a cohort of >1,100 cognitively unimpaired individuals. Metagenomic profiling identified gut bacteria encoding putative orthologs of the ImP-synthesizing enzyme, urocanate reductase (UrdA), whose abundance correlated with both cognitive measures and multiple AD biomarkers. Chronic ImP administration to mice activated neurodegenerative pathways, worsened AD-like neuropathology, and increased blood-brain barrier (BBB) permeability. Complementary in vitro studies showed that ImP compromised the integrity of human brain endothelial cells. Collectively, these findings implicate ImP in AD progression via both neurodegenerative and cerebrovascular mechanisms, identifying it as a potential target for early intervention.<br><br>ONE SENTENCE SUMMARY: Gut bacterial metabolite increases dementia risk.}, }
@article {pmid40500775, year = {2025}, author = {Liang, T and Dong, J and Zhou, W and Huang, X and Liu, H and Zhang, Y and Yang, Q and Ahmad, M and Chen, L and Ling, J}, title = {Investigation on the aerobic methanotrophic community and the dominant taxon Methylomarinum in seagrass ecosystem.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {67}, pmid = {40500775}, issn = {2524-6372}, support = {Mangrove Wetland Blue Carbon Sequestration Technology Innovation Team//Nansha District High-Level Talent Innovation Team Project in 2021/ ; Mangrove Wetland Blue Carbon Sequestration Technology Innovation Team//Nansha District High-Level Talent Innovation Team Project in 2021/ ; 2023B1212060047//Science and Technology Planning Project of Guangdong Province of China/ ; 42206129//the National Natural Science Foundation of China/ ; 41676163//the National Natural Science Foundation of China/ ; 2023A1515012124//Guangdong Basic and Applied Basic Research Foundation/ ; 2022KJCX07//Sanya Science and Technology Innovation Special Project/ ; GDNRC[2024]38//the Marine Economy Development Project of Guangdong Province/ ; 2023ZD012//Nansha Key Scientific and Technological Project, Guangdong Province/ ; ZDYF2023SHFZ172//Hainan Province Science and Technology Special Fund/ ; }, abstract = {BACKGROUND: Methanotrophs are a key biological methane sink, and aerobic methanotrophs critically reduce wetland methane emissions under global climate change. However, despite their ecological significance, investigations on aerobic methanotrophs within seagrass ecosystems remain scant. In this study, microcosmic culture experiments were used to assess aerobic methane oxidation (AMO) potential and its drivers across a vertical gradient of seagrass sediments. Moreover, the methanotrophic community structure was characterized by amplicon sequencing, and the dominant methanotroph's metagenome-assembled genome (MAG) and metabolic pathway was investigated.<br><br>RESULTS: Sediments of Halophila ovalis exhibited notable vertical differences in both physicochemical properties and methane oxidation rates. Furthermore, ammonium nitrogen (NH4[+]-N) decreased with sediment depth, and was suggested by structural equation modeling (SEM) to significantly contribute to the vertical methane oxidation variability. Microbial community structure analysis revealed that type I methanotrophs were stimulated by methane addition and significantly impacted the oxidation of elevated methane, with Methylomarinum being the dominant taxon. Through metagenomic analysis, we assembled a phylogenetically novel methanotroph, Candidatus Methylomarinum sp. MAG81, which is distantly related to the extant Methylomarinum vadi IT-4. We conducted a comparative analysis of the two genomes and discovered that MAG81 not only possesses the capability for methane oxidation but also has the ability to participate in methanol oxidation via Xox-MDH. Furthermore, MAG81 also harbors nitrogen metabolism genes, particularly those involved in nitrogen fixation (nifHDK). This genetic characteristic suggests a potential role for MAG81 in facilitating the carbon and nitrogen cycles within seagrass ecosystems.<br><br>CONCLUSIONS: In summary, our study revealed that the vertical variation of NH4[+]-N significantly affected methane oxidation and that type I methanotrophs, especially the genus Methylomarinum played an important role in oxidizing methane in seagrass sediments, shedding new insights into the methane abatement in the seagrass ecosystem, which is essential for climate change mitigation.}, }
@article {pmid40500757, year = {2025}, author = {Sussfeld, D and Lannes, R and Corel, E and Bernard, G and Martin, P and Bapteste, E and Pelletier, E and Lopez, P}, title = {New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {65}, pmid = {40500757}, issn = {2524-6372}, support = {615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; }, abstract = {BACKGROUND: Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel viruses. Such findings profoundly reshaped the structure of the known Tree of Life and emphasised the central role of investigating uncultured organisms. However, despite significant progresses, a large portion of proteins predicted from metagenomes remain today unannotated, both taxonomically and functionally, across many biomes and in particular in oceanic waters.<br><br>RESULTS: Here, we used an iterative, network-based approach for remote homology detection, to probe a dataset of 40&#xa0;million ORFs predicted in marine environments. We assessed the environmental diversity of 53 core gene families broadly distributed across the Tree of Life, with essential functions including translational, replication and trafficking processes. For nearly half of them, we identified clusters of remote environmental homologues that showed divergence from the known genetic diversity comparable to the divergence between Archaea and Bacteria, with representatives distributed across all the oceans. In particular, we report the detection of environmental clades with new structural variants of essential SMC (Structural Maintenance of Chromosomes) genes, divergent polymerase subunits forming deep-branching clades in the polymerase tree, and variant DNA recombinases in Bacteria as well as viruses.<br><br>CONCLUSIONS: These results indicate that significant environmental diversity may yet be unravelled even in strongly conserved gene families. Protein sequence similarity network approaches, in particular, appear well-suited to highlight potential sources of biological novelty and make better sense of microbial dark matter across taxonomical scales.}, }
@article {pmid40500753, year = {2025}, author = {Bograd, A and Oppenheimer-Shaanan, Y and Levy, A}, title = {Plasmids, prophages, and defense systems are depleted from plant microbiota genomes.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {163}, pmid = {40500753}, issn = {1474-760X}, support = {1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; }, mesh = {*Prophages/genetics ; *Plasmids/genetics ; *Plants/microbiology ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/virology ; }, abstract = {Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. Here, we compare 38,912 bacterial genomes and 6073 metagenomes to explore the distribution of mobile genetic elements and defense systems in plant-associated bacteria. We reveal a consistent taxon-independent depletion of prophages, plasmids, and defense systems in plant-associated bacteria, particularly in the phyllosphere, compared to other ecosystems. The mobilome depletion suggests the presence of unique ecological constraints or molecular mechanisms exerted by plants to control the bacterial mobilomes independently of bacterial immunity.}, }
@article {pmid40500273, year = {2025}, author = {Wang, H and Zhao, B}, title = {Diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing for pulmonary infections in patients with connective tissue disease: A retrospective study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20042}, pmid = {40500273}, issn = {2045-2322}, support = {2024KY1510//the Medical and Health Science and Technology Project of Zhejiang Province/ ; }, mesh = {Humans ; *Connective Tissue Diseases/complications/microbiology ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; Adult ; Aged ; *Respiratory Tract Infections/diagnosis/microbiology ; }, abstract = {Pulmonary infection is common in connective tissue diseases (CTDs) patients because of immunodeficiency. The basic characteristics of pathogens in this set of patients may differs from immunocompetent patients and largely unclear. We aimed to understand these characteristics by metagenomic next-generation sequencing (mNGS) detection in bronchoalveolar lavage fluid (BALF) from CTDs and explored the primary disease features of this group of patients. Eighty-one CTD patients who were suspected pulmonary infection and received mNGS of BALF as well as conventional microbiologic testing (CMT) were enrolled consecutively. We analysed the types of CTDs, whether accompanied with interstitial lung disease, comparison between performance of mNGS and CMT, and distribution of clinically relevant pathogens, etc. Of the 81 cases, 62 were clinically diagnosed with pulmonary infection. Among all patients, idiopathic inflammatory myopathy accounted for the highest proportion of cases infected, especially anti-MDA5 dermatomyositis and anti-synthetase syndrome. Patients in the pulmonary infection group had been previously treated with higher percentages of anti-rheumatic drugs than those in the non-infection group. The sensitivity of mNGS was higher than that of CMT (80.6% vs. 66.1%). Among the microbes detected by mNGS, the most common bacterial pathogen was Pseudomonas aeruginosa, and the most frequently fungi was Pneumocystis jirovecii. As for the specific pathogens, mNGS had great advantages over CMT in identifying Pneumocystis jirovecii. Idiopathic inflammatory myopathy was the disease most susceptible to pulmonary infections among CTDs. mNGS showed high efficiency for the detection of pathogens that cause pneumonia in BALF from patients with CTDs, especially for Pneumocystis jirovecii.}, }
@article {pmid40499773, year = {2025}, author = {Ma, Y and Dong, X and Sun, Y and Li, B and Ma, H and Li, H and Zhao, X and Ran, S and Zhang, J and Ye, Y and Li, J}, title = {Diversity and Functional Roles of Viral Communities in Gene Transfer and Antibiotic Resistance in Aquaculture Waters and Microplastic Biofilms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126636}, doi = {10.1016/j.envpol.2025.126636}, pmid = {40499773}, issn = {1873-6424}, abstract = {This study presents a comprehensive metagenomic analysis of viral communities in seawater and microplastic biofilms, uncovering their diversity, functional roles, and ecological significance. We identified 4,999 DNA and 22 RNA viral operational taxonomic units. Seawater samples exhibited greater viral diversity, while microplastic biofilms harbored specialized viral assemblages with enriched metabolic functions, particularly in carbohydrate and amino acid metabolism. Auxiliary metabolic genes were detected, suggesting viral involvement in microbial metabolism and nutrient cycling. The dominance of lytic viruses (98 and 100%) indicates a significant role in microbial regulation. Moreover, antibiotic resistance genes and virulence factors were found, highlighting microplastic biofilms as potential re2servoirs for gene transfer, raising concerns about antibiotic resistance dissemination. The detection of Klebsiella pneumoniae OmpK37 in viruses further underscores the risk of horizontal gene transfer. These findings emphasize the ecological implications of virus-host interactions in marine environments and the urgent need for continued monitoring of viral dynamics in anthropogenically influenced ecosystems.}, }
@article {pmid40499635, year = {2025}, author = {Wen, C and Guan, J and Uea-Anuwong, T and Shang, J and Peng, C and Tang, X and Magouras, I and Sun, Y and Li, F}, title = {Dissecting the gut microbial communities and resistomes of wild rats from different ecological areas in Hong Kong.}, journal = {Environmental research}, volume = {}, number = {}, pages = {122108}, doi = {10.1016/j.envres.2025.122108}, pmid = {40499635}, issn = {1096-0953}, abstract = {Antimicrobial resistance (AMR) is one of the top global public health issues shared across all One Health domains. Wild rats, as one of key intersections of the animal and environmental domains, are understudied reservoirs and spreaders for AMR. Our study employed the whole-metagenome shotgun sequencing to characterize the caecal microbiome of wild rats and examine the presence of antimicrobial resistance genes (ARGs) from different ecological areas in Hong Kong. We trapped 88 live rats, belonging to the species of Rattus norvegicus (n=57), R. tanezumi (n=24), and R. andamanensis (n=7), from city regions, livestock farms, and stables of horse-riding schools (referred to as "suburbs"). We identified 9,672 ARGs belonging to 29 ARG types and 554 ARG subtypes. Among them, aminoglycosides, macrolide-lincosamide-streptogramin and chloramphenicol, known to be predominant in livestock gut resistome or manure compost were significantly more abundant in rats from livestock farms. Moreover, some ARGs with high-risk levels, including tetM, tetL, floR, mecR1 and lnuA , as well as plasmid-borne ARGs were significantly more abundant in rats from livestock farms than from city regions or suburbs. Furthermore, zoonotic antimicrobial-resistant bacteria (ARB) were detected, including but not limited to, prioritized antimicrobial-resistant Klebsiella pneumoniae, Proteus mirabilis, Escherichia coli, Enterococcus faecium, Acinetobacter baumannii, Campylobacter jejuni, and Staphylococcus aureus. Notably, resistant zoonotic bacteria of Streptococcus suis, Campylobacter coli, and Campylobacter jejuni were more abundant in wild rats from livestock farms. Our findings provides insights into the gut resistomes and zoonotic bacteria in wild rats in Hong Kong, highlighting the potential role of wild rats in the dissemination of ARGs and zoonotic pathogens, especially for those from agricultural settings.}, }
@article {pmid40499416, year = {2025}, author = {Ye, PZ and Yang, Q and Zhang, CY and Yang, TT and Jiang, SF and Lan, R and Gao, SM and Huang, LN}, title = {Comparative metagenomic analyses of viral genomic diversity and ecosystem functions in extremely acidic copper mine tailings.}, journal = {Journal of hazardous materials}, volume = {495}, number = {}, pages = {138862}, doi = {10.1016/j.jhazmat.2025.138862}, pmid = {40499416}, issn = {1873-3336}, abstract = {Sulfidic mine tailings represent a major source of acid mine drainage (AMD), a significant environmental problem worldwide. While the prokaryotic communities in extremely acidic tailings have been extensively studied to reveal their adaptation strategies and roles in acid generation, the diversity and putative ecosystem functions of viruses potentially infecting these extremophilic prokaryotes remain unexplored. Here, we used comparative metagenomics to investigate the viral communities in a massive copper mine tailings impoundment. Our analyses identified 932 viral operational taxonomic units (vOTUs) in 22 tailings samples, with the majority of them being taxonomically unaffiliated. The viral communities were significantly more diverse in the surface tailings (mean = 531 vOTUs) than the deeper layers (mean = 249 vOTUs). Viral communities are shaped mainly by physicochemical factors related to tailings oxidation and salinity in the surface and deeper tailings, respectively. In silico prediction uncovered archaeal viruses significantly enriched in the deeper tailings layers as compared to the surface tailings, especially those putatively infecting Thermoplasmataceae. Predicted hosts included key functional microbes associated with Fe/S redox, linking the prevalent viral infection with AMD generation/bioremediation. Notably, viral-encoded auxiliary metabolic genes (AMGs) potentially contributing to the stress resistance of hosts were identified in the tailings, exhibiting higher abundance in the deeper layers. Global metatranscriptomic analyses further demonstrated the infective and functional activity of tailings viruses across diverse AMD-associated environments. Overall, our findings provide initial insights into the viral populations and putative ecosystem functions in this extreme habitat and have important implications for mitigating AMD generation in situ.}, }
@article {pmid40499367, year = {2025}, author = {Wang, X and Shen, Z and Zhang, Q and Lyu, T and Ding, Y and Bai, S}, title = {Biochar amendment and water level optimization enhance nitrogen removal and reduce N2O emissions in vertical flow constructed wetlands via metagenomic analysis.}, journal = {Journal of environmental management}, volume = {389}, number = {}, pages = {126133}, doi = {10.1016/j.jenvman.2025.126133}, pmid = {40499367}, issn = {1095-8630}, abstract = {To explore how biochar influences nitrogen cycling in unsaturated, capillary, and saturated zones of partially saturated vertical flow constructed wetlands (VFCWs), three parallel VFCWs were established to examine the effects of biochar's better water holding capacity on nitrogen removal and N2O emissions. Microbial mechanisms involved were studied by conducting ETS activity, metagenomic sequencing and performing high-throughput sequencing of 16S rRNA. Results indicated that the combination of adding 40 % biochar and maintaining water level of 45 cm facilitated TN removal and suppressed N2O emissions, achieving TN removal efficiency of 73.4 % and N2O/removed TN value of 0.3 %. Within the unsaturated zone, the relative abundance of amoA, hao, and nxrB increased by 929 %, 454 %, and 38.3 %, respectively, enhancing nitrification capacity microorganisms carrying these genes and involved in the oxidation of NH4[+]-N to NO3[-]-N included Nitrosomonas, Methylosarcina, Nitrosospira, and Methylomonas, whose relative abundance increased by 75.2 %. In the capillary zone, the 19.2 % increase in nosZ (involved in the reduction of N2O to N2) transformed it into a potential N2O consumption layer. The functional genera involved in N2O reduction (Ferrovibrio, Thauera, Ramlibacter, and Hyphomicrobium) in the capillary zone increased by 1724 %, 357 %, 707 %, and 78.5 %, respectively, and the ETS activity in the 40W-CW capillary zone was 72.5 % higher than that of QS-CW. Within the saturated zone, the relative abundance of amoA increased by 591 %, hao by 149 %, and nxrB decreased by 20.0 %, potentially facilitating short-cut denitrification.}, }
@article {pmid40499078, year = {2025}, author = {Xue, K and Wang, P and Lin, Q and Xie, J and Cong, L and Yan, Z}, title = {Uncovering the Single Amino-Acid Polymorphisms of the Human Gut Ecosystem.}, journal = {Journal of proteome research}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jproteome.5c00108}, pmid = {40499078}, issn = {1535-3907}, abstract = {Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in the gut microbial metagenome and the host genome, but they could not adequately represent the protein-level variants. Single amino-acid polymorphisms (SAP) derived from nonsynonymous SNPs can cause functional changes of proteins and are important forces of adaption. However, SAP remains quite unexplored for the human gut microbiome. Here, we present a comprehensive large-scale analysis of SAP in the gut ecosystem, introducing a rigorous computational pipeline for detecting such protein variation from 992 published human metaproteomes. We find varied yet elaborate SAP patterns, capturing both known and novel functions and adaptive strategies of gut microbes. Microbial SAP is enriched in the outermost shell, motility devices, and ribosomes. Generally, gut microbial SAP is more convergent in metabolic subpathway regions and is enriched in the initial steps of carbohydrate metabolism pathways that catalyze the formation and isomerization of phosphorylated sugars. Furthermore, microbial and host mutant peptide patterns were altered and exhibited significant correlations in both inflammatory bowel disease and type 1 diabetes. Our results highlight the functional and clinically relevant implications and potential host-microbial interactions of gut ecosystem SAP.}, }
@article {pmid40497682, year = {2025}, author = {Lei, X and Xu, X and Liu, C and Zhong, L and Yin, S and Li, B and Cao, L and Xie, Z and Li, J and Zhang, X and Guo, Y and Zhang, L and Lin, H and Zhang, S and Zhang, C and Gong, T}, title = {Clinical evaluation of two pathogen enrichment approaches for next-generation sequencing in the diagnosis of lower respiratory tract infections.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0092225}, doi = {10.1128/spectrum.00922-25}, pmid = {40497682}, issn = {2165-0497}, abstract = {The underdevelopment of microbiological tests has contributed to diagnostic delay and inappropriate use of antibiotics in patients with lower respiratory tract infections, which is ranked as the seventh leading cause of death globally. Next-generation sequencing (NGS) has emerged as a promising platform for the diagnosis of infectious diseases, albeit with high costs and challenges in result interpretation. Here we evaluated two NGS-based pathogen detection assays for the etiological diagnosis of pneumonia in a prospective cohort of 257 patients. Both assays utilized multiplex polymerase chain reaction (PCR) for pathogen enrichment. One assay was designed to promiscuously amplify and identify more than 1,000 pathogens (broad-spectrum targeted next-generation sequencing [bs-tNGS]), while the other specifically targeted 194 pathogens (pathogen-specific targeted next-generation sequencing [ps-tNGS]). The analytical and diagnostic performances of both assays were compared using a composite clinical reference standard. The specificity of ps-tNGS was higher than that of bs-tNGS (84.85% vs. 75.00%), while the sensitivities of both assays were similar (>89%). In addition, a significant overlap in the frequently detected pathogens by the two methods was observed. Moreover, the enrichment of pathogens via multiplex PCR for ps-tNGS has alleviated the requirement for deep sequencing in the shotgun metagenomic workflows and thus dramatically lowered the assay cost. This study demonstrated that ps-tNGS achieved a better overall diagnostic performance and may potentially replace bs-tNGS in the clinical application.IMPORTANCEMicrobial enrichment in metagenomic next-generation sequencing has been achieved through differential cell lysis, but the results varied, depending on experimental procedures and sample types. Therefore, direct enrichment of pathogen DNA/RNA was attempted via multiplex PCR or hybrid probe capture (targeted next-generation sequencing [tNGS]). We evaluated two enrichment methods based on multiplex PCR. One method utilized a primer design strategy to amplify over 1,000 respiratory pathogens (bs-tNGS), while the other specifically targeted 194 pathogens (ps-tNGS). Our findings disavowed the notion that "the more, the better" in tNGS workflows, since ps-tNGS exhibited equivalent sensitivity and, notably, higher specificity than bs-tNGS in a prospective cohort of 257 patients who were suspected of having pneumonia. In future evaluations of tNGS assays, researchers should pay more attention to diagnostic specificity, rather than focusing solely on sensitivity, since a low specificity may potentially lead to misdiagnosis and overuse of antibiotics in cases of non-infectious diseases.}, }
@article {pmid40497681, year = {2025}, author = {Fan, Y and Li, Y and Wang, L and Zhao, D and Zhou, Y and Houpt, ER and Liu, J}, title = {Fecal microbiome profiling of children with Shigella diarrhea from low- and middle-income countries.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0057325}, doi = {10.1128/spectrum.00573-25}, pmid = {40497681}, issn = {2165-0497}, abstract = {Shigella is one of the leading pathogens causing diarrhea in children globally. Stool culture remains the standard for diagnosing Shigella infections; however, quantitative PCR (qPCR) offers greater sensitivity. In this study, we evaluated the fecal microbiomes of 27 diarrheal children with and without Shigella identified by culture and quantitative PCR, respectively, aiming to characterize the fecal microbiome profiles of children with Shigella diarrhea and to explore the differences in microbiome and the mechanisms associated with the culturability of Shigella. Our results showed that Shigella qPCR positive cases were characterized by a significantly higher abundance of Shigella and other Proteobacteria, alongside a lower abundance of the probiotic genus Bifidobacterium. This profile was associated with specific virulence factors (VFGs) and antimicrobial resistance genes (ARGs), indicating a unique pathogenic module related to Shigella infection. While no significant difference in Shigella abundance was found between the Shigella culture positive and culture negative groups, genera Bifidobacterium and Ligilactobacillus were enriched in the culture positive group. Interestingly, the culture positive group also possessed a higher abundance of virulence factors associated with pathogenicity, likely resulting from the higher copy number of pINV plasmid. The fecal metagenomic analyses from diarrheal children suggested a potentially distinct intestinal microbial profile associated with Shigella infection and a possible correlation between increased pathogenicity and the Shigella culturability. These findings might contribute to a more comprehensive understanding of Shigella pathogenicity and improving diagnostic methods for Shigella.IMPORTANCEDiarrhea represents the fifth leading cause of mortality among children under the age of five, with Shigella representing the second most common pathogen responsible for diarrhea-related mortality. In the current study, we employed metagenomics to comprehensively characterize the fecal microbiome profiles of children infected with Shigella and to investigate the factors affecting Shigella culturability. We identified a distinct intestinal microbial profile associated with Shigella-infected diarrheal children, observed a correlation between increased pathogenicity and the Shigella culturability, and also proposed some potential factors that might promote the in vitro growth of Shigella strains. These findings might provide evidence for improving diagnostic methods for Shigella.}, }
@article {pmid40497237, year = {2025}, author = {Feng, Y and Kuang, G and Pan, Y and Wang, J and Yang, W and Wu, WC and Pan, H and Wang, J and Han, X and Yang, L and Xin, GY and Shan, YT and Gou, QY and Liu, X and Guo, D and Liang, G and Holmes, EC and Gao, Z and Shi, M}, title = {Small mammals in a biodiversity hotspot harbor viruses of emergence risk.}, journal = {National science review}, volume = {12}, number = {6}, pages = {nwae463}, pmid = {40497237}, issn = {2053-714X}, abstract = {Metagenomic sequencing has transformed the understanding of viral diversity in wildlife and the potential threats these viruses pose to human health. Despite this progress, such sequencing studies often have lacked systematic and ecologically informed sampling, thereby likely missing many potential human pathogens and the drivers behind their ecology, evolution and emergence. We conducted an extensive search for viruses in the lungs, spleens and guts of 1688 mammals from 38 species across 428 sites in Yunnan Province, China-a hotspot for zoonoses emergence. We identified 162 mammalian viruses, including 102 new ones and 24 posing potential risks to humans due to their relationships with known human pathogens associated with serious diseases or their ability to cross major host species barriers. Our findings offer an in-depth view of virus organotropism, cross-host associations, host sharing patterns, and the ecological factors influencing viral evolution, all of which are critical for anticipating and mitigating future zoonotic outbreaks.}, }
@article {pmid40496755, year = {2025}, author = {Gui, X and Qiu, X and Gao, Y and Chen, T and Qiu, Y and Liu, J and Xiao, Y}, title = {Chlamydia psittaci infection-associated acute fibrinous and organizing pneumonitis: A case report.}, journal = {IDCases}, volume = {40}, number = {}, pages = {e02217}, pmid = {40496755}, issn = {2214-2509}, abstract = {Acute fibrinous and organizing pneumonia (AFOP) is a rare type of lung injury, and while Chlamydia psittaci pneumonia is a zoonotic disease, secondary AFOP has not been previously reported. We present a 53-year-old female with a 13-day history of cough, fever, and shortness of breath. High-resolution computed tomography (HRCT) showed multiple bilateral patchy shadows and consolidations in the left lung lower lobe. Empirical treatment was ineffective, and lung lesions worsened. Metagenomic next-generation sequencing (mNGS) confirmed Chlamydia psittaci infection. After minocycline treatment, the patient's fever improved, but shortness of breath persisted. CT-guided lung biopsy revealed "fibrin balls" in the alveolar space and interstitial inflammatory infiltrates. Shortness of breath improved after glucocorticoid therapy, with significant lesion absorption noted on follow-up chest CT. This case suggests a possible association between AFOP and C. psittaci infection, supporting the use of combined antibiotic and glucocorticoid therapy.}, }
@article {pmid40496059, year = {2025}, author = {Lv, Y and Jiang, G and Gao, S and Wang, H and Zhang, Y}, title = {Severe and Rapid Progression of Tropheryma whipplei-Related Pneumonia With Septic Shock: A Case Report.}, journal = {Respirology case reports}, volume = {13}, number = {6}, pages = {e70231}, pmid = {40496059}, issn = {2051-3380}, abstract = {A 54-year-old Chinese male was admitted to our department with fever, vomiting and dyspnea. His condition rapidly worsened within 12 h with acute respiratory distress syndrome and septic shock. We performed routine laboratory tests and metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) and peripheral blood, the results of which indicated the presence of Tropheryma whipplei (TW) in BALF and no pathogens in peripheral blood. We treated him with mechanical ventilation, continuous renal replacement therapy (CRRT) for 3 days, and meropenem and trimethoprim/sulfamethoxazole (TMP/SMX), as well as other therapies for 12 days. The patient survived and showed clinical improvement, with chest computed tomography (CT) scan showing absorption of lesions. During the follow-up period, the patient was given oral TMP/SMX and cefdinir for up to 33 days, and the chest CT scan showing almost complete absorption of lesions. Clinicians should strengthen the awareness of the presence of severe TW-related pneumonia in a patient without immunodeficiency diseases. Rapid detection characteristics of mNGS can guide us to diagnose rare pathogenic bacteria and improve survival for those severe pneumonia patients.}, }
@article {pmid40495714, year = {2025}, author = {Mars Brisbin, M and McIlvin, MR and Wilburn, DB and Saunders, JK and Cohen, NR and Bhatia, M and Kujawinski, E and Searle, BC and Saito, MA}, title = {Validation and Community Sharing of Ocean Spectral Libraries Generated by Machine Learning for Data Independent Acquisition Ocean Metaproteomic Analyses.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e13971}, doi = {10.1002/pmic.13971}, pmid = {40495714}, issn = {1615-9861}, support = {//Simons Foundation/ ; R01-GM135709//NSF/ ; }, abstract = {Ocean metaproteomics provides valuable insights into the structure and function of marine microbial communities. Yet, ocean samples are challenging due to their extensive biological diversity, which results in a very large number of peptides with a large dynamic range. This study characterized the capabilities of data independent acquisition (DIA) mode for use in ocean metaproteomic samples. Spectral libraries were constructed from discovered peptides and proteins using machine learning (ML) algorithms to remove the incorporation of false positives in the libraries. When compared with 1-dimensional and 2-dimensional data dependent acquisition analyses (DDA), DIA outperformed DDA both with and without gas phase fractionation. We found that larger discovered protein spectral libraries performed better, regardless of the geographic distance between where samples were collected for library generation and where the test samples were collected. Moreover, the spectral library containing all unique proteins present in the Ocean Protein Portal (OPP) outperformed smaller libraries generated from individual sampling campaigns. However, a spectral library constructed from all open reading frames (ORFs) in a metagenome was found to be too large to be workable, resulting in low peptide identifications due to challenges in maintaining a low false discovery rate with such a large database size. Given sufficient sequencing depth and validation studies, spectral libraries generated from previously discovered proteins can serve as a community resource, saving resequencing efforts. The spectral libraries generated in this study are available at the OPP to enable future ocean proteomic studies.}, }
@article {pmid40495477, year = {2025}, author = {Hurst, C and Zobel, G and Young, W and Olson, T and Parkar, N and Bracegirdle, J and Hannaford, R and Anderson, RC and Dalziel, JE}, title = {Social Isolation Induces Sex-Specific Differences in Behavior and Gut Microbiota Composition in Stress-Sensitive Rats.}, journal = {Brain and behavior}, volume = {15}, number = {6}, pages = {e70621}, doi = {10.1002/brb3.70621}, pmid = {40495477}, issn = {2162-3279}, support = {//Smarter Lives: New opportunities for dairy products across the lifespan/ ; C10X1706//Ministry of Business, Innovation and Employment/ ; }, mesh = {Animals ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Rats ; *Social Isolation/psychology ; *Stress, Psychological/microbiology/physiopathology ; *Behavior, Animal/physiology ; Rats, Inbred WKY ; Anxiety ; *Sex Characteristics ; Sex Factors ; Cecum/microbiology ; }, abstract = {BACKGROUND: Social isolation (SI) is an established rat model of chronic stress. We applied this to the stress-sensitive Wistar Kyoto (WKY) strain to explore brain-to-gut interactions associated with mood. Whether SI stress-induced behavioral changes are sex-specific or if they affect the microbiome in WKY is unknown. We hypothesized individually housed (IH) animals would be more anxious than pair-housed (PH), with sex differences. Male and female rats were either IH or PH from 70 to 112 days old and behavior was assessed in modified open field (OFTmod), elevated plus maze (EPM), and novel object recognition (NOR) tests. Cecal content DNA was analyzed by shotgun metagenome sequencing.<br><br>RESULTS: IH rats, particularly females, spent more time in the center of the OFTmod where the semi-novel feed was presented compared to PH group rats. There was a tendency for greater distance traveled, or potential hyperactivity, in IH female rats. Males stayed in the EPM closed arms more than females. No treatment difference occurred for recognition memory. SI altered cecal microbiome composition in females where housing was associated with seven differentially abundant taxa and 49 differentially abundant KEGG Level 3 ortholog/gene categories. Several relationships were noted between behavioral traits and relative abundance of microbiome taxa. There was a greater shift in female microbiome composition.<br><br>CONCLUSIONS: In summary, behavioral responses to the housing treatment were minimal. IH animals, particularly females, spent more time in the center of an OFT that contained food; this may have been an indication of depression, as opposed to anxiety. Housing status had a differential impact on the microbiome for females compared to males. The associations between cecal microbiota and activity in the modified OFT suggest that dietary interventions that influence the relative abundance of Bifidobacteria, Alistipes, and Muribaculaceae should be explored.}, }
@article {pmid40495233, year = {2025}, author = {Ndione, MHD and Ndiaye, EH and Dieng, M and Diouf, B and Sankhé, S and Diallo, D and Kane, M and Sene, NM and Mbanne, M and Sy, FA and Diop, SMBS and Doukanda, SFM and Sall, AA and Faye, O and Dia, N and Weaver, SC and Faye, O and Diallo, M and Fall, G and Gaye, A and Diagne, MM}, title = {Mosquito-based detection of retroviruses and arboviruses in Senegal: expanding the scope of xenosurveillance.}, journal = {One health outlook}, volume = {7}, number = {1}, pages = {32}, pmid = {40495233}, issn = {2524-4655}, support = {U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151758/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151758/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; }, abstract = {BACKGROUND: Mosquitoes are well-known vectors for arthropod-borne viruses, yet their role as passive carriers of non-arthropod-borne viruses remains underexplored. Xenosurveillance, a method that utilizes blood-feeding arthropods to sample host and pathogen genetic material, has emerged as a valuable tool in viral ecology. In this study, we investigated the viral landscape of blood-fed mosquitoes from Senegal and report the first detection of Jaagsiekte Sheep Retrovirus (JSRV)-related and Enzootic Nasal Tumor Virus 2 (ENTV-2)-related sequences, alongside endemic arboviruses. Our study aimed to investigate whether mosquitoes can serve as sentinels for detecting both pathogens and host-derived markers in complex ecosystems.<br><br>METHODS: Mosquitoes were collected between 2016 and 2019 from three ecologically significant regions in Senegal (Louga, Barkedji, and Kedougou). Blood-fed mosquitoes were pooled and subjected to RNA extraction and metagenomic sequencing using Illumina NextSeq550. Sequencing data were analyzed with CZ-ID and BLAST for viral identification. RT-qPCR assays were designed to validate the presence of JSRV-related sequences, targeting conserved regions of the envelope gene and 3' untranslated region. Phylogenetic analysis was conducted using MAFFT and IQ-TREE to compare the detected sequence with global exogenous and endogenous JSRV references.<br><br>RESULTS: Sequencing revealed a broad viral diversity across mosquito species, including insect-specific viruses, arboviruses (West Nile, Sindbis, Bagaza, Usutu, Barkedji), and two retroviral sequences. A JSRV-related sequence was confirmed in a pool from Barkedji (2019) and clustered phylogenetically with endogenous JSRV. A nearly complete ENTV-2 genome, closely related to pathogenic Chinese strains, was recovered from the same pool. Other viruses grouped within established African lineages, supporting persistent regional circulation.<br><br>DISCUSSION: This study presents the first report of retroviral sequences detected in mosquitoes, alongside the identification of actively circulating arboviruses and insect-specific viruses, highlighting the broader potential of mosquitoes as environmental sentinels. While mosquitoes are not biological vectors for retroviruses, their ability to capture both host-derived retroviral material and pathogenic viral genomes through bloodmeals reinforces the value of xenosurveillance for monitoring livestock-vector-environment interactions. These findings contribute to broader efforts in integrated disease surveillance and underscore the utility of combining metagenomics with molecular diagnostics to detect diverse viral signals in high-risk ecological settings.}, }
@article {pmid40495179, year = {2025}, author = {Liu, W and Zhou, X and Xiao, L and Huang, X and Chang, D and Zhong, X and Zeng, M and Xian, Y and Zheng, Y and Huang, W and Huang, R and Huang, M}, title = {The gut microbiota-mediated ferroptosis pathway: a key mechanism of ginsenoside Rd against metabolism-associated fatty liver disease.}, journal = {Chinese medicine}, volume = {20}, number = {1}, pages = {83}, pmid = {40495179}, issn = {1749-8546}, support = {2022YFC3501200//National Key Research and Development Program of China/ ; 82274080//National Natural Science Foundation of China Projects/ ; X2024019//School Management Project of Fujian University of Traditional Chinese Medicine/ ; X2024035//School Management Project of Fujian University of Traditional Chinese Medicine/ ; 2024Y9511//Fujian Provincial Science and Technology Innovation Joint Fund Project/ ; }, abstract = {BACKGROUND: Ginsenoside Rd (G-Rd), found in Panax species, has shown therapeutic potential against metabolism-associated fatty liver disease (MAFLD), but its mechanism has not been well elucidated. This study investigated the key mechanisms of G-Rd in modulating the gut microbiome and lipid peroxidation-mediated ferroptosis pathway in MAFLD.<br><br>METHODS: A high-fat diet-induced MAFLD model was established. Ultrastructural changes in liver tissue were observed using transmission electron microscopy. Metagenomics were employed to detect alterations in gut microbiota and their metabolites. Biochemical analysis and immunohistochemistry were used to examine liver injury, blood lipids, lipid peroxidation-related indicators, and tissue iron content.<br><br>RESULTS: G-Rd significantly reduced liver injury and steatosis in MAFLD mice and downregulated the elevated relative abundance of Firmicutes and the Firmicutes/Bacteroidetes ratio. It also significantly reduced the abundances of Faecalibaculum rodentium while increasing Muribaculum intestinale, with its functional role being relevant to lipid metabolism regulation. Moreover, G-Rd ameliorated mitochondrial damage and inhibited the ferroptosis pathway in the liver, which was associated with antioxidant-related factors mediated by Nrf2 signaling. The liver protective effect of G-Rd was driven by the regulation of gut microbiota, as demonstrated by antibiotic cocktail treatment and fecal microbiota transplantation.<br><br>CONCLUSIONS: G-Rd attenuated HFD-induced MAFLD by alleviating liver oxidative stress, lipid peroxidation, and ferroptosis through modulation of the gut microbiota. The antioxidant and anti-ferroptotic actions of G-Rd, mediated via the Nrf2 pathway, were found to contribute to the amelioration of liver injury and hepatic steatosis in MAFLD.}, }
@article {pmid40494644, year = {2025}, author = {Ma, R and Shi, Y and Wu, W and Huang, C and Xue, F and Hou, R and Zhou, Y and Gu, J and Feng, F and Yu, X and Liu, J and Li, Z and Zhang, L and Lan, G and Chen, C and Bi, W and Song, X and Fu, M and Yang, H and Gu, H and Yang, J and Qi, D}, title = {The bacterial diversity and potential pathogenic risks of giant panda-infesting ticks.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0219724}, doi = {10.1128/spectrum.02197-24}, pmid = {40494644}, issn = {2165-0497}, abstract = {UNLABELLED: As common parasites in the wild, ticks significantly limit the population growth of wild giant pandas and hinder the process of reintroducing captive giant pandas into their natural habitats. Research on microbial communities and pathogens in ticks infesting giant pandas is limited, emphasizing the need for a comprehensive investigation. To thoroughly investigate the microbial communities in giant panda-infesting ticks, particularly potential pathogens, we analyzed 246 ticks collected from the ears of wild-living giant pandas using 16S rRNA and metagenomic sequencing. We found that the microbial diversity in female ticks was significantly enriched in summer. The microbial community structure carried by ticks is more significantly influenced by seasonal changes than by sex. Metagenomic results indicated that giant pandas have a higher risk of Coxiella burnetii infection in summer and a higher risk of Anaplasma phagocytophilum, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Rickettsia amblyommatis infections in autumn. Over 90% of the ticks carried pathogens, with 82.54% harboring a single potentially pathogenic symbiont and the remaining 17.46% carrying multiple pathogens, all involving Coxiella burnetii. Using the CARD database, we identified a total of 121 antibiotic resistance genes (ARGs), with 76% exhibiting antibiotic efflux mechanisms. Based on the significantly associated ARGs, we provided antibiotic treatment recommendations for infections potentially caused by pathogenic symbionts. This study provides a clear answer to the potential microbial pathogen risks of ticks infesting giant pandas and offers a framework for tick-borne diseases in reintroduced wild panda populations.<br><br>IMPORTANCE: Importance: The emergence of tick-borne bacterial diseases poses a serious threat to the population health of wild-living giant pandas. Ticks are obligate hematophagous ectoparasites that survive by feeding on the blood of various animal hosts and spreading pathogens. Although some previous studies have confirmed that wild ticks carried various viruses, the role of wild giant panda-infesting ticks in the bacterial community remains unknown. Here, the identification of the microbial community and antibiotic resistome in giant panda-infesting ticks revealed that most Ixodes ovatus ticks are potentially pathogenic symbionts, including Anaplasma phagocytophilum, Coxiella burnetii, and Rickettsia amblyommatis. Tick-borne disease control also needs to take into account the effects of season, sex, and antibiotic efflux resistance genes. Our findings highlight the contribution of the scientific management of tick-borne diseases in the giant panda population.}, }
@article {pmid40494317, year = {2025}, author = {Kane, F and Cissoko, Y and Collins, J and Diallo, D and Diarra, B and Kone, A and Dabitao, DK and Sako, O and Coulibaly, TA and Keita, D and Togo, ACG and Coulibaly, G and Tangara, CO and Diakite, M and Konate, I and Lu, XJ and Briese, T and Lipkin, WI and Odio, DC and Katzelnick, CL and Aboulhab, J and Akpa, E and Fouth-Tchos, K and Neal, AT and Shaw-Saliba, K and Dao, S and Chen, RY and Wickiser, JK and Doumbia, S}, title = {Analyzing Transmission Patterns of Two Dengue Virus Serotypes during the 2023 Outbreak in Mali, West Africa.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.25-0113}, pmid = {40494317}, issn = {1476-1645}, abstract = {Dengue fever, a vector-borne disease caused by four serotypes of dengue virus (DENV), ranges from asymptomatic to severe illness, including hemorrhagic fever and shock syndrome. A 2023 outbreak (August 2023-May 2024) in Mali affected six districts in Bamako, causing 1,422 confirmed cases with a 2.7% fatality rate. In this study, viral sequencing provided insights into the molecular epidemiology and transmission dynamics of this outbreak. From September to October 2023, 23 of 42 suspected cases detected through national dengue surveillance activities were tested using the pan-vertebrate virus metagenomics method (virome capture sequencing platform for vertebrate viruses [VirCapSeq-VERT]). Sequencing data were analyzed using the Rapid Identification of Microbes pipeline, and Bayesian phylogenetic inference with Monte Carlo methods was used to assess viral genomic evolution. Among 23 patients, 61% were male, and the median age was 37 years (range: 20-74). The most common symptoms were fever (93.1%), headache (56.5%), and asthenia (47.8%). The largest proportion experienced dengue with warning signs (65.2%), followed by dengue without warning signs (30.4%) and severe dengue (4.4%). The successful sequencing of 19 samples revealed dengue virus serotype 3 (DENV-3; genotype III) in 15 (65.21%) samples and dengue virus serotype 1 (DENV-1; genotype III) in 4 (17.39%) samples. The DENV-1 sequences were analogous to West African sequences, and the DENV-3 were clustered with West African, Asian, and Caribbean sequences. In this study of DENV in Mali, we offer insights into the molecular epidemiology of the virus and underscore the benefits of the genomic surveillance of arboviruses in West Africa.}, }
@article {pmid40494297, year = {2025}, author = {Hibbett, D and Nagy, LG and Nilsson, RH}, title = {Fungal diversity, evolution, and classification.}, journal = {Current biology : CB}, volume = {35}, number = {11}, pages = {R463-R469}, doi = {10.1016/j.cub.2025.01.053}, pmid = {40494297}, issn = {1879-0445}, mesh = {*Fungi/classification/genetics ; Phylogeny ; *Biodiversity ; *Biological Evolution ; }, abstract = {Fungi include mushrooms, molds, lichens, yeasts, and zoosporic forms that occur as free-living or symbiotic organisms in every ecosystem on Earth. About 155,000 species of Fungi have been described, and possibly millions more remain to be named. Recent focus on aquatic habitats has illuminated major groups near the boundary between Fungi and protists. Fungal systematists have made remarkable progress toward resolving the major branches of the phylogeny, although some deep nodes have proven recalcitrant. Fungal taxonomists steadily describe about 3,000 new species per year, and fungal molecular ecologists routinely detect many thousands of unidentifiable 'dark fungi' through metagenomic analyses. To assemble the complete fungal tree of life, it will be necessary to connect the main branches of the phylogeny to information on all described species and integrate the vast and rapidly growing corpus of dark fungi.}, }
@article {pmid40494146, year = {2025}, author = {de Basanta, DW and Lado, C}, title = {Phagocytes of the forest: Are myxomycetes defensive mutualists for host plants?.}, journal = {European journal of protistology}, volume = {99}, number = {}, pages = {126158}, doi = {10.1016/j.ejop.2025.126158}, pmid = {40494146}, issn = {1618-0429}, abstract = {Myxomycetes are microscopic eukaryotic organisms classified within the phylum Amoebozoa. They are naked amoebae, with or without a flagellated stage in their life cycle, capable of forming a multinucleate cell (plasmodium) and producing fruiting bodies for spore dispersal. Myxomycetes are natural bacterivores and fungivores, consistently associated with plants or plant remains in terrestrial habitats. They are commonly found on decaying wood but also occur in living plants, where they may act as mutualists. Here, we propose that these microorganisms function as primary endophytic symbionts of plants, potentially protecting them from other endophytes. We comment on published studies that support this relationship and suggest that further evidence could be obtained through molecular or genomic approaches.}, }
@article {pmid40493700, year = {2025}, author = {Han, C and Chen, Z and Xiao, Y and Yang, T and Shi, H and Cao, H and Yang, W and Gong, P}, title = {Characterizing nitrogen cycling microorganisms and genes in sediments of the Three Gorges Reservoir.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0324051}, doi = {10.1371/journal.pone.0324051}, pmid = {40493700}, issn = {1932-6203}, mesh = {*Geologic Sediments/microbiology ; *Nitrogen Cycle/genetics ; Nitrogen/metabolism ; *Bacteria/genetics/metabolism/classification ; *Lakes/microbiology ; Denitrification ; Nitrification ; }, abstract = {Microorganisms play a central role in driving the biogeochemical cycles in lakes (reservoirs). This study aims to refine the microbial-driven nitrogen cycle processes in the sediments of the Three Gorges Reservoir and assess the overall state of nitrogen cycling within these sediments. The study focuses on the Three Gorges Reservoir as the research area, using metagenomic sequencing as a research method and measuring various environmental factors in the sediment of the region, systematically investigates the nitrogen cycle microorganisms and corresponding functional gene abundance characteristics attached to sediments from upstream, midstream, and downstream areas within the region, and explores key factors that may influence the composition of nitrogen cycle microbial communities. The outcomes of the present study manifest that within the sediments of the Three Gorges Reservoir, seven principal nitrogen cycling pathways exist. These pathways are specifically nitrogen fixation, nitrification, denitrification, nitrogen transport, organic nitrogen metabolism, assimilatory nitrate reduction, and dissimilatory nitrate reduction. Furthermore, the results of this study also reveal that the anaerobic ammonium oxidation genes are barely present in the sediments of this region, which indicates that the probability of the occurrence of anaerobic ammonium oxidation reactions in this area is negligible. The abundance of nitrogen cycle related functional genes and the diversity, composition and community structure of nitrogen cycling microorganisms differ among the upstream, midstream, and downstream regions. This suggests that as sediment particle size decreases along the course from the upstream to the downstream, it may have an impact on the distribution and community structure of nitrogen cycling microorganisms.}, }
@article {pmid40493399, year = {2025}, author = {Han, S and Zhang, Q and Zhang, H and Ma, J}, title = {Eucommia ulmoides and its inhibitory effects on prevotella in piglet gut microbiome through metagenomic and metabolomic analysis.}, journal = {Animal biotechnology}, volume = {36}, number = {1}, pages = {2503753}, doi = {10.1080/10495398.2025.2503753}, pmid = {40493399}, issn = {1532-2378}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Prevotella/drug effects ; Swine/microbiology/growth &amp; development ; *Eucommiaceae/chemistry ; Animal Feed/analysis ; Metagenomics ; Metabolomics ; Diet/veterinary ; Dietary Supplements ; Feces/microbiology ; }, abstract = {Eucommia ulmoides (EU) is a traditional medicinal plant widely cultivated across China. The combination of EU and feed significantly affects the growth performance, intestinal microbiota composition, and metabolic characteristics of weaned piglets. Forty Landrace x Yorkshire piglets were randomly assigned to four groups: a control group receiving a basal diet, three treatment groups receiving a basal diet supplemented with EU and EU with mix energy (EU+ME), and EU with high protein and energy (EU+HPE), respectively. Growth performance was monitored over a 25-day feeding period, and fecal samples were collected for subsequent metagenomic sequencing and metabolomic analysis. Piglets supplemented with EU, EU+ME, and EU+HPE exhibited significantly improved growth performance, compared to the control group. Metagenomic analysis revealed significant alterations in gut microbiota composition, with increased beneficial bacterial classes and suppression of Prevotella spp. Metabolomic profiling demonstrated distinct metabolic alterations among the treatment groups, with pathway impact analysis highlighting enhanced protein synthesis and energy metabolism. Furthermore, EU supplementation did not affect porcine epidemic diarrhea virus activity in vitro but reduced LPS-induced intestinal inflammation. These findings suggest that EU could be a promising natural additive for improving piglet health and growth, with potential implications for managing post-weaning challenges in swine production.}, }
@article {pmid40493087, year = {2025}, author = {Qayyum, H and Ishaq, Z and Ali, A and Kayani, MUR and Huang, L}, title = {Genome-resolved metagenomics from short-read sequencing data in the era of artificial intelligence.}, journal = {Functional &amp; integrative genomics}, volume = {25}, number = {1}, pages = {124}, pmid = {40493087}, issn = {1438-7948}, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Metagenome ; Humans ; Computational Biology/methods ; }, abstract = {Genome-resolved metagenomics is a computational method that enables researchers to reconstruct microbial genomes from a given sample directly. This process involves three major steps, i.e. (i) preprocessing of the reads (ii) metagenome assembly, and (iii) genome binning, with (iv) taxonomic classification, and (v) functional annotation as additional steps. Despite the availability of multiple bioinformatics approaches, metagenomic data analysis encounters various challenges due to high dimensionality, data sparseness, and complexity. Meanwhile, integrating artificial intelligence (AI) at different stages of data analysis has transformed genome-resolved metagenomics. Though the application of machine learning and deep learning in metagenomic annotation started earlier, the emergence of better sequencing technologies, improved throughput, and reduced processing time have rendered the initial models less efficient. Consequently, the number of AI-based metagenomics tools is continuously increasing. The recent AI-based tools demonstrate superior performance in handling complex and multi-dimensional metagenomics data, offering improved accuracy, scalability, and efficiency compared to traditional models. In this paper, we reviewed recent AI-based tools specifically developed for short-read metagenomic data, and their underlying models for genome-resolved metagenomics. It also discusses the performance of these tools and overviews their usability in metagenomics research. We believe this study will provide researchers with insights into the strengths and limitations of current AI-based approaches, serving as a valuable resource for selecting appropriate tools and guiding future advancements in genome-resolved metagenomics.}, }
@article {pmid40492778, year = {2025}, author = {Buthelezi, ZM and Pierneef, RE and Bezuidt, OKI and Makhalanyane, TP}, title = {High-quality metagenomic-assembled genomes from sea ice and seawater of the Southern Ocean.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0129824}, doi = {10.1128/mra.01298-24}, pmid = {40492778}, issn = {2576-098X}, abstract = {We provide high-quality metagenome-assembled genomes (MAGs) derived from seawater and sea ice samples collected in the Southern Ocean. Several MAGs encode genes associated with dimethylsulfoniopropionate (DMSP) lyase activity and methane oxidation. This resource provides insights regarding the role of microbial communities in the production of key volatile compounds.}, }
@article {pmid40492767, year = {2025}, author = {Musundi, S and Okanda, D and Lambisia, A and Morobe, JM and Muthanje, E and Ochola-Oyier, LI and Carter, DP and Agoti, CN and Kiiru, J and Githinji, G}, title = {The genome sequence of varicella-zoster virus (Varicellovirus humanalpha3) obtained by metagenomics from a patient presenting with an exanthem rash.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0024825}, doi = {10.1128/mra.00248-25}, pmid = {40492767}, issn = {2576-098X}, abstract = {Here, we report a partial genome sequence of varicella-zoster virus, recovered through metagenomic sequencing from a skin lesion sample collected from a 31-year-old male from Mombasa, Kenya, in August 2024. Phylogenetic analysis placed this isolate in varicella-zoster virus clade 5.}, }
@article {pmid40492765, year = {2025}, author = {Jin, W and Wang, M and Wang, Y and Zhu, B and Wang, Q and Zhou, C and Li, P and Hu, C and Liu, J and Pan, J and Chen, J and Hu, B}, title = {Targeted next-generation sequencing: a promising approach for Mycobacterium tuberculosis detection and drug resistance when applied in paucibacillary clinical samples.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0312724}, doi = {10.1128/spectrum.03127-24}, pmid = {40492765}, issn = {2165-0497}, abstract = {Tuberculosis (TB) returns to be the leading infectious killer globally after coronavirus disease 2019. The World Health Organization (WHO) formally included targeted next-generation sequencing (tNGS) in its list of recommendations for Mycobacterium tuberculosis (MTB) and drug resistance (DR). In this study, we explored the application of various clinical sample types for TB diagnosis and DR profiles. In comparison to the composite reference standard, the overall sensitivity values of culture, Xpert, metagenomic next-generation sequencing (mNGS), and tNGS were 0.458, 0.614, 0.772, and 0.760, respectively. tNGS had sensitivity similar to mNGS, which had advantages over culture and Xpert, respectively, despite different classification of sample types. In comparison to the microbiological reference standard, the overall sensitivity values of culture, Xpert, mNGS, and tNGS were 0.606, 0.811, 0.856, and 0.884, respectively. Suprisingly, in extrapulmonary tissue and serous effusion, mNGS and tNGS had advantages over Xpert. DR-related mutations were detected in 15 cases (13.2%). There were 51 (44.7%) applicable for all DR genes, with 22 (19.3%) not applicable for DR genes. DR genes were partially applicable in 41 (36.0%) samples. However, in culture-negative TB cases, tNGS can additionally provide 52.7% first-line DR profiles. Sanger sequencing was performed on 14 samples to confirm gene mutation identified by tNGS, and the results were entirely consistent. It was concluded that the tNGS assay was a promising approach in the initial diagnostic test of MTB and DR-related genes in different clinical samples, even for the smear- and culture-negative paucibacillary samples.IMPORTANCEtNGS combines gene-specific amplification with next-generation sequencing to detect MTB and drug-resistant genes by amplifying numerous loci directly from clinical samples. The WHO implemented tNGS for the purpose of monitoring respiratory specimens for MTB detection and DR-TB due to its high sensitivity and specificity, culture independence, and ability to report heterogeneous/silent mutations. The sensitivity outperformed both culture and Xpert, and the turnaround time was significantly less than that of culture-based assays. The tNGS assay used in this study costs USD 96 and has a 12 hour turnaround time. Nonetheless, tNGS has a great deal of promise for enhancing TB detection while also addressing DR strains.}, }
@article {pmid40492742, year = {2025}, author = {Edwin, NR and Duff, A and Deveautour, C and Brennan, F and Abram, F and O'Sullivan, O}, title = {Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0105924}, doi = {10.1128/msystems.01059-24}, pmid = {40492742}, issn = {2379-5077}, abstract = {Microbes play an important role in soil functioning, underpinning food production systems and delivering an array of essential ecosystem services. To elucidate how these microbes relate to ecosystem functions, accurate identification and classification of soil microorganisms are important. We evaluated the comparability of shotgun and amplicon sequencing approaches by profiling soil microbiota from 131 diverse temperate grassland soils across Ireland. We assessed method comparability in terms of (i) detection and classification of the most abundant phyla, (ii) their capacity to differentiate samples based on their microbial community, and (iii) their capacity to link microbial communities to measured nitrogen cycle functions. Our findings reveal that both methods offer moderately similar outcomes, providing consistent detection of major phyla, similar microbial community differentiation patterns, and largely identifying the same relationships between the phyla and nitrogen functions. The variations observed between the two methods were mostly associated with differences in the choice of reference taxonomy. Amplicon sequencing represents a cost-effective, less computationally demanding option, while shotgun sequencing provides deeper taxonomic resolution and access to the latest databases, making it suitable for detailed microbial profiling. Our study underscores the need for careful method selection based on project requirements, database availability, and financial resources.IMPORTANCEStudying the microorganisms in soil remains a challenge as soils are one of the most complex and diverse environments. Compounding these challenges is the lack of culturable representatives in soil, with over 99% of soil microorganisms yet to be cultivated in a laboratory setting. Leveraging next-generation sequencing technologies, which bypass traditional culture-dependent methods, scientists are now able to attain low-cost, high-throughput DNA sequencing that can detect even the rarest microorganisms within samples. The present study rigorously compares amplicon and shotgun sequencing techniques in profiling microbial communities across diverse temperate grassland soil samples, focusing on how different databases, classifiers, and sequencing methods influence the results. Our study underscores the crucial need for a harmonized taxonomic database that could greatly enhance comparability and accuracy in the understanding of soil microbiomes.}, }
@article {pmid40492740, year = {2025}, author = {Green, EA and Klepacki, I and Klassen, JL}, title = {Isolation and characterization of mollicute symbionts from a fungus-growing ant reveals high niche overlap leading to co-exclusion.}, journal = {mBio}, volume = {}, number = {}, pages = {e0089325}, doi = {10.1128/mbio.00893-25}, pmid = {40492740}, issn = {2150-7511}, abstract = {UNLABELLED: Two mollicute species belonging to the Mesoplasma and Spiroplasma genera have been detected in several species of fungus-growing ants using molecular methods. However, their ecological roles remain largely inferred from metagenomic data. To better understand their diversity and specialization, we cultured both of these Mesoplasma and Spiroplasma symbionts from the fungus-growing ant Trachymyrmex septentrionalis, providing the first isolated mollicutes from any fungus-growing ant species. The genomes of our isolates and related metagenome-assembled genomes (MAGs) from T. septentrionalis fungus gardens comprise two unique phylogenetic lineages compared to previously described Mesoplasma and Spiroplasma species, and from related MAGs previously sequenced from the leaf-cutting ant Acromyrmex echinatior. This suggests that the T. septentrionalis symbionts comprise undescribed species that can exclude each other from a niche that is largely shared between them. Mesoplasma genomes and MAGs also demonstrate regional specificity with their T. septentrionalis ant hosts. Both Mesoplasma and Spiroplasma strains from T. septentrionalis can catabolize glucose and fructose; both sugars are common in the ant's diet. Similarly, both these Mesoplasma and Spiroplasma can catabolize arginine, but only Mesoplasma can catabolize N-acetylglucosamine; both could produce ammonia for the ants or fungus garden. Based on our genomic and phenotypic analyses, we describe these T. septentrionalis symbionts as Mesoplasma whartonense sp. nov. and Spiroplasma attinicola sp. nov., providing insight into their genomic and phenotypic diversity and cultures to facilitate future studies of how these common but poorly understood members of the fungus-growing ant symbiosis separately colonize different ant colonies despite having highly overlapping niches.<br><br>IMPORTANCE: Fungus-growing ants partner with multiple microbial symbionts to obtain food and remain free from disease. Of these symbionts, those inhabiting the ant gut remain the least understood and are known only from environmental surveys. Such surveys can infer potential functions of gut symbionts, but cultures are required to experimentally validate these hypotheses. Here, we describe the first cultures of the ant gut symbionts of the fungus-growing ant Trachymyrmex septentrionalis, using comparative genomics and phenotypic experiments to describe them as two novel species: Mesoplasma whartonense sp. nov. and Spiroplasma attinicola sp. nov. This genomic analysis suggests that these species are highly specialized to T. septentrionalis and are distinct from related environmental data generated from the related ant species Acromyrmex echinatior, implying substantial host specificity. Our phenotypic experiments and genomic reconstructions highlight the highly overlapping niches and likely costs and benefits of these symbionts to their ant host, setting the stage for further experimentation.}, }
@article {pmid40462952, year = {2025}, author = {Zhou, H and Chen, J and Zhang, X}, title = {BMDD: A Probabilistic Framework for Accurate Imputation of Zero-inflated Microbiome Sequencing Data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40462952}, issn = {2692-8205}, abstract = {Microbiome sequencing data are inherently sparse and compositional, with excessive zeros arising from biological absence or insufficient sampling. These zeros pose significant challenges for downstream analyses, particularly those that require log-transformation. We introduce BMDD (BiModal Dirichlet Distribution), a novel probabilistic modeling framework for accurate imputation of microbiome sequencing data. Unlike existing imputation approaches that assume unimodal abundance, BMDD captures the bimodal abundance distribution of the taxa via a mixture of Dirichlet priors. It uses variational inference and a scalable expectation-maximization algorithm for efficient imputation. Through simulations and real microbiome datasets, we demonstrate that BMDD outperforms competing methods in reconstructing true abundances and improves the performance of differential abundance analysis. Through multiple posterior samples, BMDD enables robust inference by accounting for uncertainty in zero imputation. Our method offers a principled and computationally efficient solution for analyzing high-dimensional, zero-inflated microbiome sequencing data and is broadly applicable in microbial biomarker discovery and host-microbiome interaction studies. BMDD is available at: https://github.com/zhouhj1994/BMDD.}, }
@article {pmid40492738, year = {2025}, author = {Mori, K and Hidaka, K and Tamazawa, S and Hosoyama, A and Tamaki, H and Kakegawa, T and Hanada, S}, title = {Isolation and characterization of a bacterium affiliated with the hitherto uncultured candidate phylum WOR-3 from a deep-sea hydrothermal fluid.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0018825}, doi = {10.1128/aem.00188-25}, pmid = {40492738}, issn = {1098-5336}, abstract = {UNLABELLED: A pure cultured representative, designated strain sy37, in the candidate WOR-3 lineage was obtained from a deep-sea hydrothermal fluid. This lineage was named as the candidate phylum, "Candidatus Caldipriscota," "Candidatus Hydrothermota," or "Candidatus Stahliibacteriota," based on metagenome-assembled genomes of samples from various environments. The isolated strain was a thermophilic, microaerophilic, and chemoheterotrophic rod and obtained energy through aerobic/anaerobic respiration using oxygen and elemental sulfur. The strain could not use thiosulfate, sulfate, sulfite, fumarate, nitrate, nitrite, selenate, selenite, arsenate, ferric citrate, or ferrihydrite as an electron acceptor. Genomic annotation suggested that strain sy37 possesses a novel sulfur reduction mechanism. Among members of the WOR-3 lineage, only the group containing strain sy37 possessed the oxidative phosphorylation pathway with V-type ATPase and cytochrome c oxidase and may be capable of evolving to adapt to modern oxidative environments.<br><br>IMPORTANCE: Genome analysis from various environments has revealed the overall diversity of microorganisms. However, there are many lineages for which culture representatives do not yet exist, and the characteristics and ecological significance of many of these microorganisms remain unclear: the WOR-3 lineage is one of these and has been found in various environments through the 16S rRNA gene analysis. In recent years, the metagenome-assembled genomes have been determined from the environments. In this study, we report on the successful isolation of a thermophilic microaerobic chemoorganoheterotroph, strain sy37, which is phylogenetically belonging to the WOR-3 lineage, from a deep-sea hydrothermal environment for the first time.}, }
@article {pmid40492703, year = {2025}, author = {Alam, I and Marasco, R and Momin, AA and Aalismail, N and Laiolo, E and Martin, C and Sanz-Sáez, I and Foix, BB and Sá, EL and Kamau, A and Guzmán-Vega, FJ and Jamil, T and Acinas, SG and Gasol, JM and Gojobori, T and Agusti, S and Daffonchio, D and Arold, ST and Duarte, CM}, title = {Widespread distribution of bacteria containing PETases with a functional motif across global oceans.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf121}, pmid = {40492703}, issn = {1751-7370}, abstract = {Accumulating evidence indicates that microorganisms respond to the ubiquitous plastic pollution by evolving plastic-degrading enzymes. However, the functional diversity of these enzymes and their distribution across the ocean, including the deep sea, remain poorly understood. By integrating bioinformatics and artificial intelligence-based structure prediction, we developed a structure- and function-informed algorithm to computationally distinguish functional polyethylene terephthalate-degrading enzymes (PETases) from variants lacking PETase activity (pseudo-PETase), either due to alternative substrate specificity or pseudogene origin. Through in vitro functional screening and in vivo microcosm experiments, we verified that this algorithm identified a high-confidence, searchable sequence motif for functional PETases capable of degrading PET. Metagenomic analysis of 415 ocean samples revealed 23 PETase variants, detected in nearly 80% of the samples. These PETases mainly occur between 1000 and 2000 m deep and at the surface in regions with high plastic pollution. Metatranscriptomic analysis further identified PETase variants that were actively transcribed by marine microorganisms. In contrast to their terrestrial counterparts-where PETases are taxonomically diverse-those in marine ecosystems were predominantly encoded and transcribed by members of the Pseudomonadales order. Our study underscores the widespread distribution of PETase-containing bacteria across carbon-limited marine ecosystems, identifying and distinguishing the PETase motif that underpins the functionality of these specialised cutinases.}, }
@article {pmid40492429, year = {2025}, author = {Meng, R and Li, J and Wang, W and Liang, D and Li, Z and Mao, C and Li, Q and Zhang, Y and Chen, H and Tang, J and Hu, P and Niu, Q and Huang, X and Shen, B and Zhang, J}, title = {Engineered Cas12j-8 is a Versatile Platform for Multiplexed Genome Modulation in Mammalian Cells.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e02593}, doi = {10.1002/advs.202502593}, pmid = {40492429}, issn = {2198-3844}, support = {2022YFC2702705//National Key Research and Development Project of China/ ; 82221005//Creative Research Groups of China/ ; 32371546//National Natural Science Foundation of China/ ; 82071434//National Natural Science Foundation of China/ ; 81971398//National Natural Science Foundation of China/ ; }, abstract = {Cas12j-8 is a compact Cas nuclease discovered from the metagenome of giant bacteriophages, consisting of only 717 amino acids and recognizing the '5-TTN-3' protospacer adjacent motif (PAM) sequence. However, its low gene editing efficiency in mammalian cells limits its application in therapeutic gene editing. To address this limitation, structure-guided mutagenesis is employed to replace key negatively charged residues with arginine, strengthening DNA binding. The resulting quintuple mutant, engineered Cas12j-8 (enCas12j-8), demonstrates robust on-target editing efficiency comparable to LbCas12a while maintaining low off-target effects. Cytosine base editors (CBEs) and adenine base editors (ABEs) are developed using enCas12j-8, achieving up to 29.54-fold C-to-T and 36.57-fold A-to-G conversion efficiency compared with the wild-type at the dominated sites, respectively. Notably, enCas12j-8 enables multiplexed editing of three genomic loci simultaneously via a single crRNA array, achieving efficiencies comparable to single-guide approaches. Additionally, enCas12j-8-ABE facilitates the disruption of splice acceptor sites, effectively inducing exon skipping in the SOD1 gene. This strategy holds potential significance for therapeutic genome modulation. These findings establish enCas12j-8 as a versatile, high-precision tool for genome engineering, combining efficient delivery, multiplexing capability, and compatibility with diverse editing modalities.}, }
@article {pmid40491974, year = {2025}, author = {Nyström-Persson, J and Bapatdhar, N and Ghosh, S}, title = {Precise and scalable metagenomic profiling with sample-tailored minimizer libraries.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {2}, pages = {lqaf076}, pmid = {40491974}, issn = {2631-9268}, mesh = {*Metagenomics/methods ; Algorithms ; *Gene Library ; *Software ; *Metagenome ; }, abstract = {Reference-based metagenomic profiling requires large genome libraries to maximize detection and minimize false positives. However, as libraries grow, classification accuracy suffers, particularly in k-mer-based tools, as the growing overlap in genomic regions among organisms results in more high-level taxonomic assignments, blunting precision. To address this, we propose sample-tailored minimizer libraries, which improve on the minimizer-lowest common ancestor classification algorithm from the widely used Kraken 2. In this method, an initial filtering step using a large library removes non-resemblance genomes, followed by a refined classification step using a dynamically built smaller minimizer library. This 2-step classification method shows significant performance improvements compared to the state of the art. We develop a new computational tool called Slacken, a distributed and highly scalable platform based on Apache Spark, to implement the 2-step classification method, which improves speed while keeping the cost per sample comparable to Kraken 2. Specifically, in the CAMI2 'strain madness' samples, the fraction of reads classified at species level increased by 3.5×, while for in silico samples, it increased by 2.2×. The 2-step method achieves the sensitivity of large genomic libraries and the specificity of smaller ones, unlocking the true potential of large reference libraries for metagenomic read profiling.}, }
@article {pmid40491912, year = {2025}, author = {Li, Y and Ye, J and Zhang, C and Gao, W and Zhang, H and Zheng, C and Feng, Z and Song, M and Hao, J and Zuo, H and Zhao, Z and Guo, Y and Zhang, L}, title = {Case Report: Pulmonary mixed infection by Nocardia cyriacigeorgica, Stenotrophomonas maltophilia, and human cytomegalovirus in a patient with minimal change nephrotic syndrome.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1599958}, pmid = {40491912}, issn = {1664-3224}, mesh = {Humans ; Male ; *Stenotrophomonas maltophilia ; Adolescent ; *Cytomegalovirus Infections/diagnosis/drug therapy ; *Nocardia Infections/diagnosis/drug therapy ; *Nocardia ; *Cytomegalovirus ; *Gram-Negative Bacterial Infections/diagnosis/drug therapy ; *Coinfection/diagnosis/microbiology/drug therapy ; }, abstract = {To our knowledge, this is the first reported case of a pulmonary mixed infection involving Nocardia cyriacigeorgica, Stenotrophomonas maltophilia, and human cytomegalovirus (HCMV) in a patient with minimal change nephrotic syndrome (MCNS), which is of great clinical significance. We report the case of an 18-year-old male with a two-month history of MCNS who was admitted due to fever, cough, and bright red hemoptysis. Upon admission, he was treated with piperacillin/tazobactam and moxifloxacin for one week; however, the therapeutic response was suboptimal. Metagenomic Next-Generation Sequencing (mNGS) and microbiological culture of bronchoalveolar lavage fluid identified a pulmonary mixed infection involving N. cyriacigeorgica, S. maltophilia, and HCMV. Following the initiation of combination therapy with linezolid, trimethoprim-sulfamethoxazole, and ganciclovir, the patient's condition improved markedly, and he was discharged in a stable condition. One-year follow-up revealed complete recovery with no recurrence. This case highlights the critical role of incorporating advanced molecular diagnostic tools such as mNGS into clinical practice and the need to be vigilance about opportunistic infections involving multiple pathogens, especially in patients receiving immunosuppressive therapy.}, }
@article {pmid40491838, year = {2025}, author = {Tian, C and Zhang, Z}, title = {Sociobiome signals by high income for increased mobile genetic elements in the gut microbiome of Chinese individuals.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1596101}, pmid = {40491838}, issn = {1664-302X}, abstract = {INTRODUCTION: Mobile genetic elements (MGEs) play a crucial role in the dissemination of antibiotic resistance genes (ARGs), posing significant public health concerns. Despite their importance, the impact of socioeconomic factors on MGEs within the human gut microbiome remains poorly understood.<br><br>METHODS: We reanalyzed 1,382 publicly available human gut metagenomic datasets from Chinese populations, including 415 individuals from high-income eastern regions and 967 individuals from low- and middle-income western regions. MGEs were identified and categorized into functional groups, and statistical analyses were conducted to assess regional differences and correlations with economic indicators.<br><br>RESULTS: A total of 638,097 nonredundant MGEs were identified. Among these, MGEs related to integration/excision had the highest mean abundance, while those involved in stability/transfer/defense had the lowest. The abundance of MGEs was significantly higher in the eastern population compared to the western population. Moreover, MGE abundance was positively correlated with regional GDP per capita and with ARG abundance within individuals.<br><br>DISCUSSION: Our findings suggest that socioeconomic development and industrialization are associated with increased MGE abundance in the human gut microbiome, which may in turn facilitate the spread of ARGs. These results highlight a potential unintended consequence of economic advancement on public health through microbiome-mediated antibiotic resistance.}, }
@article {pmid40491516, year = {2025}, author = {Xue, Y and Cerqueira, FM and Stevenson, HL and Williams-Bouyer, N and Fang, R}, title = {Culture-negative liver abscess identified with plasma microbial cell-free DNA sequencing: A case report.}, journal = {Infectious medicine}, volume = {4}, number = {2}, pages = {100180}, pmid = {40491516}, issn = {2772-431X}, abstract = {Pyogenic liver abscess (PLA) is a potentially life-threatening disease. Early diagnosis and appropriate treatment are crucial to ensure high-quality healthcare for patients with PLA. However, this is complicated by their non-specific clinical symptoms. In addition, the etiologic organisms responsible for PLA are frequently culture-negative, thus complicating clinical decision-making. Here, we report a case of PLA caused by Streptococcus intermedius, as identified via DNA metagenomic sequencing of plasma.}, }
@article {pmid40491436, year = {2025}, author = {Li, D and Zhang, DY and Chen, SJ and Lv, YT and Huang, SM and Chen, C and Zeng, F and Chen, RX and Zhang, XD and Xiong, JX and Chen, FD and Jiang, YH and Chen, Z and Mo, CY and Chen, JJ and Zhu, XL and Zhang, LJ and Bai, FH}, title = {Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1565887}, pmid = {40491436}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; *Fungi/classification/genetics/isolation &amp; purification ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Adult ; Middle Aged ; Feces/microbiology ; SARS-CoV-2 ; *Mycobiome ; Probiotics ; Metagenomics ; China ; }, abstract = {OBJECTIVE: COVID-19 has had a profound impact on public health globally. However, most studies have focused on patients with long COVID or those in the acute phase of infection, with limited research on the health of individuals who have recovered from mild COVID-19. This study investigates the long-term changes in bacterial and fungal communities in individuals recovering from mild COVID-19 and their clinical relevance.<br><br>METHODS: Healthy individuals from Hainan Province were enrolled before the COVID-19 outbreak, along with individuals recovering from COVID-19 at 3 months and 6 months post-recovery. Stool, blood samples, and metadata were collected. Metagenomic sequencing and Internal Transcribed Spacer (ITS) analysis characterized bacterial and fungal communities, while bacterial-fungal co-occurrence networks were constructed. A random forest model evaluated the predictive capacity of key taxa.<br><br>RESULTS: The gut microbiota of COVID-19 recoverees differed significantly from that of healthy individuals. At 3 months post-recovery, probiotics (e.g., Blautia massiliensis and Kluyveromyces spp.) were enriched, linked to improved metabolism, while at 6&#xa0;months, partial recovery of probiotics (e.g., Acidaminococcus massiliensis and Asterotremella spp.) was observed alongside persistent pathogens (e.g., Streptococcus equinus and Gibberella spp.). Dynamic changes were observed, with Acidaminococcus massiliensis enriched at both baseline and 6 months but absent at 3 months. Co-occurrence network analysis revealed synergies between bacterial (Rothia spp.) and fungal (Coprinopsis spp.) taxa, suggesting their potential roles in gut restoration. The bacterial random forest model (10 taxa) outperformed the fungal model (8 taxa) in predicting recovery status (AUC = 0.99 vs. 0.80).<br><br>CONCLUSION: These findings highlight the significant long-term impacts of mild&#xa0;COVID-19 recovery on gut microbiota, with key taxa influencing metabolism and immune regulation, supporting microbiome-based strategies for recovery management.}, }
@article {pmid40491430, year = {2025}, author = {Chen, Z and Liu, X and Tan, L and Lyu, X and Long, Q and Wu, W and Guo, Z and Liu, Z and Li, Z and Hu, M}, title = {Comparative of metagenomic and targeted next-generation sequencing in lower respiratory tract fungal infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1534519}, pmid = {40491430}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Sensitivity and Specificity ; Aged ; Adult ; China ; *Fungi/genetics/isolation &amp; purification/classification ; *Respiratory Tract Infections/microbiology/diagnosis ; Bronchoalveolar Lavage Fluid/microbiology ; *Lung Diseases, Fungal/diagnosis/microbiology ; Young Adult ; }, abstract = {OBJECTIVES: This study aims to compare the diagnostic efficiency and consistency of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in patients with lower respiratory tract fungal infections.<br><br>METHODS: A total of 115 patients with probable pulmonary infection between September 2022 and April 2023 were enrolled at the Second Xiangya Hospital, Changsha, China, of which 61 were clinically diagnosed with invasive pulmonary fungal infection (IPFI) and 54 were non-IPFI cases. All patients received bronchoalveolar lavage, with mNGS, tNGS, and cultures being conducted paralleled. Diagnostic effectiveness and consistency in detecting microorganisms were compared.<br><br>RESULTS: Both mNGS and tNGS showed high sensitivity rates of 95.08% each, with specificity of 90.74% and 85.19%, respectively. They also demonstrated positive predictive values (PPVs) of 92.1% and 87.9% and negative predictive values (NPVs) of 94.2% and 93.9%, respectively, in diagnosing IPFI. The sensitivity and NPV of mNGS and tNGS were superior to that of any individual or combined conventional microbiological tests (CMTs) (P < 0.05). The consistency of culture with mNGS and tNGS was 48.70% and 50.43%, respectively. For fungal detection, Pneumocystis jirovecii (26/61, 42.6%; and 28/61, 45.9%), Candida albicans (19/61, 31.1%; and 21/61, 34.4%), and Aspergillus fumigatus (16/61, 26.2%; and 15/61, 24.6%) are most prevalent for mNGS and tNGS in enrolled cases, and the detection rate was greatly higher than that of culture. Furthermore, mNGS and tNGS were capable of diagnosing mixed infections in 65 and 55 out of the 115 cases, whereas only nine cases of bacterial-fungal infection were detected by culture.<br><br>CONCLUSION: The diagnostic efficacy of mNGS and tNGS was comparable to that of identified IPFI. NGS-based methodologies present a promising tool for detecting IPFI, which can be a good supplement to CMT.}, }
@article {pmid40491146, year = {2025}, author = {Li, YH and Zhao, YX and Liu, PL and Wang, YY and Tian, CL and Dong, YJ and Zhang, LJ and Chen, G}, title = {[Severe pneumonia, intracranial infection, and reversible splenial lesion syndrome caused by chlamydia psittacosis infection].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {48}, number = {6}, pages = {557-559}, doi = {10.3760/cma.j.cn112147-20240809-00474}, pmid = {40491146}, issn = {1001-0939}, mesh = {Humans ; *Psittacosis/complications/drug therapy ; Male ; Chlamydophila psittaci/isolation &amp; purification ; Minocycline/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {A patient with severe pneumonia, central nervous system infection, and reversible splenial lesion syndrome was described in this article. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid and cerebrospinal fluid revealed chlamydia psittacosis. After treatment with minocycline, the patient was cured. His respiratory and neurological symptoms all disappeared.}, }
@article {pmid40490984, year = {2025}, author = {Vargas, BO and Carazzolle, MF and Galhardo, JP and José, J and de Souza, BC and Correia, JBL and Santos, JRD and Pereira, GAG and de de Mello, FDSB}, title = {Engineering Saccharomyces Cerevisiae With Novel Functional Xylose Isomerases From Rumen Microbiota for Enhanced Biofuel Production.}, journal = {Biotechnology journal}, volume = {20}, number = {6}, pages = {e70050}, doi = {10.1002/biot.70050}, pmid = {40490984}, issn = {1860-7314}, support = {//National Agency of Petroleum, Natural Gas and Biofuels/ ; JPG: 88887.479699/2020-0//National Council for the Improvement of Higher Education/ ; JRS: 142340/2020-0//National Council for the Improvement of Higher Education/ ; BCS: 2022/05001-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa no Estado de S&#xe3;o Paulo/ ; }, mesh = {*Saccharomyces cerevisiae/genetics/metabolism/enzymology ; Animals ; *Rumen/microbiology ; *Biofuels ; Sheep ; Xylose/metabolism ; Cattle ; Camelus/microbiology ; *Metabolic Engineering/methods ; Ethanol/metabolism ; Fermentation ; Microbiota/genetics ; Aldose-Ketose Isomerases ; }, abstract = {Xylose metabolism in Saccharomyces cerevisiae remains a significant bottleneck due to the difficulty in identifying functional and efficient xylose isomerases (XI). In the present study, publicly available metagenomic and metatranscriptomic datasets of rumen microbiota from different herbivorous mammals were used to prospect novel XIs sequences. Seven putative XIs from moose, camel, cow, and sheep were cloned into a strain modified for xylose metabolism. Out of those, five XIs demonstrated activity and efficiently converted xylose into xylulose, resulting in ethanol as the final product. A XI from camel rumen microbiota exhibited a KM of 16.25 mM, indicating high substrate affinity. The strains expressing enzymes XI11 and XI12, obtained from sheep rumen microbiota, were able to deplete 40 g/L of xylose within 72 and 96 h, achieving theoretical ethanol yields of 90% and 88%, respectively. These results are comparable to those obtained with Orpinomyces sp. ukk1 XI, a benchmark enzyme previously reported as highly efficient in S. cerevisiae. This study also provides the first report on the successful expression of XIs mined from the ruminal microbiotas of sheep and camels in S. cerevisiae, expanding the perspectives for the optimization of fermentation processes and the production of lignocellulosic biofuels from xylose.}, }
@article {pmid40490486, year = {2025}, author = {Hendricks, H and Israel, S and Weitkamp, JH and Pakala, S and Rajagopala, S and Banerjee, R}, title = {Associations between antibiotic exposure intensity, intestinal microbiome perturbations, and outcomes in premature neonates with bacteremia.}, journal = {Journal of perinatology : official journal of the California Perinatal Association}, volume = {}, number = {}, pages = {}, pmid = {40490486}, issn = {1476-5543}, support = {5UL1TR002243-03//Vanderbilt Institute for Clinical and Translational Research (VICTR)/ ; }, abstract = {BACKGROUND: Neonatal microbiome dysbiosis is associated with infectious complications.<br><br>METHODS: Prospective weekly stools were collected over 1 year from hospitalized preterm infants with birthweight &#x2264;2000&#x2009;g and postnatal age (PNA)&#x2009;&#x2264;2 months. Neonates with bacteremia (cases) were matched to uninfected controls. Stools were analyzed using whole metagenome sequencing. Intensity of antibiotic exposure was compared using an Antibiotic Spectrum Index (ASI).<br><br>RESULTS: We analyzed 398 stools from 40 cases and 39 controls. Cases had lower &#x3b1; diversity beyond 4 weeks PNA. Cases with subsequent infections after index bacteremia had persistently lower &#x3b1; diversity, while cases without subsequent infections demonstrated recovery of microbiome diversity. Compared to controls, cases had greater ASI at multiple timepoints, higher Enterococcus spp. and lower anaerobe abundance.<br><br>CONCLUSIONS: Compared to controls, premature neonates with bacteremia had intestinal microbiomes with lower &#x3b1; diversity, higher Enterococcus spp. and lower anaerobe abundance. These changes were associated with recurrent infectious complications.}, }
@article {pmid40489796, year = {2025}, author = {Andersen, S and Kennedy, GA and Banks, M and Flanagan, BM and Henden, AS}, title = {Prebiotic fibre enteral supplementation post allogeneic transplantation; feasibility and impact on the microbiome.}, journal = {Blood advances}, volume = {}, number = {}, pages = {}, doi = {10.1182/bloodadvances.2024015703}, pmid = {40489796}, issn = {2473-9537}, abstract = {The decline in diversity of the gastrointestinal microbiome during haematopoietic stem cell transplantation (HSCT) is associated with poorer clinical outcomes. While provision of enteral nutrition (EN) is common during HSCT, provision of a prebiotic fibre containing formula has not been explored. This pilot study compared tolerance, clinical, microbiome and metabolomic outcomes between patients who received standard EN (n= 10) versus prebiotic fibre EN (n=20) post allogeneic HSCT. Stool samples were collected at baseline and at peri-engraftment and were analysed with shotgun metagenomic sequencing. Provision of prebiotic EN increased daily fibre intake post-transplant to an average 22g per day compared with 4g per day in the standard care group. High tolerance of both EN formulas was observed with only 20% (n=2) of the standard and 15% of the prebiotic group (n=3) requiring parenteral nutrition (p=1.0). There was no difference in the amount of EN provided, EN duration or clinical outcomes. Microbial diversity declined in both groups with no difference post EN provision (p=0.93), however, there was a significant difference in relative abundance of lactobacillus_C rhamnosus with an increase in the prebiotic group only (p=0.022). The relative abundance of faecalicatena gnavus increased in the standard group and declined in the prebiotic group (p=0.0027). Functional analysis of the microbial genome showed decreased expression of antibiotic resistance genes in the prebiotic group only post EN provision (p = 0.00035). A longer fibre intervention should be trialled to optimise clinical outcomes and a more diverse microbiome. The trial was registered at www.anzctr.org.au as ACTRN12621000832875.}, }
@article {pmid40489603, year = {2025}, author = {Cao, J and He, Q and Zhang, M and Zhou, R and Feng, C}, title = {Characteristics and Clinical Significance of Gut Microbiota in Patients with Invasive Pulmonary Aspergillosis.}, journal = {Polish journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.33073/pjm-2025-011}, pmid = {40489603}, issn = {2544-4646}, abstract = {Gut microbiota acts on the lungs through the gut-lung axis and play an important role in lung diseases. However, there are no reports on the gut microbiota characteristics in patients with invasive pulmonary aspergillosis (IPA). We aimed to analyze changes in gut microbiota in IPA patients, correlate these changes with clinical indicators and disease prognosis, and explore the application value of these characteristic changes in diagnosing IPA. The objective was to provide a theoretical basis for preventing and treating individual immunity. We conducted metagenomic next-generation sequencing of fecal samples from 43 patients with IPA and 31 healthy controls to analyze changes in the gut microbiota of these patients. We also built a random forest model for diagnosing IPA based on the gut microbiota. Compared to healthy controls, IPA patients showed a decrease in gut microbiota diversity and metabolic levels. Changes in the microbiota were characterized by a significant reduction in anti-inflammatory species that produce short-chain fatty acids, such as Faecalibacterium, Blautia, Roseburia, Phocaeicola, and Bacteroides. In contrast, opportunistic pathogens, such as Enterococcus, Corynebacterium, Escherichia, Staphylococcus, Haemophilus, and Finegoldia, were significantly enriched. The classification model based on Clostridium fessum, Blautia wexlerae, Streptococcus pseudopneumoniae, Corynebacterium striatum, and Faecalibacterium prausnitzii showed high value in distinguishing patients with IPA from healthy controls. Patients with IPA exhibit gut microbiota imbalance. The gut microbiota can serve as a biomarker that helps in diagnosing IPA. Our findings support the potential use of gut microbiota as a target for IPA prevention and treatment.}, }
@article {pmid40489326, year = {2025}, author = {Sun, Y and Guo, K and Tang, J and Zhao, J and Zhang, X and Yan, Y and Yuan, L and Zhang, Y and Qiu, C and Luo, J and Zhang, W and Fang, H and Chen, J}, title = {Changes of respiratory microbiota associated with prognosis in pulmonary infection patients with invasive mechanical ventilation-supported respiratory failure.}, journal = {Annals of medicine}, volume = {57}, number = {1}, pages = {2514093}, doi = {10.1080/07853890.2025.2514093}, pmid = {40489326}, issn = {1365-2060}, mesh = {Humans ; Male ; Female ; Retrospective Studies ; *Respiration, Artificial/methods/adverse effects ; Prognosis ; *Respiratory Insufficiency/therapy/microbiology/mortality ; Middle Aged ; Aged ; *Microbiota/genetics ; Intensive Care Units/statistics &amp; numerical data ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/microbiology/mortality ; Anti-Bacterial Agents/therapeutic use ; Risk Factors ; }, abstract = {BACKGROUND: Respiratory failure (RF) is an important cause of intensive care unit (ICU) admission and mortality due to respiratory diseases. This study aimed to evaluate the clinical performance of metagenomic next-generation sequencing (mNGS) testing in pathogen diagnosis, medication guidance and to explore dynamic changes in the respiratory microbiota associated with prognosis.<br><br>METHODS: This multicenter retrospective study enrolled ICU patients from five hospitals who underwent invasive mechanical ventilation (IMV) and had pathogenic microorganisms identified by both mNGS and conventional microbiological tests (CMT) from December 2021 to April 2024. Patients were classified into two groups based on discharge outcomes: survivors (n=122) and non-survivors (n=35).<br><br>RESULTS: Compared with the survivors, non-survivors had a significantly higher proportion of smokers, dyspnea, type I RF, blood urea nitrogen, and C-reactive protein (p < 0.05). All the above indicators were identified as independent risk factors for mortality, except for type I RF. mNGS showed a better performance for pathogen identification than CMT in both groups, and nearly 60% showed consistent results between the two methods. Among survivors, antibiotic adjustment was mainly based on mNGS results (35.25%), whereas non-survivors more frequently received adjustments based on mNGS and CMT results (34.29%). The richness and abundance of lung microorganisms in the non-survivors were significantly lower than those in the survivors (p < 0.05).<br><br>CONCLUSIONS: mNGS is a promising method for identifying pathogens in pulmonary infections in IMV-supported RF patients and for exploring changes in lung microbial composition to provide a reference for patient prognosis.}, }
@article {pmid40489211, year = {2025}, author = {Gautam, P and Yadav, R and Vishwakarma, RK and Shekhar, S and Pathak, A and Singh, C}, title = {An Integrative Analysis of Metagenomic and Metabolomic Profiling Reveals Gut Microbiome Dysbiosis and Metabolic Alterations in ALS: Potential Biomarkers and Therapeutic Insights.}, journal = {ACS chemical neuroscience}, volume = {}, number = {}, pages = {}, doi = {10.1021/acschemneuro.5c00254}, pmid = {40489211}, issn = {1948-7193}, abstract = {ALS is a severe neurodegenerative disorder characterized by motor neuron degeneration, gut dysbiosis, immune dysregulation, and metabolic disturbances. In this study, shotgun metagenomics and [1]H nuclear magnetic resonance (NMR)-based metabolomics were employed to investigate the altered gut microbiome and metabolite profiles in individuals with ALS, household controls (HCs), and nonhousehold controls (NHCs). The principal component analysis (PCA) explained 33% of the variance, and the partial least-squares discriminant analysis (PLS-DA) model demonstrate R[2] and Q[2] values of 0.97 and 0.84, respectively, indicating an adequate model fit. The relative bacterial abundance was 99.34% in the ALS group and 98.94% in the HC group. Among the ten identified genera, Bifidobacterium, Lactobacillus, and Enterococcus were more prevalent in ALS individuals, while Lactiplantibacillus and Klebsiella were more abundant in the HC group. We identified 70 metabolites, including short-chain fatty acids (SCFAs), branched-chain amino acids (BCAAs), carbohydrates, and aromatic compounds, using NMR. Orthogonal partial least-squares discriminant analysis (O-PLS-DA) explained 15.8% of the variance, with a clear separation between the ALS and HC groups. Univariate receiver operating characteristic (ROC) analysis identified three fecal metabolites with AUC values above 0.70, including butyrate (0.798), propionate (0.727), and citrate (0.719). These metabolites may serve as potential biomarkers for ALS. The statistical model for metabolic pathway analysis revealed interconnected pathways, highlighting the complexity of metabolic dysregulation, as well as potential microbial and metabolic biomarkers in ALS. These results highlight the role of gut microbiome alterations in ALS and suggest potential avenues for therapeutic intervention.}, }
@article {pmid40488951, year = {2025}, author = {Liu, Y and Huang, G and Wei, F and Hu, Y}, title = {Non-negligible role of gut morphology in shaping mammalian gut microbiomes.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {40488951}, issn = {1869-1889}, abstract = {Because of the overemphasis on the roles of diet and phylogeny in shaping the gut microbiome, the gut morphology is seldom independently considered and even often ignored. To address this research gap, we investigated a large-scale dataset of mammalian gut microbiomes, comprising 16S ribosomal RNA and metagenomic sequencing data from 292 species spanning 20 orders. We dissected the effects of various factors on the gut microbiome across four distinct gut morphology categories (foregut/hindgut/simple, foregut/hindgut, functional ruminant/ruminant-like, and colon fermenter/cecum fermenter) and uncovered the synergistic effect between phylogeny and gut morphology. Moreover, we identified the significant role of gut morphology in the gut microbiomes of hosts occupying specific niches, as well as those within the same taxonomic order but with different gut morphologies. We also identified three enterotype indices-Fusobacterium, UCG-005, and Prevotella-which could predict the three gut morphology types of mammals: simple, foregut, and hindgut. These findings enhance our understanding of mammalian gut microbial assembly and provide novel insights into host-microbe coevolution.}, }
@article {pmid40488937, year = {2025}, author = {Paul, C and Roy, T and Roy, M and Rajeev, AC and Pan, A and Maitra, M and Das, N}, title = {Genome wide analysis of Priestia aryabhattai_OP, an endobacterium, modulating growth, development and biochemical compositions of sporophores in edible oyster mushroom Pleurotus ostreatus (MTCC 1802).}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {6}, pages = {194}, pmid = {40488937}, issn = {1573-0972}, support = {G.O. No. 52-Edn (B)/5B-15/2017//by Higher Education Department, Govt. of West Bengal, India as fellowship/ ; BT/INF/22/SP41296/2020//Department of Biotechnology (DBT), Govt. of India as DBT Builder Grant/ ; }, mesh = {*Pleurotus/growth &amp; development/metabolism ; *Genome, Bacterial ; Phylogeny ; Laccase/metabolism/biosynthesis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Siderophores/metabolism ; Whole Genome Sequencing ; Fruiting Bodies, Fungal/growth &amp; development ; }, abstract = {The increasing global interest in the consuming and producing of edible oyster mushrooms (Pleurotus spp.) is driven by their well-documented nutritional and health benefits. The metagenomic analysis of fruiting body revealed a distinct microbial composition in P. ostreatus, predominantly comprising Pseudomonodota (~ 82%) and Bacillota (~ 10%). An endobacterium Priestia aryabhattai_OP, associated with internal tissue of P. ostreatus (MTCC 1802), was isolated and characterized through biochemical and microscopic analyses as well as 16 S rRNA and whole genome sequencing. Co-cultivation of P. ostreatus with this bacterium significantly enhanced the in vitro production of laccase, a key growth-promoting enzyme. Additionally, the endobacterium improved the biological efficiency (BE) of the mushroom, enriched its nutraceutical profile, and facilitated the biosynthesis of beneficial compounds, including IAA, siderophores, and antimicrobials like lassopeptides, phosphonates, non-ribosomal iron-binding siderophores (NI- siderophore), carotenoids, paeninodins, synechobactins, and surfactins. The present findings offer novel insights into microbe-microbe interactions and their pivotal roles in fungal biology, with significant implications for sustainable mushroom production as well as nutrient enrichment and biotechnological advancements.}, }
@article {pmid40488750, year = {2025}, author = {Jin, L and Huaijie, J and Shuaiyang, Z and Qiaoyun, R and Qingli, N and Jifei, Y and Obaid, MK and Guiquan, G and Guangyuan, L and Hong, Y}, title = {Microbial Pathogen Community in Ornithodoros lahorensis (Acari: Argasidae) in China.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {11}, pages = {e70694}, doi = {10.1096/fj.202500105R}, pmid = {40488750}, issn = {1530-6860}, support = {2021YFD1800101//MOST | National Key Research and Development Program of China (NKPs)/ ; }, mesh = {Animals ; *Ornithodoros/virology/microbiology ; China ; Phylogeny ; Genome, Viral ; *RNA Viruses/genetics ; }, abstract = {The prevalence of tick-borne bacterial and viral diseases, which pose a serious threat to human and livestock health, is increasing worldwide. At present, only a limited number of tick-borne pathogens have been reported, and no analysis of the microbial pathogen community in ticks has been carried out. We sequenced the viral metagenome of Ornithodoros lahorensis species of ticks from the Chinese mainland and identified 390 RNA viruses with unique microbial compositions. A total of 992 assembled viral transcriptomes revealed the breadth and diversity of the genome structure of tick-borne viruses, reflecting the importance of ticks as RNA viral pools. We analyzed the phylogeny of different virus families to investigate virus evolution and found that the most diverse tick-associated viruses belonged to the family Siphoviridae, which diverged earlier in evolutionary time than other arboviruses. There were only a few tick-specific viruses, whereas the number of vertebrate-infecting viruses in ticks was greater. We hope that our virus sequencing dataset will facilitate future important research on viruses carried by ticks that can infect vertebrates.}, }
@article {pmid40488653, year = {2025}, author = {Shajahan, RM and M, A and A, FT and Sreekumaran, S and Lakshmanan, D and Jaiswal, M and K, RE}, title = {Targeted Antimicrobial Resistance Gene Screening from Metagenomic DNA of Raw Milk Samples Identifies the Presence of Multiple Genes Including the mcr9.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {}, doi = {10.1089/fpd.2024.0187}, pmid = {40488653}, issn = {1556-7125}, abstract = {The current study has investigated the prevalence of antimicrobial resistance (AMR) genes in cow and goat raw milk samples. The misuse of antibiotics in the livestock sector has already been reported to be a major factor contributing to AMR risk. For the study, milk samples were collected from five different farms, and metagenomic DNA was extracted. Then, PCR amplification was carried out using primers specific to 15 different AMR genes. From the results obtained, the prevalence of β-lactam resistance genes, particularly blaTEM (24%), along with other genes like blaZ (12%) and blaSHV (8%), were observed in addition to the transmissible mcr9 gene (12%) conferring resistance to colistin. These findings underscore the urgent need for monitoring AMR genes and regulating antibiotic use in dairy farming to safeguard public health, as it poses a potential risk with the consumption of unpasteurized milk.}, }
@article {pmid40488505, year = {2025}, author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Hassan, J and Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT}, title = {Mapping of urban garden soil microbiomes in Bangladesh.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0037525}, doi = {10.1128/mra.00375-25}, pmid = {40488505}, issn = {2576-098X}, abstract = {Shotgun metagenomics revealed distinct microbiome profiles in the garden soils of Dhaka and Gazipur district, Bangladesh, with Bacillus spp. demonstrating ecological dominance (>53% relative abundance) and location-specific distribution patterns. These findings highlight Bacillus species as prevalent microbes in urban garden soils.}, }
@article {pmid40488500, year = {2025}, author = {Berríos-Farías, V and Guajardo-Leiva, S and Gallardo-Cerda, J and Galbán-Malagón, C and Ballesteros, G and Egas, C and Molina-Montenegro, M and Castro-Nallar, E}, title = {Rhizosphere and soil metagenomes and metagenome-assembled genomes from the Byers Peninsula, Livingston Island (62°S), Antarctica.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0017125}, doi = {10.1128/mra.00171-25}, pmid = {40488500}, issn = {2576-098X}, abstract = {Rhizosphere microbes establish functional interactions with their hosts, impacting plant fitness. To further understand plant effects on microbial composition and functional diversity, we present 52 metagenomes and 1,484 metagenome-assembled genomes (MAGs) from soil and the rhizosphere of Colobanthus quitensis and Deschampsia antarctica.}, }
@article {pmid40488474, year = {2025}, author = {Li, P and Chen, Y and Cao, X and Wang, Z and Sai, L and Wang, L}, title = {Diagnosis of invasive pulmonary aspergillosis using metagenomic next-generation sequencing and conventional microbial tests post-COVID-19 pandemic.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0012125}, doi = {10.1128/spectrum.00121-25}, pmid = {40488474}, issn = {2165-0497}, abstract = {UNLABELLED: Early recognition and timely diagnosis are crucial for improving the clinical outcome of invasive pulmonary aspergillosis (IPA) patients. Metagenomic next-generation sequencing (mNGS) shows immense advantages in identifying responsible complex pathogens, especially with the gradual ease of COVID-19 control policies in China since 2022. A total of 327 patients with suspected Aspergillus infection in non-neutropenic populations were enrolled in the current study. The diagnostic efficacy with mNGS and conventional microbial tests (CMTs) in suspected IPA patients was assessed, and the incidence and risk factors for Aspergillus infection were also investigated. mNGS exhibited excellent performance in detecting Aspergillus. The sensitivity of mNGS (80.58%) was superior to that of CMTs, as demonstrated by comparisons with smears (22.30%, P < 0.001), culture (30.94%, P < 0.001), serum GM (22.62%, P < 0.001), BALF GM (55.40%, P < 0.001), and combined CMTs (61.87%, P < 0.001). The results of mNGS caused a direct shift in the management of 212 (64.8%) positive effect patients, making a clear diagnosis and instructing antifungal therapy. Notably, in addition to the common risk factors, the patients with a history of COVID-19 infection were more prone to IPA. The occurrence of IPA increased significantly with the gradual ease of COVID-19 control policies (47.62% vs 30.21%, P = 0.004). Meanwhile, mixed infections were commonly observed in IPA patients, with Human gammaherpesvirus and Acinetobacter baumannii being the most common co-pathogens. Our study demonstrated that mNGS might present a feasible and remarkably sensitive approach for detecting Aspergillus, thereby serving as a valuable auxiliary tool for CMTs.<br><br>IMPORTANCE: Our study is the first to focus on Aspergillus infection after the COVID-19 pandemic and find that (i) mNGS is a feasible and highly sensitive method for detecting Aspergillus post-COVID-19 pandemic, thereby serving as a valuable auxiliary tool for CMTs. (ii) mNGS has the potential to revolutionize the management of fungal infections. (iii) The history of COVID-19 infection is an independent risk factor for IPA. Identification of this risk factor for IPA may raise clinical attention and require careful follow-up of high-risk individuals post-COVID-19 infection. (iv) Mixed infections were commonly observed in IPA patients, with Human gammaherpesvirus and Acinetobacter baumannii being the most common co-pathogens.}, }
@article {pmid40488469, year = {2025}, author = {Rissanen, AJ and Mangayil, R and Tveit, AT and Maanoja, ST and Khanongnuch, R}, title = {Dissolved organic matter and sulfide enhance the CH4 consumption of a psychrophilic lake methanotroph, Methylobacter sp. S3L5C.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0313324}, doi = {10.1128/spectrum.03133-24}, pmid = {40488469}, issn = {2165-0497}, abstract = {Gammaproteobacterial methanotrophic bacteria (gMOB) are dominant methanotrophs in the water column of oxygen-stratified boreal and subarctic lakes and ponds. (Meta)genomic data suggest that, besides methane (CH4), gMOB potentially use dissolved organic matter (DOM) and reduced sulfur compounds (e.g., sulfide) as electron sources. To study the DOM and sulfide metabolism of lake gMOB, we subjected a psychrophilic lake water strain, Methylobacter sp. S3L5C, first to different sulfide levels (Na2S, 0-5 mM) to test the toxicity, and subsequently, to freshwater DOM (60 mg L[-1]) either alone or with sulfide (0.05 mM) at 1 and 20% CH4 levels. The growth, CH4 and O2 consumption, CO2 production, and mRNA expression patterns of S3L5C were analyzed. Sulfide concentrations of 0-0.5 mM had no effect, while 1 and 5 mM concentrations inhibited the strain's growth. At 20% CH4, DOM addition enhanced CH4 consumption, CO2 production, and growth of S3L5C, while the addition of sulfide+DOM led to further increases in these variables. The addition of sulfide+DOM enhanced CH4 consumption even at 1% CH4. The effect of DOM on the S3L5C's metabolism was accompanied by enhanced expression of the cyc2 gene, which has been suggested to mediate the extracellular electron transfer from DOM. Furthermore, the addition of sulfide+DOM enhanced the expression of the sqr and soxB genes encoding dissimilatory sulfide and thiosulfate oxidation, respectively. Together with previous metagenomic data, these results suggest that the usage of DOM and reduced sulfur compounds as electron sources is a trait that enhances methanotrophy among gMOB of boreal and subarctic lakes and ponds.IMPORTANCEGammaproteobacterial methanotrophic bacteria (gMOB) are crucial mitigators of methane emissions of many ecosystems, like boreal and subarctic lakes and ponds. Metagenomic data suggest that besides using methane, gMOB have genetic potential to use dissolved organic matter (DOM) and sulfide, typically present in lakes and ponds, as electron donors. To test the effect of DOM and sulfide on the methane metabolism of gMOB of oxygen-stratified boreal lakes, we subjected our recently isolated lake gMOB strain, Methylobacter sp. S3L5C, to additions of freshwater DOM and sulfide. We show that DOM and sulfide enhance methane consumption and growth of S3L5C. Furthermore, the expression of genes mediating the electron transfer from DOM and sulfide is enhanced. Our results suggest that the usage of DOM and reduced sulfur compounds as electron sources is a trait that enhances methanotrophy among gMOB and adds significantly to the growing body of literature highlighting the enormous metabolic versatility of gMOB.}, }
@article {pmid40488467, year = {2025}, author = {Liu, Y and Qiu, Q and Chen, Y and Deng, Y and Huang, W and Sun, C and Shang, X and Chen, X and Wang, C and Han, L and Chen, S and Yuan, J and Xu, F and Yang, Z and Fang, X and Huang, L}, title = {Integrated multi-omics analysis reveals the functional signature of microbes and metabolomics in pre-diabetes individuals.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0145924}, doi = {10.1128/spectrum.01459-24}, pmid = {40488467}, issn = {2165-0497}, abstract = {Pre-diabetes (PD) represents a critical stage in the progression toward type 2 diabetes, with significant alterations observed in the human microbial community among pre-diabetic individuals in observational studies. However, understanding the interaction between human microbiota and the host during pre-diabetes remains limited. Therefore, this study aims to understand the alterations in the human microbial community during pre-diabetes, a critical stage toward type 2 diabetes. Using an integrated analysis of human microbiota and metabolomics data, we seek to identify the functional signature associated with PD and gain insights into potential mechanisms driving its progression to type 2 diabetes. These findings could inform the development of early intervention strategies for those at high risk. Samples were collected from pre-diabetes, diabetes, and healthy control groups. Through metagenome and 16S rRNA sequencing, we analyzed the gut microbial and tongue coating compositions, respectively. Untargeted metabolomics techniques were also applied for comprehensive plasma data. Using integrated multi-omics analysis, we aim to understand the metabolic potentials of the human microbiome, its molecular links with host targets, and their effects on pre-diabetes, thereby deepening our understanding of microbiome-host interactions in this context. The pre-diabetes group exhibited distinct clinical characteristics, particularly in blood glucose levels and a higher average level of γ-glutamyl transferase. We identified 509 intestinal bacterial species, with Megamonas funiformis and Parabacteroides merdae showing higher abundance in the PD group. In tongue coating samples, we found 1,122 bacterial genera, with the PD group showing altered levels of Corynebacterium and Johnsonella. Furthermore, we detected 795 metabolites, primarily involved in carbohydrate and lipid metabolism. Importantly, our integrated multi-omics analysis suggested Flavonifractor plautii's role in modulating blood glucose through influencing carbohydrate metabolism. Our integrated multi-omics analysis revealed significant alterations in several regulatory pathways associated with pre-diabetes, particularly emphasizing the impact of gut bacterium Flavonifractor plautii on blood glucose levels through its influence on carbohydrate metabolism. These intricate relationships among gut microbiota, metabolites, and blood glucose levels underscore the significance of personalized treatment approaches and preventive strategies for pre-diabetes. The insights gained from this research hold considerable promise for advancing our understanding and management of pre-diabetes.IMPORTANCEThis study investigates alterations in the human microbial community during PD, a critical stage leading to type 2 diabetes. Through integrated analysis of metagenomic and metabolomics data from pre-diabetes, diabetes, and healthy control groups, we identified distinct clinical characteristics in the PD group, including elevated blood glucose levels and γ-glutamyl transferase. A total of 509 intestinal bacterial species were identified, with Flavonifractor plautii playing a key role in modulating blood glucose levels via its influence on carbohydrate metabolism. Our findings underscore the complex interactions among gut microbiota, metabolites, and blood glucose levels, highlighting the potential for personalized treatment approaches and early intervention strategies for individuals at high risk of developing type 2 diabetes.}, }
@article {pmid40488405, year = {2025}, author = {Ricci, F and Leung, PM and Hutchinson, T and Nguyen-Dinh, T and Frank, AH and Hood, AVS and Salazar, VW and Eate, V and Wong, WW and Cook, PLM and Greening, C and McClelland, H}, title = {Chemosynthesis enhances net primary production and nutrient cycling in a hypersaline microbial mat.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf117}, pmid = {40488405}, issn = {1751-7370}, abstract = {Photosynthetic microbial mats are macroscopic microbial ecosystems consisting of a wide array of functional groups and microenvironments arranged along variable redox gradients. Light energy ultimately drives primary production and a cascade of daisy-chained metabolisms. Heterotrophic members of these communities remineralise organic material, decreasing net primary production, and returning nutrients to the aqueous phase. However, reduced inorganic and one-carbon substrates such as trace gases and those released as metabolic byproducts in deeper anoxic regions of the mat, could theoretically also fuel carbon fixation, mitigating carbon loss from heterotrophy and enhancing net primary production. Here, we investigated the intricate metabolic synergies that sustain community nutrient webs in a biomineralising microbial mat from a hypersaline lake. We recovered 331 genomes spanning 40 bacterial and archaeal phyla that influence the biogeochemistry of these ecosystems. Phototrophy is a major metabolic potential found in 17% of the genomes, but over 50% encode enzymes to harness energy from inorganic substrates and 12% co-encode chemosynthetic carbon fixation pathways that use sulfide and hydrogen as electron donors. We experimentally demonstrated that the microbial community oxidises ferrous iron, ammonia, sulfide, and reduced trace gas substrates aerobically and anaerobically. Furthermore, carbon isotope assays revealed that diverse chemosynthetic pathways contribute significantly to carbon fixation and organic matter production alongside photosynthesis. Chemosynthesis in microbial mats results from a complex suite of spatially organised metabolic interactions and continuous nutrient cycling, which decouples carbon fixation from the diurnal cycle, and enhances the net primary production of these highly efficient ecosystems.}, }
@article {pmid40488306, year = {2025}, author = {Yoshimura, E and Hamada, Y and Hatamoto, Y and Nakagata, T and Nanri, H and Nakayama, Y and Iwasaka, C and Hayashi, T and Suzuki, I and Ando, T and Ishikawa-Takata, K and Tanaka, S and Ono, R and Araki, M and Kawashima, H and Chen, YA and Park, J and Hosomi, K and Mizuguchi, K and Kunisawa, J and Miyachi, M}, title = {Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2514137}, doi = {10.1080/19490976.2025.2514137}, pmid = {40488306}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/chemistry/microbiology ; Cross-Over Studies ; Male ; *Serotonin/analysis/metabolism ; Adult ; Female ; Young Adult ; *Tryptophanase/metabolism/analysis/genetics ; Energy Metabolism ; *Diet ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, we investigated the effects of short-term energy loads on changes in gut microbiome-derived tryptophanase and fecal serotonin levels and their association with variations in energy absorption. This randomized crossover energy-load intervention study included 15 healthy participants subjected to three dietary conditions - overfeeding, control, and underfeeding - for eight days. The effects of the dietary conditions on energy absorption (digestible and metabolizable energy) were assessed using a bomb calorimeter. Fecal serotonin levels were assessed using LC-MS/MS, and the gut microbiota was analyzed using the 16S rRNA gene and metagenomic shotgun analysis. Significant differences were observed in digestible energy (p < 0.001), with higher values in the overfeeding than in the control (p = 0.032) conditions. Furthermore, significant differences were noted in metabolizable energy and gut transit time (p < 0.001), both of which were higher in the overfeeding than in the control (metabolizable energy: p = 0.001; gut transit time: p = 0.014) and underfeeding (metabolizable energy: p < 0.001; gut transit time: p = 0.004) conditions. Fecal serotonin levels differed significantly (p < 0.001), with significantly lower levels in the overfeeding than in the control (p = 0.005) and underfeeding (p < 0.001) conditions. Tryptophanase exhibited significant differences (p = 0.0019), with lower gene abundance in the overfeeding than in the underfeeding (p = 0.001) condition. Tryptophanase positively correlated with Bacteroides abundance under all conditions (correlation coefficient: 0.696-0.896). Intra-individual variability in fecal serotonin levels was significantly negatively associated with digestible energy (β = -0.077, p = 0.019). The findings suggest that short-term energy loads dynamically alter fecal serotonin, Bacteroides, and tryptophanase levels. Moreover, changes in fecal serotonin levels might be indirectly associated with energy absorption.}, }
@article {pmid40487918, year = {2025}, author = {Boak, EN and Bowen, BP and Louie, KB and Northen, TR and Kroeger, ME}, title = {Bacterial and fungal composition and exometabolites control the development and persistence of soil water repellency.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf084}, pmid = {40487918}, issn = {2730-6151}, abstract = {Soil water repellency (SWR), the reduced affinity of soil for water, is a phenomenon that affects soils globally. With worsening climate change, SWR is expected to increase emphasizing the need to understand the mechanisms driving SWR development and persistence. The importance of the soil microbes in SWR has been postulated for decades, but limited research has been conducted into whole-community interactions and the role of community metabolic activity. To address this gap in knowledge, we investigated the direct effect of microbial community composition, activity, and diversity, as well as their associated metabolites on the development and persistence of SWR by inoculating microcosms containing model soils with 15 different microbial communities and quantified respiration and SWR over time. Six communities that consistently produced either a hydrophobic or hydrophilic phenotype were characterized using metagenomics and metabolomics to determine the impact of microbial and metabolite composition and diversity on SWR. We identified several bacterial genera with significant changes in abundance between SWR phenotypes including Nocardiopsis and Kocuria in hydrophilic and Streptomyces and Cutibacterium in hydrophobic. We discovered that hydrophilic communities were more positively connected when compared to hydrophobic communities, which could be due to an increase in defense mechanism genes. Additionally, we identified specific metabolites associated with hydrophilic and hydrophobic phenotypes including an increase in the osmolyte ectoine in hydrophilic and an increase in plant-derived decomposition products in hydrophobic communities. Finally, our research suggests that fungi, previously thought to cause hydrophobicity, may actually contribute to hydrophilicity through their preferential consumption of hydrophobic compounds.}, }
@article {pmid40487916, year = {2025}, author = {Okazaki, Y and Nishikawa, Y and Wagatsuma, R and Takeyama, H and Nakano, SI}, title = {Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf086}, pmid = {40487916}, issn = {2730-6151}, abstract = {Characterizing virus-host pairs and the infection state of individual cells is the major technical challenge in microbial ecology. We addressed these challenges using state-of-the-art single-cell genome technology (SAG-gel) combined with extensive metagenomic datasets targeting the bacterial and viral communities in Lake Biwa. From two water layers and two seasons, we obtained 862 single-cell amplified genomes (SAGs), including 176 viral (double-stranded DNA phage) contigs, which identified novel virus-host pairs involving dominant freshwater lineages. The viral infection rate, estimated by mapping the individual SAG's raw reads to viral contigs, showed little variation among samples (12.1%-18.1%) but significant variation in host taxonomy (4.2%-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were attributed to collective infection by diverse viruses, suggesting weak density-dependent virus-host selection, presumably due to their nonpersistent interactions with viruses resulting from fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their codominance with viruses is achieved by genomic microdiversification, which diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Notably, we discovered viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. These viruses showed extremely high read coverages in cellular and virion metagenomes but were detected in <1% of host cells, suggesting a low infection rate and high burst size. Overall, we revealed highly diverse virus-host interactions within and between host lineages that were overlooked at the metagenomic resolution.}, }
@article {pmid40487915, year = {2025}, author = {Wu, X and Liu, Y and He, Z and Zhou, X and Liesack, W and Peng, J}, title = {Coevolution and cross-infection patterns between viruses and their host methanogens in paddy soils.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf088}, pmid = {40487915}, issn = {2730-6151}, abstract = {Methanogens play a critical role in global methane (CH4) emissions from rice paddy ecosystems. Through the integration of metagenomic analysis and meta-analysis, we constructed a CRISPR spacer database comprising 14 475 spacers derived from 351 methanogenic genomes. This enabled the identification of viruses targeting key methanogenic families prevalent in rice paddies, including Methanosarcinaceae, Methanotrichaceae, Methanobacteriaceae, Methanocellaceae, and Methanomassiliicoccaceae. We identified 419 virus-host linkages involving 56 methanogenic host species and 189 viruses, spanning the families Straboviridae, Salasmaviridae, Kyanoviridae, Herelleviridae, and Demerecviridae, along with 126 unclassified viral entities. These findings highlight a virome composition that is markedly distinct from those observed in gut environments. Cross-infection patterns were supported by the presence of specific viruses predicted to infect multiple closely related methanogenic species. Evidence for potential virus-host coevolution was observed in 24 viruses encoding anti-CRISPR proteins, likely facilitating evasion of host CRISPR-mediated immunity. Collectively, this study reveals a complex and dynamic network of virus-host interactions shaping methanogen communities in rice paddy ecosystems.}, }
@article {pmid40487637, year = {2025}, author = {Chen, M and Peng, Y and Hu, Y and Kang, Z and Chen, T and Zhang, Y and Chen, X and Li, Q and Yuan, Z and Wu, Y and Xu, H and Zhou, G and Liu, T and Zhou, H and Yuan, C and Huang, W and Zhang, W}, title = {A critical role for Phocaeicola vulgatus in negatively impacting metformin response in diabetes.}, journal = {Acta pharmaceutica Sinica. B}, volume = {15}, number = {5}, pages = {2511-2528}, pmid = {40487637}, issn = {2211-3835}, abstract = {Metformin has been demonstrated to attenuate hyperglycaemia by modulating the gut microbiota. However, the mechanisms through which the microbiome mediates metformin monotherapy failure (MMF) are unclear. Herein, in a prospective clinical cohort study of newly diagnosed type 2 diabetes mellitus (T2DM) patients treated with metformin monotherapy, metagenomic sequencing of faecal samples revealed that Phocaeicola vulgatus abundance was approximately 12 times higher in nonresponders than in responders. P. vulgatus rapidly hydrolysed taurine-conjugated bile acids, leading to ceramide accumulation and reversing the improvements in glucose intolerance conferred by metformin in high-fat diet-fed mice. Interestingly, C22:0 ceramide bound to mitochondrial fission factor to induce mitochondrial fragmentation and impair hepatic oxidative phosphorylation in P. vulgatus-colonized hyperglycaemic mice, which could be exacerbated by metformin. This work suggests that metformin may be unsuitable for P. vulgatus-rich T2DM patients and that clinicians should be aware of metformin toxicity to mitochondria. Suppressing P. vulgatus growth with cefaclor or improving mitochondrial function using adenosylcobalamin may represent simple, safe, effective therapeutic strategies for addressing MMF.}, }
@article {pmid40487313, year = {2025}, author = {Wei, H and Thammasit, P and Amsri, A and Pruksaphon, K and Deng, F and Nosanchuk, JD and Youngchim, S}, title = {An overview of rapid non-culture-based techniques in various clinical specimens for the laboratory diagnosis of Talaromyces marneffei.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1591429}, pmid = {40487313}, issn = {2235-2988}, mesh = {*Talaromyces/isolation &amp; purification/genetics ; Humans ; *Mycoses/diagnosis/microbiology ; Sensitivity and Specificity ; Molecular Diagnostic Techniques/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {Talaromyces marneffei (T. marneffei) is a temperature-dependent biphasic deep opportunistic infectious fungus that primarily affects individuals with advanced HIV disease and other immunocompromised populations. Traditional diagnostic methods rely on fungal culture, but this process, although sensitive, is time-consuming and susceptible to contamination. Therefore, non-culture techniques serve as important complementary and alternative methods for diagnosing talaromycosis. They enable faster and more convenient pathogen identification, improving diagnostic efficiency and facilitating earlier initiation of treatment. Patients with talaromycosis can present with a wide range of clinical symptoms, and different clinical samples require different detection techniques. Blood samples are the most versatile, as laboratory technologists can utilize a wide range of diagnostic methods to obtain accurate results, particularly in the setting of a suspected disseminated infection. In contrast, urine diagnosis relies primarily on immunological methods that detect an antigen abundantly secreted during an infection. Moreover, for invasive samples like bronchoalveolar lavage fluid or cerebrospinal fluid, metagenomic next-generation sequencing is likely to be of significant importance for the early diagnosis due to its high sensitivity and specificity, though this approach is not yet standardized or widely available. For tissue samples, histopathology for light microscopy analysis is a well-established basic method, but it relies on experienced laboratory personnel, is time-consuming, and the histological appearance of other fungi can overlap with T. marneffei. Recent advances in rapid non-culture-based methods diagnostics underscore the growing importance of these tools in clinical settings, particularly for resource-limited areas where culture facilities are inadequate or unavailable. These methods improve diagnostic turnaround time and may lead to better clinical outcomes, especially for vulnerable patient populations. This review emphasizes the need for ongoing development and validation of non-culture diagnostics, with a focus on standardization, accessibility, and integration of rapid molecular and immunological tools to improve early detection and patient management in endemic regions.}, }
@article {pmid40487152, year = {2025}, author = {Leys, SP and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Erpenbeck, D and Niu, H and McKenna, V and ,  and ,  and ,  and ,  and , }, title = {The chromosome-level genome sequences of the freshwater sponge, Spongilla lacustris (Linnaeus, 1759) and the chlorophyte cobiont Choricystis sp., and the associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {222}, pmid = {40487152}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Spongilla lacustris (freshwater sponge; Porifera; Demospongiae; Spongillida; Spongillidae). The genome sequence is 248.7 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.04 kilobases in length. A 14.6-megabase genome assembly of the green algal cobiont Choricystis sp. (Chlorophyta; Trebouxiophyceae) was scaffolded into 16 chromosomal pseudomolecules. Additionally, three bacterial metagenome bins were recovered from the same sample. Gene annotation of this assembly at Ensembl identified 30,435 protein coding genes.}, }
@article {pmid40486693, year = {2025}, author = {Witonsky, JI and Elhawary, JR and Eng, C and Oh, SS and Salazar, S and Contreras, MG and Medina, V and Secor, EA and Zhang, P and Everman, JL and Fairbanks-Mahnke, A and Pruesse, E and Sajuthi, SP and Chang, CH and Guerrero, TR and Fuentes, KC and Lopez, N and Montañez-López, CA and Morales, EV and Morales, NV and Otero, RA and Rivera, RC and Rodriguez, L and Vazquez, G and Hu, D and Huntsman, S and Jackson, ND and Li, Y and Morin, A and Nieves, NA and Rios, C and Serrano, G and Williams, BJM and Ziv, E and Moore, CM and Sheppard, D and Burchard, EG and Seibold, MA and Rodríguez-Santana, JR}, title = {The PRIMERO birth cohort: Design and baseline characteristics.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {4}, number = {3}, pages = {100470}, pmid = {40486693}, issn = {2772-8293}, abstract = {BACKGROUND: Although early-life respiratory illnesses (RIs) are linked to childhood asthma, it is unclear whether children are predisposed to both conditions or if RIs induce alterations that lead to asthma. Puerto Rican children, who bear a disproportionate burden of early-life RIs and asthma, are an important population for studying this relationship.<br><br>OBJECTIVE: We sought to describe the design and baseline characteristics of the Puerto Rican Infant Metagenomic and Epidemiologic Study of Respiratory Outcomes (PRIMERO) birth cohort.<br><br>METHODS: PRIMERO is designed to examine the role of respiratory viruses on the development of RIs and asthma. Pregnant women were recruited at Hospital Interamericano de Medicina Avanzada-San Pablo in Caguas, Puerto Rico. Questionnaires at birth and annual follow-ups gather clinical, social, and environmental data. Collected samples include postterm maternal blood; infant cord blood; the child's blood at year 2; and the child's nasal airway epithelium at birth, during RIs over the first 2 years, and annually until age 5.<br><br>RESULTS: We enrolled 2,100 mother-child dyads into the PRIMERO study between February 2020 and June 2023, representing 59% of births at Hospital Interamericano de Medicina Avanzada. As of April 29, 2024, 2,069 participants remain active, with high rates of biospecimen collection and annual visit participation. Illness surveillance detected 6,076 RIs, with 38.4% involving the lower respiratory tract.<br><br>CONCLUSION: The PRIMERO birth cohort study, with its comprehensive data on viral exposures, respiratory outcomes, and airway molecular phenotypes in a high-risk population of Puerto Rican children, is uniquely positioned to address long-standing questions about the early-life determinants and mechanisms underlying virus-related asthma development.}, }
@article {pmid40486234, year = {2025}, author = {Shilov, S and Korotetskiy, I and Kuznetsova, T and Zubenko, N and Ivanova, L and Solodova, E and Tugeyeva, A and Kaziyev, A and Korotetskaya, N and Izmailov, T}, title = {The chicken gut resistome data from different regions of Kazakhstan.}, journal = {Data in brief}, volume = {60}, number = {}, pages = {111608}, pmid = {40486234}, issn = {2352-3409}, abstract = {Antibiotic resistance (AR) is a serious global health problem affecting both human medicine and animal agriculture. The poultry farming, especially industrial poultry, antibiotics are widely used for disease prevention and growth promotion, leading to the accumulation and dissemination of antibiotic resistance genes (ARGs) within the intestinal microbiomes of birds. Poultry, which often have close contact with humans, can serve as reservoirs for resistant microorganisms, posing potential public health risks. Determination of avian intestinal resistomes through metagenomic sequencing and bioinformatics analysis enables the identification of diversity and transmission dynamics of ARGs, and to evaluate the influence of environmental factors and conditions of poultry on resistance gene distribution. The article presents data of resistome analysis of gut microbiota in populations of chickens from different regions of Kazakhstan. The data obtained will allow to develop a strategy to reduce the spread of antibiotic-resistant pathogens and improve safety in poultry farming, as well as to predict the risk of transmission of resistant microorganisms between animals and humans.}, }
@article {pmid40485833, year = {2025}, author = {Sibalekile, A and Araya, T and Castillo Hernandez, J and Kotzé, E}, title = {Glyphosate-microbial interactions: metagenomic insights and future directions.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570235}, pmid = {40485833}, issn = {1664-302X}, abstract = {Glyphosate [N-(phosphonomethyl) glycine] is the most widely used systematic non-selective herbicide worldwide. However, there is increasing concern about its potential impacts on soil microbial communities, which play crucial roles in maintaining soil functions, plant health, and crop productivity. While glyphosate can be inactivated in soil through strong sorption, desorption remains a significant challenge as glyphosate residues and metabolites can exert toxicity effects on agroecosystems, particularly by altering microbial diversity and functionality. This review synthesizes current knowledge on glyphosate's behavior in soils and advancements in metagenomics approaches (including their limitations) to better understand the complex interactions between glyphosate and microbial communities in genetically modified (GM) cropping systems. Glyphosate has demonstrated antimicrobial properties, inhibiting the growth of various bacteria and fungi. Conversely, other studies suggest that glyphosate may enhance microbial richness, promoting the proliferation of potential glyphosate degraders (e.g., Bacillus, Stenetrophomonas, Pseudomonas, Sphingomonas, and Phenylobacterium) and N2 fixing bacteria (e.g., Bradyrhizobium, Rhizobium, and Devosia) in the bulk soil and rhizosphere of GM crops. These contrasting findings are influenced by factors such as soil types, glyphosate rates, and crop varieties. Moreover, the review highlights that methodological discrepancies, including variations in next-generation sequencing (NGS) platforms and reference databases, contribute significantly to inconsistencies in the literature. These differences stem from varying levels of accuracy or annotation standards in the databases and NGS technologies used. To address these challenges, this study underscores the need for standardized molecular and bioinformatics approaches. Integrating advanced long-read sequencing technologies, such as Oxford Nanopore and PacBio, with compatible reference databases could provide more accurate and consistent analyses of microbial community composition at finer taxonomic levels. Such advancements could improve our understanding of how glyphosate influences the balance between pathogenic microorganisms and plant-growth-promoting microbes in GM cropping systems, ultimately informing sustainable agricultural practices.}, }
@article {pmid40484974, year = {2025}, author = {Smith, ME and Kavamura, VN and Hughes, D and Mendes, R and Lund, G and Clark, I and Mauchline, TH}, title = {Uncovering functional deterioration in the rhizosphere microbiome associated with post-green revolution wheat cultivars.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {64}, pmid = {40484974}, issn = {2524-6372}, support = {FR2021-02017//Svenska Forskningsr&#xe5;det Formas/ ; BB/N016246/1//Bilateral BBSRC-Embrapa gran/ ; BBS/E/C/00005196//Bilateral BBSRC-Embrapa grant/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; }, abstract = {BACKGROUND: During the Green Revolution, one of the biggest developments of wheat domestication was the development of new cultivars that respond well to fertilisers and produce higher yields on shorter stems to prevent lodging. Consequently, this change has also impacted the wheat microbiome, often resulting in reduced selection of taxa and a loss of network complexity in the rhizospheres of modern cultivars. Given the importance of rhizosphere microbiomes for plant health and performance, it is imperative that we understand if and how these changes have affected their function. Here, we use shotgun metagenomics to classify the functional potential of prokaryote communities from the rhizospheres of pre-green revolution (heritage) cultivars to compare the impact of modern wheat breeding on rhizosphere microbiome functions.<br><br>RESULTS: We found distinct taxonomic and functional differences between heritage and modern wheat rhizosphere communities and identified that modern wheat microbiomes were less distinct from the communities in the surrounding soil. Of the 113 functional genes that were differentially abundant between heritage and modern cultivars, 95% were depleted in modern cultivars and 65% of differentially abundant reads best mapped to genes involved in staurosporine biosynthesis (antibiotic product), plant cell wall degradation (microbial mediation of plant root architecture, overwintering energy source for microbes) and sphingolipid metabolism (signal bioactive molecules).<br><br>CONCLUSIONS: Overall, our findings indicate that green revolution breeding has developed wheat cultivars with a reduced rhizosphere effect. The consequences of this are likely detrimental to the development of microbiome-assisted agriculture which will require a strong rhizosphere selective environment for the establishment of a beneficial plant root microbiome. We believe our results are of striking importance and highlight that implementation of microbiome facilitated agriculture will benefit from deliberately incorporating the development of beneficial plant-microbiome interactions, alongside traditional yield traits, to advance sustainable wheat production.}, }
@article {pmid40484531, year = {2025}, author = {Hu, Q and Cheng, S and Qian, D and Wang, Y and Xie, G and Peng, Q}, title = {Identification of core microbial communities and their influence on flavor-oriented traditional fermented sour cucumbers.}, journal = {Food microbiology}, volume = {131}, number = {}, pages = {104810}, doi = {10.1016/j.fm.2025.104810}, pmid = {40484531}, issn = {1095-9998}, mesh = {Volatile Organic Compounds/metabolism/analysis ; Fermentation ; *Cucumis sativus/microbiology/chemistry ; *Fermented Foods/microbiology/analysis ; Taste ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Flavoring Agents/metabolism ; Humans ; *Microbial Consortia ; Food Microbiology ; *Microbiota ; }, abstract = {Sour cucumber is a traditional fermented vegetable with global popularity, yet its fermentation process often leads to inconsistencies in quality and flavor due to the reliance on natural fermentation. This study identifies 12 core volatile organic compounds (VOCs) contributing to its unique flavor and investigates the key microbial species involved in the fermentation process. Using a synthetic microbial consortium constructed from core microbial species, we successfully replicated the flavor profile of naturally fermented sour cucumbers while enhancing safety by reducing nitrite levels. This approach also reduced bitterness and astringency, while improving sourness and umami, providing a robust framework for standardized production of high-quality fermented vegetables. These findings offer practical solutions for improving flavor quality and ensuring the safety of fermented foods.}, }
@article {pmid40484397, year = {2025}, author = {Adachi, A and Dominguez, JJ and Utami, YD and Fuji, M and Kirita, S and Imai, S and Murakami, T and Hongoh, Y and Shinjo, R and Kamiya, T and Fujiwara, T and Minamisawa, K and Ono, N and Kanaya, S and Saijo, Y}, title = {Field Dynamics of the Root Endosphere Microbiome Assembly in Paddy Rice Cultivated under No Fertilizer Input.}, journal = {Plant &amp; cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcaf045}, pmid = {40484397}, issn = {1471-9053}, abstract = {Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and the underlying mechanisms driving them, particularly in crops adapting to the field conditions, are not well understood. Here, we investigate the root endosphere microbiome of rice (Oryza sativa ssp. japonica) across four consecutive cultivation seasons in a high-yield, non-fertilized, and pesticide-free paddy field, compared to a neighboring fertilized and pesticide-treated field. Using 16S rRNA amplicon and metagenome sequencing, we analyzed three Japonica cultivars-Nipponbare, Hinohikari, and Kinmaze. Our findings reveal that the root endosphere microbiomes diverge based on fertilization regime and plant developmental stages, while the effects of cultivar variation are less significant. Machine learning model and metagenomic analysis of nitrogenase (nif) genes suggest enhanced nitrogen fixation activity in the non-fertilized field-grown roots, highlighting a potential role of diazotrophic, iron-reducing bacteria Telmatospirillum. These results provide valuable insights into the assembly of the rice root microbiome in nutrient-poor soil, which can aid in managing microbial homeostasis for sustainable agriculture.}, }
@article {pmid40483623, year = {2025}, author = {Chi, Y and Luo, M and Ding, C}, title = {The role of microbiota in fish spoilage: biochemical mechanisms and innovative preservation strategies.}, journal = {Antonie van Leeuwenhoek}, volume = {118}, number = {7}, pages = {89}, pmid = {40483623}, issn = {1572-9699}, support = {202411049301XJ//National College Student Innovation and Entrepreneurship Training Program Funding Project/ ; }, mesh = {*Fishes/microbiology ; *Microbiota ; Animals ; *Food Preservation/methods ; *Food Microbiology ; *Seafood/microbiology ; *Bacteria/metabolism/classification/genetics ; }, abstract = {Fish spoilage is a microbially-mediated biochemical process resulting in quality deterioration, economic losses, and food safety risks. Studies have indicated that spoilage microbiota are phylogenetically diverse, with Gram-negative bacteria (Pseudomonas, Shewanella, Photobacterium) representing primary spoilage organisms, and Gram-positive bacteria (Lactobacillus, Brochothrix) causing spoilage only under specific conditions. Microorganisms cause spoilage through the utilization of three main metabolic processes: (i) proteolytic degradation of muscle proteins, (ii) lipolytic breakdown of triglycerides, and (iii) production of volatile bioactive organic compounds and biogenic amines. By combining high-throughput sequencing with metabolomics, researchers have been uncovering strain-specific metabolic networks and how they are influenced by environmental factors such as temperature, pH, and packaging. This review systematically examines: (1) patterns of taxonomic succession in spoilage microbiota, (2) enzymatic and biochemical pathways involved in spoilage, and (3) innovative preservation strategies targeting spoilage consortia. Emerging technologies, such as bacteriocin-mediated biopreservation, phage therapy, and modified atmosphere packaging, show considerable promise in inhibiting spoilage organisms while maintaining the sensory qualities of the fish. Microbiome-directed interventions combined with predictive modeling and precision storage systems also represent a novel approach to fish preservation. There is a critical need to integrate traditional microbiology with the use of multi-omic technologies for the development of sustainable, microbiota-based preservation strategies that address global seafood security challenges.}, }
@article {pmid40483486, year = {2025}, author = {Bergholm, J and Tessema, TS and Blomström, AL and Berg, M}, title = {Metagenomic insights into the complex viral composition of the enteric RNA virome in healthy and diarrheic calves from Ethiopia.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {188}, pmid = {40483486}, issn = {1743-422X}, support = {2021-04343//Vetenskapsr&#xe5;det/ ; 2021-04343//Vetenskapsr&#xe5;det/ ; 2021-04343//Vetenskapsr&#xe5;det/ ; 2021-04343//Vetenskapsr&#xe5;det/ ; }, mesh = {Animals ; Cattle ; Ethiopia/epidemiology ; *Diarrhea/veterinary/virology ; *Virome ; Metagenomics ; *Cattle Diseases/virology ; Feces/virology ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; Genome, Viral ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Viruses and the virome have received increased attention in the context of calf diarrhea and with the advancement of high-throughput sequencing the detection and discovery of viruses has been improved. Calf diarrhea, being the main contributor to calf morbidity and mortality, is a major issue within the livestock sector in Ethiopia. However, studies on viruses and the virome in calves is lacking in the country. Therefore, we utilized viral metagenomics to investigate the diversity of RNA viruses in healthy and diarrheic calves from central Ethiopia.<br><br>METHODS: Fecal material from 47 calves were collected, pooled, and sequenced using Illumina. Following sequencing, the virome composition and individual viral sequences were investigated using bioinformatic analysis.<br><br>RESULTS: The metagenomic analysis revealed the presence of several RNA viruses, including rotavirus and bovine coronavirus, known causative agents in calf diarrhea. In addition, several enteric RNA viruses that have not been detected in cattle in Ethiopia previously, such as norovirus, nebovirus, astrovirus, torovirus, kobuvirus, enterovirus, boosepivirus and hunnivirus were identified. Furthermore, a highly divergent viral sequence, which we gave the working name suluvirus, was found. Suluvirus showed a similar genome structure to viruses within the Picornaviridae family and phylogenetic analysis showed that it clusters with crohiviruses. However, due to its very divergent amino acid sequence, we propose that suluvirus represent either a new genus within the Picornaviridae or a new species within crohiviruses.<br><br>CONCLUSIONS: To our knowledge, this is the first characterization of the RNA virome in Ethiopian cattle and the study revealed multiple RNA viruses circulating in both diarrheic and healthy calves, as well as a putative novel virus, suluvirus. Our study highlights that viral metagenomics is a powerful tool in understanding the divergence of viruses and their possible association to calf diarrhea, enabling characterization of known viruses as well as discovery of novel viruses.}, }
@article {pmid40483351, year = {2025}, author = {Koblitz, J and Reimer, LC and Pukall, R and Overmann, J}, title = {Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {897}, pmid = {40483351}, issn = {2399-3642}, support = {K280/2019//Leibniz-Gemeinschaft (Leibniz Association)/ ; }, mesh = {*Machine Learning ; *Bacteria/genetics ; Phenotype ; Software ; Computational Biology/methods ; }, abstract = {Predicting prokaryotic phenotypes-observable traits that govern functionality, adaptability, and interactions-holds significant potential for fields such as biotechnology, environmental sciences, and evolutionary biology. In this study, we leverage machine learning to explore the relationship between prokaryotic genotypes and phenotypes. Utilizing the highly standardized datasets in the BacDive database, we model eight physiological properties based on protein family inventories, evaluate model performance using multiple metrics, and examine the biological implications of our predictions. The high confidence values achieved underscore the importance of data quality and quantity for reliably inferring bacterial phenotypes. Our approach generates 50,396 completely new datapoints for 15,938 strains, now openly available in the BacDive database, thereby enriching existing phenotypic resources and enabling further research. The open-source software we provide can be readily applied to other datasets, such as those from metagenomic studies, and to various applications, including assessing the potential of soil bacteria for bioremediation.}, }
@article {pmid40483244, year = {2025}, author = {Duong, JT and Hayden, HS and Verster, AJ and Pope, CE and Miller, C and Kelsi Penewit,  and Salipante, SJ and Rowe, SM and Solomon, GM and Nichols, D and Kelly, A and Schwarzenberg, SJ and Freedman, SD and Hoffman, LR}, title = {Fecal microbiota changes in people with cystic fibrosis after 6 months of elexacaftor/tezacaftor/ivacaftor: Findings from the promise study.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2025.05.006}, pmid = {40483244}, issn = {1873-5010}, abstract = {BACKGROUND: People with cystic fibrosis (PwCF) often have fecal dysbioses relative to those without CF, characterized by increased pro-inflammatory microbiota and gastrointestinal (GI) inflammation as measured by fecal calprotectin, suggesting that inflammation contributes to CF GI disease. The multicenter observational PROMISE study (NCT04038047) found that calprotectin decreased in PwCF treated with elexacaftor/tezacaftor/ivacaftor (ETI). To better understand the dynamics between fecal dysbiosis and GI inflammation, we characterized the microbiomes of fecal samples from PROMISE and the relationships with calprotectin before, 1-month post, and 6-months post ETI.<br><br>METHODS: Fecal microbiota from participants &#x2265;12 y/o were determined by shotgun metagenomic sequencing with random forest modeling and multivariate linear regression analysis to define relationships between microbiota, calprotectin, and deltaF508 genotype before and after ETI.<br><br>RESULTS: We analyzed 345 samples from 124 participants. At baseline, we observed community-level differences in the fecal microbiota among participants with abnormal compared to normal calprotectin. With ETI, the relative abundances of 7 bacterial species - Escherichia coli, Staphylococcus aureus, Clostridium scindens, Enterocloster clostridioformis, Clostridium butyricum, Anaeroglobus geminatus, and Ruminococcus gnavus - decreased significantly, correlating with calprotectin decrease. We detected community-level differences in the fecal microbiota based on CFTR genotype and a distinct pattern of microbiota change in F508del homozygous compared to heterozygous participants after ETI.<br><br>CONCLUSIONS: We identified 7 species for which fecal abundances decreased with ETI and correlated with calprotectin decrease, supporting a close relationship between fecal microbiota and inflammation in PwCF. Future work will define these relationships with metabolites and GI symptoms during long-term ETI therapy.}, }
@article {pmid40482930, year = {2025}, author = {Adiningrat, A and Maulana, I and Fadhlurrahman, AG and Yumoto, H}, title = {Probiotic bacteria from asymptomatic necrotic tooth can regulate the microbiome homeostasis.}, journal = {Microbial pathogenesis}, volume = {206}, number = {}, pages = {107791}, doi = {10.1016/j.micpath.2025.107791}, pmid = {40482930}, issn = {1096-1208}, abstract = {OBJECTIVE: This study was performed to identify and isolate the dominant bacteria from a chronic asymptomatic necrotic root canal and investigate in vitro its potential postbiotics effect at the biofilm maturation maintaining root canal microbiome homeostasis.<br><br>METHODS: For bacterial identification of an in vivo root canal sample, metagenomic analysis was applied, followed by single colony isolation and PCR analysis. Cell free supernatant (CFS) was then cultivated through serial L paracasei culture procedures prior antibiofilm analysis. Antibiofilm effects of the CFS product were evaluated using in vitro biofilm analysis against S. mutans and E. faecalis. Biofilm mass analysis was measured by using colorimetric approach with cresyl-vast violet staining, morphological appearance was observed using both phase-contrast and scanning electron microscope (SEM). Shapiro-Wilk analysis was applied for normality test, followed by the ANOVA to compare multiple groups or a student t-test for independent two groups mean comparisons.<br><br>RESULTS: The isolated root canal bacteria produced biofilm mass that was similar to the Enterococcus faecalis control pathogenic biofilm. From the morphological analysis suggested that population of the isolated bacteria were predominantly occupied by rod-shaped rather than cocci-shaped inhabitants. Further metagenomic analysis indicated that the isolated dominant bacteria in the mixed culture were mainly identified as probiotic bacteria, Lacticaseibacillus paracasei. Moreover, the functional analysis revealed that the L. paracasei cell free supernatant product (CFS) exhibited a promising positive effect in biofilm structure integrity disturbances of S. mutans and E. faecalis.<br><br>CONCLUSIONS: The isolated Lacticaseibacillus paracasei from the root canal of a chronic asymptomatic necrotic tooth, produces potential postbiotic products that demonstrated a disruptive ability against Streptococcus mutans and Enterococcus faecalis biofilm integrity.}, }
@article {pmid40482668, year = {2025}, author = {Garcia-Mauriño, C and Shao, Y and Miltz, A and Lawley, TD and Rodger, A and Field, N}, title = {Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101072}, doi = {10.1016/j.lanmic.2024.101072}, pmid = {40482668}, issn = {2666-5247}, abstract = {BACKGROUND: Early-life gut microbiota affects immune system development, including the lung immune response (gut-lung axis). We aimed to investigate whether gut microbiota composition in neonates in the first week of life is associated with hospital admissions for viral lower respiratory tract infections (vLRTIs).<br><br>METHODS: The Baby Biome Study (BBS) is a prospective birth cohort, which enrolled mother-baby pairs between Jan&#xa0;1,&#xa0;2016,&#xa0;and Dec 31, 2017, at three UK hospitals. In the present study, we only included BBS babies with a sequenced first-week stool sample and successful data linkage. Stool was collected in the first week of life for shotgun-metagenomic sequencing. We examined the following microbiota features: alpha diversity (Chao1, Shannon, and Simpson indices) and community structures (cluster-partitioning against medoids method). The participants were followed up through linkage to the Hospital Episode Statistics-Admitted Patient Care (HES-APC) database to determine vLRTI hospital admission incidence in the first 2&#xa0;years of life. We used Poisson mixed-effects models for univariable and multivariable analyses to evaluate the association between microbiota features and vLRTI hospital admission incidence, adjusting for confounders identified through direct acyclic graphs.<br><br>FINDINGS: 3305 (95%) of the 3476&#xa0;BBS-enrolled babies for whom consent to data linkage was obtained were included in the present study. 1111 (34%) babies had a first-week sequenced stool sample, of whom 1082 (97%; 564&#xa0;born vaginally and 518&#xa0;born by caesarean section) were successfully linked to HES-APC, and had median follow-up of 2&#xb7;0&#xa0;years (IQR&#xa0;1&#xb7;4-2&#xb7;9). Most babies were born at term (996 [92%] &#x2265;37&#xa0;weeks gestational age and 1070 [99%] >35&#xa0;weeks gestational age) and healthy (1050 [97%] had no comorbidities), and 520 (48%) were female and 562 (52%) were male. Higher first-week gut microbiota alpha diversity was associated with reduced rates of vLRTI hospital admission (Chao1 Index adjusted hazard ratio [HR] 0&#xb7;92 [95% CI 0&#xb7;85-0&#xb7;99]; Shannon Index adjusted HR 0&#xb7;57&#xa0;[0&#xb7;33-0&#xb7;98]; and Simpson Index adjusted HR 0&#xb7;36 [0&#xb7;11-1&#xb7;20]). Three microbiota clusters were identified. Cluster 1&#xa0;had a mixed composition and cluster 2&#xa0;was dominated by Bifidobacterium breve, with both clusters observed in babies born vaginally and by caesarean section. Cluster 3&#xa0;was found only in vaginally born babies and was dominated by Bifidobacterium longum. Having cluster 1 (mixed) or cluster 2 (B&#xa0;breve dominated) was independently associated with increased rates of vLRTI hospital admission compared with cluster 3 (B&#xa0;longum dominated; cluster&#xa0;1 [mixed] 3&#xb7;05 [1&#xb7;25-7&#xb7;41] and cluster 2 [B&#xa0;breve dominated] 2&#xb7;80 [1&#xb7;06-7&#xb7;44]).<br><br>INTERPRETATION: We report observational evidence that first-week gut microbiota differences are associated with clinically severe vLRTI in young children. This study identified bacterial species that could be of interest for vLRTI prevention. This finding has important implications for the design of future research and intervention strategies.<br><br>FUNDING: The Wellcome Trust and Wellcome Sanger Institute core funding.}, }
@article {pmid40482531, year = {2025}, author = {Yan, R and Manjunatha, V and Thomas, A and Shankar, V and Lumpkins, B and Hoerr, FJ and Greene, A and Jiang, X}, title = {Comparative effects of vegetarian diet and rendered animal by-product on the chicken gut health.}, journal = {Poultry science}, volume = {104}, number = {9}, pages = {105360}, doi = {10.1016/j.psj.2025.105360}, pmid = {40482531}, issn = {1525-3171}, abstract = {Rendered animal proteins and fats can provide vital nutrients for poultry at affordable prices. With growing interest in reintroducing rendered animal by-products into poultry diets, this study investigated the effects of replacing a portion of soybean meal and vegetable fat with rendered animal proteins and fats in a standard vegetarian chicken diet. The study focused on the changes in gut and liver histopathology, and gut microbiome composition and functions. Five diet treatments were formulated to be isocaloric and isonitrogenous and balanced for amino acids, including a standard vegetarian control diet and four diets containing rendered animal by-products. A total of 15 pens with 50 chickens each were assigned one of the five diets from hatch to 42 days of age, with three replicate pens per treatment. On days 28 and 42, six birds were randomly selected from two pens per treatment and humanely euthanized by cervical dislocation. Cecal samples were collected for microbial enumeration and DNA extraction, while gut and liver histopathology analyses were conducted on day 42. Enumeration of Clostridium perfringens was performed under anaerobic conditions using selective media and metagenomic sequencing was used to assess taxonomic and functional profiles of the microbiome. Statistical analysis included data transformation, permutational multivariate analysis of variance, and differential abundance testing. No significant differences were observed between the vegetarian control and rendered animal by-product diets in gut or liver histopathology, C. perfringens levels, or microbiome composition, indicating that inclusion of animal by-products did not significantly affect broiler intestinal health or microbial functions over a 42-day period. These findings suggest that partially replacing soybean meal and vegetable fat with rendered animal by-products can be a safe and cost-effective alternative to plant-based ingredients in poultry diets.}, }
@article {pmid40482428, year = {2025}, author = {Roy, S and King, GM and Hernández, M}, title = {Classification of MAGs associated with trace gas metabolism in volcanic soils named following SeqCode rules.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {4}, pages = {126622}, doi = {10.1016/j.syapm.2025.126622}, pmid = {40482428}, issn = {1618-0984}, abstract = {Trace gas metabolism is important for nutrient flow in all ecosystems, particularly volcanic ecosystems. Microbes in volcanic ecosystems are among the early colonisers and can play key roles in ecological succession. Here, we describe the taxonomic and functional characteristics of two new metagenome-assembled genomes (MAGs), one belonging to Bacteria (MAG_1957-2.1) and one to Archaea (MAG_C2-3), retrieved from soils in volcanoes located in Chile (Llaima) and the USA (Kilauea), respectively. MAG_1957-2.1 has a genome size of 6.36Mb with 96.21 % completeness. MAG_C2-3 has a genome size of 3.02Mb with 97.57 % completeness. Phylogenetic analyses of the bacterial MAGs placed MAG_1957-2.1 in the class Ktedonobacteria, while the archaeal MAG_C2-3 was placed in the class Nitrososphaeria. Functional characterisation for potential trace gas metabolism showed that MAG_1957-2.1 contains a coxL gene encoding the large subunit of form I carbon monoxide dehydrogenase (CoxL), which is associated with the oxidation of carbon monoxide (CO). It also contains the form I cox gene cluster with a coxMSL arrangement. On the other hand, MAG_C2-3 contains gene subunit A (amoA) as well as subunit B (amoB), which encode for ammonia monooxygenase, the enzyme that catalyses the oxidation of ammonia. Based on the sequence characteristics and phylogenomic analyses we propose the names Paraktedonobacter carboxidivorans sp. nov for MAG_1957-2.1 and Nitrososphaera maunauluensis sp. nov for MAG_C2-3. The names are proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).}, }
@article {pmid40482427, year = {2025}, author = {Mao, YL and Tan, S and Wang, BB and Yang, XY and Hou, J and Cui, HL}, title = {Halosimplex amylolyticum sp. nov., Halosimplex halobium sp. nov., Halosimplex marinum sp. nov., Halosimplex rarum sp. nov., Halovenus amylolytica sp. nov., Halovenus halobia sp. nov., and Halovenus marina sp. nov., halophilic archaea isolated from a marine tidal flat, a marine solar saltern, three coarse sea salts, and two saline lakes.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {4}, pages = {126626}, doi = {10.1016/j.syapm.2025.126626}, pmid = {40482427}, issn = {1618-0984}, abstract = {Seven novel halophilic archaeal strains DYHT-AS-1[T], GDY60[T], TS25[T], XH63[T], SHR40[T], SYNS179[T], and ZY30[T] were isolated from tidal flat, saline lakes, marine solar saltern and coarse sea salts from different regions of China. Metagenomic and amplicon analyses indicated that the abundance of these seven strains in respective habitats was low. Phylogenetic and comparative genomic analyses indicated that strains DYHT-AS-1[T], GDY60[T], TS25[T], and XH63[T] formed a tight cluster with Halosimplex species, exhibiting high 16S rRNA gene sequence similarity (90.4-99.4 %). The ANI, dDDH, and AAI values among these four strains and current Halosimplex species were 80.8-92.3 %, 24.5-53.3 %, and 77.8-91.5 %, respectively. Strains SHR40[T], SYNS179[T], and ZY30[T] were related to Halovenus species, with 16S rRNA gene sequence similarities ranging from 88.8 % to 98.4 %. The ANI, dDDH, and AAI values among these three strains and current Halovenus species were 69.9-77.8 %, 19.4-21.5 %, and 62.1-78.1 %, respectively. These values are significantly lower than the thresholds for species demarcation. The optimal growth conditions for these seven strains in terms of NaCl, MgCl2, temperature, and pH were 3.1-3.4 M, 0.05-0.5 M, 35-40 °C, and 6.5-7.5, respectively. According to phenotypic differences in nutrition, biochemical activity, and antibiotic sensitivity, these seven strains can be distinguished from their related species. Based on the above results, strains DYHT-AS-1[T], GDY60[T], TS25[T], and XH63[T] represent four new species of the genus Halosimplex, and strains SHR40[T], SYNS179[T], and ZY30[T] represent three novel species of the genus Halovenus.}, }
@article {pmid40482059, year = {2025}, author = {Rendina, M and Turnbaugh, PJ and Bradley, PH}, title = {Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkaf131}, pmid = {40482059}, issn = {2160-1836}, abstract = {Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some cases by homologous enzymes. We conducted a systematic search for all known human proteins with gut microbial homologs. Because gene fusion and fission can obscure homology detection, we built a pipeline to identify not only full-length homologs, but also cases where microbial homologs were split across multiple adjacent genes in the same neighborhood or operon ("split homologs"). We found that human proteins with full-length gut microbial homologs disproportionately participate in xenobiotic metabolism. While this included many different enzyme classes, short-chain and aldo-keto reductases were the most frequently detected, especially in prevalent gut microbes, while cytochrome P450 homologs were largely restricted to lower-prevalence facultative anaerobes. In contrast, human proteins with split homologs tended to play roles in central metabolism, especially of nucleobase-containing compounds. We identify twelve specific drugs that gut microbial split homologs may metabolize; two of these, 6-mercaptopurine by xanthine dehydrogenase (XDH) and 5-fluorouracil by dihydropyrimidine dehydrogenase (DPYD), have been recently confirmed in mouse models. This work provides a comprehensive map of homology between the human and gut microbial proteomes, indicates which human xenobiotic enzyme classes are most likely to be shared by gut microorganisms, and finally demonstrates that split homology may be an underappreciated explanation for microbial contributions to drug metabolism.}, }
@article {pmid40481853, year = {2025}, author = {Chaverri, P and Escudero-Leyva, E and Mora-Rojas, D and Calvo-Obando, A and González, M and Escalante-Campos, E and Mesén-Porras, E and Wicki-Emmenegger, D and Rojas-Gätjens, D and Avey-Arroyo, J and Campos-Hernández, M and Castellón, E and Moreira-Soto, A and Drexler, JF and Chavarría, M}, title = {Differential Microbial Composition and Fiber Degradation in Two Sloth Species (Bradypus variegatus and Choloepus hoffmanni).}, journal = {Current microbiology}, volume = {82}, number = {7}, pages = {327}, pmid = {40481853}, issn = {1432-0991}, support = {VI 809-C3-102//Vicerrector&#xed;a de Investigaci&#xf3;n, Universidad de Costa Rica/ ; 57592642//Deutscher Akademischer Austauschdienst/ ; }, mesh = {Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Gastrointestinal Microbiome ; Cellulose/metabolism ; *Dietary Fiber/metabolism ; *Fungi/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics ; }, abstract = {Sloths have the slowest digestion among mammals, requiring 5-20 times longer to digest food than other herbivores, which suggests differences in their gut microbiota, particularly in plant-fiber-degrading microorganisms. Bradypus variegatus has a lower metabolic rate and moves less than Choloepus hoffmanni. However, no comprehensive studies have compared the microbiota (e.g., fungi) of these species. We hypothesized that differences in digestion and metabolism between the two species would be reflected in their microbiota composition and functionality, which we characterized using metagenomics, metabarcoding, and cellulose degradation. Results revealed significant differences in microbiota composition and functionality. Both species are dominated by bacteria; fungi comprised only 0.06-0.5% of metagenomic reads. Neocallimastigomycota, an anaerobic fungus involved in fiber breakdown in other herbivores, was found in low abundance, especially in B. variegatus. Bacterial communities showed subtle differences: C. hoffmanni was dominated by Bacillota and Bacteroidota, while B. variegatus showed higher Actinomycetota. Expected herbivore bacterial taxa (e.g., Fibrobacter and Prevotella) were scarce. Functional analysis showed a low abundance of carbohydrate-active enzymes essential for polysaccharide breakdown. Cellulose degradation assays confirmed that sloths digest only ~ 3-30% of ingested plant material. This research sheds light on the potential multidirectional links between the gut microbiota, metabolism, and digestion.}, }
@article {pmid40481811, year = {2025}, author = {Baeza, JA and Rosales, SM}, title = {The complete mitochondrial genome of the 'maze' coral Meandrina meandrites (Scleractinia: Vacatina: Meandrinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {}, number = {}, pages = {1-8}, doi = {10.1080/24701394.2025.2504422}, pmid = {40481811}, issn = {2470-1408}, abstract = {The shallow water reef-building 'maze' or 'brain' stony coral Meandrina meandrites (fam. Meandrinidae) is currently experiencing major environmental problems in the Caribbean Sea. In this study, we assembled the mitochondrial genome of M. meandrites to support future conservation of this imperiled coral. We also explored the phylogenetic position of this coral in the Class Scleractinia utilizing the phylogenetic signal provided by translated mitochondrial protein-coding genes (PCGs). A complete mitochondrial genome of M. meandrites, 17,196 bp in length, was assembled using short-reads next-generation sequencing (NGS) sequencing with the target-restricted-assembly pipeline GetOrganelle. The newly assembled mitochondrial genome of M. meandrites encoded 13 PCGs, two ribosomal genes (ribosomal RNA), and two transfer genes (tRNAs). It also contains two relatively long non-coding regions 400 and 1,877 bp long. A group I intron bisected the nad5 PCG. Each of the two tRNAs exhibited a canonical 'cloverleaf' secondary structure. The mitochondrial genome of M. meandrites is identical to that of a conspecific assembled using HiFi PacBio long reads (available in GenBank with accession number OY855917 but without a companion paper) with the exception of four single nucleotide variants. The aforementioned comparison indicates that the mitochondrial genome assembled from a short-read NGS dataset is reliable (complete and accurate). A maximum-likelihood phylomitogenomic analysis based on PCGs (translated) supported the monophyly of the order Scleractinia and placed M. meandrites in a moderately to well-supported clade with Astrangia sp. (family Astrangidae). This newly assembled mitochondrial genome can be used as a reference to support conservation planning, including biomonitoring of this stony coral using environmental DNA.}, }
@article {pmid40481438, year = {2025}, author = {Babalola, OO and Osuji, IE and Akanmu, AO}, title = {Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {40}, pmid = {40481438}, issn = {2730-6844}, }
@article {pmid40481394, year = {2025}, author = {Lu, X and Chen, J and Miao, S and Xie, Y}, title = {Two cases of Talaromyces marneffei tracheobronchial infection in HIV-negative patients.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {800}, pmid = {40481394}, issn = {1471-2334}, abstract = {OBJECTIVES: In recent years, the incidence and prevalence of Talaromyces marneffei (TM) have been on the rise. This infection predominantly affects immunocompromised or immunodeficient individuals, especially those with acquired immunodeficiency syndrome (AIDS). There has been a notable increase in the incidence of TM and its associated infections. The majority of cases occur within immunocompromised or immunodeficient populations, with a high prevalence among AIDS patients. However, cases are also occasionally detected in HIV - negative individuals. Due to the insidious and slow - growing nature of TM, the disease can be misdiagnosed as other conditions such as tuberculosis, bacterial pneumonia, and lung cancer, particularly in non - endemic regions. Such misdiagnosis significantly impacts the patient’s prognosis.<br><br>METHODS: Two HIV-negative patients with TM infection from non - endemic areas were hospitalized with a high suspicion of co-infection with lung cancer and poor symptomatic treatment response. These patients underwent a comprehensive diagnostic workup, including lung puncture biopsy, sputum, blood, pleural, and peritoneal fluid cultures, as well as Metagenomics Next Generation Sequencing (mNGS) analysis. Eventually, both patients were diagnosed with TM tracheobronchial infection.<br><br>RESULTS: The patients were treated with voriconazole antifungal therapy, combined with methylprednisolone (used for reducing inflammation, relieving spasms, and treating asthma) and acyclovir (used for treating viral infections). The 49 - year - old patient was cured and discharged from the hospital, while the 79 - year - old male patient&#x2019;s condition continued to deteriorate, and he ultimately died.<br><br>CONCLUSION: It has been determined that TM infection, presenting primarily with respiratory symptoms, is highly susceptible to misdiagnosis in the early stages of the disease. This can lead to treatment delays and a negative impact on the prognosis. It is crucial for medical professionals to be more aware of the possibility of TM infection in non - HIV - infected and non - endemic populations. Collecting respiratory and lung tissue specimens from the infection sites at the earliest possible stage is essential for diagnosing TM infection. Integrating mNGS and mass spectrometry results is crucial for improving the detection and early diagnosis of TM infection, which is of great value for enhancing the efficacy of clinical treatment and the prognosis of patients.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40480048, year = {2025}, author = {Yang, J and Liu, J and Gu, H and Song, W and Zhang, H and Wang, J and Yang, P}, title = {Gut microbiota, metabolites, and pulmonary hypertension: Mutual regulation and potential therapies.}, journal = {Microbiological research}, volume = {299}, number = {}, pages = {128245}, doi = {10.1016/j.micres.2025.128245}, pmid = {40480048}, issn = {1618-0623}, abstract = {Pulmonary hypertension is a progressive condition characterized by increased pulmonary vascular pressure and resistance, ultimately leading to right heart failure and death. Increasing evidence has underscored the importance of the gut-lung axis in the development of respiratory and cardiovascular diseases. Notably, significant changes in the gut microbiota, including altered microbial composition and function, have been observed in pulmonary hypertension. Specifically, microbiota-derived metabolites, including short chain fatty acids, trimethylamine N-oxide, bile acids and tryptophan, play a significant role in the development of pulmonary hypertension. The identification of key bacteria and metabolites, along with recent advances in gut microbiota-targeting technologies and metabolic pathway-targeting inhibitors/agonists, holds potential for developing diagnostic, prognostic, and therapeutic strategies for pulmonary hypertension. Emerging research directions include metagenomic analysis of viruses and fungi, artificial intelligence-aided prediction models, novel metabolites and their associated enzymes, drug-microbiota interactions, selective antibiotics, and advanced microbiota transplantation. This review synthesizes clinical and experimental evidence linking the gut microbiota to pulmonary hypertension, highlighting their interplay as a promising avenue for further investigation and translational applications.}, }
@article {pmid40478725, year = {2025}, author = {Wang, J and den Bakker, HC and Denes, TG}, title = {A critical review of metagenomic approaches for foodborne pathogen surveillance.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/10408398.2025.2503453}, pmid = {40478725}, issn = {1549-7852}, abstract = {High-throughput sequencing methods (e.g., whole-genome sequencing and metagenomics) are rapidly changing multiple fields of microbiology, including food safety and pathogen surveillance. Current foodborne pathogen surveillance relies heavily on resource-intensive, isolate-based approaches, limiting large-scale implementation. To facilitate more efficient public health responses, innovative technologies that can rapidly and accurately identify diverse foodborne pathogens are essential. Metagenomics-based approaches represent a potential transformative advancement in food safety diagnostics. These techniques enable unbiased and comprehensive analysis of foodborne pathogen genetic material from clinical, food product, processing facility, and environmental samples, positioning metagenomics as a promising strategy for foodborne pathogen surveillance. Here, we explore how metagenomics can be applied to foodborne pathogen surveillance and outbreak detection, focusing on recent advances in both short- and long-read sequencing technologies. The challenges limiting potential applications are reviewed, including the detection and characterization of low-abundance pathogens, the complexity of assembly-based analysis, and the identification of antimicrobial resistance genes. Finally, we discuss a future outlook for metagenomics impacting public health response to foodborne pathogens. It is anticipated that through continuous improvements in sequencing and analytical technologies, that metagenomic approaches to foodborne pathogen detection and characterization will become routine, with the potential to reduce the foodborne illness burden.}, }
@article {pmid40478660, year = {2025}, author = {Nicolas, M and Lemaitre, C and Vicedomini, R and Frioux, C}, title = {Mapler: A pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf334}, pmid = {40478660}, issn = {1367-4811}, abstract = {SUMMARY: Metagenome assembly seeks to reconstruct the most high-quality genomes from sequencing data of microbial ecosystems. Despite technological advancements that facilitate assembly, such as Hi-Fi long reads, the process remains challenging in complex environmental samples consisting of hundreds to thousands of populations. Mapler is a metagenome assembly and evaluation pipeline with a focus on evaluating the quality of Hi-Fi long read metagenome assemblies. It incorporates several state-of-the-art metrics, as well as novel metrics assessing the diversity that remains uncaptured by the assembly process. Mapler facilitates the comparison of assembly strategies and helps identify methodological bottlenecks that hinder genome reconstruction.<br><br>Mapler is open source and publicly available under the AGPL-3.0 licence at https://github.com/Nimauric/Mapler. Source code is implemented in Python and Bash as a Snakemake pipeline. A snapshot of the code is available on Software Heritage at swh:1:snp:df4f5f02e22ebbab285ec14af58d4d88436ee5d6.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid40478429, year = {2025}, author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN}, title = {Hydrological regime and niche partitioning drive fungal community structure and function in arid wetlands sediments of South Africa.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {40478429}, issn = {1614-7499}, support = {DST/CON0197/2017//Department of Science and Innovation, South Africa/ ; }, abstract = {Arid wetlands are ecologically significant yet understudied ecosystems shaped by extreme conditions and hydrological variability. However, the structure and ecological functional of fungal communities in these habitats remain poorly understood, especially in southern Africa. This study integrated shotgun metagenomics, FUNGuild functional profiling, and multivariate analyses to examine fungal diversity, functional composition, and environmental drivers in seasonal and permanent arid wetlands of South Africa. Distinct fungal assemblages emerged, primarily shaped by hydrological regimes and ionic stress. Seasonal wetlands were dominated by Mucoromycota (79%), particularly arbuscular mycorrhizal (AM) fungus (Rhizophagus, 62%), while permanent wetlands had higher Ascomycota (54%), with Aspergillus (50%) prevalent in oxygen-limited sediments. Although alpha diversity showed no significant difference, beta diversity confirmed significant mycobiome differentiation. Total dissolved solids (TDS), electrical conductivity (EC), and salinity were key predictors of fungal composition, with TDS the strongest determinant (p < 0.01). Functional guild analysis highlighted niche differentiation, with saprotrophs dominating permanent wetlands (59.7% vs. 21.5%; p < 0.05), while symbiotrophs, particularly AM fungi, were enriched in seasonal wetlands (69.3% vs. 36.1%; p < 0.001). Indicator taxa identified via LefSe (LDA > 3, p < 0.05) and random forest modeling included Rhizophagus, Trichoderma, Fusarium, and Entomophthora in seasonal wetlands, and Aspergillus in permanent wetlands. This study provides the first integrative insight into fungal ecology in South Africa's arid wetlands, demonstrating that hydrological regime shapes fungal structure and function through environmental filtering and niche specialization, with implications for guiding conservation and adaptive management of these fragile ecosystems.}, }
@article {pmid40478395, year = {2025}, author = {Zhang, T and Liu, Y and Li, J and Yuan, M and Qiao, C and Huang, X and Yang, X and Gao, B and Lou, C and Yang, Y and Cao, Y}, title = {Toad's survivability and soil microbiome alterations impacted via individual abundance.}, journal = {Biologia futura}, volume = {}, number = {}, pages = {}, pmid = {40478395}, issn = {2676-8607}, support = {CI2021A04012//CACMS Innovation Fund/ ; ZZ16-YQ-04//Fundamental Research Funds of CACMS/ ; H2023406026//Hebei Natural Science Foundation/ ; QN2024119//Science Research Project of Hebei Education Department/ ; }, abstract = {Artificial breeding is a valid strategy for the reverse of current extinction tendency in wild population of amphibian like toads. Considering public health, an alternative to antibiotics is demanded for ameliorating survival of toads during the culture period. Relying on the cognition of probiotics or antagonistic bacteria, the present work investigated viability and soil microorganism variations induced by distribution characteristic on toads using high-throughput sequencing technology. Comparison and analysis of soil metagenome from clustered and depopulated groups distinguished by toad behavior showed differences of bacterial community composition (e.g., Proteobacteria bacterium TMED72 and Nannocystis exedens) and antibiotic resistance genes involving antibiotic efflux and inactivation (e.g., mdtB and acrF). There were 18 and 10 distribution-typical genes independently enriched in Proteobacteria bacterium TMED72 and bacterium TMED88 of clustered group and Nannocystis exedens of depopulated group. In Nannocystis exedens, one of the distribution-typical genes was annotated as 6-phosphogluconate dehydrogenase acting role on bacterial growth restriction. It implied that, compared with the group emerging rare traces, the reduction of soil bacteria which possess genes retarding bacterial growth putatively impairs competitiveness to pathogenic bacteria and results in poor survivability of toads under clustering behavior. With the co-occurrence of virulence genes, more evidences are needed on the antagonistic bacteria Nannocystis exedens as antibiotic substitute.}, }
@article {pmid40476734, year = {2025}, author = {Marcos-Zambrano, LJ and Lacruz-Pleguezuelos, B and Aguilar-Aguilar, E and Marcos-Pasero, H and Valdés, A and Loria-Kohen, V and Cifuentes, A and Ramirez de Molina, A and Diaz-Ruiz, A and Pancaldi, V and Carrillo de Santa Pau, E}, title = {Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0014325}, doi = {10.1128/msystems.00143-25}, pmid = {40476734}, issn = {2379-5077}, abstract = {UNLABELLED: Non-responsive celiac disease (NRCD) challenges clinicians due to persistent symptoms despite a gluten-free diet (GFD). We present a cross-sectional pilot study including 39 NRCD patients to describe the underlying mechanisms contributing to symptom persistence by integrating different levels of data (fecal shotgun metagenomics, mucosal integrity markers, and metabolomic profiles) and using microbial networks to unravel the community structure of the patient's microbiome. Two distinct clusters of patients were identified based on clinical and demographic variables not influenced by gluten consumption. Cluster 1, labeled "Low-grade symptoms," displayed milder symptoms and lower inflammatory markers and a fragmented microbial network characterized by high modularity and a reliance on localized hubs, suggesting a microbial community under stress but capable of maintaining limited functionality. Cluster 2, named "High-grade symptoms," exhibited more severe symptoms, elevated inflammatory markers, and a more connected but antagonistic microbial network with a greater number of keystone taxa, including taxa associated with Th17 activation and inflammation. In contrast, the control network, representing asymptomatic treated celiac disease (tCD) patients, was highly interconnected, resilient, and cooperative, with a robust structure maintained even under simulated disruptions. Metabolomic analysis revealed differential metabolites between clusters, particularly those involved in amino acid metabolism pathways and microbial-derived metabolites such as indolelactic acid and mannitol, which were associated with symptom severity. This study identifies NRCD subgroups based on the gut microbiome and metabolic signatures associated with clinical manifestations, highlighting variations in microbial network stability and metabolite profiles as contributors to symptom persistence and potential therapeutic targets.<br><br>IMPORTANCE: Celiac disease (CD) is a chronic immune-mediated systemic disorder caused by consuming gluten in genetically susceptible individuals. There is currently no cure for CD, and the most effective treatment is maintaining a strict, lifelong gluten-free diet (GFD). This nutritional therapy aims to prevent the immune reaction triggered by gluten and promote the healing of the intestinal lining, resolving the clinical, serological, and histological abnormalities within 6-12 months. However, up to 30% of patients may continue to experience symptoms or exhibit laboratory abnormalities or intestinal inflammation suggestive of active CD, despite following a GFD. This challenge, which encompasses various diagnoses, is known as nonresponsive celiac disease (NRCD). In this study, we explored the role of intestinal microbiota in causing NRCD, finding an association between the persistence of symptoms and changes in mucosal integrity biomarkers, with different gut microbiome structures among NRCD patients, indicating a significant role of the microbiome in NRCD.}, }
@article {pmid40475999, year = {2025}, author = {Hwang, D and Chong, E and Li, Y and Li, Y and Roh, K}, title = {Deciphering the gut microbiome's metabolic code: pathways to bone health and novel therapeutic avenues.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1553655}, pmid = {40475999}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bone and Bones/metabolism ; Animals ; Probiotics/therapeutic use ; *Bone Remodeling/physiology ; *Osteoporosis/metabolism/microbiology/therapy ; Prebiotics ; Fecal Microbiota Transplantation ; Bone Diseases/metabolism/microbiology/therapy ; }, abstract = {The gut microbiome plays an important role in the protection against various systemic diseases. Its metabolic products profoundly influence a wide range of pathophysiological events, including the regulation of bone health. This review discusses the recently established connections between the gut microbiome and bone metabolism, focusing on the impact of microbiome-derived metabolites such as SCFAs, Bile Acids, and tryptophan to the control of bone remodeling and immunoreactions. Recent advances in metagenomics and microbiome profiling have unveiled new exciting therapeutic opportunities, ranging from the use of probiotics, prebiotics, engineered microbes, and to fecal microbiota transplantation. Understanding of the interplay among diet, microbiota, and bone health provides new avenues for tailored interventions aimed at reducing disease risk in osteoporosis and other related disorders. By drawing knowledge from microbiology, metabolism, and bone biology, this review highlights the potential of microbiome-targeted therapies to transform skeletal health and the management of bone diseases.}, }
@article {pmid40475488, year = {2025}, author = {Price, A and Rasolofomanana-Rajery, S and Manpearl, K and Robertson, CE and Krebs, NF and Frank, DN and Krishnan, A and Hendricks, AE and Tang, M}, title = {Network-based representation learning reveals the impact of age and diet on the gut microbial and metabolomic environment of U.S. infants in a randomized controlled feeding trial.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.01.621627}, pmid = {40475488}, issn = {2692-8205}, abstract = {While studies have explored differences in gut microbiome development for infant liquid diets (breastmilk, formula), little is known about the impact of complementary foods on infant gut microbiome development. Here, we investigated how different protein-rich foods (i.e., meat vs. dairy) affect fecal metagenomics and metabolomics during early complementary feeding from 5-12 months in U.S. formula-fed infants from a randomized controlled feeding trial. We used a network representation learning approach to model the time-dependent, complex interactions between microbiome features, metabolite compounds, and diet. We then used the embedded space to detect features associated with age and diet type and found the meat diet group was enriched with microbial genes encoding amino acid, nucleic acid, and carbohydrate metabolism. Compared to a more traditional differential abundance analysis, which analyzes features independently and found no significant diet associations, network node embedding represents the infant samples, microbiome features, and metabolites in a single transformed space revealing otherwise undetected associations between infant diet and the gut microbiome.}, }
@article {pmid40475394, year = {2025}, author = {Ebadi, M and Gem, H and Sebastian, G and Abasaeed, R and Lloid, M and Tseng, YD and Mian, OY and Minot, S and Dean, DR and Rashidi, A}, title = {Different Patterns of Oral Mucositis and Microbiota Injury After Total Body Irradiation- Versus Chemotherapy-Based Myeloablative Allogeneic Hematopoietic Cell Transplantation.}, journal = {Advances in radiation oncology}, volume = {10}, number = {6}, pages = {101787}, pmid = {40475394}, issn = {2452-1094}, abstract = {PURPOSE: Oral mucositis (OM) is a common complication of allogeneic hematopoietic cell transplantation, causing pain, infections, swallowing/speech impairment, and poor quality of life. We hypothesized that patterns (severity and dynamics) of OM and oral microbiota disruptions may be different after high-dose total body irradiation (TBI)- versus chemotherapy-based myeloablative conditioning.<br><br>METHODS AND MATERIALS: We conducted an exploratory study including comprehensive, longitudinal mucositis assessment, paired with supragingival plaque and saliva collection. OM was assessed at baseline and days +7, +14, +21, +28, and +84. Total mucositis score at each timepoint was calculated from objective findings in 2 domains and 9 oral sites using a validated scoring system. Plaque and saliva samples (baseline and days +14, +28, and +84) were profiled using shotgun metagenomic sequencing.<br><br>RESULTS: A total of 249 OM assessments were performed and 342 samples were collected from 47 patients (27 chemotherapy-based, 20 TBI-based). Salivary flow rate remained stable in the chemotherapy-based cohort, but steadily declined in the TBI-based cohort, reaching a significantly lower level in the TBI-based cohort at day +84 both compared to baseline and the chemotherapy-based cohort. OM severity peaked at day +7 in the TBI-based cohort versus day +14 in the chemotherapy-based cohort. Day +14 OM was significantly more severe in the chemotherapy-based cohort; other timepoints were not different. Although the cohorts were similar in plaque microbiota composition at baseline, they became significantly different at all post- hematopoietic cell transplantation timepoints. Salivary microbiota composition was not significantly different between the 2 cohorts. Day +84 plaque microbiota diversity was significantly higher in the TBI-based cohort.<br><br>CONCLUSIONS: We demonstrated different patterns of OM, microbiota injury, and salivary flow rate after TBI- versus chemotherapy-based conditioning. If validated in future studies, our findings could enhance evidence-based pretransplant counseling on oral toxicity and have implications for short- and long-term oral health in transplant survivors.}, }
@article {pmid40475346, year = {2025}, author = {Wang, Z and Wei, X and Piao, L and Zhang, X and Wang, H}, title = {Gut microbiota dysbiosis and metabolic shifts in pediatric norovirus infection: a metagenomic study in Northeast China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1600470}, pmid = {40475346}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; China/epidemiology ; *Caliciviridae Infections/microbiology/virology ; *Norovirus ; Metagenomics ; Feces/microbiology ; Male ; Female ; *Gastroenteritis/virology/microbiology ; Child, Preschool ; Child ; Infant ; Bacteria/classification/genetics/isolation &amp; purification ; Longitudinal Studies ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Norovirus (NoV) is a leading cause of acute gastroenteritis in pediatric populations worldwide. However, the role of gut microbiota in NoV pathogenesis remains poorly understood.<br><br>METHODS: We conducted a longitudinal metagenomic analysis of fecal samples from 12 NoV-infected children and 13 age-matched healthy controls in Northeast China. Microbial composition and functional pathways were assessed using high-throughput shotgun sequencing and bioinformatic profiling.<br><br>RESULTS: NoV infection was associated with significant gut microbial dysbiosis, including increased alpha diversity and distinct taxonomic shifts. Notably, Bacteroides uniformis, Veillonella spp., and Carjivirus communis were enriched in infected individuals. Functional analysis revealed upregulation of metabolic pathways involved in carbohydrate and lipid processing. These microbial and functional alterations persisted over time and correlated with disease severity.<br><br>CONCLUSIONS: Our findings reveal novel associations between NoV infection and gut microbiota dysbiosis, particularly the enrichment of Bacteroides uniformis, which may influence host-pathogen interactions via metabolic or immune mechanisms. The identified microbial and metabolic signatures offer potential biomarkers for diagnosis and targets for microbiota-based therapeutic strategies in pediatric NoV infection.}, }
@article {pmid40475274, year = {2025}, author = {Lv, Y and Peng, S and Liu, Y and Yang, H and Li, G and Peng, Y}, title = {Cross-omics analysis reveals microbe-metabolism interactions characteristic of gingival enlargement associated with fixed orthodontic in adolescents.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2513739}, pmid = {40475274}, issn = {2000-2297}, abstract = {OBJECTIVES: To investigate the oral microbiome and metabolome longitudinal changes associated with orthodontic treatment-induced gingival enlargement (OT-GE).<br><br>METHODS: Twenty-six subjects were divided into case and control groups based on the gingival overgrowth index (GOi). The OT-GE group was divided into the no gingival enlargement (OT-GE0, n&#x2009;=&#x2009;5) and persistent gingival enlargement (OT-GE1, n&#x2009;=&#x2009;11). The control group included orthodontic treatment periodontal health (OT-GH, n&#x2009;=&#x2009;5), and no orthodontic treatment periodontal health (NOT-GH, n&#x2009;=&#x2009;5). Microbial composition and metabolites in saliva were investigated using cross-omics.<br><br>RESULTS: Longitudinal analysis linked orthodontic treatment-induced gingival enlargement to distinct oral microbiome and metabolome shifts. The OT-GE group showed significantly higher bleeding on probing (BOP), plaque scores (p&#x2009;<&#x2009;0.001), probing depth, GOi, and ligature wire differences (p&#x2009;<&#x2009;0.05) versus controls. Microbial diversity and species richness were elevated in OT-GE (p&#x2009;<&#x2009;0.05), though no differences emerged between OT-GE0 and OT-GE1) subgroup (p&#x2009;>&#x2009;0.05). Cross-omics identified specific periodontal pathogens and metabolites linked to gingival enlargement. Disrupted amino acid biosynthesis pathways, particularly citrulline metabolism, correlated with functional gene dysregulation and microbial imbalance. Aberrant citrulline intake appeared to drive dysbiosis, potentially contributing to gingival overgrowth.<br><br>CONCLUSIONS: OT-GE pathogenesis involves functional gene-regulated metabolite metabolism influencing periodontal pathogens.}, }
@article {pmid40475154, year = {2025}, author = {Cotto, I and Durán-Viseras, A and Jesser, KJ and Zhou, NA and Hemlock, C and Albán, V and Ballard, AM and Fagnant-Sperati, CS and Lee, GO and Hatt, JK and Royer, C and Eisenberg, JNS and Trueba, G and Konstantinidis, KT and Levy, K and Fuhrmeister, ER}, title = {Environmental Exposures and the Human Gut Resistome in Northwest Ecuador.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.05.23.25327954}, pmid = {40475154}, abstract = {Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We used metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Escherichia coli , Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) were detected across all age groups, but the highest abundance was found in children compared to mothers. In mothers, higher animal exposure trended towards a higher number of unique ARGs compared to low animal exposure (β= -5.58 [95% CI: -11.46, 0.29]) and was significantly associated with greater taxonomic diversity (β= -1.29 [-1.96, -0.63]). In addition, mothers with sewer systems or septic tanks and piped drinking water had fewer unique ARGs (β= -3.52 [-6.74, -0.30]) compared to those without, and mothers with longer duration of drinking water access had lower total ARG abundance (β= -0.05 [-0.1, -0.01]). In contrast, few associations were observed in children, likely due to the dynamic nature of the gut microbiome during early childhood. Improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut.}, }
@article {pmid40477893, year = {2023}, author = {Yu, Y and Zhang, Q and Zhang, Z and Xu, N and Li, Y and Jin, M and Feng, G and Qian, H and Lu, T}, title = {Assessment of residual chlorine in soil microbial community using metagenomics.}, journal = {Soil ecology letters}, volume = {5}, number = {1}, pages = {66-78}, pmid = {40477893}, issn = {2662-2297}, abstract = {Chlorine-containing disinfectants have been widely used around the world for the prevention and control of the COVID-19 pandemic. However, at present, little is known about the impact of residual chlorine on the soil micro-ecological environment. Herein, we treated an experimental soil-plant-microbiome microcosm system by continuous irrigation with a low concentration of chlorine-containing water, and then analyzed the influence on the soil microbial community using metagenomics. After 14-d continuous chlorine treatment, there were no significant lasting effect on soil microbial community diversity and composition either in the rhizosphere or in bulk soil. Although metabolic functions of the rhizosphere microbial community were affected slightly by continuous chlorine treatment, it recovered to the original status. The abundance of several resistance genes changed by 7 d and recovered by 14 d. According to our results, the chlorine residue resulting from daily disinfection may present a slight long-term effect on plant growth (shoot length and fresh weight) and soil micro-ecology. In general, our study assisted with environmental risk assessments relating to the application ofchlorine-containing disinfectants and minimization of risks to the environment during disease control, such as COVID-19.}, }
@article {pmid40474246, year = {2025}, author = {Denison, ER and Pound, HL and Gann, ER and Gilbert, NE and Weston, DJ and Pelletier, DA and Wilhelm, SW}, title = {Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {62}, pmid = {40474246}, issn = {2524-6372}, support = {DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-SC0020362//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; DE-AC05-00OR22725//U.S. Department of Energy/ ; DE-AC05-00OR22725//U.S. Department of Energy/ ; }, }
@article {pmid40474206, year = {2025}, author = {Tubbesing, T and Schlüter, A and Sczyrba, A}, title = {subMG automates data submission for metagenomics studies.}, journal = {BioData mining}, volume = {18}, number = {1}, pages = {38}, pmid = {40474206}, issn = {1756-0381}, support = {101081957//HORIZON EUROPE European Research Council/ ; 460129525 (NFDI4Microbiota)//Deutsche Forschungsgemeinschaft/ ; NNF200C0062223//Novo Nordisk Fonden/ ; }, abstract = {BACKGROUND: Publicly available metagenomics datasets are crucial for ensuring the reproducibility of scientific findings and supporting contemporary large-scale studies. However, submitting a comprehensive metagenomics dataset is both cumbersome and time-consuming. It requires including sample information, sequencing reads, assemblies, binned contigs, metagenome-assembled genomes (MAGs), and appropriate metadata. As a result, metagenomics studies are often published with incomplete datasets or, in some cases, without any data at all. subMG addresses this challenge by simplifying and automating the data submission process, thereby encouraging broader and more consistent data sharing.<br><br>RESULTS: subMG streamlines the process of submitting metagenomics study results to the European Nucleotide Archive (ENA) by allowing researchers to input files and metadata from their studies in a single form and automating downstream tasks that otherwise require extensive manual effort and expertise. The tool comes with comprehensive documentation as well as example data tailored for different use cases and can be operated via the command-line or a graphical user interface (GUI), making it easily deployable to a wide range of potential users.<br><br>CONCLUSIONS: By simplifying the submission of genome-resolved metagenomics study datasets, subMG significantly reduces the time, effort, and expertise required from researchers, thus paving the way for more numerous and comprehensive data submissions in the future. An increased availability of well-documented and FAIR data can benefit future research, particularly in meta-analyses and comparative studies.}, }
@article {pmid40473843, year = {2025}, author = {Wu, S and Wang, S and Wu, Z and Chen, M and Chen, X and Lei, D and Peng, C}, title = {Comparative analysis of the clinical characteristic and lung microbiota in adult and elderly patients with pulmonary tuberculosis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19777}, pmid = {40473843}, issn = {2045-2322}, support = {2023K146//Quzhou City science and technology plan project/ ; }, mesh = {Humans ; Middle Aged ; Male ; Female ; *Tuberculosis, Pulmonary/microbiology/diagnosis/diagnostic imaging ; Aged ; Adult ; *Lung/microbiology/diagnostic imaging ; *Microbiota/genetics ; Retrospective Studies ; Age Factors ; High-Throughput Nucleotide Sequencing ; Young Adult ; Aged, 80 and over ; }, abstract = {The proportion of elderly people infected with tuberculosis (TB) is increasing, and misdiagnosis and missed diagnosis are common. This study aimed to explore the diagnostic value of metagenomic next-generation sequencing (mNGS) for pulmonary TB (PTB) and to investigate age-related differences in lung microbial composition, clinical characteristics and imaging findings among PTB patients. We retrospectively recruited 162 suspected PTB patients, and finally 143 patients were used in this analysis. Patients were classified into two groups: adult (18 ≤ age < 60, n = 66) and elderly (Age ≥ 60, n = 77). Differences and associations in clinical characteristics, imaging findings, and lung microbiota were analyzed. Compared to adult patients, elderly patients had a higher prevalence of hypertension (31.17% vs. 9.09%, P = 0.0012), fever (20.78% vs. 4.55%, P = 0.0044) and chest tightness (24.68% vs. 10.61%, P = 0.0297), but a lower prevalence of chest pain (7.58% vs. 0%, P = 0.0139). For TB identification, mNGS had the highest positive rate (100%), followed by T-spot (74.75%), GeneXpert (37.80%) and acid-fast staining (AFS) (7.30%), and all the conventional methods showed slight higher positive rates in the elderly group compared to the adult group (P > 0.05). Bilateral lung infection was more common in elderly patients (79.22% vs. 60.61%, P = 0.0148), with infiltration (32.17%, 46/143), shadows (26.57%, 38/143), nodules (20.28%, 29/143), and bronchiectasis (20.28%, 29/143) being the most common imaging features. The diversity of the lung microbial communities was significantly lower in elderly patients compared to adults (P < 0.05). Clinical characteristics, imaging findings, and the top 20 most abundant species in lung microbiota showed significantly positive correlation. This study demonstrates that mNGS has excellent diagnostic value for PTB in both adult and elderly patients. Significant differences in clinical characteristics, imaging, and lung microbial composition were observed between the two groups. Understanding these differences may aid in the diagnosis and treatment of tuberculosis in elderly patients.}, }
@article {pmid40473402, year = {2025}, author = {Barnich, N and Arthur, JC and Buisson, A and Campbell, BJ and Carbonnel, F and Chassaing, B and Coombes, BK and Denizot, J and Dogan, B and Faith, J and Kamada, N and Longman, RS and Martinez-Medina, M and O'Brien, CL and Sartor, RB and Zhang, S and ,  and Colombel, JF and Simpson, KW and , }, title = {Adherent-invasive Escherichia coli in Crohn's disease: the 25th anniversary.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-335331}, pmid = {40473402}, issn = {1468-3288}, abstract = {In 1998, Arlette Darfeuille-Michaud, Christel Neut and Jean-Frederic Colombel discovered a novel pathovar of Escherichia coli, adherent and invasive Escherichia coli (AIEC), in the ileum of patients with Crohn's disease (CD), that was genetically distinct from diarrheagenic E. coli, could adhere to and invade intestinal epithelial cells and survive in macrophages. The consistent association between AIEC and CD (approximately 30% across the world), their ability to exploit CD-associated genetic traits, and virulence in preclinical colitis models but not healthy hosts spurred global research to elucidate their pathogenicity. Research focused on integrating AIEC with the microbiome, metabolome, metagenome, host response and the impact of diet and antimicrobials has linked the luminal microenvironment and AIEC metabolism to health and disease. This deeper understanding has led to therapeutic trials and precision medicine targeting AIEC-colonised patients. In November 2023, prominent members of the AIEC research community met to present and discuss the many facets of basic, translational and clinical AIEC fields at 'AIEC: past, present and future' in NYC. This review is a summary of this international meeting highlighting the history of AIEC, knowledge accumulated over the past 25 years about its pathogenic properties and proposes a standardised approach for screening patients for AIEC.}, }
@article {pmid40473141, year = {2025}, author = {Luo, Y and Liao, H and Wu, L and Wu, M and Luo, Y and Yao, Y and Ji, W and Gao, L and Xia, X}, title = {Temperature adaptability drives functional diversity and horizontal gene transfer within microbial communities in Daqu solid-state fermentation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132770}, doi = {10.1016/j.biortech.2025.132770}, pmid = {40473141}, issn = {1873-2976}, abstract = {The spontaneous solid-state fermentation of high-temperature Daqu (HTD) is a temperature-dependent stacking bioprocessing for enriching microbiota and enzymes to guarantee efficient substrate utilization and fermentation. However, there is a lack of clarity regarding how temperature adaptability affects HTD microbial assembly, domestication direction, and metabolic profile. Here, the flavor substances, microbial assembly, metabolic network, and horizontal gene transfer (HGT) events of three HTDs from Renshu (RS), Jiushang (JS), and Maoyuan (MY) were analyzed. 125 volatile compounds were identified, tetramethylpyrazine, 3-methyl-butanoic acid, phenylethyl alcohol, and trimethylpyrazine were clarified as the typical flavor substances. Bacillus and Kroppenstedtia were the shared dominant bacterial genera. Paecilomyces, Aspergillus, Rasamsonia, and Lichtheimia were dominant fungal genera. Differences in flavor metabolism, microbial structure, and key enzyme metabolism are strongly correlated with sample distance. As proximity decreases, the microbial structural and functional metabolic traits tend to exhibit greater similarity. The frequency of HGT events was analyzed using MetaCHIP, 49, 9 and 69 groups of HGT events occurred in RS, JS, and MY, respectively. HGT events occurred most abundantly in Bacillaceae, and the microbial taxa with a closer phylogenetic relationship possessed the highest incidence of HGT. Specifically, the occurrence of HGT was mainly associated with high-temperature adaptability. It was also linked to characteristic flavor metabolism. Our results revealed the effects of temperature stress on microbial regulation of HTD and adaptive transfer of relevant genes in stacked fermented HTDs. This work provides important insights into HTD quality classification and regulation of solid-state fermentation quality and efficiency through microbial domestication.}, }
@article {pmid40473125, year = {2025}, author = {Darwiche, S and Gacesa, R and Ferraro, RB and Alwan, W and Oben, JA and Rashidghamat, E and Long, PF}, title = {Prevalence of skin fungi markedly declines in the lesions of two patients with moderate Hidradenitis Suppurativa.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107778}, doi = {10.1016/j.micpath.2025.107778}, pmid = {40473125}, issn = {1096-1208}, abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disorder affecting hair follicles in intertriginous regions, leading to painful nodules, sinus tracts, and scarring. The pathogenesis of HS is far from clear, but alterations in the bacterial community of the skin microbiome has been debated, yet the potential involvement of fungi - the mycobiome - has received almost no attention. Large areas of skin were sampled for amplicon metagenomics sequencing to negate the inference of low-sequence counts with the objective of examining the provenance of fungi between lesion and lesion-free skin from the same individuals. The DNA from skin swabs was isolated and the V4 region of the 18S rRNA gene was amplified and sequenced. Total fungal counts were inferred from taxonomic assignment of unique operational taxonomic units and absolute numbers then compared between skin sites. There were dramatically lower numbers of fungi in HS lesions with Malassezia dominance, as expected, across samples. This finding suggested, for the first time, that fungal depletion in lesions might be linked to HS pathology through disruption of normal skin barrier function and immunity, potentially due to reduced sebum production essential for fungal growth.}, }
@article {pmid40472755, year = {2025}, author = {Chen, M and Xing, L and Gao, S and Guo, Y and Qiu, T and Wang, X and Gao, M}, title = {Metagenomic analysis deciphers airborne pathogens with enhanced antimicrobial resistance and virulence factors in composting facilities.}, journal = {Environment international}, volume = {201}, number = {}, pages = {109569}, doi = {10.1016/j.envint.2025.109569}, pmid = {40472755}, issn = {1873-6750}, abstract = {The composting process has been shown to effectively reduce antimicrobial resistance (AMR) in animal manure, but its influence on surrounding airborne AMR remains unknown, particularly with regard to human-pathogenic antibiotic-resistant bacteria (HPARB). In this study, air and paired compost samples were collected from a full-scale composting facility, and the antibiotic resistome, microbiome, and HPARB were systematically analyzed in both two habitats using metagenomic analysis. Current result uncovered the profiles of HPARB in air, showing that significantly more airborne HPARB were assembled than that in compost samples. Airborne pathogens harboredan increased abundance and diversity of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in comparison with compost-borne HPARB. The core antibiotic resistome represents 18.58% of overall ARG subtypes, contributing to 86.31% of ARG abundance. A higher number of enriched core ARGs (2.16- to 13.36-times higher), including mexF, tetW, and vanS, were observed in air samples compared to compost samples. As an important human pathogen, Mycobacterium tuberculosis was prevalent in the air and carried more ARG (6) and VFG (130) subtypes than those in compost. A significantly higher risk score was detected for airborne AMR in the composting facility compared to that in hospital and urban environments. This study revealed the enhanced airborne HPARB through comparative experiments between air and composting habitats. It highlighted the unrecognized AMR risks associated with air in composting site and provided a scientific basis for accurately assessing health outcomes caused by occupational exposure.}, }
@article {pmid40472476, year = {2025}, author = {Wang, JZ and Wang, JB and Yuan, D and Sun, CH and Hou, LL and Zhang, Y and Yang, XH and Xie, HX and Gao, YX}, title = {Metagenomic next-generation sequencing-based diagnosis of Pneumocystis jirovecii pneumonia in patients without human immunodeficiency virus infection: A dual-center retrospective propensity matched study.}, journal = {Journal of infection and public health}, volume = {18}, number = {9}, pages = {102831}, doi = {10.1016/j.jiph.2025.102831}, pmid = {40472476}, issn = {1876-035X}, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP), caused by Pneumocystis jirovecii (PJ), is an opportunistic infection prevalent in clinical settings. However, large-scale studies on the efficacy of metagenomic next-generation sequencing (mNGS)-based diagnosis of PJP in patients without human immunodeficiency virus infection (HIV) are lacking.<br><br>METHODS: The study included 168 patients diagnosed with either PJP (84) or other pneumonia types (non-PJP patients; 84) who underwent mNGS-mediated bronchoalveolar lavage fluid (BALF) analysis, Gomori methenamine silver (GMS) staining and peripheral blood 1,3-beta-D-glucan (BDG) testing. Additionally, patients with PJP were categorized into survival (n&#x202f;=&#x202f;55) and non-survival (n&#x202f;=&#x202f;29) groups based on a 28-day in-hospital outcome to compare clinical characteristics, inflammatory markers, PJ sequence counts in BALF, and serum BDG levels.<br><br>RESULTS: Serum BDG levels, the proportion of patients with serum BDG of >&#x202f;60&#x202f;pg/mL and >&#x202f;200&#x202f;pg/mL were notably higher in the PJP group compared with that in the non-PJP group (all P< 0.05). The sensitivity and specificity of mNGS in diagnosing PJP were higher than those of serum BDG testing (sensitivity: 100&#x202f;% vs. 63.0&#x202f;%; specificity: 96.4&#x202f;% vs. 90.4&#x202f;%; both P< 0.05). The most common coinfection was viral (30.9&#x202f;%), followed by bacterial-viral coinfections (13.0&#x202f;%). Treatment regimens were altered for 83.3&#x202f;% of patients based on the mNGS results. The patients in the non-survival group showed markedly higher serum BDG levels (142.5 [32.7, 277.7] vs. 123.0 [34.0, 164.0]) and a higher proportion of PJ sequence counts of >&#x202f;1&#x202f;&#xd7;&#x202f;10[5] (13.7&#x202f;% vs. 0, P= 0.005) relative to those in the survival group.<br><br>CONCLUSION: The mNGS showed superior performance over serum BDG testing and GMS staining in diagnosing PJP in non-HIV patients and identified a broader range of coinfections.}, }
@article {pmid40472426, year = {2025}, author = {Zhuang, X and Wu, J and Liu, X and Lin, J and Wang, Z and Wang, Y}, title = {The synergistic corrosion of carbon steel by sulfate-reducing bacteria and methanogenic archaea microbial communities.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {166}, number = {}, pages = {109015}, doi = {10.1016/j.bioelechem.2025.109015}, pmid = {40472426}, issn = {1878-562X}, abstract = {The impact of sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) on the corrosion of carbon steel was examined through weight loss tests, electrochemical measurements, surface analyses, and metagenomic analyses. The findings indicated that SRB and MA exhibited a synergistic effect on the corrosion process. This resulted in a significant increase in corrosion weight loss in the SRB + MA group (16.05 mg/cm[2]), which was 8.64 times that of the SRB group (1.86 mg/cm[2]) and 1.58 times that of the MA group (10.14 mg/cm[2]). This synergistic effect can be attributed to the influence of SRB and MA on the formation of corrosion products, producing more corrosion products such as FeS in the mixed group. In addition, the corrosion of carbon steel is further enhanced by electron transfer process between carbon steel and microorganisms in the mixed group.}, }
@article {pmid40472396, year = {2025}, author = {Zheng, F and Guo, X and Zhang, W and Wang, Y and Hu, E and Guo, X and Su, H and Deng, C}, title = {Insights into the functional characteristics of rhubarb (Rheum officinale Baill) treatment on experimental traumatic brain injury through network pharmacology with metagenomics.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {143}, number = {}, pages = {156853}, doi = {10.1016/j.phymed.2025.156853}, pmid = {40472396}, issn = {1618-095X}, abstract = {BACKGROUND: Traumatic brain injury (TBI) imposes a heavy burden on society and families owing to its high morbidity and mortality. Rhubarb has been noticed in the Chinese herb for treating TBI. The pharmacological effects include anti-inflammation, anti-bacterial, and purgative. But little is known about its potential mechanism when treating TBI.<br><br>PURPOSE: In this study, we profiled the pharmacological and intestinal functional characteristics of rhubarb in post-TBI mice.<br><br>METHODS: Fifty adult male C57BL/6 mice were randomly allocated into five groups, including sham, controlled cortical impact (CCI), and rhubarb extract administered at low, medium, and high doses. The impaired neurobehavioral function was assessed using the modified neurological severity score (mNSS) and the wire hang test. hematoxylin-eosin (HE) and Nissl staining, terminal deoxynucleotidyl transferase-mediated dUTP-nick-end labeling (TUNEL) and immunoglobulin-&#x3b3; (IgG) staining, immunostaining for GFAP, TNF-&#x3b1; and IL-1&#x3b2; were applied to detect the histological damage, neuronal apoptosis and blood-brain barrier (BBB) permeability, respectively. Subsequently, the network pharmacology approaches was used to identify putative therapeutic targets and the relevant pathway of rhubarb on TBI. In addition, metagenomics and targeted metabolomics revealed the alterations in composition and functions of gut flora and gut-derived serum short-chain fatty acids (SCFAs). Finally, we depleted the gut microbiota with an antibiotic cocktail (ampicillin, metronidazole, neomycin, vancomycin) to uncover the critical role of gut microbiota on rhubarb function.<br><br>RESULTS: Rhubarb reduced brain IgG leakage and neuronal apoptosis after TBI. The network pharmacology analysis identified seven genes as key potential therapeutic targets of rhubarb, and the genes were related to inflammation, oxidant and apoptosis. The enrichment analysis showed that three of the top signal pathways were involved in anti-inflammation, anti-apoptosis and anti-oxidant. The metagenomics analysis showed that rhubarb reshaped the structure and abundance of gut microbiota in TBI. The altered function of gut microbiota was enriched in the improvement of carbohydrate metabolism, gut-derived serum SCFAs and microbial resistance. Finally, gut microbiota depletion confirmed the effects of rhubarb on post-TBI IgG leakage and neuronal apoptosis were depended on gut microbiota.<br><br>CONCLUSIONS: Rhubarb may treat TBI by effects of targeting inflammatory factors and oxidant factors to inhibit neuronal apoptosis and protect the BBB. The therapeutic effects of rhubarb are partly mediated by altering gut microbiota. Our findings not only highlight a holistic and microbial potential of rhubarb's therapeutic functional actions but also elucidate previously unrecognized therapeutic development of novel targets and strategies for TBI therapies by rhubarb.}, }
@article {pmid40472050, year = {2025}, author = {Kawashima, A and Yanagawa, Y and Chikata, T and Shimogawara, R and Mizushima, D and Tsuchiya, K and Yagita, K and Gatanaga, H and Watanabe, K}, title = {Optimization of TaqMan-based quantitative PCR diagnosis for Entamoeba histolytica using droplet digital PCR.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {6}, pages = {e0012935}, doi = {10.1371/journal.pntd.0012935}, pmid = {40472050}, issn = {1935-2735}, abstract = {BACKGROUND: TaqMan-probed quantitative PCR (qPCR) is highly valued for diagnosing Entamoeba histolytica infections (amebiasis). However, unclear cycle threshold (Ct) values often yield low-titer positive results, complicating interpretation. This study aimed to optimize qPCR primer-probe sets with logically determined cut-off Ct value using droplet digital PCR (ddPCR).<br><br>Amplification efficacy was evaluated using ddPCR by measuring absolute positive droplet counts (APD) and mean fluorescence intensity at different PCR cycles and annealing temperatures (AT). A primer-probe specific cut-off Ct value was determined from a standard curve by correlating Ct values with APD. Twenty primer-probe sets targeting small subunit rRNA gene regions (X64142) were designed from previous papers. Amplification efficacy remained consistent at high PCR cycles (50 cycles), but differed at lower PCR cycles (30 cycles), identifying five sets with higher amplification efficiency than other candidates. Of these, only two sets maintained efficiency at higher AT (62&#xb0;C). Ct value was inversely proportional to the square of APD, defining the specific cut-off Ct value as 36 cycles. Selected primer-probe set with a cut-off effectively differentiated E. histolytica infection in clinical specimens. However, discordant results between Ct value and APD were seen in some cases with high Ct value. Shotgun metagenomic sequencing suggested microbial-independent false positive reactions contributed to these discrepancies, although specific reactants were unidentified.<br><br>CONCLUSIONS/SIGNIFICANCE: The combination use of ddPCR with qPCR revealed that false positive reactions of qPCR and/or ddPCR commonly happen in stool specimens. Also, this study emphasizes the value of ddPCR for establishing accurate cut-off values with efficient primer-probes.}, }
@article {pmid40471671, year = {2025}, author = {Alam, AM and Houlihan, CF and Bharucha, T}, title = {Novel techniques for the diagnosis of neurological infections.}, journal = {Current opinion in neurology}, volume = {}, number = {}, pages = {}, doi = {10.1097/WCO.0000000000001395}, pmid = {40471671}, issn = {1473-6551}, abstract = {PURPOSE OF REVIEW: On World Encephalitis Day 19th February 2025, Encephalitis International launched the World Health Organization technical brief on encephalitis, highlighting the growing public health challenge and need for improved diagnostics. This review summarizes the published literature over the last 18 months on novel methods of identifying the aetiology of neurological infections and existing research gaps.<br><br>RECENT FINDINGS: There is an increased availability and sensitivity of multiplex polymerase chain reaction assays and untargeted metagenomic sequencing in clinical practice. This is contributing to increasing diagnostic yield in suspected neurological infections. Preliminary results suggest that novel serological methods such as phage immunoprecipitation sequencing (Phip-seq) may be useful where molecular approaches are negative.<br><br>SUMMARY: Significant progress in improving diagnostics has been made in the last decade. Going forward, multicentre studies and meta-analyses are needed to achieve adequate power in ascertaining the role of novel diagnostic methods in neurological infections. Studies need to investigate the impact on patient management and cost-effectiveness. The role of other omics methods in identifying host biomarkers for utilization in diagnostic algorithms needs further work.}, }
@article {pmid40470551, year = {2025}, author = {Yang, L and Yang, Q and Li, J and Zhang, L and Liu, S and Lian, C}, title = {Pneumocystis jirovecii pneumonia in anti-MDA5-positive dermatomyositis: characterisation, risk factors and prognosis.}, journal = {Clinical and experimental rheumatology}, volume = {}, number = {}, pages = {}, doi = {10.55563/clinexprheumatol/hpx173}, pmid = {40470551}, issn = {0392-856X}, abstract = {OBJECTIVES: This study aimed to identify risk and prognostic factors of Pneumocystis jirovecii pneumonia (PJP) in patients with anti-melanoma differentiation-associated gene 5 antibody-positive dermatomyositis (anti-MDA5+DM).<br><br>METHODS: We conducted a retrospective cohort study of anti-MDA5+DM patients who underwent metagenomic next-generation sequencing analysis of bronchoalveolar lavage fluid or lung tissue at our center between January 2019 and February 2023. Eligible patients were stratified into PJP+ and PJP- groups based on PJP status. Potential risk factors and prognostic indicators for PJP were analysed using univariate and multivariate logistic regression analysis.<br><br>RESULTS: A total of 107 anti-MDA5+DM patients were enrolled, of whom 47 were assigned to the PJP+ group. Multivariate logistic regression analysis revealed older age and high cumulative dosage of glucocorticoids within 3 months preceding PJP diagnosis were independent risk factors for PJP development. Conversely, prophylactic-dose trimethoprim-sulfamethoxazole (TMP/SMZ) was associated with a significantly reduced risk of PJP (all p<0.05). The 30-day mortality rate in the PJP+ group was 55.3%. Short disease duration and immunosuppressive therapy exposure, severe hypoxia, extensive radiological interstitial lung disease, moderate to severe acute respiratory distress syndrome, mechanical ventilation were associated with unfavourable prognosis (all p<0.05). Glucocorticoids therapy was more frenquently administered in survivors (p<0.05).<br><br>CONCLUSIONS: PJP significantly increases early mortality of anti-MDA5+DM patients. Clinicians should identify high-risk patients early and administer prophylactic-dose TMP/SMZ for PJP prophylaxis.}, }
@article {pmid40469774, year = {2025}, author = {Levy Karin, E and Steinegger, M}, title = {Cutting-edge deep-learning based tools for metagenomic research.}, journal = {National science review}, volume = {12}, number = {6}, pages = {nwaf056}, pmid = {40469774}, issn = {2053-714X}, abstract = {Recent years have seen incredible progress in the development of deep-learning (DL) tools for the analysis of biological data, with the most prominent example being AlphaFold2 for accurate protein structure prediction. DL-based tools are especially useful for identifying patterns and connections within sparsely labeled datasets. This makes them essential for the analysis of metagenomic data, which is mostly unannotated and bears little sequence similarity to known genes and proteins. In this review, we chose to present 12 tools which we deem as offering novel capabilities for metagenomic analysis by utilizing interesting DL techniques. This review is thus intended to be a solid starting point for any data scientist looking to apply advanced methods to explore metagenomic datasets. For each DL-based tool, we present its computational principles, followed by relevant examples of its application where possible and a note on its limitations.}, }
@article {pmid37732396, year = {2025}, author = {Lajmi, A and Glinka, F and Privman, E}, title = {Optimizing ddRAD sequencing for population genomic studies with ddgRADer.}, journal = {Molecular ecology resources}, volume = {25}, number = {5}, pages = {e13870}, doi = {10.1111/1755-0998.13870}, pmid = {37732396}, issn = {1755-0998}, support = {2017319//US-Israel Binational Science Foundation/ ; }, mesh = {*Sequence Analysis, DNA/methods ; *Genetics, Population/methods ; *Software ; *Computational Biology/methods ; *Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; }, abstract = {Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is widely used to generate genomic data for non-model organisms in evolutionary and ecological studies. Along with affordable paired-end sequencing, this method makes population genomic analyses more accessible. However, multiple factors should be considered when designing a ddRADseq experiment, which can be challenging for new users. The generated data often suffer from substantial read overlaps and adaptor contamination, severely reducing sequencing efficiency and affecting data quality. Here, we analyse diverse datasets from the literature and carry out controlled experiments to understand the effects of enzyme choice and size selection on sequencing efficiency. The empirical data reveal that size selection is imprecise and has limited efficacy. In certain scenarios, a substantial proportion of short fragments pass below the lower size-selection cut-off resulting in low sequencing efficiency. However, enzyme choice can considerably mitigate inadvertent inclusion of these shorter fragments. A simple model based on these experiments is implemented to predict the number of genomic fragments generated after digestion and size selection, number of SNPs genotyped, number of samples that can be multiplexed and the expected sequencing efficiency. We developed ddgRADer - http://ddgrader.haifa.ac.il/ - a user-friendly webtool and incorporated these calculations to aid in ddRADseq experimental design while optimizing sequencing efficiency. This tool can also be used for single enzyme protocols such as Genotyping-by-Sequencing. Given user-defined study goals, ddgRADer recommends enzyme pairs and allows users to compare and choose enzymes and size-selection criteria. ddgRADer improves the accessibility and ease of designing ddRADseq experiments and increases the probability of success of the first population genomic study conducted in labs with no prior experience in genomics.}, }
@article {pmid40469735, year = {2025}, author = {Heisel, T and Gonia, S and Dillon, A and Hoops, SL and Al-Ghalith, GA and Gohl, D and Mukhopadhyay, S and Puopolo, K and Kennedy, P and Sadowsky, MJ and Knights, D and Johnson, AJ and Gerber, JS and Gale, CA}, title = {Gut mycobiome maturation and its determinants during early childhood: a comparison of ITS2 amplicon and shotgun metagenomic sequencing approaches.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1539750}, pmid = {40469735}, issn = {1664-302X}, abstract = {INTRODUCTION: Microbial colonization of the gut in early life is important for the development of metabolism, immunity, and the brain. Fungi and bacteria both colonize the human infant gut. The relatively smaller contribution of fungi to the gut microbiome, as compared to bacteria, has posed technical challenges for the precise characterization of fungal communities (mycobiomes) and limited the ability to longitudinally examine mycobiome development.<br><br>BACKGROUND: The aims of this study were to (1) characterize mycobiome maturation and identify clinical determinants of mycobiome compositional variation during the first 2&#x202f;years of life and (2) compare two sequencing approaches (ITS2 amplicon and whole genome metagenomics) for characterizing mycobiome maturational features. Longitudinal fecal samples and associated clinical metadata were obtained from subjects enrolled as part of the MAGIC (Microbiome, Antibiotics and Growth Infant Cohort) study.<br><br>RESULTS: Overall, fungal richness increased and mycobiome composition changed in a similar ordered pattern during the first 2&#x202f;years of life utilizing either amplicon or metagenomic sequencing approaches. Less resolution of taxa to species and genera levels was observed for the metagenomic dataset. The predominant taxa identified by both sequencing approaches, Candida albicans, Saccharomyces/S. cerevisiae, and Malassezia restricta, each exhibited similar dynamics in abundances and prevalences over the first 2&#x202f;years of life, irrespective of sequencing approach. Antibiotic exposure and breastfeeding status contributed to time-specific mycobiome compositional variation, results that were consistent for both types of sequence datasets. Candida albicans exhibited altered abundance dynamics in association with perinatal antibiotic exposure and birth mode for both sequencing approaches. Post hoc analyses suggested that the birth mode association could be driven by exposure to perinatal antibiotics in children delivered by cesarean section rather than by birth mode itself.<br><br>DISCUSSION: In summary, amplicon and metagenomic sequencing approaches provide generally similar results with respect to mycobiome maturational dynamics and the contribution of clinical variables to variation. Differences in taxa identification by the two approaches likely due to sequence database differences, primer/genome sequence variation, and/or sequencing depth should be taken into consideration.}, }
@article {pmid40469725, year = {2025}, author = {Moumi, NA and Ahmed, S and Brown, C and Pruden, A and Zhang, L}, title = {ARGContextProfiler: extracting and scoring the genomic contexts of antibiotic resistance genes using assembly graphs.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1604461}, pmid = {40469725}, issn = {1664-302X}, abstract = {Antibiotic resistance (AR) presents a global health challenge, necessitating an improved understanding of the ecology, evolution, and dissemination of antibiotic resistance genes (ARGs). Several tools, databases, and algorithms are now available to facilitate the identification of ARGs in metagenomic sequencing data; however, direct annotation of short-read data provides limited contextual information. Knowledge of whether an ARG is carried in the chromosome or on a specific mobile genetic element (MGE) is critical to understanding mobility, persistence, and potential for co-selection. Here we developed ARGContextProfiler, a pipeline designed to extract and visualize ARG genomic contexts. By leveraging the assembly graph for genomic neighborhood extraction and validating contexts through read mapping, ARGContextProfiler minimizes chimeric errors that are a common artifact of assembly outputs. Testing on real, synthetic, and semi-synthetic data, including long-read sequencing data from environmental samples, demonstrated that ARGContextProfiler offers superior accuracy, precision, and sensitivity compared to conventional assembly-based methods. ARGContextProfiler thus provides a powerful tool for uncovering the genomic context of ARGs in metagenomic sequencing data, which can be of value to both fundamental and applied research aimed at understanding and stemming the spread of AR. The source code of ARGContextProfiler is publicly available at GitHub.}, }
@article {pmid40469537, year = {2025}, author = {Yu, X and Zou, Y and Li, M and Wang, L and Feng, W and Wei, L and Yang, L and He, J and Bu, H and Li, Y}, title = {Auto-Immune Glial Fibrillary Acidic Protein Astrocytopathy with Active Intrathecal Epstein-Barr Virus: A Single-Center Case Series Report.}, journal = {Neuropsychiatric disease and treatment}, volume = {21}, number = {}, pages = {1119-1130}, pmid = {40469537}, issn = {1176-6328}, abstract = {PURPOSE: Auto-immune glial fibrillary acidic protein (GFAP) astrocytopathy is a disease with unclear mechanisms and no diagnostic and treatment guidelines. Epstein-Barr virus (EBV) infection is reportedly involved in glial activities. However, the relationship between GFAP astrocytopathy and EBV infection is not clear. This study reports a case series of auto-immune GFAP astrocytosis with positive cerebrospinal fluid (CSF) EBV DNA, describing its clinical manifestations and treatment experience.<br><br>PATIENTS AND METHODS: In the serial case study, we reported six patients diagnosed with GFAP astrocytopathy having intrathecal EBV.<br><br>RESULTS: The significant signs included headache, fever and urination disorder, ataxia, limb weakness, numbness, consciousness disorder, psychological disorder, and blindness, among others. CSF analysis showed increased pressure, white blood cell count, abnormal biochemical components, positive GFAP antibody, and EBV. The positive results of metagenomic next-generation sequencing (mNGS) and PCR in CSF indicated that there might be active replication of EBV in the CSF of patients. The results of EBV-associated antibodies in blood suggest no evidence of acute primary EBV infection in six patients. Initial single antivirus therapy did not show satisfactory effects, but all patients showed improvement in clinical features and laboratory analysis after immunotherapy.<br><br>CONCLUSION: This study indicated that intrathecal EBV activity was closely related to auto-immune GFAP astrocytopathy, of which the mechanism remains to be further studied.}, }
@article {pmid40469517, year = {2025}, author = {Zhang, F and Li, R and Liu, Y and Liang, J and Gong, Y and Xiao, C and Cai, J and Wang, T and You, Q and Zhang, J and Chen, H and Xiao, J and Zhang, Y and Yang, Y and Li, H and Yao, J and Zhang, Q and Zheng, J}, title = {Integrative cross-tissue analysis unveils complement-immunoglobulin augmentation and dysbiosis-related fatty acid metabolic remodeling during mammalian aging.}, journal = {iMeta}, volume = {4}, number = {3}, pages = {e70027}, pmid = {40469517}, issn = {2770-596X}, abstract = {Aging-related decline and adaptation are complex, multifaceted processes that affect various tissues and increase risk of chronic diseases. To characterize key changes in cross-tissue aging, we performed comprehensive proteomic and metabolomic analyses across 21 solid tissues and plasma samples, alongside shotgun metagenomic profiling of fecal microbial communities in young and aged mice. Our findings revealed widespread aging-rewired chronic inflammation, characterized by complement system activation in plasma and universal immunoglobulins accumulation across multiple solid tissues. This inflammatory remodeling significantly enhanced vulnerability to aging-related tissue injury. Moreover, we identified organ-specific and organ-enriched proteins with high functional specificity. Among these, aging-related proteins were closely linked to disorders arising from lipid metabolism dysfunction. Analysis of multi-tissue metabolomic and fecal metagenomic profiles revealed that aging significantly disrupted inter-tissue metabolic coupling, activities of polyunsaturated fatty acids metabolism, and gut microbiota homeostasis. Aged mice exhibited a marked decrease in Escherichia and an increase in Helicobacter, strongly correlating with alterations in omega-3 and omega-6 fatty acid abundances. Through multi-omics integration, we identified key molecular hubs driving organismal responses to aging. Collectively, our study uncovers extensive aging-associated alterations across tissues, emphasizing the interplay between systemic inflammation and dysbiosis-driven fatty acid remodeling. These findings provide deeper insights into the development of healthy aging from a cross-tissue perspective.}, }
@article {pmid40469508, year = {2025}, author = {Zhao, S and Zhong, H and He, Y and Li, X and Zhu, L and Xiong, Z and Zhang, X and Zheng, N and Morgavi, DP and Wang, J}, title = {Leveraging core enzyme structures for microbiota targeted functional regulation: Urease as an example.}, journal = {iMeta}, volume = {4}, number = {3}, pages = {e70032}, pmid = {40469508}, issn = {2770-596X}, abstract = {Microbial communities play critical roles in various ecosystems. Despite extensive research on the taxonomic and functional diversity of microbial communities, effective approaches to regulate targeted microbial functions remain limited. Here, we present an innovative methodology that integrates core enzyme identification, protein structural characterization, regulator virtual screening, and functional validation to achieve precise microbiome functional regulation. As a proof of concept, we focused on the regulation of urea decomposition by the rumen microbiota in ruminants. Through metagenomic analysis, we identified the core urease gene and its corresponding microbial genome (MAG257) affiliated with the unclassified Succinivibrionaceae, and reconstructed its complete gene cluster. Structural analysis of the urease catalytic subunit (UreC) via cryo-electron microscopy (cryo-EM) revealed detailed features of its active site, guiding molecular docking studies that identified epiberberine, a natural compound with potent urease inhibitory activity. Validation in a rumen simulation system demonstrated that epiberberine significantly reduced urea decomposition and enhanced nitrogen utilization. This study establishes a robust framework that combines structural biology and computational screening to achieve targeted microbiome functional regulation, offering a promising tool for microbiome engineering and broader applications in animal productivity, human health, environmental improvement, and biotechnology.}, }
@article {pmid40469506, year = {2025}, author = {Li, X and Wu, Y and Yi, B and Chen, M and Zhang, G and Shao, X and Jiang, X and Cui, Y and Chen, L and Dong, X and Zhang, S and Zhao, Y and Deng, Y and Li, X and Wang, Y and Wu, L and Fu, Y and Ran, D and Peng, C and Yang, X and Zhang, L and Wang, Y and Zhu, Y and Sun, D and Ran, Y and Zheng, D and Yin, X and Chen, Y and Long, Y and Wang, W and Zhao, X and Liu, E and Xu, T and Li, Q and Zhong, W}, title = {A multi-centered prospective birth cohort study in Western China.}, journal = {iMeta}, volume = {4}, number = {3}, pages = {e70049}, pmid = {40469506}, issn = {2770-596X}, abstract = {The Western China Birth Cohort (WCBC) is a large-scale, multi-centered, prospective birth cohort study designed to address critical gaps in maternal and child health research in Western China, a region with diverse altitudes, ethnic groups, and unique environmental exposures. WCBC had enrolled 15,093 pregnant women across eight clinical centers in five provinces (Qinghai, Gansu, Guizhou, Chongqing, and Sichuan), spanning from the high-altitude Qinghai-Tibet Plateau to lowland regions. WCBC has collected over 220,000 medical records, 80,000 questionnaires, and 12 different types of biological samples, including peripheral blood, cord blood, dried blood spots, placenta, umbilical cord, decidua, saliva, feces, throat and nasal swabs, vaginal swabs, and breast milk. By integrating advanced multi-omics measurement, including genomics, proteomics, exosome profiling, metabolomics, spatial transcriptomics, single-cell RNA sequencing, culturome, metagenomics, and virosome analysis, WCBC provides a valuable platform to explore gene-environment interplay, early-life determinants of health, and long-term disease risks in diverse populations in Western China.}, }
@article {pmid40468884, year = {2025}, author = {Lee, Y and Ko, YM and Kwak, YS}, title = {Genetic and Nutritional Dynamics of SynCom in Suppressing Apple Fire Blight.}, journal = {The plant pathology journal}, volume = {41}, number = {3}, pages = {380-391}, doi = {10.5423/PPJ.OA.03.2025.0040}, pmid = {40468884}, issn = {1598-2254}, support = {RS-2020-RD009282//Rural Development Administration/ ; RS-2025-00516084//National Research Foundation of Korea/ ; }, abstract = {Fire blight disease, caused by Erwinia amylovora, occurs in apples and other Rosaceae plants and is known to cause significant economic damage. The pathogen usually infects flowers during the reproductive growth period of plants, colonizes, and penetrates by producing exopolysaccharides in the stigma. A synthetic microbial community (SynCom) is an artificial community of microorganisms designed to enhance host viability. To construct SynCom, we attempted to identify and utilize the microbial characteristics of apple trees that are not infected with the pathogen compared to those that are infected. In our previous study, we composed SynCom with strains expected to reduce the density of fire blight pathogens through microbiome analysis, strain isolation, and continuous replacement culture. We are able to observe the disease control effect of the constructed SynCom. However, no study has been conducted to clearly determine the genetic mechanism underlying this effect of the SynCom. Here, we present that potential secondary metabolite candidates and nutritional competition with the pathogen were confirmed as biochemical mechanisms through whole genome analysis of SynCom strains. Additionally, by co-cultivating SynCom with the pathogen in limited nutrient conditions, such as apple blossom extracts, which are susceptible to the pathogen, we confirmed the potential of SynCom treatment to reduce the pathogen densities. This study demonstrates that genetic selection using metagenomics can effectively identify microorganisms with potential functional capabilities.}, }
@article {pmid40468453, year = {2025}, author = {Hu, F and Gebeyew, K and Wu, Z and Chen, B and Jiao, J and Tan, Z and Tian, D and He, Z}, title = {Fat-rich diet promotes microbiome-dependent ATP synthesis in sheep model.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {81}, pmid = {40468453}, issn = {1674-9782}, support = {XDA26040304//Strategic Priority Research Program/ ; XDA26050102//Strategic Priority Research Program/ ; 32072760//National Natural Science Foundation of China/ ; 2022JJ10054//Natural Science Foundation of Hunan Province of China/ ; }, abstract = {BACKGROUND: The ketogenic diet that forces adenosine triphosphate (ATP) production by beta-oxidation of fatty acids instead of carbohydrate glycolysis, has gained consensus on host metabolism. However, the mechanisms how a ketogenic diet alters gastrointestinal microbiome and its downstream consequences on microbial nutrient availability and energy metabolism remain to be elucidated. Here, we used the sheep model fed with fat-rich diet to evaluate the symbiotic microbiome across three regions of the gastrointestinal tract (rumen, ileum, and colon) to gain a comprehensive understanding of the microbial energy metabolism and microbe-mediated ATP biosynthesis.<br><br>RESULTS: Results showed that sheep fed a fat-rich diet had a greater ADG and increased reliance on fat oxidation for fuel utilization. Metagenomics analysis showed the loss of the specialized fiber-degrading bacteria (genus_Fibrobacter) in the rumen and enrichment of genera RUG420 and Eubacterium,&#xa0;which are involved in lipid metabolism and bile acid processing, in the ileum. A significant functional shift related to energy metabolism was shared across three regions of the gastrointestinal microbiomes. These shifts were dominated by glycolysis/gluconeogenesis and TCA cycle in the rumen and by fatty acid degradation and bile acid transformation in the ileum, indicating adaptation to nutrient availability and energy acquisition. Notably, the abundance of substrate-level phosphorylation (SLP) enzymes was significantly increased in the rumen, ileum and colon, while the ATP-producing capacity through electron transport phosphorylation (ETP) by family_Bacteroidaceae in rumen and Acutalibacteraceae in ileum of sheep with fat-rich diet.<br><br>CONCLUSIONS: Altogether, the ATP-related microbiome encoding SLP and ETP in rumen, ileum, and colon contributed 36.95% to the host's weight variation. Our study is the first one demonstrating the microbial potential in the ATP synthesis under the shift in dietary energy source, providing a new perspective on the energy metabolism and precise human macronutrients nutrition.}, }
@article {pmid40468444, year = {2025}, author = {Tang, Q and Yin, X and Wen, G and Luo, Z and Zhang, L and Tan, S}, title = {Unraveling the composition and function of pig gut microbiome from metagenomics.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {60}, pmid = {40468444}, issn = {2524-4671}, support = {No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; }, abstract = {The gut microbiome plays a crucial role in intestinal maturation, metabolism, and immunoregulation, significantly influencing the host's health and growth performance. This review highlights the use of metagenomic techniques to the composition, function, and dynamic changes of the pig gut microbiota. Research has revealed that environmental and host factors, particularly diet, drive significant variations in microbial composition, which in turn shape host epigenetics through microbial components and metabolites. Furthermore, the strong correlation between the gut microbiota and host health presents opportunities for improving growth performance in the livestock industry.}, }
@article {pmid40468439, year = {2025}, author = {Ravelo, AD and Ruch, M and Suazo, M and Ferm, P and Su, R and Chen, C and Crooker, BA and Noyes, NR and Salfer, IJ and Caixeta, LS}, title = {Associations between hyperketonemia and the rumen metagenome and metabolome in Holstein cows during the first 2 weeks postpartum.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {59}, pmid = {40468439}, issn = {2524-4671}, support = {1025222//U.S. Department of Agriculture/ ; }, abstract = {Hyperketonemia (HYK) is characterized by elevated levels of blood ketone bodies in dairy cows. Despite previous research on the physiological events related to HYK, associations between the rumen metagenome, metabolome, and HYK have not been well described. Therefore, the objective of this study was to compare rumen metagenome and metabolome profiles of cows with naturally occurring HYK to those without HYK during the first two weeks postpartum. Blood beta-hydroxybutyrate (BHB) concentrations at d 5, 10 and 14 postpartum were used to classify 16 rumen cannulated Holstein cows as either hyperketonemic (+ HYK; ≥1.2 mmol/L BHB at any of the collection days) or non-hyperketonemic (-HYK). Five + HYK cows were identified and were paired with 5 -HYK cows based on parity and calving date. Microbial DNA was extracted from rumen fluid and sequenced using shotgun metagenomics with the Illumina platform. Kraken2 was used to map reads to microbial taxonomic groups and Humann3.8 was used to predict potential functions. Metabolome profiling of rumen fluid was conducted using high-resolution liquid chromatography-mass spectroscopy. MetaboAnalyst6.0 was used to identify potential changes in metabolic pathways. Metagenomes and metabolomes comparisons were conducted using mixed models that included the fixed effects of group, day, their interaction, and the random effect of cow. There was minimal difference detected in alpha diversity for the metagenome, but differences in the metabolome were detected by HYK status. The concentration of asparagine and p-cresol was greater in + HYK cows compared to -HYK, but citrulline was greater in -HYK cows throughout all days considered. On d5 the concentration of ornithine was greater in + HYK compared to-HYK cows, and on d10 acetate was greater in the -HYK cows. There were no differences detected in the pathway analysis from the metabolites quantified by HYK status. Overall, modest differences in rumen metabolome were observed between + HYK and -HYK cows in early lactation. Future studies should explore associations between the rumen environment and HYK as this could be informative for treatment and management practices.}, }
@article {pmid40468436, year = {2025}, author = {Kilama, J and Islam, MS and Amat, S}, title = {Bovine ocular microbiome: the next frontier in managing Pinkeye in cattle.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {58}, pmid = {40468436}, issn = {2524-4671}, abstract = {Infectious bovine keratoconjunctivitis (IBK), or pinkeye, represents a significant economic challenge to dairy and beef cattle industries resulting in decreased productivity and increased treatment costs. The current IBK prevention and control strategies in cattle face challenges owing to the multifactorial nature of the disease, the rise of antibiotic resistance in IBK pathogens, and inconsistent efficacy of IBK vaccines. Recent efforts in metagenomic characterization of the eye microbiome in humans and animals, including cattle, have revealed that the ocular surface is colonized by relatively diverse and dynamic microbial community that is essential for maintaining ocular health and can be leveraged to enhance resistance against infectious ocular diseases. In this narrative review, we provide comprehensive insights into the ocular microbiota by summarizing the amplicon and metagenomic sequencing- and culture-based studies conducted in cattle, and by reviewing relevant findings from humans and other animal species. We also explore the potential of the ocular microbiome as a new frontier in managing IBK. Finally, we examine the gut-eye-microbiome axis and discuss its potential contribution in improving the resistance of cattle against IBK.}, }
@article {pmid40468430, year = {2025}, author = {Khoiri, AN and Costa, NR and Crusciol, CAC and Pariz, CM and Costa, C and Calonego, JC and de Castilhos, AM and de Souza, DM and de Lima Meirelles, PR and Cru, IV and Moretti, LG and Bossolani, JW and Kuramae, EE}, title = {Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {60}, pmid = {40468430}, issn = {2524-6372}, support = {#2014/21772-4 and #2014/14935-4//S&#xe3;o Paulo Research Foundation (FAPESP)/ ; #458225/2014-2//National Council for Scientific and Technological Development (CNPq)/ ; 1378/14//Funda&#xe7;&#xe3;o Agrisus/ ; }, abstract = {BACKGROUND: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.<br><br>RESULTS: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M&#x2009;+&#x2009;PG&#x2009;+&#x2009;PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M&#x2009;+&#x2009;PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.<br><br>CONCLUSIONS: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.}, }
@article {pmid40468269, year = {2025}, author = {Li, B and Yang, Y and Xu, B and Song, P and Jiang, F and Gao, H and Cai, Z and Gu, H and Zhang, T}, title = {Comparative macrogenomics reveal plateau adaptation of gut microbiome in cervids.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {154}, pmid = {40468269}, issn = {1741-7007}, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Deer/microbiology/genetics ; Phylogeny ; Metagenome ; Metagenomics ; *Adaptation, Physiological/genetics ; Energy Metabolism ; Biological Evolution ; }, abstract = {BACKGROUND: Diverse gut microbiota in animals significantly influences host physiology, ecological adaptation, and evolution. However, the specific functional roles of gut microbiota in facilitating host adaptation, as well as the coevolutionary dynamics between microbiota and their hosts, remain largely understudied.<br><br>RESULTS: A total of 41,847 metagenome-assembled genomes and 3193 high-quality species-level genome bins were generated, establishing a comprehensive gut microbiome catalog for cervids in this study. Phylogenetic analysis revealed a coevolutionary relationship between cervids and their gut microbiota. Comparative metagenomic analyses further indicated that the gut microbiota of plateau cervids have undergone genome-level adaptations related to energy metabolism. At the genus level, species-level genome bins from the genera Alistipes and Faecousia in plateau cervids exhibit enhanced energy metabolism capabilities. Structural variations analysis revealed that the insertion and duplications structural variations in the gut microbiota of plateau cervids were significantly enriched in energy metabolism pathways. In contrast, the deletions and contractions in structural variations were predominantly enriched with metabolic pathways involved in the biosynthesis of diverse biochemical molecules.<br><br>CONCLUSIONS: Our study provides a comprehensive gut microbiome catalog of the cervid gut microbiota, revealing the coevolutionary relationship between cervid gut microbiota and hosts. These findings highlight the adaptive genomic evolution of the gut microbiota in contributing to the plateau adaptability of cervids and offer new insights into the mechanisms by which the gut microbiota help hosts adapt to extreme environments.}, }
@article {pmid40468214, year = {2025}, author = {Yang, X and Chen, H and Wu, L and Guo, X and Xue, D}, title = {Diversity and correlation analysis of microbiomes and metabolites of Sphagnum palustre in various microhabitats.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {761}, pmid = {40468214}, issn = {1471-2229}, support = {2019QZKK0304//Second Tibetan Plateau Scientific Expedition/ ; QNTS202201//Youth Innovation Program of CIB/ ; 2022376//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2021JDTD011//Youth Science and Technology Innovation Team Program of Sichuan Province of China/ ; }, mesh = {*Microbiota ; *Sphagnopsida/microbiology/metabolism ; Ecosystem ; Soil Microbiology ; Bacteria/genetics/metabolism ; }, abstract = {BACKGROUND: Sphagnum peat mosses are crucial contributors to global carbon sequestration and are a dominant presence in many northern peatland environments. These mosses host a wide variety of microorganisms, which reside within their tissues and on their surfaces. Despite this close association, the connection between these microorganisms and the production of metabolites across different parts of Sphagnum remains unclear.<br><br>RESULTS: This research explored the connection between microbial diversity and metabolite production in various microhabitats of Sphagnum palustre by employing metagenomic and metabolomic techniques. Our results indicate that the S. palustre microbiome composition is more strongly influenced by microhabitat than by geographic location. Microbiome diversity microbiomes related to S. palustre showed a steady decrease from soil to near soil, from X to CAP, and from belowground to aboveground habitats. In contrast, network complexity increased. Species abundance analysis indicated that Proteobacteria was the most prevalent bacterial phylum across CAP, S, Z, and X. Additionally, Ascomycota emerged as the predominant fungal phylum. There were significant differences in nitrogen fixation activity, methane oxidation activity, total nitrogen, and total carbon among different microhabitats. The FAPROTAX analysis revealed differences in the metabolic potential of the carbon (C) and nitrogen (N) cycles across the four microhabitats. LC-MS/MS technology was employed to quantitatively assess metabolites across various S. palustre microhabitats. A total of 3,822 metabolites and 353 differential metabolites were detected, predominantly including lipids, organic acids, and carboxylic acids. The majority of these differential metabolites were associated with metabolic pathways such as carotenoid biosynthesis, steroid biosynthesis, secondary bile acid biosynthesis, as well as the biosynthesis of neomycin, kanamycin, and gentamicin. Correlation analysis revealed both positive and negative relationships between microorganisms and differential metabolites. Methylocystis, which was significantly enriched in X and T, showed a strong positive correlation with differential metabolites in S vs T and Z vs X, but a negative correlation with those in X vs T (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: In summary, our study demonstrates that Sphagnum palustre microbiomes are primarily influenced by microhabitats rather than specific environmental conditions at different sites. We identified significant variations in microbial community diversity across various S. palustre microhabitats. Correlation analysis revealed links between microorganisms and differential metabolic processes. This comprehensive investigation of aboveground and belowground microbiomes and metabolites in S. palustre provides new insights into the distribution of microbial communities and metabolites across different microhabitats.}, }
@article {pmid40468175, year = {2025}, author = {Lin, Z and Chen, Y and Yu, Z and Zhang, Z and Lin, Y and Zhang, W and Li, W and Guo, Y and Fang, X}, title = {Early and Accurate Pathogen Identification Based on mNGS: Key to Timely Therapy for Mycoplasma Prosthetic Joint Infection.}, journal = {Orthopaedic surgery}, volume = {}, number = {}, pages = {}, doi = {10.1111/os.70069}, pmid = {40468175}, issn = {1757-7861}, support = {2023J01597,2023J01315//Natural Science Foundation of Fujian Province/ ; 2023CXA020//Fujian Medical Innovation Grant, China/ ; }, abstract = {OBJECTIVES: Prosthetic joint infection (PJI) caused by Mycoplasma infection is relatively rare in clinical practice; all cases are primarily reported as individual case reports, and the characteristics of PJI induced by Mycoplasma infection have not been clearly studied. This case-control study was designed to systematically compare demographic profiles, clinical histories, diagnostic modalities, and therapeutic outcomes between Mycoplasma PJI and conventional bacterial PJI through retrospective analysis.<br><br>METHODS: This retrospective single-center study included 6 cases of simplex Mycoplasma PJI, 4 cases of mixed Mycoplasma PJI, 33 cases of Staphylococcus aureus, and 21 cases of Staphylococcus epidermidis infection from January 1, 2017 to January 1, 2024. Perioperative inflammatory markers, pathogen cultures, metagenomic next-generation sequencing (mNGS) results, history of invasive urinary catheterization, clinical presentation, treatment, and rate of treatment success were recorded and analyzed for the four groups. Continuous variables were compared two-by-two between the four groups using independent t-tests or the Mann-Whitney U test based on the distribution of the data. The categorical variables were compared using the chi-square test or Fisher's exact test.<br><br>RESULTS: The proportion of invasive urinary catheterization history in the mixed versus simplex Mycoplasma group was significantly higher than that in the Staphylococcus aureus and Staphylococcus epidermidis control groups (p&#x2009;<&#x2009;0.05). Routine microbial culture positivity was significantly lower in the mixed versus simplex Mycoplasma group than in the control group (p&#x2009;<&#x2009;0.01), but positive results for Mycoplasma can be detected by mNGS. Of note, one patient in the simplex Mycoplasma group was cured with targeted antibiotic-only therapy and avoided surgery. There was no statistically significant difference in cure rates between the mixed and simplex Mycoplasma groups and the Staphylococcus aureus and Staphylococcus epidermidis control groups (p&#x2009;=&#x2009;1.000).<br><br>CONCLUSION: Prior invasive urinary catheterization represents a significant risk factor for Mycoplasma PJI. The synergistic use of mNGS, optimized culture methods, and 16S rRNA PCR enables early detection of Mycoplasma. This multimodal diagnostic approach significantly enhances pathogen identification accuracy, minimizes diagnostic oversights, and provides essential guidance for effective therapeutic intervention.}, }
@article {pmid40468098, year = {2025}, author = {Srivastava, A and Rai, PK and Agnihotri, VK and Choure, K and Vishvakarma, R}, title = {Metagenomic analysis of viral communities in the polluted Varuna River reveals site-specific diversity patterns associated with environmental aspects.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40468098}, issn = {1618-1905}, abstract = {Varuna River, which is native to Varanasi, is of great importance as a water reservoir for the people and is contaminated with heavy pollutants due to urbanization. In this study, four sites (VR1, VR2, VR3, and VR4) of Varuna River water were sampled to assess the viral diversity. The metagenomics approach was used to study the viral diversity and functional analysis, suggesting the overall quality of the water at the sampled location. The analysis shows that VR1 had the most species richness (3000 species), followed by VR3 (2500), VR2 (2000), and VR4 (1500). The PCA analysis revealed distinct spatial patterns and community differentiation where VR2 and VR4 clustered while VR1 and VR3 were distant.Diversity analysis showed that Negarnaviricota dominated all samples at the phylum level. Yunchangviricetes, a non-reported virus, and Insthoviricetes were the dominant classes. Pakpunavirus was the leading genus, followed by the human pathogen Mimivirus. The highest species abundance in VR1 and VR2 was Mimivirus, Megavirus, chilensis, while VR3 and VR4 had Hpunavirus and Pseudomonas phage O4, indicating human involvement. Functional analyses of enzymatic activity and KEGG Orthology in microbial communities from VR1 to VR4 samples showed that VR4 exhibited maximal enzymatic activity, genetic flexibility, and advanced regulatory control compared to the other samples. The increased presence of transporter genes alongside signal transduction proteins and metabolic enzymes in VR4 indicates enhanced functional diversity, which aids in coping with environmental stresses. On the basis of viral species, ecological, biotechnological aspects were also interpreted. This study concluded that the Negarnaviricota plays a key role in maintaining the overall water quality and there is an urgent need for remediation of the Varuna River especially at site VR4 (25° 19' 46.7″ N 83° 02' 38.3″ E).}, }
@article {pmid40468041, year = {2025}, author = {Lin, D and Du, S and Zhao, Z and Zhang, T and Wang, L and Zhang, Q and Zhou, SY and Graham, DW and Tissue, DT and Zhu, D and Zhu, YG and Penuelas, J and Reich, PB}, title = {Climate warming fuels the global antibiotic resistome by altering soil bacterial traits.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {40468041}, issn = {2397-334X}, support = {2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (Youth Innovation Promotion Association CAS)/ ; 42222701//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090063//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Understanding the implications of global warming on the spread of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) within soil ecosystems is crucial for safeguarding human well-being and sustaining ecosystem health. However, there is currently a lack of large-scale, systematic underpinning data needed to examine this issue. Here, using an integrative approach that combines field experiments, extensive global metagenomic data and microbial culturing, we show that warming enriches bacteria with ARGs and VFGs, increases metabolic complexity and adaptability in bacteria, and accelerates genetic alterations related to ARG and VFGs development. Our validation experiments confirm that the warming effect is more pronounced in colder regions. Machine learning predictions further suggest that warming will increase the soil ARG abundance, especially in some areas that rely heavily on fossil fuels. These results suggest another major negative consequence of global warming, highlighting the importance of developing and implementing sustainability policies that simultaneously combat climate change and antibiotic resistance.}, }
@article {pmid40467587, year = {2025}, author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y}, title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5186}, pmid = {40467587}, issn = {2041-1723}, support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; }, abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.}, }
@article {pmid40467492, year = {2025}, author = {Tonomura, S and Hattori, Y and Ishibashi, T and Ikeda, S and Noda, K and Chiba, T and Kato, Y and Asano, R and Fukuma, K and Edamoto-Taira, Y and Motooka, D and Inagaki, T and Okazawa, M and Nakamura, S and Koga, M and Toyoda, K and Nomura, R and Nakano, K and Friedland, RP and Takeda, K and Takahashi, R and Ihara, M and Nakaoka, Y}, title = {Oral Pathobiont Streptococcus Anginosus Is Enriched in the Gut of Stroke Patients and Predicts 2-Year Cardiovascular Outcome.}, journal = {Circulation journal : official journal of the Japanese Circulation Society}, volume = {}, number = {}, pages = {}, doi = {10.1253/circj.CJ-24-0872}, pmid = {40467492}, issn = {1347-4820}, abstract = {BACKGROUND: Several cross-sectional studies have implicated gut dysbiosis caused by an abundance of oral commensals in stroke, but the effect on long-term prognosis is still unknown. Therefore, we longitudinally investigated oral pathobionts in the gut and their clinical relevance to stroke.<br><br>METHODS AND RESULTS: We analyzed the salivary and gut microbiomes collected from 189 acute stroke and 55 non-stroke subjects, and found that Streptococcus anginosus was significantly more abundant in both the saliva (median [IQR], 0.01 [0.00-0.14] vs. 0.00 [0.00-0.03], P=0.02) and gut (0.09 [0.00-0.28] vs. 0.00 [0.00-0.02], P<0.001) of the stroke patients compared with their non-stroke counterparts. Network analysis revealed S. anginosus as a central hub in gut dysbiosis. After adjusting for vascular risks, S. anginosus (odds ratio 1.20, 95% confidence interval 1.06-1.36, P<0.01), Anaerostipes hadrus (0.82, [0.73-0.93], P<0.01), and Bacteroides plebeius (0.86, [0.86-0.93], P=0.01) in the gut were independent predictors of stroke. Longitudinally, S. anginosus in the gut was significantly associated with increased rates of death and major cardiovascular events (P=0.04; log-rank test), whereas A. hadrus and B. plebeius were not (P=0.45 and P=0.19). After adjusting for vascular risks, S. anginosus in the gut was a residual risk for increased rates of death and major cardiovascular events (hazard ratio 4.78, 95% confidence interval 1.08-21.18, P=0.04)Conclusions: S. anginosus in the gut may increase the risk of stroke and a poor prognosis.}, }
@article {pmid40467356, year = {2025}, author = {Messadi, A and Sayhi, S and Ghedira, K and Zaouaoui, C and Arfaoui, B and Khouikhi, S and Rebai, M and Guediche, NEH and Abdelhafidh, N and Louzir, B and Faida, A}, title = {Microbial diversity investigation using 16S metagenomics in Tunisian patients with systemic lupus erythematosus.}, journal = {Revista Argentina de microbiologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ram.2025.04.002}, pmid = {40467356}, issn = {0325-7541}, abstract = {Systemic lupus erythematosus (SLE) is a multisystemic autoimmune disease associated with significant morbidity and mortality. It is characterized by a loss of self-immune tolerance and autoantibody production, leading to multiple organ damage. Emerging investigations have confirmed the role of gut microbiota dysbiosis in patients with SLE, although the underlying mechanisms remain unclear to date. In this study, we aim to investigate the bacterial profile of SLE including phylum/class/genus relative abundance and diversity, to compare them with healthy controls and to study the correlation of relative abundance of different patterns with clinical/biological parameters. In this case-control study, the bacterial profile was investigated in 7 SLE patients and 7 healthy controls using 16S metagenomics clustering. The present study reported a low abundance of the class Bacilli (0.58% in SLE vs 1.26% in the controls), the genus Lactobacillus (0.43% vs 0.74%), as well as a higher abundance of the genera Gammaproteobacteria (2.37% vs 0.77%) and Escherichia-Shigella (2.04% vs 0.51%) in SLE samples compared to the controls (p<0.05). We also found an association between the class Betaproteobacteria (4.42% vs 1.57%) and the genus Faecalibacterium (11.34% vs 3.35%) and renal manifestations (p<0.05). The phylum Actinobacteria (0.21% vs 3.8%, p=0.036) and the genus Bifidobacterium levels were lower in active SLE compared to the healthy controls. This study is the first report on the gut microbiota of SLE and the first case-control study in Tunisia and North Africa. We obtained a particular profile of bacterial gut microbiota for the SLE group. We found a specific clustering when compared to the healthy controls.}, }
@article {pmid40467297, year = {2025}, author = {Waterworth, SC and Egbert, S and Sorensen, J and O'Keefe, BR and Beutler, JA}, title = {A Biosynthetic and Taxonomic Atlas of the Global Lichen Holobiont.}, journal = {Environmental microbiology}, volume = {27}, number = {6}, pages = {e70112}, doi = {10.1111/1462-2920.70112}, pmid = {40467297}, issn = {1462-2920}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; ZIA BC 011471/CA/NCI NIH HHS/United States ; ZIA BC 011469/CA/NCI NIH HHS/United States ; }, mesh = {*Lichens/microbiology/classification/genetics ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Fungi/genetics/classification/metabolism/isolation &amp; purification ; Multigene Family ; Biosynthetic Pathways/genetics ; Phylogeny ; Secondary Metabolism ; Metagenomics ; Metagenome ; Symbiosis ; }, abstract = {Lichens are pioneer species in several ecosystems, and as such are found in a variety of geographic regions and environments. Here, inspection of metagenomic data from 794 lichen samples from 34 countries reveals the presence of a complex holobiont harbouring remarkable biosynthetic capabilities, particularly in the bacterial consortia, a component that has been somewhat underappreciated. While bacteria were consistently present, their abundance varied among lichen taxa. Common bacterial genera included Microbacterium, Terribacillus, and JABEUN01 (an Acidimicrobiaceae bacterium awaiting Latin binomial naming assignment) albeit in low abundance. Lichenihabitans and Sphingomonas genera were moderately abundant, present in approximately 30% of samples, and exhibited an enrichment in the number of biosynthetic gene clusters (BGCs) predicted to encode secondary metabolites (biosynthetic potential). We found that both fungal and bacterial biosynthetic repertoires appeared to follow genus-specific patterns but that there was greater relative homogeneity of BGCs in the fungal genera. The substantial biosynthetic diversity within lichen holobionts is evident in our findings, with the lichen-associated bacteria emerging as a promising potential source for sustainable drug discovery.}, }
@article {pmid40467244, year = {2025}, author = {Li, S and Rao, C and Zang, X and Yang, Y and Yang, W and Huang, X and Li, J and Sun, J and Liu, Y and Ye, D}, title = {Characterization of aroma active compounds and microbial communities in spontaneously fermented Vitis quinquangularis wines.}, journal = {Food research international (Ottawa, Ont.)}, volume = {214}, number = {}, pages = {116676}, doi = {10.1016/j.foodres.2025.116676}, pmid = {40467244}, issn = {1873-7145}, mesh = {*Wine/analysis/microbiology ; *Fermentation ; *Vitis/microbiology/chemistry ; *Odorants/analysis ; *Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; *Microbiota ; *Food Microbiology ; }, abstract = {This study comprehensively investigated volatile compounds and microbial communities of spontaneously fermented Vitis quinquangularis wines from the Guangxi production regions. The aroma profiles of V. quinquangularis wines were analyzed by GC-O-MS, GC-QQQ-MS/MS, and quantitative descriptive analysis. The wines exhibit predominantly fruity and floral notes, with contributions from esters and (E)-β-damascenone. A distinctive and typical "green and earthy" aroma was observed, with contributions from C6 compounds and volatile phenols such as 1-hexanol, (E)-3-hexen-1-ol, hexanoic acid, 4-vinylguaiacol, eugenol, and isoeugenol. Metagenomics and culturomics analyses indicated that the dominant strains involved in the spontaneous fermentation process were Hanseniaspora opuntiae, Saccharomyces cerevisiae, Paenibacillus sp., Sphingomonas sp., and Bacillus sp. Additionally, microorganisms from sixteen generas, including Actinomycetospora and Ameyamaea, etc., along with six enzymes like EC 1.1.1.1 and EC 1.1.1.318, etc., were implicated in the production of the "green and earthy" aroma in V. quinquangularis wines.}, }
@article {pmid40467108, year = {2025}, author = {Ghensi, P and Heidrich, V and Bazzani, D and Asnicar, F and Armanini, F and Bertelle, A and Dell'Acqua, F and Dellasega, E and Waldner, R and Vicentini, D and Bolzan, M and Trevisiol, L and Tomasi, C and Pasolli, E and Segata, N}, title = {Shotgun Metagenomics Identifies in a Cross-Sectional Setting Improved Plaque Microbiome Biomarkers for Peri-Implant Diseases.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.14121}, pmid = {40467108}, issn = {1600-051X}, support = {//Italian Society of Periodontology and Implantology (SIdP)/ ; //Eklund Foundation/ ; //International Team for Implantology (ITI)/ ; /ERC_/European Research Council/International ; //CLC Scientific S.r.l./ ; //PreBiomics S.r.l./ ; }, abstract = {AIM: This observational study aimed to verify and improve the predictive value of plaque microbiome of patients with dental implant for peri-implant diseases.<br><br>MATERIALS AND METHODS: Patients were included in one of the following study groups according to the health status of their dental implants: (a) healthy, (b) affected by mucositis and (c) affected by peri-implantitis. From each patient, submucosal plaque microbiome samples were collected from the considered dental implant and from a contralateral healthy implant/tooth. After shotgun metagenomic sequencing, the plaque microbiome was profiled taxonomically and functionally with MetaPhlAn 4 and HUMAnN 3, respectively. Taxonomic and functional profiles were fed into machine-learning models, which were then evaluated with cross-validation to assess the extent to which the plaque microbiome could be used to pinpoint peri-implant diseases.<br><br>RESULTS: Shotgun metagenomics sequencing was performed for a total of 158 samples spanning 102 individuals. Four-hundred and forty-seven prokaryotic species were identified as part of the peri-implant microbiome, 34% of which were currently uncharacterized species. At the community level, the peri-implant microbiome differed according to the health status of the implant (p&#x2009;&#x2264;&#x2009;0.006 for all pairwise comparisons) but this was site-specific, as healthy contralateral sites showed no discriminating microbiome features. Peri-implantitis microbiomes further showed lower inter-subject variability than healthy plaque microbiomes (p&#x2009;<&#x2009;0.001), while mucositis-associated microbiomes were in the middle of the continuum between health and peri-implantitis. Each health condition was associated with a strong signature of taxonomic and functional microbiome biomarkers (log10 LDA score &#x2265;&#x2009;2.5), 30% and 13% of which represented uncharacterized microbial functions and unknown species, respectively. Distinct Fusobacterium nucleatum clades were associated with implant status, highlighting the subspecies F. nucleatum's functional and phenotypic diversity. Machine-learning models trained on taxonomic or functional plaque microbiome profiles were highly accurate in differentiating clinical groups (AUC&#x2009;=&#x2009;0.78-0.96) and highlighted the extent to which the peri-implant microbiome is associated with peri-implant clinical parameters (AUC&#x2009;=&#x2009;0.79-0.87).<br><br>CONCLUSIONS: Plaque microbiome profiling with shotgun metagenomics revealed consistent associations between microbiome composition and peri-implant diseases. In addition to pointing to peri-implant-associated microbes, warranting further mechanistic studies, we showed high-resolution plaque microbiome evaluation via metagenomics as an effective tool. Its utility within protocols for clinical management of peri-implant diseases should be explored in the future.}, }
@article {pmid40467013, year = {2025}, author = {Valmas, MI and Kormas, K and Karpouzas, DG and Konstantinidis, KT and Rozman, SD and Udiković-Kolić, N and Remus-Emsermann, MNP and Vasileiadis, S}, title = {Targeted analysis of metagenomes: divide and conquer.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {108619}, doi = {10.1016/j.biotechadv.2025.108619}, pmid = {40467013}, issn = {1873-1899}, abstract = {The rapidly developing field of targeted analysis of metagenomes focuses on retrieving information about specific genes and/or genome(s) from environmental DNA. The traditional shotgun sequencing methods overemphasise dominant microorganisms and often fail to confidently assign the entirety of the analysed genetic material to specific species, genomovars, or strains. The ultimate goal of the targete methods is to overcome this limitation of throughput and precision of current shotgun metagenomics when analysing complex microbial communities in the quest of refined information. Here, we discuss recent technological advances that are designed to focus the analytical power of diagnostic tools like sequencing, towards phylogenetically or functionally distinct and rare microbial groups and enhance e.g. the confidence in the assignment of genetic elements to their respective owning organisms. We specifically showcase the capabilities of these technological advances for targeted analysis of metagenomes, identify suitable related applications, discuss methodological limitations, and propose solutions for addressing these limitations. This review aspires to inspire highly relevant experimental designs in the future that will unlock unknown and important aspects of microbial ecology, and the yet-uncultivated microbial majority.}, }
@article {pmid40467000, year = {2025}, author = {Potrykus, M and Kurpas, M and Gałęzowska, G and Gajewska, M}, title = {Linking Chemical Contamination to Composition of Bacterial Communities in Urban Beach Sands of a Brackish Sea Under Anthropogenic Pressure.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126596}, doi = {10.1016/j.envpol.2025.126596}, pmid = {40467000}, issn = {1873-6424}, abstract = {The water quality on recreational beaches is constantly monitored. However, given that beachgoers often spend more time in contact with the sand than the seawater, it is essential to also regularly assess beach sand quality. In this study, 34 beach sand samples were collected in seven locations along the south shore of the Baltic Sea (Europe) between 2022 and 2023. The samples were obtained from recreational beaches with significant anthropogenic pressure. Since the use of new chemicals is widespread, it is imperative to not only monitor known contaminants but also to actively search for the presence of new ones in the environment. In order to establish the connection between the bacterial biodiversity and their possible resilience in the contaminated marine environment, the bacterial abundances in the beach sand were compared based on 16S rDNA sequencing with chemical contamination examined with non-targeted GC-MS. One hundred forty-nine (149) distinct chemicals were detected, many of which are of human health concern. The presence of polycyclic aromatic hydrocarbons, plasticizers and benzothiazoles in the sand samples was observed, and these contaminants were found to be associated with alterations in the bacterial community structure, characterized by a decrease or increase in certain taxonomic groups. Notably, the bacterial communities exhibited specificity to each location and demonstrated stability throughout the seasons. Furthermore, the presence of DNA from 31 potential human pathogens was detected in the sand. These findings emphasize the necessity for regular monitoring of beach sand for the presence of toxic chemicals and pathogens to safeguard public health and the environment.}, }
@article {pmid40466780, year = {2025}, author = {Yang, Y and Abdelfattah, A and Jia, H and Kumar, V and Jiang, Y and Cheng, L}, title = {Enhanced nitrogen removal by Comamonas 110 colonization and bioaugmentation in sequencing batch activated sludge bioreactor.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132759}, doi = {10.1016/j.biortech.2025.132759}, pmid = {40466780}, issn = {1873-2976}, abstract = {While pure functional strains demonstrate high pollutant removal efficiency, their environmental persistence remains challenging. This study optimized Comamonas 110 inoculation strategies in activated sludge systems, enhancing nitrogen removal efficiency (44 % of nitrogen removal at day 180) and achieving stable colonization (15.22 % abundance at day 180) through 30 % initial dosage combined with operational parameter regulation. Monod modeling and 16S rRNA sequencing revealed Comamonas 110 suppressed Nitrite-Oxidizing Bacteria (NOB) while boosting Ammonia-Oxidizing Bacteria (AOB). Denitrifying enzymes (NAR and NIR) increased significantly in inoculated reactors, attributing to the substantial presence of Comamonas 110. Metagenomics revealed upregulated (tricarboxylic acid) TCA cycle genes and nitrogen metabolism pathways, optimizing electron transfer for denitrification. Concurrently, Extracellular Polymeric Substance (EPS) synthesis-related genes were activated, promoting co-aggregation with native EPS-producing microbes. This study provides new insights into colonization dynamics of bioaugmentation strains through microbiome-environment interplay.}, }
@article {pmid40466474, year = {2025}, author = {Zhang, J and Zeng, W and Meng, Q and Liu, H and Lu, Y and Li, S and Peng, Y}, title = {Insights into synergistic metabolism mechanisms of carbon, nitrogen and phosphorus in Tetrasphaera-dominated partial denitrifying phosphorus removal and anammox (PDPRA) process.}, journal = {Water research}, volume = {284}, number = {}, pages = {123901}, doi = {10.1016/j.watres.2025.123901}, pmid = {40466474}, issn = {1879-2448}, abstract = {The partial denitrifying phosphorus removal coupled with anammox (PDPRA) technology holds great promise for the simultaneous removal of carbon, nitrogen, and phosphorus. However, its widespread application is hindered by the instability of nitrite accumulation and the strong dependence on volatile fatty acids (VFAs) of traditional denitrifying polyphosphate accumulating organisms (DPAOs). This study first proposes coupling partial denitrifying phosphorus removal, driven by Tetrasphaera, a novel fermentative DPAO, with anammox for efficiently treating wastewater rich in complex organic matter (e.g., amino acids and proteins). A comprehensive investigation was conducted on the synergistic metabolic mechanisms between DPAOs and anammox bacteria (AnAOB). Under a low carbon to nitrogen (C/N) ratio of 3.1 ± 0.1, Tetrasphaera utilized intracellular amino acids, particularly proline, to drive the stable and efficient nitrite accumulation, leading to a contribution of 82.64 % to total nitrogen removal through anammox. This PDPRA system ultimately achieved remarkable removal efficiency of chemical oxygen demand (COD, 84.8 ± 0.8 %), total inorganic nitrogen (TIN, 92.3 ± 0.9 %) and orthophosphate (PO4[3-]-P, 92.0 ± 1.5 %). Microbial community analysis and metagenomic sequencing revealed the high abundance of Tetrasphaera and Candidatus Brocadia, with their high contribution to key functional genes (narGHI, napAB, ppk1, ppk2, hzs, hdh) confirming the co-existence and co-prosperity metabolic relationship between DPAO and AnAOB. Additionally, an even spatial distribution of Tetrasphaera and AnAOB within the biofilm was developed, further ensuring the stable and efficient removal performance. The findings of this study contribute to the broader application of the PDPRA process and provide a new approach for treating wastewater containing complex organic matter.}, }
@article {pmid40465720, year = {2025}, author = {de Porto, AP and Dylla, NP and Stutz, M and Lin, H and Khalid, M and Mullowney, MW and Little, J and Rose, A and Moran, D and McMillin, M and Burgo, V and Smith, R and Woodson, C and Metcalfe, C and Ramaswamy, R and Lehmann, C and Odenwald, M and Bandealy, N and Zhao, J and Kim, M and Adler, E and Sundararajan, A and Sidebottom, A and Kress, JP and Wolfe, KS and Pamer, EG and Patel, BK}, title = {Fecal metabolite profiling identifies critically ill patients with increased 30-day mortality.}, journal = {Science advances}, volume = {11}, number = {23}, pages = {eadt1466}, doi = {10.1126/sciadv.adt1466}, pmid = {40465720}, issn = {2375-2548}, mesh = {Humans ; *Critical Illness/mortality ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Intensive Care Units ; *Metabolome ; Dysbiosis/mortality/microbiology ; Metabolomics/methods ; Prospective Studies ; }, abstract = {Critically ill patients admitted to the medical intensive care unit (MICU) have reduced intestinal microbiota diversity and altered microbiome-associated metabolite concentrations. Metabolites produced by the gut microbiota have been associated with survival of patients receiving complex medical treatments and thus might represent a treatable trait to improve clinical outcomes. We prospectively collected fecal specimens, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived fecal metabolites by mass spectrometry from 196 critically ill patients admitted to the MICU for non-COVID-19 respiratory failure or shock to correlate microbiota features and metabolites with 30-day mortality. Microbiota compositions of the first fecal sample after MICU admission did not independently associate with 30-day mortality. We developed a metabolic dysbiosis score (MDS) that uses fecal concentrations of 13 microbiota-derived metabolites, which predicted 30-day mortality independent of known confounders. The MDS complements existing tools to identify patients at high risk of mortality by incorporating potentially modifiable, microbiome-related, independent contributors to host resilience.}, }
@article {pmid40465264, year = {2025}, author = {Liu, M and Geng, J and Jin, S and Hu, P and Wang, X and Liu, X}, title = {Alterations of the Enteric Virome in Vogt-Koyanagi-Harada Disease.}, journal = {Investigative ophthalmology &amp; visual science}, volume = {66}, number = {6}, pages = {15}, doi = {10.1167/iovs.66.6.15}, pmid = {40465264}, issn = {1552-5783}, mesh = {Humans ; *Uveomeningoencephalitic Syndrome/virology/microbiology ; Male ; Female ; *Virome/genetics ; Adult ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Middle Aged ; Bacteria/genetics ; Metagenomics ; Young Adult ; }, abstract = {PURPOSE: This study aims to explore the enteric virome characteristics of Vogt Koyanagi Harada (VKH) disease and its potential role in this disease.<br><br>METHODS: Shotgun metagenomic sequencing was used to detect the enteric virome and 16S rRNA to detect the bacteriome in new-onset, untreated patients with VKH (n = 25) and age- and sex-matched healthy controls without autoimmune diseases (n = 25).<br><br>RESULTS: Patients with VKH exhibited different enteric viral communities from healthy controls, characterized by decreased richness of core viral communities (present in > 80% of samples) and increased richness of common viral communities (present in 50%-80% of samples). Notably, within the core virus community, bacteriophage richness was markedly reduced, whereas eukaryotic virus richness significantly increased in patients with VKH. The case-control analysis identified 42 differentially abundant viruses, including a decrease in crAss-like phages, the eukaryotic virus Moumouvirus_moumou, and an enrichment of the Chlamydiamicrovirus_CPG1. Most of the differential phages predominantly targeted bacteria from the phyla Pseudomonadota and Firmicutes. The gut virome-bacteria community correlation analysis revealed a shift in the interactions between the core viruses and bacterial communities. Additionally, Wroclawvirus PA5oct (a Pseudomonas phage) correlated with leukotrichia, a clinically relevant symptom of VKH (P = 0.042). The impact of multiple Pseudomonas phages on the host folate biosynthesis was significantly enhanced in patients with VKH. Moreover, the protein (Earp361-372) encoded by VKH-enriched Pseudomonas was identified to share homology with the melanin antigen gp10044-59.<br><br>CONCLUSIONS: The gut virome of patients with VKH differs significantly from healthy controls, suggesting its disturbance may contribute to gut microbiome imbalance and VKH development.}, }
@article {pmid40464977, year = {2025}, author = {Lewis, R and Hammond, R and Wilkinson, M and Allenby, N}, title = {Technological developments driving industrial natural product discovery.}, journal = {Natural product reports}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4np00072b}, pmid = {40464977}, issn = {1460-4752}, abstract = {Covering: up to 2025Bacterial natural products have long been the foundation for many therapeutic agents. However, traditional culture-based approaches to discovering these products have been deprioritised by pharmaceutical companies, primarily due to the high rates of rediscovery. To revitalise the pipeline of new drugs, especially antibiotics-an area where natural products have historically played a crucial role-new technologies are essential. Culture-independent, or metagenomic, techniques combined with long-read sequencing technologies are now enabling the identification of novel biosynthetic gene clusters (BGCs). When paired with the heterologous expression of DNA extracted directly from environmental samples (eDNA), these approaches may provide access to untapped microbial biosynthetic diversity. This review explores industrial screening for new compounds and examines how modern technologies such as metagenomics, in situ cultivation, and pico-droplet-based screening are advancing the search for novel natural products. These approaches have the potential to greatly expand the discovery of new bioactive compounds, helping to address the growing need for new therapeutic agents.}, }
@article {pmid40464921, year = {2025}, author = {Shropshire, WC and Hanson, BM and Shelburne, SA}, title = {Genome-wide approaches to bacterial strain typing: a history and review of recent methodological advances.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1097/QCO.0000000000001118}, pmid = {40464921}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: Whole genome sequencing (WGS) has transformed bacterial strain typing, an essential tool for outbreak detection, antimicrobial resistance surveillance, and tracking clonal emergence across clinical, research, and public health settings. Herein, we will review recent advances in WGS-based bacterial strain typing methods for purposes of comparison and classification with a focus on improvements in variant identification, strain classification, and transmission assessment.<br><br>RECENT FINDINGS: Advances in sequencing technologies as well as variant calling methodologies and parameter optimization have enhanced the precision and accuracy of single nucleotide variant identification. Hierarchical clustering of gene-by-gene strain typing, combined with novel data management and classification strategies, has improved standardized pathogen typing schemes in an effort to streamline inter-laboratory comparison. Additionally, novel approaches to defining transmission thresholds now better account for species-specific traits, while progress in metagenomic sequencing enables strain identification and tracking within mixed microbial communities.<br><br>SUMMARY: Recent developments have enhanced the accuracy, portability, scalability, and standardization of bacterial typing methods, integrating variant calling and gene-by-gene approaches into unified genotyping systems. However, challenges still remain in nomenclature consistency, inter-laboratory variant calling compatibility, and capturing bacterial heterogeneity. Future work should focus on refining genotyping frameworks to enhance surveillance and optimize detection of pathogen transmission while accounting for microbial diversity across various environments.}, }
@article {pmid40464915, year = {2025}, author = {Kim, R and Oh, S and Woo, KA and Shin, CM and Park, KU and Lee, JY}, title = {Blood microbiome signatures in the REM sleep behavior disorder-Lewy body disease continuum.}, journal = {Journal of neural transmission (Vienna, Austria : 1996)}, volume = {}, number = {}, pages = {}, pmid = {40464915}, issn = {1435-1463}, abstract = {Although systemic inflammation triggered by alterations in microbiota from various body sites has been proposed as a potential mechanism underlying Lewy body diseases (LBDs), the association between the blood microbiome and LBDs remains uncertain. This study aimed to investigate the blood microbiome profiles across the REM sleep behavior disorder (RBD)-LBD continuum and to explore their potential as biomarkers reflecting disease phenotypes and clinical severity. Blood samples were collected from 106 patients across the RBD-LBD continuum, including 41 with isolated RBD (iRBD), 45 Parkinson's disease with probable RBD, and 20 dementia with Lewy bodies with probable RBD, as well as from 94 healthy controls. All patients were evaluated with the Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and comprehensive neuropsychological tests. Microbiome taxonomic compositions were analyzed using 16 S rRNA metagenomic sequencing. Significant microbial shifts were observed in the RBD-LBD continuum group compared to controls, with reduced microbial alpha diversity and distinct beta diversity patterns. Specifically, the genus Stenotrophomonas was enriched, while the genera Acetobacter, Enhydrobacter, and Lactobacillus were depleted in the RBD-LBD continuum group. The combined model using these genera demonstrated high predictive accuracy for the RBD-LBD continuum, with the area under the receiver-operating-characteristic curve (AUC) of 0.970 (95% confidence interval [CI]: 0.950-0.980). This model also successfully distinguished the iRBD subgroup from controls, achieving an AUC of 0.956 (95% CI, 0.914-0.987). Alpha and beta diversity were significantly associated with MDS-UPDRS Parts I and II scores in the RBD-LBD continuum group. Our findings suggest that patients within the RBD-LBD continuum may share specific blood microbiome signatures.}, }
@article {pmid40464558, year = {2025}, author = {Ruan, Y and Zhu, T and Yang, R and Su, F and An, C and Hu, Z and Li, X and Li, Y and Chen, P and Shao, X and Qin, J and Chen, H and Chen, R}, title = {Donor-derived microbial engraftment and gut microbiota shifts associated with weight loss following fecal microbiota transplantation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0012025}, doi = {10.1128/aem.00120-25}, pmid = {40464558}, issn = {1098-5336}, abstract = {Fecal microbiota transplantation (FMT) is a promising treatment for microbiota dysbiosis and may provide metabolic benefits for obesity. However, its mechanisms and variability in clinical outcomes remain poorly understood. This 12-week multicenter, single-arm study evaluated the efficacy of FMT for weight loss and explored the role of donor-derived microbial engraftment and functional shifts in mediating weight loss among overweight and obese individuals. Twenty-three participants (body mass index ≥24 kg/m[2]) without diabetes received three biweekly FMT sessions via a nasojejunal tube. Fecal samples from participants and donors were analyzed using metagenomic sequencing. By week 12, 52% of participants were classified as responders, achieving significant weight loss of ≥5% from baseline, with an average weight loss of 7.98 ± 2.69 kg (P < 0.001). In contrast, non-responders lost 2.90 ± 1.89 kg (P < 0.001). Responders exhibited a significantly higher proportion of donor-derived microbial strains post-FMT compared to non-responders (37.8% vs 15.2%, P = 0.020). Notably, key taxa, including Phascolarctobacterium (P = 0.034) and Acidaminococcaceae (P = 0.012), increased significantly in abundance in responders post-FMT, indicating successful microbial engraftment as a critical determinant of therapeutic success. These findings suggest that FMT is a viable intervention for weight loss in obese individuals. Successful donor-derived microbial engraftment strongly correlates with weight loss efficacy, highlighting the potential of microbiota-targeted therapies in obesity management and providing insights into the mechanisms underlying FMT outcomes.IMPORTANCEPrior research indicates that fecal microbiota transplantation (FMT) is a promising treatment for diseases related to microbiota imbalance, potentially providing metabolic benefits for obesity. However, the specific role of donor-derived microbial engraftment in driving clinical efficacy has remained unclear. In this study, we evaluated the efficacy of FMT in promoting weight loss and explored the role of donor-derived bacterial strains in this process. Our findings demonstrate that the successful engraftment of specific donor-derived taxa, such as Phascolarctobacterium and Acidaminococcaceae, is strongly associated with significant weight loss. This highlights the critical interplay between donor microbiota and recipient gut environment. These findings underscore the potential of microbiota-targeted therapies as a novel strategy for obesity management.CLINICAL TRIALSThis study is registered with the Chinese Clinical Trial Registry as ChiCTR1900024760.}, }
@article {pmid40463963, year = {2025}, author = {Coblentz, M and Evans, JD and Kothe, CI and Mak, T and Valerón, NR and Chwalek, P and Wejendorp, K and Garg, S and Pless, L and Mak, S and Sörensen, PM and Jahn, LJ and Ekblaw, A}, title = {Food fermentation in space: Opportunities and challenges.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112189}, pmid = {40463963}, issn = {2589-0042}, abstract = {Space exploration is expanding, which demands new technologies and enables new scientific questions. Food, as a bridge between disciplines, can bring these fundamental and applied goals together. Here, we investigate whether food fermentation in space is possible and if so, how it compares with fermentation on Earth. We fermented a miso, a traditional Japanese condiment, on the International Space Station over 30 days and compared it with two earthbound controls. Based on environmental metadata, shotgun metagenomics, whole-genome sequencing, untargeted metabolomics, colorimetry, and sensory analysis, we found that overall, the space miso is recognizable as a miso, indicating fermentation in space is possible. We also found some key microbiological and sensory differences in the space miso, which suggest distinctive features of the space environment. These findings can be harnessed to create more flavorful, nourishing foods for long-term space missions and invite further research questions across science, health, technology, and society.}, }
@article {pmid40463955, year = {2025}, author = {Zhang, E and Breselge, S and Carlino, N and Segata, N and Claesson, MJ and Cotter, PD}, title = {A genomics-based investigation of acetic acid bacteria across a global fermented food metagenomics dataset.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112139}, pmid = {40463955}, issn = {2589-0042}, abstract = {Developing a better understanding of the genomic and metabolic features of acetic acid bacteria (AABs) has the potential to facilitate an improvement of the taste or flavor of fermented foods. Here, we conducted a high-resolution analysis of AABs present in fermented foods based on the investigation of 337 high-quality metagenomic-assembled genomes (MAGs) recovered from 223 metagenomic samples. Firstly, by integrating these MAGs, we built a phylogenetic tree of high-quality MAGs using GTDB-Tk. We found that AABs MAGs from food-related samples and those from other environments are generally phylogenetically distinct, with the majority of those from fermented foods being assigned to a relatively small number of genera. Functional metagenomic analysis also revealed that the fermented food-associated AABs MAGs are associated with the production of carbohydrate-active enzymes, antibiotic resistance genes, and secondary metabolites. Through these investigations, we have gained substantial insights into the diversity, function, and roles of AABs in fermented food microbiomes.}, }
@article {pmid40463945, year = {2025}, author = {Wu, C and Mi, Y and Song, J and Zhang, M and Wang, C}, title = {The Regulatory Effect of Human Umbilical Cord Mesenchymal Stem Cells on the Gut Microbiota in Diabetic Nephropathy Rats.}, journal = {Iranian journal of biotechnology}, volume = {23}, number = {1}, pages = {}, pmid = {40463945}, issn = {1728-3043}, abstract = {BACKGROUND: Chronic inflammation is increasingly recognized as a key factor in the progression of diabetic kidney disease (DKD). By discovering that the regulation of gut microbiota plays an important role in diabetic kidney disease, human umbilical cord mesenchymal stem cells (HU-MSCs) explore the mechanism of fibrosis in diabetic kidney disease through the regulation of chronic inflammation, providing new clinical insights for the prediction, diagnosis, and treatment of diabetic kidney disease.<br><br>OBJECTIVES: This study explores the regulatory effects of HU-MSCs on gut microbiota and their protective role on the intestinal barrier in diabetic nephropathy rats.<br><br>MATERIAL AND METHOD: Diabetic kidney disease (DKD) was induced in SD rats via intraperitoneal injection of streptozotocin. Three groups were established: control group, diabetic kidney disease (DKD) group, and treatment group (DKD+HU-MSCs) (10 rats each). After diabetic kidney disease (DKD) modeling, rats in the treatment group (DKD+HU-MSCs) received 2&#xd7;10[6] HU-MSCs via tail vein injection weekly for four weeks. Blood, urine, kidney, and colon tissues were collected post-treatment. Pathological changes were observed microscopically; immunohistochemistry detected tight junction proteins ZO-1 and Occludin in colon tissues. DiR-labeled HU-MSCs distribution was assessed with in vivo imaging, and immunohistochemistry evaluated human mesenchymal stem cell markers CD44 and CD90. Fecal samples underwent metagenomic sequencing for gut microbiota analysis.<br><br>RESULTS: HU-MSCs transplantation significantly reduced Blood Urea Nitrogen (BUN), Serum Creatinine (SCr), and 24-hour urinary protein levels (all P < 0.05) and improved renal pathology. Markers CD44 and CD90 were present in DKD rat colon tissues. Tight junction proteins Occludin and ZO-1 were decreased in DKD rats but increased following HU-MSCs treatment. Metagenomic analysis showed enhanced abundance of beneficial bacteria (Bifidobacterium and Lactobacillus) with HU-MSCs. Urinary protein was positively correlated with Prevotella and negatively with Ligilactobacillus (p < 0.05).<br><br>CONCLUSIONS: HU-MSCs may improve intestinal barrier function in diabetic kidney disease (DKD) rats by restoring gut microbiota structure and increasing intestinal tight junction proteins, offering a potential pathway for enhancing renal function.}, }
@article {pmid40463537, year = {2025}, author = {De Chiara, L and Doughty, R and Estévez-Gómez, N and Gallego-García, P and Alvariño, P and Díez-Martín, A and Piñón, PD and Treangen, TJ and Cubiella, J and Posada, D}, title = {A Comparison of Methods for the Optimal Recovery of the Human Fecal Virome.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.05.12.25327428}, pmid = {40463537}, abstract = {Human virome studies are gaining attention as viruses are increasingly acknowledged as key modulators of microbial communities and human health. However, viral metagenomics presents distinct challenges, including the low abundance and diversity of viruses in biological samples, the lack of universal marker genes, and protocol-induced biases. Although various virome protocols have been benchmarked using viral particles or nucleic acids from mock communities, these often fail to replicate the complexity and heterogeneity of natural viromes. In this study, we systematically evaluated protocol modifications for the metagenomic analysis of human fecal samples, testing alternatives for viral enrichment, nucleic acid extraction, genome amplification, and library preparation. We assessed the impact of each modification on key inferences, including taxonomic and functional assignment, contig quality, viral diversity, and genome structure. Our results highlight important trade-offs between viral genome recovery and contamination removal, underscoring how methodological choices can shape virome composition. Based on our findings, we propose an optimized protocol that enhances the recovery of viral DNA and RNA genomes while minimizing contamination from non-viral sequences, providing a robust framework for future gut virome studies.}, }
@article {pmid40463520, year = {2025}, author = {Patel, SM and Farirai, J and Patel, MZ and Boiditswe, S and Tawe, L and Lekalake, S and Matshaba, M and Steenhoff, AP and Arscott-Mills, T and Feemster, KA and Shah, SS and Thielman, N and Cunningham, CK and David, LA and Murdoch, DM and Kelly, MS}, title = {Alterations of the upper respiratory microbiome among children living with HIV infection in Botswana.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2022.12.19.22283664}, pmid = {40463520}, abstract = {Children living with HIV (CLWH) are at high risk of colonization and infection by bacterial respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on development of the upper respiratory microbiome during childhood is poorly understood, and we sought to address this knowledge gap by identifying associations between HIV infection and the nasopharyngeal microbiomes of children in Botswana. We enrolled Batswana CLWH (<5 years) and age- and sex-matched HIV-exposed, uninfected (HEU) and HIV-unexposed, uninfected (HUU) children in a cross-sectional study. We used shotgun metagenomic sequencing to compare the nasopharyngeal microbiomes of children by HIV status. Among the 143 children in this study, HIV infection and HIV-associated immunosuppression were associated with alterations in nasopharyngeal microbiome composition, including lower abundances of Corynebacterium species associated with respiratory health. These findings suggest that the upper respiratory microbiome may contribute to the high risk of bacterial respiratory infections among CLWH.}, }
@article {pmid40463435, year = {2025}, author = {Strokach, A and Zoruk, P and Boldyreva, D and Morozov, M and Olekhnovich, E and Veselovsky, V and Babenko, V and Selezneva, O and Zakharevich, N and Larin, A and Koldman, S and Koldman, V and Odorskaya, M and Yunes, R and Pavlov, V and Kudryavtseva, A and Danilenko, V and Klimina, K}, title = {Comparative evaluation of sequencing technologies and primer sets for mouse gut microbiota profiling.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1584359}, pmid = {40463435}, issn = {1664-302X}, abstract = {BACKGROUND: Advancements in sequencing technologies, such as Illumina and Oxford Nanopore Technologies (ONT), have significantly improved microbiome research. However, variations in sequencing platforms, primer selection, and DNA quality may influence microbial diversity assessments, particularly in studies of gut microbiota. This study systematically evaluates these factors in mouse gut microbiota analysis, comparing 16S rRNA gene sequencing and metagenome sequencing (MS) across both platforms.<br><br>RESULTS: Our findings highlight the critical influence of primer selection on 16S rRNA sequencing results, with certain primer combinations detecting unique taxa that others miss. Despite these variations in taxonomic resolution, all tested primer sets consistently revealed significant differences between experimental groups, indicating that key microbial shifts induced by bacterial cultures remain detectable regardless of primer choice. A comparative analysis of Illumina and ONT 16S rRNA sequencing revealed notable differences in microbial diversity profiling, with ONT capturing a broader range of taxa. In contrast, MS on both platforms showed a high degree of correlation, indicating that ONT sequencing errors have minimal impact on taxonomic diversity estimations. Furthermore, the type of extracted DNA (high molecular weight vs. standard DNA) had little on microbial diversity outcomes, underscoring the robustness of these sequencing technologies.<br><br>CONCLUSION: These results highlight the advantages and limitations of different sequencing strategies in microbiota research. While 16S rRNA sequencing remains a cost-effective tool for assessing bacterial diversity, MS provides superior taxonomic resolution and more precise species identification. Our study advocates for a hybrid approach that combines multiple sequencing technologies to achieve a more comprehensive and accurate representation of microbial communities.}, }
@article {pmid40463374, year = {2025}, author = {Gu, J and Ma, Y and Chang, Q and Chen, L}, title = {Influence of programmed death ligand 1 (PD-L1) knockout on gut microbiota in experimental autoimmune uveitis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1600673}, pmid = {40463374}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Uveitis/immunology/microbiology/genetics ; *B7-H1 Antigen/genetics/deficiency ; *Autoimmune Diseases/immunology/microbiology/genetics ; Mice, Knockout ; Mice ; Female ; Disease Models, Animal ; Mice, Inbred C57BL ; }, abstract = {PURPOSE: Programmed death ligand 1 (PD-L1) is a potential target for autoimmune disease therapies. The gut microbiota plays a critical role in autoimmunity, and may influence therapeutic outcomes of immune therapies in cancer. However, the relationship between PD-L1 and gut microbiota in autoimmune conditions remains unclear. This study aims to investigate the effect of PD-L1 knockout on gut microbiota in an experimental autoimmune uveitis (EAU) model.<br><br>METHODS: EAU was induced via immunization with interphotoreceptor retinoid-binding protein peptide 651-670 (IRBP651-670) in either wild type (WT) or PD-L1 knockout (KO) C57BL/6J female mice. Sham adjuvant was administered to WT or PD-L1 KO mice as healthy controls. The severity of EAU was evaluated through clinical evaluation and histopathological gradings. The characteristics of gut microbiota was analyzed using metagenomic sequencing.<br><br>RESULTS: Each group consisted of three biological replicates. The clinical and histopathological scores of EAU were significantly higher in KO_EAU mice than in WT_EAU mice. WT_EAU mice exhibited lower microbial richness than their healthy controls (WT mice), while PD-L1 KO in EAU mice (KO_EAU group) led to increased richness when compared to wild type EAU mice (WT_EAU group). EAU induced a reduction in the abundance of Akkermansia muciniphila A and an increased in CAG-485 sp002362485. PD-L1 knockout in EAU led to an increased abundance of families Bacteroidaceae, Lachnospiraceae and Ruminococcaceae. EAU was associated with declining microbial tryptophan metabolism and up-regulated functions related to lipid and carbohydrate metabolism; PD-L1 knockout in EAU further increased the metabolism of glycan and biosynthesis of 3-deoxy-&#x3b1;-D-manno-2-octulosonate (Kdo), a key component of bacterial lipopolysaccharide (LPS).<br><br>CONCLUSION: Both EAU and PD-L1 knockout modulate gut microbiota, affecting microbial composition - particularly Akkermansia, CAG-485, Bacteroidaceae, Lachnospiraceae and Ruminococcaceae - and microbial functions such as lipid, carbohydrate and glycan metabolism.}, }
@article {pmid40462844, year = {2025}, author = {Morra, M and Marradi, D and Gandini, L and Ivagnes, V and Ottolini, G and Bovio, A and Jabali, G and Maraschi, L and Dada, IA and Chawanda, TV and Gorla, M and Tarasiuk, O and Mocchetti, C and Soluri, MF and Boccafoschi, F and Sblattero, D and Cotella, D}, title = {A non-hypothesis-driven practical laboratory activity on functional metagenomics: "fishing" protein-coding DNA sequences from microbiomes.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {13}, number = {}, pages = {1602982}, pmid = {40462844}, issn = {2296-4185}, abstract = {Practical laboratory of the most functional metagenomics courses focuses on activities aimed at providing specific skills in bioinformatics through the analysis of genomic datasets. However, sequence-based analyses of metagenomes should be complemented by function-based analyses, to provide evidential knowledge of gene function. A "true" functional metagenomic approach relies on the construction and screening of metagenomic libraries - physical libraries that contain DNA cloned from metagenomes of various origin. The information obtained from functional metagenomics will help in future annotations of gene function and serve as a complement to sequence-based metagenomics. Here, we describe a simple protocol for the construction of a metagenomic DNA library, optimized and tested by a team of undergraduate biotechnology students. This protocol is based on a technique developed in our laboratory and currently used for research. Using this protocol, libraries of protein domains can be quickly generated, from the DNA of any intron-less genome, such as those of bacteria or phages. Therefore, these libraries provide a valuable platform for training students in various validation tools, including computational methods - for example, metagenome assembly, functional annotation - and proteomics techniques, including protein expression and analysis. By varying the biological source and validation pipeline, this approach offers virtually limitless opportunities for innovative thesis research projects.}, }
@article {pmid40462511, year = {2025}, author = {Qian, LM and Wang, SX and Zhou, W and Qin, ZX and Wang, YN and Zhao, Q and Xu, RH}, title = {Individualized metagenomic network model for colorectal cancer diagnosis: insights into viral regulation of gut microecology.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {3}, pages = {}, doi = {10.1093/bib/bbaf208}, pmid = {40462511}, issn = {1477-4054}, support = {Y-HR2020QN-0474//Beijing Xisike Clinical Oncology Research Foundation/ ; 84000-31630002//Sun Yat-sen University clinical research 5010 program/ ; CIRP-SYSUCC-0004//Cancer Innovative Research Program of Sun Yat-sen University Cancer Center/ ; 2019-I2M-5-036//CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; 82173128//National Natural Science Foundation of China/ ; 81930065//National Natural Science Foundation of China/ ; 82321003//National Natural Science Foundation of China/ ; }, mesh = {*Colorectal Neoplasms/diagnosis/virology/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; *Metagenome ; Dysbiosis/virology ; }, abstract = {The role of gut microbiota, especially viruses, in colorectal cancer (CRC) pathogenesis remains unclear. This study investigated the interplay between gut microbiota and CRC development. We developed a viral/bacterial sequence analysis pipeline to reanalyze gut metagenomic datasets from eight CRC studies. A multisample co-occurrence network was constructed to delineate microbiota species interconnections. Our analysis confirmed dysbiosis in CRC patients and revealed enrichment of viral species, particularly those hosted by Lactococcus and Escherichia. These viruses were identified as central hubs in the multikingdom interaction network. We developed a network-based model using single sample networks (SSN) that distinguished CRC patients from controls with an area under the curve (AUC) of 0.93. Models combining relative abundance and SSN assessment achieved an AUC of 0.97, outperforming SSN-based models without viral data. This study highlights the crucial role of viruses in the gut microbiome network and their potential as targets for CRC prevention and intervention. Our approach offers a new perspective on noninvasive diagnostic criteria for CRC.}, }
@article {pmid40462354, year = {2025}, author = {Li, X and Xu, L and Demaree, B and Noecker, C and Bisanz, JE and Weisgerber, DW and Modavi, C and Turnbaugh, PJ and Abate, AR}, title = {Microbiome Single Cell Atlases Generated with a Commercial Instrument.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2409338}, doi = {10.1002/advs.202409338}, pmid = {40462354}, issn = {2198-3844}, support = {//Florida State University Start-up fund/ ; COA7000-138420-7030928-45-A73H5//UCSF Benioff Center for Microbiome Medicine (BCMM) Trainee Pilot Award/ ; R01HG008978//Foundation for the National Institutes of Health/ ; U01AI129206//Foundation for the National Institutes of Health/ ; R01AI149699//Foundation for the National Institutes of Health/ ; R01EB019453//Foundation for the National Institutes of Health/ ; R01HL122593//Foundation for the National Institutes of Health/ ; R01AT011117//Foundation for the National Institutes of Health/ ; F32GM140808//Foundation for the National Institutes of Health/ ; }, abstract = {Single-cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single-cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, EASi-seq (Easily Accessible Single microbe sequencing) is presented. By adapting the single-cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbial genomes. EASi-seq allows tens of thousands of microbes to be sequenced per run and, as it is shown, can generate detailed atlases of human and environmental microbiomes. The ability to capture large genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, a companion bioinformatic pipeline is developed that clusters genome by sequence similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, the integration of metagenomic contigs with the EASi-seq datasets is demonstrated to reduce capture bias and increase coverage. EASi-seq enables high-quality single-cell genomic sequencing for microbiome samples using a simple workflow run on a commercially available platform.}, }
@article {pmid40462165, year = {2025}, author = {Gao, H and Bai, H and Su, Y and Gao, Y and Fang, H and Li, D and Yu, Y and Lu, X and Xia, D and Mao, D and Luo, Y}, title = {Fecal microbiota transplantation from Helicobacter pylori carriers following bismuth quadruple therapy exacerbates alcohol-related liver disease in mice via LPS-induced activation of hepatic TLR4/NF-κB/NLRP3 signaling.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {627}, pmid = {40462165}, issn = {1479-5876}, support = {42377426//National Natural Science Foundation of China/ ; 42077382//National Natural Science Foundation of China/ ; 21JCYBJC01200//Tianjin Municipal Natural Science Foundation/ ; 2023220//Research Project on Integrated Traditional Chinese and Western Medicine of Tianjin Municipal Health Commission/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation/adverse effects ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; *Helicobacter pylori/physiology/drug effects ; *Signal Transduction/drug effects ; Lipopolysaccharides/pharmacology ; *Bismuth/therapeutic use/pharmacology ; *Toll-Like Receptor 4/metabolism ; Gastrointestinal Microbiome/drug effects ; *NF-kappa B/metabolism ; *Liver/pathology/metabolism/drug effects ; *Liver Diseases, Alcoholic/microbiology/therapy/pathology ; Male ; Mice ; Mice, Inbred C57BL ; Helicobacter Infections/microbiology ; Disease Models, Animal ; Humans ; Dysbiosis ; }, abstract = {BACKGROUND: Helicobacter pylori infection is common in patients with alcohol-related liver disease (ALD), and bismuth quadruple therapy (BQT) is widely used for eradication. However, its impact on ALD remains unclear. This study aims to characterize BQT-induced gut microbiota alterations in asymptomatic H. pylori carriers and evaluate their effect on an ALD mouse model.<br><br>METHODS: Metagenomic sequencing was conducted to assess the gut microbiota composition of individuals before and after BQT. Fecal microbiota transplantation (FMT) from these donors was performed in an ALD mouse model. Gut microbiota in mice was analyzed by 16S rRNA sequencing. Liver and intestinal parameters were assessed using western blot, RT-qPCR, histopathology, ELISA, and flow cytometry.<br><br>RESULTS: BQT treatment significantly altered the gut microbiota in H. pylori carriers, increasing the abundance of opportunistic pathogens, including Klebsiella pneumoniae, Escherichia coli, Klebsiella quasipneumoniae, and Klebsiella variicola, while decreasing beneficial bacteria such as Bifidobacterium, Eubacterium, Bacteroides, Faecalibacterium, and Blautia. In ALD mice receiving FMT from post-BQT donors, exacerbated gut dysbiosis was observed, marked by an enrichment of Enterobacteriaceae and Escherichia-Shigella. These microbiota changes were associated with impairment of intestinal barrier integrity, as evidenced by reduced levels of mucins, tight junction proteins, and antimicrobial peptides, along with a decrease in Treg cells and an increase in Th17 and Th1 cells. Additionally, this dysbiosis led to elevated serum lipopolysaccharide (LPS) levels, which activated the hepatic NLRP3 inflammasome pathway and subsequently increased IL-18 and IL-1&#x3b2; levels. Furthermore, liver function and oxidative stress markers, including ALT, AST, MDA, GSSG/GSH ratio, and SOD, were significantly elevated, indicating severe liver dysfunction and increased oxidative stress. Finally, probiotic supplementation effectively mitigated the negative effects of BQT-induced gut microbiota remodeling on ALD in mice.<br><br>CONCLUSIONS: BQT markedly alters the gut microbiota in H. pylori carriers, promoting dysbiosis that exacerbates ALD in mice via LPS-mediated activation of hepatic inflammatory pathways. These findings highlight the need for careful consideration of BQT use in ALD patients.}, }
@article {pmid40462041, year = {2025}, author = {Luo, Y and Wu, R and Wu, W and Zhao, D and Jiang, Y and Gu, H}, title = {Differences in pulmonary microbiota of severe community-acquired pneumonia with different pathogenic microorganisms in children.}, journal = {BMC pediatrics}, volume = {25}, number = {1}, pages = {449}, pmid = {40462041}, issn = {1471-2431}, support = {82200008//the Youth Program of National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Community-Acquired Infections/microbiology ; Male ; Female ; Child, Preschool ; Haemophilus influenzae/isolation &amp; purification ; Infant ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota ; *Lung/microbiology ; Streptococcus pneumoniae/isolation &amp; purification ; Mycoplasma pneumoniae/isolation &amp; purification ; *Pneumonia, Bacterial/microbiology ; Child ; Severity of Illness Index ; Pneumonia, Mycoplasma/microbiology ; C-Reactive Protein/analysis ; Community-Acquired Pneumonia ; }, abstract = {BACKGROUND: Community-acquired pneumonia (CAP) is the leading cause of hospitalization and death in children under 5 years old. Recently, the number of children with severe CAP (SCAP) has increased significantly, and local or systemic complications may occur. However, changes in the pulmonary microbiota of SCAP with different pathogens and their relationship with the clinical features of SCAP remain unclear.<br><br>METHODS: This study collected bronchoalveolar lavage fluid (BALF) from 105 children with SCAP for metagenomics next generation sequencing (mNGS). According to the first pathogen of mNGS, the enrolled children were divided into the Streptococcus pneumoniae (SP), Mycoplasma pneumoniae (MP) and Haemophilus influenzae (HI) groups. We aimed to explore differences in clinical features and pulmonary microbiota of SCAP with different pathogens, and clarify the correlation between pulmonary microbiota and clinical features.<br><br>RESULTS: Fever days and the levels of C-reactive protein (CRP), procalcitonin (PCT), lactate dehydrogenase (LDH), D-dimer and heparin-binding protein (HBP) of children in MP group were significantly higher than those in HI group. The level of LDH of children in MP group was significantly higher than that in SP group. The abundance of MP was also positively correlated with fever days and the levels of PCT, LDH and D-dimer. The &#x3b1; diversity of SP group was significantly increased compared to MP group and HI group.<br><br>CONCLUSION: Compared to SP-infected and HI-infected children with SCAP, children with SCAP infected with MP tend to have a more intense inflammatory response. The &#x3b1; diversity was higher in the lower airways of children with SCAP and SP infections compared to MP-infected and HI-infected children with SCAP.}, }
@article {pmid40461820, year = {2025}, author = {Piccinno, G and Thompson, KN and Manghi, P and Ghazi, AR and Thomas, AM and Blanco-Míguez, A and Asnicar, F and Mladenovic, K and Pinto, F and Armanini, F and Punčochář, M and Piperni, E and Heidrich, V and Fackelmann, G and Ferrero, G and Tarallo, S and Nguyen, LH and Yan, Y and Keles, NA and Tuna, BG and Vymetalkova, V and Trompetto, M and Liska, V and Hucl, T and Vodicka, P and Bencsiková, B and Čarnogurská, M and Popovici, V and Marmorino, F and Cremolini, C and Pardini, B and Cordero, F and Song, M and Chan, AT and Derosa, L and Zitvogel, L and Huttenhower, C and Naccarati, A and Budinska, E and Segata, N}, title = {Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {40461820}, issn = {1546-170X}, support = {101045015//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 825410//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; CGCATF-2023/100036//Cancer Research UK (CRUK)/ ; CGCATF-2023/100041//Cancer Research UK (CRUK)/ ; 1OT2CA297205-01//U.S. Department of Health &amp; Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics)/ ; OT2CA297680//U.S. Department of Health &amp; Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics)/ ; }, abstract = {Associations between the gut microbiome and colorectal cancer (CRC) have been uncovered, but larger and more diverse studies are needed to assess their potential clinical use. We expanded upon 12 metagenomic datasets of patients with CRC (n = 930), adenomas (n = 210) and healthy control individuals (n = 976; total n = 2,116) with 6 new cohorts (n = 1,625) providing granular information on cancer stage and the anatomic location of tumors. We improved CRC prediction accuracy based solely on gut metagenomics (average area under the curve = 0.85) and highlighted the contribution of 19 newly profiled species and distinct Fusobacterium nucleatum clades. Specific gut species distinguish left-sided versus right-sided CRC (area under the curve = 0.66) with an enrichment of oral-typical microbes. We identified strain-specific CRC signatures with the commensal Ruminococcus bicirculans and Faecalibacterium prausnitzii showing subclades associated with late-stage CRC. Our analysis confirms that the microbiome can be a clinical target for CRC screening and characterizes it as a biomarker for CRC progression.}, }
@article {pmid40461259, year = {2025}, author = {Esser, SP and Turzynski, V and Plewka, J and Nuy, J and Moore, CJ and Banas, I and Soares, AR and Lee, J and Woyke, T and Probst, AJ}, title = {Differential Expression of Core Metabolic Functions in Candidatus Altiarchaeum Inhabiting Distinct Subsurface Ecosystems.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70096}, doi = {10.1111/1758-2229.70096}, pmid = {40461259}, issn = {1758-2229}, support = {DFG PR1603/2-1//Ministerium f&#xfc;r Kultur und Wissenschaft des Landes Nordrhein- Westfalen ("Nachwuchsgruppe Dr. Alexander Probst") and the German Research Foundation/ ; //Aker B.P.: GeneOil Project/ ; //U.S. Department of Energy Joint Genome Institute/ ; //DOE Office of Science User Facility/ ; //the Office of Science of the U.S. Department of Energy operated/ ; }, mesh = {*Ecosystem ; Germany ; Groundwater/microbiology ; Symbiosis ; Transcriptome ; Gene Expression Profiling ; Genome, Archaeal ; Multigene Family ; }, abstract = {Candidatus Altiarchaea are widespread across aquatic subsurface ecosystems and possess a highly conserved core genome, yet adaptations of this core genome to different biotic and abiotic factors based on gene expression remain unknown. Here, we investigated the metatranscriptome of two Ca. Altiarchaeum populations that thrive in two substantially different subsurface ecosystems. In Crystal Geyser, a high-CO2 groundwater system in the USA, Ca. Altiarchaeum crystalense co-occurs with the symbiont Ca. Huberiarchaeum crystalense, while in the Muehlbacher sulfidic spring in Germany, an artesian spring high in sulfide concentration, Ca. A. hamiconexum is heavily infected with viruses. We here mapped metatranscriptome reads against their genomes to analyse the in situ expression profile of their core genomes. Out of 537 shared gene clusters, 331 were functionally annotated and 130 differed significantly in expression between the two sites. Main differences were related to genes involved in cell defence like CRISPR-Cas, virus defence, replication, transcription and energy and carbon metabolism. Our results demonstrate that altiarchaeal populations in the subsurface are likely adapted to their environment while influenced by other biological entities that tamper with their core metabolism. We consequently posit that viruses and symbiotic interactions can be major energy sinks for organisms in the deep biosphere.}, }
@article {pmid40461059, year = {2025}, author = {Laiola, M and Koppe, L and Larabi, A and Thirion, F and Lange, C and Quinquis, B and David, A and Le Chatelier, E and Benoit, B and Sequino, G and Chanon, S and Vieille-Marchiset, A and Herpe, YE and Alvarez, JC and Glorieux, G and Krukowski, H and Geert, HRB and Raes, J and Fouque, D and Massy, ZA and Ehrlich, SD and Stengel, B and Wagner, S and , }, title = {Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2024-334634}, pmid = {40461059}, issn = {1468-3288}, abstract = {BACKGROUND: The gut microbiota has been linked to non-communicable diseases, including chronic kidney disease (CKD). However, the relationships between gut microbiome composition changes, uraemic toxins (UTs) accumulation, and diet on CKD severity and progression remain underexplored.<br><br>OBJECTIVE: To characterise relationships between gut microbiome composition and functionality, UTs diet, and CKD severity and progression, as well as assess microbial contributions to UTs accumulation through mice faecal microbiota transplantation (FMT).<br><br>DESIGN: This study profiled the gut microbiome of 240 non-dialysis patients with CKD (CKD-REIN cohort) using shotgun metagenomics, with follow-up in 103 patients after 3 years, with comparisons with healthy volunteers from the Milieu Int&#xe9;rieur cohort. A multiomics approach identifies features associated with CKD severity (and progression), with validation in an independent Belgian cohort. Experimental models used FMT to test CKD gut microbiome effects on UTs and kidney fibrosis. Changes in gut microbiome over time were evaluated, and the impact of diet on these changes was assessed.<br><br>RESULTS: Compared with matched healthy controls, patients with CKD exhibited gut microbiota alteration, with enrichment of UT precursor-producing species. Patients with severe CKD exhibited higher UT levels and greater enrichment of UT (precursor)-producing species in the microbiota than patients with moderate CKD. Over time, UT (precursor)-producing species increased, and a plant-based low protein diet appeared to mitigate these changes. FMT from patients with CKD to antibiotic-treated CKD model mice increased serum UT levels and exacerbated kidney fibrosis.<br><br>CONCLUSIONS: This study highlights the role of the microbiome and UTs in CKD, suggesting a potential therapeutic target to slow disease progression.}, }
@article {pmid40460917, year = {2025}, author = {Lian, ZH and You, Z and Han, PY and Qiu, Y and Zhang, YZ and Ge, XY}, title = {Decoding the virome reveals diverse novel viruses in tree shrews (Tupaia belangeri) in Yunnan Province.}, journal = {Virologica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.virs.2025.05.011}, pmid = {40460917}, issn = {1995-820X}, abstract = {Viruses circulating in small mammals possess the potential to infect humans. Tree shrews are a group of small mammals inhabiting widely in forests and plantations, but studies on viruses in tree shrews are quite limited. Herein, viral metagenomic sequencing was employed to detect the virome in the tissue and swab samples from seventy-six tree shrews that we collected in Yunnan Province. As the results, genomic fragments belonging to eighteen viral families were identified, thirteen of which contain mammalian viruses. Through polymerase chain reaction (PCR) and Sanger sequencing, twelve complete genomes were determined, including five parvoviruses, three torque teno viruses (TTVs), two adenoviruses, one pneumovirus, and one hepacivirus, together with three partial genomes, including two hepatitis E virus and one paramyxovirus. Notably, the three TTVs, named TSTTV-HNU1, TSTTV-HNU2, and TSTTV-HNU3, may compose a new genus within the family Anelloviridae. Notably, TSParvoV-HNU5, one of the tree shrew parvoviruses detected, was likely to be a recombination of two murine viruses. Divergence time estimation further revealed the potential cross-species-transmission history of the tree shrew pneumovirus TSPenV-HNU1. Our study provides a comprehensive exploration of viral diversity in wild tree shrews, significantly enhancing our understanding of their role as natural virus reservoirs.}, }
@article {pmid40460905, year = {2025}, author = {Memon, FU and Li, C and Ahmad, S and Cui, Y and Feng, X and Zeng, P and Nabi, F and Huang, Z and Tettamanti, G and Chen, T and Tian, L}, title = {Efficiency of microbial fermentation on microbial shifts, enzymatic activity, and transcriptions in black soldier fly larvae during the sugarcane waste conversion.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126588}, doi = {10.1016/j.envpol.2025.126588}, pmid = {40460905}, issn = {1873-6424}, abstract = {Sugarcane trash, consisting mainly of dried leaves, tops and cans, is often burned in fields, posing serious risks to human health, contributing to environmental pollution, and depleting soil nutrients. Black soldier fly larvae (BSFL) offer a promising solution for organic waste management by converting it into insect proteins. This study aimed to develop a microbial fermentation method to utilize sugarcane waste as feed for BSFL and investigate underlying mechanisms. Our results revealed that all fermented groups exhibited enhanced growth and developmental performance, with the combination of Bacillus subtilis, Enterococcus faecalis, and Saccharomyces cerevisiae leading to the highest increases in larval body weight, survival rate, substrate conversion efficiency, and protein content compared to the unfermented group. Metagenomic analysis revealed a notable increase in the phylum Firmicutes, along with its beneficial strains such as Bacillus licheniformis, B. safensis, B. pumilus, Cytobacillus kochii, and Lysinibacillus fusiformis, in the gut of BSFL reared on fermented sugarcane waste, leading to improved gut homeostasis and reduced pathogenic loads. Additionally, the BSFL fed with fermented sugarcane waste exhibited high abundances of carbohydrate-active enzymes (CAZymes) involved in cellulose, hemicellulose, and starch degradation at both class and family levels. Transcriptome analysis further indicated the upregulation of key genes associated with key physiological processes, such as carbohydrate metabolism, chitin biosynthesis, and defense mechanisms. Collectively, these findings demonstrate the synergistic potential of microbial fermentation and BSFL for sustainable sugarcane waste management while advancing the understanding of host-microbe-diet interactions in insect-based bioconversion systems.}, }
@article {pmid40460824, year = {2025}, author = {Gogokhia, L and Tran, N and Grier, A and Nagayama, M and Xiang, G and Funez-dePagnier, G and Lavergne, A and Ericsson, C and Ben Maamar, S and Zhang, M and Battat, R and Scherl, E and Lukin, DJ and Longman, RS}, title = {Donor composition and fiber promote strain engraftment in a randomized controlled trial of fecal microbiota transplant for ulcerative colitis.}, journal = {Med (New York, N.Y.)}, volume = {}, number = {}, pages = {100707}, doi = {10.1016/j.medj.2025.100707}, pmid = {40460824}, issn = {2666-6340}, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an emerging treatment for ulcerative colitis (UC), but the impact of prebiotic fiber on FMT efficacy for UC is unclear. We performed a randomized, double-blind, placebo-controlled clinical trial to examine the efficacy of FMT with and without dietary fiber supplementation in patients with UC.<br><br>METHODS: 27 patients with mild to moderate UC were randomized to receive a single FMT or placebo with or without psyllium fiber supplementation for 8 weeks. The primary outcome was clinical response at week 8, and secondary outcomes included endoscopic improvement and clinical remission. Metagenomic sequencing of fecal DNA was analyzed to determine taxonomic profiles and donor strain engraftment.<br><br>FINDINGS: The trial was terminated early due to manufacturer discontinuation of FMT product. FMT induced clinical response, remission, and endoscopic improvement in UC patients compared to placebo (p < 0.05), but fiber did not improve clinical outcomes of FMT. Recipient microbiome composition post-FMT shifted toward donor composition in responders and non-responders, but the durability of this change was stronger in responders. Clinical response and durable change in microbiome composition following FMT was donor dependent. Strain tracking analysis also demonstrated a donor-dependent variability in the rate of successful engraftment and identified a consortium of engrafted bacteria associated with treatment response or fiber supplementation.<br><br>CONCLUSIONS: Single-dose FMT demonstrated clinical efficacy for mild to moderate UC compared to placebo but revealed no benefit of fiber supplementation. These results highlight proof of concept that donor selection and prebiotic fiber can shape strain-level engraftment. This study was registered at ClinicalTrials.gov: NCT03998488.<br><br>FUNDING: National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK128257, to R.S.L.).}, }
@article {pmid40460798, year = {2025}, author = {Vermote, L and Chun, BH and Khan, SA and De Vuyst, L and Jeon, CO and Weckx, S}, title = {Metagenomic and meta-metabolomic analysis of traditional Korean rice vinegar productions shows a large variability between producers.}, journal = {International journal of food microbiology}, volume = {440}, number = {}, pages = {111283}, doi = {10.1016/j.ijfoodmicro.2025.111283}, pmid = {40460798}, issn = {1879-3460}, abstract = {Cereal vinegars have been used for thousands of years, especially in Asian countries. These vinegars are still produced in a traditional way by a spontaneous, consecutive, alcoholic and acetic acid fermentation process in open vats under non-sterile conditions, which can lead to an unstable and inconsistent flavor and quality. The present study characterized the microbial diversity of complete, traditional Korean rice vinegar productions at two producers (A and B), from steamed rice to rice vinegar, applying high-throughput amplicon-based and shotgun metagenomic sequencing, in combination with meta-metabolomic analysis. Functional analysis based on metagenome-assembled genomes provided insights into the genetic potential of the different microorganisms involved. Producer A used nuruk, a traditional starter, and seed vinegar to start the alcoholic and acetic acid fermentation phases, respectively, which resulted in highly controlled productions even when different fermentation vessels were used. Producer B used only nuruk to start the vinegar productions, and the spontaneous inoculation of acetic acid bacteria did fail in one of the productions. The addition of nuruk resulted in a simultaneous rice starch saccharification and alcoholic fermentation phase characterized by producer-specific moulds, yeasts, and lactic acid bacteria (LAB). During the acetic acid fermentation phase at both producers (a) novel Acetobacter species, related to A. pasteurianus was found. The simultaneous presence of several LAB species made it hard to link them with the production of specific metabolites. Also, the species contributing to ester formation, important for the flavor, was not clear and requires further research.}, }
@article {pmid40460633, year = {2025}, author = {Zheng, Z and Lyu, H and Wang, L and Tang, J}, title = {Microplastic biofilm may shape microbial community enriched with antibiotic resistance genes to enhance nitrogen transformation under antibiotic stress.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138796}, doi = {10.1016/j.jhazmat.2025.138796}, pmid = {40460633}, issn = {1873-3336}, abstract = {The response of nitrogen transformation to microplastic biofilm under antibiotics (ATs) stress as well as the interrelationships between functional genes and microorganisms in surface water are not very well understood and need further investigation. This study investigated the response of nitrogen transformation by analyzing changes in various nitrogen forms and explored the interaction between nitrogen transformation functions and antibiotic resistance genes (ARGs) under exposure to ATs (ciprofloxacin (CIP) and tetracycline (TC)) and PVC biofilm. Compared to the control, exposure to mature polyvinyl chloride (PVC) biofilm increased nitrate nitrogen (NO3[-]-N) and ammonia nitrogen (NH4[+]-N) removal by 12.48 % and 8.79 %, with the NO3[-]-N removal rate constant reaching 0.17. However, co-exposure to CIP significantly inhibited nitrogen transformation, reducing the NO3[-]-N removal rate constant to 0.08. In PVC biofilm, more active nitrogen transformation and enhanced horizontal transfer of ARGs led to a stronger positive correlation between nitrogen transformation genes (NTGs) and ARGs. Microorganisms carrying NTGs largely overlapped with ARGs host species, including Hydrogenophaga, Rhodococcus, and Ignavibacterium, which exhibited high abundance of both gene types. This indicated that PVC biofilm facilitated nitrogen transformation under ATs stress by enriching nitrogen transformation microorganisms carrying high ARGs abundance. These results extended knowledge of effects of ATs and microplastics (MPs) on nitrogen transformation in surface water and provided theoretical support for unique ecological effects of microplastic biofilm.}, }
@article {pmid40460618, year = {2025}, author = {Achudhan, AB and Saleena, LM}, title = {In silico analysis to identify novel amidase enzymes from unclassified bacteria present in coal metagenome.}, journal = {Computational biology and chemistry}, volume = {119}, number = {}, pages = {108525}, doi = {10.1016/j.compbiolchem.2025.108525}, pmid = {40460618}, issn = {1476-928X}, abstract = {Amidase enzymes are essential for converting amide groups into carboxylic acids, which have a variety of applications in various industries, including food, flavorings, and pharmaceuticals. The purpose of this study is to utilize metagenomic analysis to identify and analyze novel amidase enzymes produced by unclassified bacteria present in the coal. Initially, metagenomic DNA was extracted from coal and sequenced using the Illumina platform. Analysis of the annotated coal metagenomic data revealed two novel amidase enzymes from microorganisms belonging to the unclassified Oxalobacteraceae family and the unclassified Betaproteobacteria class. These enzymes belong to the amidase signature family, as identified using the InterProScan database. The three-dimensional (3D) structures of these enzymes were predicted with high per-residue confidence scores of approximately 97.34 and 95.31 using the neural network-based AlphaFold2. Molecular docking analysis suggested caprolactam has the highest binding affinity with the enzymes. Molecular dynamics simulations were performed for 200 ns to assess the protein stability. The modelled protein Amidase 1 and Amidase 2 complexes showed higher binding free energy and better stability when compared with the PDB database amidase structures. Overall, this study demonstrates the identification of novel enzymes from unclassified bacteria belonging to the amidase signature family through in-silico mining of the coal metagenome. Novel amidase enzymes found in the coal metagenome exhibit good stability and high substrate binding affinity compared to the crystal structures in the PDB, indicating potential applications in various industries.}, }
@article {pmid40460542, year = {2025}, author = {Smirnova, AV and Verbeke, TJ and Furgason, CC and Albakistani, EA and Nwosu, FC and Kim, JJ and Haupt, ES and Sheremet, A and Lee, ES and Trang, E and Richardson, E and Dacks, JB and Dunfield, PF}, title = {Microbial community development in an oil sands pit lake.}, journal = {The Science of the total environment}, volume = {987}, number = {}, pages = {179764}, doi = {10.1016/j.scitotenv.2025.179764}, pmid = {40460542}, issn = {1879-1026}, abstract = {Surface mining and extraction of oil sands in Canada produces fluid tailings that contain several compounds of concern for the environment. One option for mine reclamation is the construction of Pit Lakes (PLs) to contain and remediate these tailings. Ultimately, PLs should support food webs typical of boreal lakes. From 2015 to 2021, we applied 16S/18S rRNA gene amplicon sequencing and metagenomics to monitor prokaryotic and eukaryotic microbes in the only full-scale PL of the oil sands industry (Base Mine Lake or BML), and compared it to two control environments: a freshwater reservoir unaffected by tailings, and active tailings ponds receiving regular industrial input. Microbial communities in BML were always intermediate to the two control environments based on alpha and beta diversity analyses. BML communities were highly variable with year, season, and water depth, and contained fewer core species than the freshwater reservoir. Several hydrocarbon degraders and sulfur cycling bacteria were identified as indicator species of tailings ponds, while several phototrophs were indicative of freshwater. However, all of these species were abundant in BML, suggesting that the PL supports food webs characteristic of each control environment. Over the 6-year study, the relative abundances of some common freshwater phytoplankton (Cryptomonas, Mychonastes, Trebouxiophyceae, Cyanobium) and heterotrophic bacteria (Sporichthyaceae, Ca. Fonsibacter, Ilumatobacteraceae, Microbacteriaceae, Ca. Planktophila) increased in BML. The results suggest that microbial communities and processes in BML represent an intermediate state between a tailings pond and a natural freshwater system, and did not stabilize within 10 years of its creation.}, }
@article {pmid40460541, year = {2025}, author = {Kang, MG and Kwak, MJ and Kang, A and Park, J and Lee, DJ and Mun, J and Kim, S and Mun, D and Lee, W and Choi, H and Seo, E and Choi, Y and Jeong, KC and Oh, S and Kim, J and Kim, Y}, title = {Metagenome-based microbial metabolic strategies to mitigate ruminal methane emissions using Komagataeibacter-based symbiotics.}, journal = {The Science of the total environment}, volume = {987}, number = {}, pages = {179793}, doi = {10.1016/j.scitotenv.2025.179793}, pmid = {40460541}, issn = {1879-1026}, abstract = {Global warming increasingly threatens organisms in equatorial regions, where temperatures often exceed physiological limits. Rumen methanogens are a major biological source of anthropogenic methane, a potent greenhouse gas. Therefore, ruminal methane mitigation strategies that preserve animal productivity are urgently needed. Our In vitro analysis of Holstein steer rumen fluid-integrating gas production, volatile fatty acid (VFA) profiles, and metagenomic data-demonstrated that kombucha, a fermented beverage, effectively reduces methane emissions by modulating ruminal fermentation. Rumen fluid was incubated for 60 h under three treatments (control, 3-NOP, and kombucha). During the initial 30 h, kombucha reduced methane by 15.07 % compared to the control but was 17.54 % higher than 3-NOP. In the subsequent 30 h, kombucha achieved sustained reductions of 34.72 % versus the control and 26.28 % versus 3-NOP, highlighting its uniquely sustained methane-reducing effect. A metagenomics-guided screening and in vitro validation identified Komagataeibacter intermedius SLAM-NK6B as a key strain underlying the methane-reducing effect of kombucha. The genome of SLAM-NK6B encodes biosynthetic gene clusters for cellulose, malate, citrate, and methanobactin-metabolites that can modulate the rumen microbiota. SLAM-NK6B supplementation reduced methanogen abundance by 53.32 % and increased hydrogen pressure, shifting microbial metabolism. Excluding acetate, VFA production increased significantly, with propionate levels elevated by 15.39-43.81 %. Metagenomic data further indicated activation of alternative hydrogen sink pathways, including citrate-to-propionate and malate-to-propionate conversions. This study proposes a novel microbial metabolic strategy for methane mitigation, enabling both methane reduction and enhanced fermentation efficiency. Such metabolic guidance of the rumen microbiome offers a sustainable approach to low-emission ruminant production.}, }
@article {pmid40459709, year = {2025}, author = {Quoc, NB and Nhu, LTT and Chau, NNB}, title = {Identification of diet resources of big-eyed bug Geocoris ochropterus (Fieber) (Hemiptera: Geocoridae) by multiplex PCR and shotgun metagenomic approaches.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {537}, pmid = {40459709}, issn = {1573-4978}, support = {E2022.02.1//&#x110;&#x1ea1;i h&#x1ecd;c M&#x1edf; Th&#xe0;nh ph&#x1ed1; H&#x1ed3; Ch&#xed; Minh/ ; }, mesh = {Animals ; *Metagenomics/methods ; Multiplex Polymerase Chain Reaction/methods ; *Hemiptera/genetics ; Diet ; Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; }, abstract = {BACKGROUND: Big-eyed bugs (Geocoris spp.) are important generalist predators in agricultural ecosystems, playing a crucial role in natural pest control.<br><br>METHODS: To better understand their dietary sources, we assessed the plant and animal food sources in the gut of Geocoris ochropterus using multiplex PCR and shotgun metagenomic analysis. The PCR assays targeted genetic markers from both animal (COI) and plant (matK and rbcL) DNA.<br><br>RESULTS: Results revealed the presence of both animal and plant-derived DNA in the gut samples, indicating that Geocoris ochropterus feeds on a mixed diet. Additionally, the results of shotgun metagenomic sequencing of the gut microbiota showed a predominance of Eukaryota, with over 80% of sequences belonging to this domain, while a diverse range of taxonomic groups were identified, including arthropods, plants, bacteria, and fungi. Arthropods particularly insects from the orders Lepidoptera, Hemiptera, Hymenoptera, Coleoptera, Phasmatodea and plants belonging to the orders Brassicales, Cucurbitales, and Poales constituted the most abundant dietary components. At the genus level, notable taxa included Maniola (family Nymphalidae), Carposina (Carposinidae), Helicoverpa (Noctuidae), and Solanum (Solanaceae). Species-level analysis confirmed the dominance of several insect species, including Maniola hyperanthus, Carposina sasakii, and Bombyx mori, alongside plant species such as Cucumis melo, Gossypium hirsutum, and Digitaria exilis.<br><br>CONCLUSIONS: These findings provide a comprehensive characterization of the diet of Geocoris ochropterus, highlighting its role as a generalist predator with a diverse diet consisting of both insect and plant food sources. This study contributes to the understanding of Geocoris ochropterus as a potential biocontrol agent in agricultural systems.}, }
@article {pmid40458954, year = {2025}, author = {Wang, Y and Pan, Z and Shi, Y and Bai, Y and Liang, J and Wang, A and Qu, J}, title = {MnOxGeneTool: A Comprehensive Tool for Identifying and Quantifying Mn(II)-Oxidizing Genes, Revealing Phylogenetic Diversity and Environmental Drivers of Mn(II)-Oxidizers.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c01235}, pmid = {40458954}, issn = {1520-5851}, abstract = {Manganese (Mn) oxides are crucial for degrading organic pollutants and driving biogeochemical cycles. Microorganisms drive Mn(II) oxidation, but traditional cultivation-dependent identification methods are inefficient and error-prone. To overcome these limitations, we developed MnOxGeneTool, a bioinformatics tool for identifying and quantifying Mn(II)-oxidizing genes from genomic and metagenomic data. MnOxGeneTool consists of three main components: (1) a curated database of known Mn(II)-oxidizing proteins and their homologues, (2) a hidden Markov models (HMMs) database derived from this protein data set, and (3) a computational pipeline that integrates bioinformatics tools (e.g., HMMER and BLASTX) to identify and quantify Mn(II)-oxidizing genes. We assessed the accuracy and sensitivity of these HMMs through cross-validation, demonstrating their effectiveness in identifying Mn(II)-oxidizing genes in bacterial genomes. Using MnOxGeneTool, we explored the phylogenetic diversity of Mn(II)-oxidizers and identified 824 bacterial genera containing Mn(II)-oxidizing genes, significantly expanding previous knowledge in this field. Additionally, we analyzed metagenomic data from various environments to explore environmental drivers of Mn(II)-oxidizing genes, identifying two potential drivers: oligotrophic conditions and alkaline environments. These findings enable targeted discovery of novel Mn(II)-oxidizers and genetic determinants through identification of their ecological niches and expression optima, thereby expanding MnOxGeneTool's predictive coverage of uncatalogued Mn(II)-oxidizing proteins. By providing an innovative bioinformatics tool that enables efficient identification and quantification of Mn(II)-oxidizing genes from both genomic and metagenomic data, this study offers significant advancements in the research of biogenic Mn(II) oxidation. The tool is available at https://github.com/wyh19990121/MnOxGeneTool.}, }
@article {pmid40458218, year = {2025}, author = {Qush, A and Assaad, N and Alkhayat, FA and Al-Kuwari, MS and Al-Khalaf, N and Bassil, M and Yassine, HM and Zeidan, A and Razali, R and Kamareddine, L}, title = {Insects in agricultural greenhouses: a metagenomic analysis of microbes in Trialeurodes vaporariorum infesting tomato and cucumber crops.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1581707}, pmid = {40458218}, issn = {1664-462X}, abstract = {INTRODUCTION: With the predicted 9-10 billion world population increase by 2050 and its accompanying need for sustainable food production, and with the harsh climate conditions challenging agriculture and food security in many countries world-wide, employing "horticultural protected cultivation practices" in farming for seasonal and off-seasonal crop production is on the rise, among which is the use of agricultural greenhouses. The importance of greenhouse farming has been, indeed, evident by the perceived increase in year-round crops production, curtail in production risks, upsurge in agricultural profits, outreaching food stability and security in many countries globally. Yet, and despite this acknowledged success of employing greenhouses in farming, many constraints, including the presence of insect pests, still chaperoned this practice over the years, significantly impacting crop quality and production.<br><br>METHODS: As such, we assessed in this study the status of "insect pests" in the greenhouse model by collecting insects from different greenhouse sectors grown with tomatoes and cucumbers and identified the collected insects using relevant identification keys. To further explore the pest paradigm in greenhouses, we then focused on particularly studying Trialeurodes vaporariorum (TRIAVA), a key insect species among the collected and identified insects in the studied greenhouse model and a significant pest with an impactful effect on many crops worldwide. To do so, we traced the abundance of TRIAVA in the tomato and cucumber grown greenhouse sectors over the period of the study, analyzed its metagenome and associated its abundance with crop yield.<br><br>RESULTS AND DISCUSSION: Our findings revealed TRIAVA hosted microbes with aptitudes to either serve as symbiotic microorganisms and protect TRIAVA against pathogens or to potentially cause damage to crops. This work provides additional insight into the insect pests paradigm in greenhouses, an upshot that could serve integrated insect pest management strategies in greenhouses for optimal agricultural practices.}, }
@article {pmid40456950, year = {2025}, author = {Kocharovskaya, Y and Delegan, Y and Sevostianov, S and Bogun, A and Demin, DV}, title = {Metagenomic Analysis of Pulp and Paper Wastes and Prospects for Their Self-purification.}, journal = {Current microbiology}, volume = {82}, number = {7}, pages = {320}, pmid = {40456950}, issn = {1432-0991}, mesh = {*Paper ; *Metagenomics ; Lignin/metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Industrial Waste/analysis ; Biodegradation, Environmental ; *Microbiota ; High-Throughput Nucleotide Sequencing ; }, abstract = {Thousands of tons of waste accumulate, as a result of the activities of the pulp and paper industry, which is often stored in the form of dumps. However, intensifying the use of lignocellulose for more efficient bioremediation remains highly challenging. Therefore, the study of microbiomes with potentially desirable characteristics for the decomposition of pulp and paper wastes is currently an important task. In this study, a comprehensive assessment of the microbiota biodiversity of these dumps was carried out using high-throughput, high-resolution sequencing. In study 472 million high-quality clean reads assembled into 6,413,337 contigs with a total length of 4306 Mb, of which 3,633,174 open reading frames (ORFs) were identified. The core microbiome was composed of four phyla from Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Representatives of phylum Proteobacteria prevailed in samples. Annotation using the KEGG database in the Metabolism category resulted in 654,234 ORFs and 5138 ORFs encoding enzymes/proteins involved in degradation of lignocellulose which formed main pool of the wastes. By use of the created database, the search for lignocellulose degradation genes showed that genera Shewanella, Achromobacter, and Delftia covered significant part of the reads. The results indicate that the established microbiome of local landfills can be considered as an important source for improving lignocellulose bioremediation, provided that lignocellulosic fungi are sufficiently active. In whole, these new data can be used as a scientific basis to form an efficient eco-biotechnology for auto-remediation of pulp and paper industry waste.}, }
@article {pmid40456770, year = {2025}, author = {Zhou, XQ and Chen, KH and Yu, RQ and Yang, M and Liu, Q and Hao, YY and Li, J and Liu, HW and Feng, J and Tan, W and Huang, Q and Gu, B and Liu, YR}, title = {Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5102}, pmid = {40456770}, issn = {2041-1723}, support = {42425701//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177022//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Methylmercury Compounds/metabolism/toxicity ; *Oryza/metabolism/microbiology ; *Soil Microbiology ; Biodegradation, Environmental ; Metagenomics ; *Soil Pollutants/metabolism/toxicity ; *Bacteria/metabolism/genetics/classification ; Soil/chemistry ; }, abstract = {Toxic methylmercury (CH3Hg[+]) is produced by microbial conversion of inorganic mercury in hypoxic environments such as rice paddy soils, and can accumulate in rice grains. Although microbial demethylation has been recognized as a crucial pathway for CH3Hg[+] degradation, the identities of microbes and pathways accountable for CH3Hg[+] degradation in soil remain elusive. Here, we combine [13]CH3Hg[+]-DNA stable-isotope probing experiments with shotgun metagenomics to explore microbial taxa and associated biochemical processes involved in CH3Hg[+] degradation in paddy and upland soils. We identify Pseudarthrobacter, Methylophilaceae (MM2), and Dechloromonas as the most significant taxa potentially engaged in the degradation of [13]CH3Hg[+] in paddy soil with high mercury contamination. We confirm that strains affiliated with two of those taxa (species Dechloromonas denitrificans and Methylovorus menthalis) can degrade CH3Hg[+] in pure culture assays. Metagenomic analysis further reveals that most of these candidate [13]CH3Hg[+] degraders carry genes associated with the Wood-Ljungdahl pathway, dicarboxylate-hydroxybutyrate cycle, methanogenesis, and denitrification, but apparently lack the merB and merA genes involved in CH3Hg[+] reductive demethylation. Finally, we estimate that microbial degradation of soil CH3Hg[+] contributes to 0.08-0.64 fold decreases in CH3Hg[+] accumulation in rice grains across China (hazard quotient (HQ) decrements of 0.62-13.75%). Thus, our results provide insights into microorganisms and pathways responsible for CH3Hg[+] degradation in soil, with potential implications for development of bioremediation strategies.}, }
@article {pmid40456641, year = {2025}, author = {Wen, M and Liu, Y and Feng, CY and Ji, W and Li, ZQ}, title = {Differences of key processes in soil nitrogen cycling and their driving factors under different land-use types.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {36}, number = {5}, pages = {1387-1397}, doi = {10.13287/j.1001-9332.202505.036}, pmid = {40456641}, issn = {1001-9332}, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Nitrogen Cycle ; *Nitrogen/analysis/metabolism ; China ; Nitrification ; *Ecosystem ; Denitrification ; Forests ; Wetlands ; Grassland ; Agriculture ; Nitrogen Fixation ; }, abstract = {To investigate the responses and drivers of soil microbial nitrogen (N)-cycling functional genes under different land-use types, we analyzed five representative ecosystems in the Yellow River alluvial plain: Tamarix chinensis forests, Fraxinus chinensis forests, grasslands, wetlands, and farmlands. With metagenomic sequencing, we quantified the relative abundances of 22 functional genes associated with six critical N-cycling processes. Soil physicochemical properties were characterized. There were significant variations in soil nitrogen (N)-cycling functional gene abundances across land-use types. Wetlands exhibited the highest relative abundances of nitrogen fixation (1.28×10[-5]), nitrification (4.91×10[-4]), and denitrification (7.03×10[-4]) genes, but the lowest assimilatory nitrate reduction potential (1.84×10[-4]). Farmlands showed maximal assimilatory nitrate reduction gene abundance (3.31×10[-4]), while grasslands dominated in ammonification gene expression (2.35×10[-4]), significantly higher than other ecosystems. T. chinensis forests maintained the most constrained N-cycling profile, with minimal nitrification (2.77×10[-4]) and denitrification (5.25×10[-4]) relative gene abundances. Redundancy analysis identified soil total nitrogen, organic carbon, total potassium, and electrical conductivity as the key environmental drivers of these variations. Our findings demonstrated that land-use types could shape microbial N-cycling functional gene abundances by altering soil nutrient conditions, with consequence on fundamental processes of soil nitrogen transformation.}, }
@article {pmid40456384, year = {2025}, author = {Nayyar, J and Bedu-Ferrari, C and Patangia, D and Hurley, E and Feeley, L and Ross, RP and Stanton, C and Brady, P}, title = {Gut and oral microbial profile associations to oral cancer.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {105848}, doi = {10.1016/j.jdent.2025.105848}, pmid = {40456384}, issn = {1879-176X}, abstract = {The human microbiome is widely known to be associated with health and disease. The oral microbiome has been linked with oral diseases and infections, though not many studies have explored the relation between oral and gut microbiome with oral cancer based on lesion histology METHODS: This study uniquely explores the oral and gut microbiota in 30 participants (n=30) divided into three groups based on histology; Benign (B) (n=15), Potentially Malignant (PM) (n=8), and Malignant (M) (n=7) oral lesions. Using shotgun metagenomic sequencing, we analysed microbiota profiles to determine their potential as biomarkers for oral malignancy RESULTS: Distinct gut microbial profiles were observed between Benign and Malignant groups and the association of specific microbes in oral saliva, such as Haemophilus parainfluenzae, Veillonella parvula, Fusobacterium nucleatum and Rothia mucilaginosa were strongly associated with malignancy CONCLUSION: The data from this exploratory study suggest that oral and gut microbiomes could act as possible biomarkers and aid in early detection and assessment of oral cancer risk. With regard to potentially malignant lesions, future research could study individual Oral Potentially Malignant Disorders (OPMDs) as distinct entities due to the wide variation in clinical and histological presentation. Further research is required to develop definitive biomarkers in both potentially malignant and malignant oral lesions CLINICAL SIGNIFICANCE: While smoking and alcohol are known risk factors for oral cancer, a biomarker such as the saliva/stool microbiome profile could help identify a risk indicator or a potential risk factor. Additionally such a biomarker could help identify patients with OPMDs that are likely to undergo malignant transformation.}, }
@article {pmid40456327, year = {2025}, author = {Zhao, F and Yang, Z and Wang, J and Bartlam, M and Wang, Y}, title = {Enantioselective effects of chiral antibiotics on antibiotic resistance gene dissemination and risk in activated sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132749}, doi = {10.1016/j.biortech.2025.132749}, pmid = {40456327}, issn = {1873-2976}, abstract = {Misuse of antibiotics drives the spread of antibiotic resistance genes (ARGs). Although reducing residual antibiotic concentrations can help curb ARG proliferation, the biodegradation and transformation of antibiotic stereoisomers may exacerbate resistance development. However, the impact of antibiotic enantiomers on ARG proliferation remains poorly understood. This study employed metagenomic analysis to investigate the enantiomer-specific selection and resistance risks of chiral antibiotic ofloxacin (OFL) and its (S)-enantiomer, levofloxacin (LEV), in activated sludge. Results showed that LEV primarily promoted the enrichment of ARGs related to aminoglycoside and mupirocin resistance by selecting for pathogenic bacteria carrying virulence factors under high toxicity stress. OFL-driven ARG proliferation involved more diverse mechanisms, including increased gene mobility, co-selection with heavy metals, broader host range, and elevated pathogenicity. The antibiotic resistome risk index (ARRI) further demonstrated a higher environmental risk under OFL treatment than LEV. These findings offer critical insights into the enantioselective resistance risks posed by chiral antibiotics.}, }
@article {pmid40455595, year = {2025}, author = {Fetters, AM and Cantalupo, PG and Robles, MTS and Pipas, JM and Ashman, TL}, title = {Sharing Pollinators and Viruses: Virus Diversity of Pollen in a Co-Flowering Community.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icaf073}, pmid = {40455595}, issn = {1557-7023}, abstract = {Co-flowering plant species frequently share pollinators, flower-inhabiting bacteria, and fungi, but whether pollen-associated viruses are shared is unknown. Given that pollen-associated viruses are sexually transmitted diseases, their diversity is expected to increase with pollinator sharing. We conducted a metagenomic study to identify pollen-associated viruses from 18 co-flowering plant species to determine whether 1) life history, floral traits, or pollination generalism were associated with viral richness, and 2) plants shared pollen-associated viruses. We demonstrated that pollination generalism influences pollen-associated virus richness and the extent of pollen virus sharing between plant species. We also revealed that perenniality, multiple flowers, and bilateral floral symmetry were associated with high pollen viral richness locally, confirming and extending patterns observed previously at a continental scale. Our results highlight the importance of plant-pollinator interactions as drivers of plant-viral interaction diversity.}, }
@article {pmid40455399, year = {2025}, author = {Qayyum, H and Raziq, MF and Manzoor, H and Zaidi, SSA and Ali, A and Kayani, MUR}, title = {Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers.}, journal = {Interdisciplinary sciences, computational life sciences}, volume = {}, number = {}, pages = {}, pmid = {40455399}, issn = {1867-1462}, abstract = {De novo assembly and genome binning are fundamental steps for genome-resolved metagenomics analyses. However, the availability of limited computational resources and extensive processing time limit the broader application of these analyses. To address these challenges, the optimization of the parameters employed in these processes can improve the effective utilization of available metagenomics tools. Therefore, this study tested three sets of k-mers (default, reduced, and extended) for their efficiency in metagenome assembly and suitability in recovering metagenome-assembled genomes. The results demonstrate that the reduced set of k-mers outperforms the other two sets in computational efficiency and the quality of results. The assemblies from the default set are comparable with those from the reduced set; however, less complete and highly contaminated metagenome-assembled genomes are obtained at the expense of higher processing time. The extended set of k-mers yields less contiguous but computationally expensive assemblies. This set takes approximately 3-times more processing time than the reduced k-mers and recovers the lowest proportions of high and medium-quality metagenome-assembled genomes. Contrarily, the reduced set produces better assemblies, substantially improving the number and quality of the recovered metagenome-assembled genomes in significantly reduced processing time. Validation of the reduced k-mer set on previously published metagenome datasets further demonstrates its effectiveness not only for human metagenomes but also for the metagenomes of environmental origin. These findings underscore that the reduced k-mer set is optimal for efficient metagenome analyses of varying complexities and origins. This optimization of the k-mer set used in metagenome assemblers significantly reduces computational time while improving the quality of the assemblies and recovered metagenome-assembled genomes. This efficient solution will facilitate the widespread application of genome-resolved analyses, even in resource-limited settings, and help the recovery of better-quality metagenome-assembled genomes for downstream analyses.}, }
@article {pmid40455288, year = {2025}, author = {Hu, J and Yu, W and Cui, J and Zhang, L and Yu, W}, title = {Recent advances in diagnostic technologies for postoperative central nervous system infections: a review.}, journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology}, volume = {}, number = {}, pages = {}, pmid = {40455288}, issn = {1590-3478}, abstract = {Postoperative central nervous system infections (PCNSIs), including meningitis, cerebral abscesses, and implant-associated infections, represent critical complications following neurosurgical procedures. These infections pose significant risks to patient outcomes due to delayed diagnosis, escalating antimicrobial resistance, and limited therapeutic efficacy. Conventional diagnostic approaches, such as cerebrospinal fluid (CSF) analysis, microbial cultures, and neuroimaging, exhibit notable limitations in sensitivity, specificity, and rapidity. This review highlights transformative technologies reshaping PCNSI diagnostics, including molecular assays (e.g., quantitative PCR, digital droplet PCR), metagenomic next-generation sequencing (mNGS), CRISPR-based pathogen detection platforms, metabolomics, and advanced molecular imaging modalities. Furthermore, we address translational challenges in clinical adoption, including cost barriers, standardization gaps, and the need for interdisciplinary collaboration. Emerging artificial intelligence (AI)-driven strategies are proposed to optimize pathogen identification, predict antimicrobial resistance profiles, and tailor personalized therapeutic regimens.}, }
@article {pmid40455149, year = {2025}, author = {da Silva, AF and Wallau, GL}, title = {Bioinformatic Identification of Viral Genomes from High-Throughput Metagenomic Sequencing Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2927}, number = {}, pages = {1-22}, pmid = {40455149}, issn = {1940-6029}, mesh = {*Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Computational Biology/methods ; *Viruses/genetics ; Phylogeny ; }, abstract = {Virus identification has historically been performed through cell culture isolation and low-throughput methodologies that are limited often requiring previous information about the investigated viruses. These classical virological methods have been pivotal to many discoveries, but overall, they have a limited capacity for characterization of highly divergent and novel viruses. Nowadays, new technologies such as next-generation sequencing have revolutionized the virology field, enabling unbiased high-throughput viral genome characterization. But although the sequencing bottleneck has been surpassed, we could not say the same for the bioinformatics bottleneck of fishing new viral genomes from these large datasets littered with host and other microbes sequencing data. Here, we describe a bioinformatic framework to process metagenomic or metatranscriptomic data, aiming to assemble, identify, and study the evolutionary relationship of viral sequences and genomes.}, }
@article {pmid40454874, year = {2025}, author = {Pfister, CA and Berlinghof, J and Bogan, M and Cardini, U and Gobet, A and Hamon-Giraud, P and Hart, J and Jimenez, N and Siegel, A and Stanfield, E and Vallet, M and Leblanc, C and Rousseau, C and Thomas, F and Stock, W and Dittami, SM}, title = {Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0099624}, doi = {10.1128/msphere.00996-24}, pmid = {40454874}, issn = {2379-5042}, abstract = {UNLABELLED: Seaweeds harbor a rich diversity of bacteria, providing them with metabolic resources and a surface for attachment and biofilm development. The host's unique environment potentially shapes the bacterial genomes and promotes adaptations for a symbiotic lifestyle. To investigate whether the genomes of seaweed-associated bacteria are genetically and metabolically distinct from their close free-living relatives in seawater, we compared both the seaweed-associated and free-living counterparts of 72 bacterial genera across 16 seaweed hosts using whole-genome sequences or high-quality metagenome-assembled genomes. While taxonomic affiliation strongly influenced genome characteristics such as GC content, gene number, and size, host association had a lower effect overall. A reduced genome size was suggested only in Nereocystis luetkeana-associated microbes, while only Ascophyllum nodosum-associated bacteria had an increased GC content. Metabolic adaptations were indicated from the genomes of seaweed-associated bacteria, including enriched pathways for B vitamin production, complex carbohydrate utilization, and amino acid biosynthesis. In particular, Flavobacteriia showed the most pronounced differences between host-associated and free-living strains. We further hypothesized that bacteria associated with seaweed might have evolved to complement their host's metabolism and tested this inference by analyzing the genomes of both the seaweed Ectocarpus subulatus and its 28 bacterial associates but found no evidence for such complementarity. Our analyses of 72 paired bacterial genomes highlighted significant metabolic differences in seaweed-associated strains with implications for carbon, nitrogen, and sulfur cycling in the coastal ocean.<br><br>IMPORTANCE: We hypothesized that the unique environment of seaweeds in coastal oceans shapes bacterial genomes and promotes a symbiotic lifestyle. We compared the genomes of bacteria isolated from seaweed with bacteria from the same genus found free-living in seawater. For genome features that included the number of genes, the size of the genome, and the GC content, taxonomy was of greater importance than bacterial lifestyle. When we compared metabolic abilities, we again found a strong effect of taxonomy in determining metabolism. Although several metabolic pathways differed between free-living and host-associated bacteria, this was especially prominent for Flavobacteriia in the phylum Bacteroidota. Notably, bacteria living on seaweeds had an increased occurrence of genes for B vitamin synthesis, complex carbohydrate use, and nitrogen uptake, indicating that bacterial genomes reflect both their evolutionary history and the current environment they inhabit.}, }
@article {pmid40454811, year = {2025}, author = {Millard, SA and Vendrov, KC and Young, VB and Seekatz, AM}, title = {Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice.}, journal = {mBio}, volume = {}, number = {}, pages = {e0110825}, doi = {10.1128/mbio.01108-25}, pmid = {40454811}, issn = {2150-7511}, abstract = {UNLABELLED: Colonization resistance provided by the gut microbiota is essential for resisting both initial Clostridioides difficile infection (CDI) and potential recurrent infection (rCDI). Although fecal microbiota transplantation (FMT) has been successful in treating rCDI by restoring microbial composition and function, mechanisms underlying the efficacy of standardized stool-derived products remain poorly understood. Using a combination of 16S rRNA gene-based and metagenomic sequencing alongside metabolomics, we investigated microbiome recovery following FMT from human and murine donor sources in a mouse model of rCDI. We found that a human-derived microbiota was less effective in clearing C. difficile compared to a mouse-derived microbiota, despite recovery of taxonomic diversity, compositional changes, and bacterial functions typically associated with clearance. Metabolomic analysis revealed deficits in secondary metabolites compared to those that received murine FMT, suggesting a functional remodeling between human microbes in their new host environment. Collectively, our data revealed additional environmental, ecological, or host factors to consider in FMT-based recovery from rCDI.<br><br>IMPORTANCE: Clostridioides difficile is a significant healthcare-associated pathogen, with recurrent infections presenting a major treatment challenge due to further disruption of the microbiota after antibiotic administration. Despite the success of fecal microbiota transplantation (FMT) for the treatment of recurrent infection, the mechanisms mediating its efficacy remain underexplored. This study reveals that the effectiveness of FMT may be compromised by a mismatch between donor microbes and the recipient environment, leading to deficits in key microbial metabolites. These findings highlight additional factors to consider when assessing the efficacy of microbial-based therapeutics for C. difficile infection (CDI) and other conditions.}, }
@article {pmid40454480, year = {2025}, author = {Lynch, LE and Lahowetz, R and Maresso, C and Terwilliger, A and Pizzini, J and Melendez Hebib, V and Britton, RA and Maresso, AW and Preidis, GA}, title = {Present and future of microbiome-targeting therapeutics.}, journal = {The Journal of clinical investigation}, volume = {135}, number = {11}, pages = {}, pmid = {40454480}, issn = {1558-8238}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; *Phage Therapy/trends/methods ; Bacteriophages ; Animals ; }, abstract = {A large body of evidence suggests that single- and multiple-strain probiotics and synbiotics could have roles in the management of specific gastrointestinal disorders. However, ongoing concerns regarding the quality and heterogeneity of the clinical data, safety in vulnerable populations, and the lack of regulation of products containing live microbes are barriers to widespread clinical use. Safety and regulatory issues must be addressed and new technologies considered. One alternative future strategy is the use of synthetic bacterial communities, defined as manually assembled consortia of two or more bacteria originally derived from the human gastrointestinal tract. Synthetic bacterial communities can model functional, ecological, and structural aspects of native communities within the gastrointestinal tract, occupying varying nutritional niches and providing the host with a stable, robust, and diverse gut microbiota that can prevent pathobiont colonization by way of colonization resistance. Alternatively, phage therapy is the use of lytic phage to treat bacterial infections. The rise of antimicrobial resistance has led to renewed interest in phage therapy, and the high specificity of phages for their hosts has spurred interest in using phage-based approaches to precisely modulate the microbiome. In this Review, we consider the present and future of microbiome-targeting therapies, with a special focus on early-life applications, such as prevention of necrotizing enterocolitis.}, }
@article {pmid40454439, year = {2025}, author = {Rosam, K and Steixner, S and Bauer, A and Lass-Flörl, C}, title = {Non-conventional diagnostic methods for invasive fungal infections.}, journal = {Expert review of molecular diagnostics}, volume = {}, number = {}, pages = {}, doi = {10.1080/14737159.2025.2509026}, pmid = {40454439}, issn = {1744-8352}, abstract = {INTRODUCTION: Biomarkers have revolutionized the field of fungal diagnostics by enabling early detection, risk assessment, and monitoring treatment response. Their value in clinical practice is influenced by a wide range of determinants including diagnostic performance (sensitivity and specificity), predictive value in diverse patient groups, host immune status and comorbidities, technical standardization and antifungal treatment.<br><br>AREA COVERED: This review provides a comprehensive overview of the current antigen and DNA-based methods used for the detection of invasive fungal infections (IFIs), with a particular focus on the clinically significant pathogens Aspergillus spp. Candida spp. and Mucorales. It examines the advantages and limitations of the available diagnostic tools, emphasizing their role in early detection, specificity, and clinical application.<br><br>EXPERT OPINION: The selection of fungal biomarkers should be tailored based on the patient population, the clinical setting, and the type of fungal infection suspected. Using a combination of biomarkers often improves diagnostic accuracy, particularly in high-risk populations like hematologic malignancy patients. Fungal biomarkers do not provide definitive proof of an active fungal infection; instead, they serve as indirect indicators of the presence of fungal components. Their primary role is to support the diagnosis, assess risk, and guide clinical decisions, but they must be interpreted within the broader clinical context to follow current guidelines for diagnosing fungal infections (EORTC/MSG).}, }
@article {pmid40454309, year = {2025}, author = {Xu, J and Li, Y and Wang, X and Mu, Y}, title = {Case Report: A Case of Visceral Leishmaniasis Misdiagnosed as Brucellosis.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {2673-2677}, pmid = {40454309}, issn = {1178-6973}, abstract = {Visceral leishmaniasis (VL) is an infectious disease caused by protozoan parasites of the genus Leishmania and transmitted through the bites of infected female sandflies. Due to its nonspecific clinical presentation, VL is prone to misdiagnosis and underdiagnosis. Though rare, VL is endemic in regions of Africa, South America, Asia, and parts of Europe, including the Mediterranean. This report describes a case of VL initially misdiagnosed as brucellosis due to a history of close contact with sheep. The patient tested negative for brucellosis via serum agglutination, blood culture, and bone marrow smear, and showed no improvement with a combination of omadacycline and rifampin therapy. Definitive diagnosis was achieved through metagenomic next-generation sequencing (mNGS) and confirmation with the rk39 antigen test. The patient was successfully treated with amphotericin B cholesterol sulfate complex and recovered fully. This case highlights the need to consider rare pathogens when epidemiological history and clinical response to treatment are incongruent and emphasizes the value of mNGS in timely diagnosis of VL.}, }
@article {pmid40454150, year = {2025}, author = {Du, R and Mao, H and Li, WM and Liu, D and Wang, K}, title = {Case Report: Empyema secondary to percutaneous transthoracic needle biopsy in three cases.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1531909}, pmid = {40454150}, issn = {2296-858X}, abstract = {Percutaneous transthoracic needle biopsy (PTNB) is a widely utilized diagnostic procedure for pulmonary lesions, with the current literature predominantly documenting pneumothorax and hemorrhage as primary complications. While empyema represents a rare complication, its clinical implications warrant special attention. In this study, we report the cases of three patients with unidentified pulmonary masses who developed empyema after PTNB. All cases exhibited fever (24-48 h post-procedure) and radiographic evidence of pleural effusion progression shortly after the procedure, which was successfully managed through pleural drainage and antibiotic treatment. These findings suggest that pre-procedural infectious foci may be prone to iatrogenic pleural seeding during PTNB. This report emphasizes the necessity of monitoring infectious indicators in patients undergoing biopsy of cavitary or necrotic lesions. Physicians should exercise caution when puncturing lumps suspected of abscesses and remain vigilant for empyema secondary to PTNB if the patient shows signs of infection.}, }
@article {pmid40453877, year = {2025}, author = {Ma, R and Yin, Y and Zhang, JP and Zhang, MX and Zhou, JR and He, Y and Gai, W and Zhang, XH and Wang, Y and Xu, LP and Liu, KY and Huang, XJ and Sun, YQ}, title = {Metagenomic Next-generation Sequencing Compared With Blood Culture as First-line Diagnostic Method for Bloodstream Infection in Hematologic Patients With Febrile Neutropenia: A Multicenter, Prospective Study.}, journal = {Open forum infectious diseases}, volume = {12}, number = {6}, pages = {ofaf288}, pmid = {40453877}, issn = {2328-8957}, abstract = {Bloodstream infection (BSI) is a frequent but lethal complication in hematologic patients with febrile neutropenia (FN). However, blood culture (BC) only detects an organism in 20%-30% of patients with FN. We aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) as a first-line diagnostic method in BSI. This study was prospectively performed in 4 Chinese hematologic centers. In patients aged ≥15 years with hematologic diseases, peripheral blood specimens were collected per patient for simultaneous BC and mNGS at the onset of FN. The clinical physician and mNGS analysis team were double-blinded, and the adjudication of the clinical diagnosis was evaluated by another expert panel of 4 specialists. The primary endpoint of this study was the diagnostic performance of mNGS. This study was registered on ClinicalTrials.gov. Three hundred FN events were enrolled, including 62 definite BSI, 61 probable BSI, 116 infectious FN other than BSI, 55 noninfectious FN events, and 6 FN of indeterminate cause. Among 62 definite BSI cases, mNGS identified causative pathogens in 59 (95.2%). Concurrent BC initially detected pathogens in 59 cases, and 3 additional pathogens consistent with mNGS were later identified in repeated BC testing. The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were 95.2%, 94.6%, 95.2%, and 94.6%, respectively. The diagnostic time of mNGS was significantly shorter than that of BC (39.7 ± 15.0 vs 119.8 ± 31.9 hours, P < .0001). The findings suggest that the mNGS approach has excellent diagnostic performance for the first-line diagnosis of BSI in patients with FN. The study will promote early diagnosis and better management of the patients.}, }
@article {pmid40453711, year = {2025}, author = {Zhou, J and Kamau, E and Wei, Q}, title = {Editorial: Targeted metagenomics in pathogen detection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1612802}, pmid = {40453711}, issn = {2235-2988}, }
@article {pmid40452057, year = {2025}, author = {Francioli, D and Kampouris, ID and Kuhl-Nagel, T and Babin, D and Sommermann, L and Behr, JH and Chowdhury, SP and Zrenner, R and Moradtalab, N and Schloter, M and Geistlinger, J and Ludewig, U and Neumann, G and Smalla, K and Grosch, R}, title = {Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {148}, pmid = {40452057}, issn = {1474-760X}, support = {031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 031B0514A- E//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {*Zea mays/microbiology/growth &amp; development ; *Rhizosphere ; *Microbiota ; *Stress, Physiological ; Bacillus ; Plant Roots/microbiology ; Soil Microbiology ; *Agricultural Inoculants/physiology ; }, abstract = {BACKGROUND: Field inoculation of crops with beneficial microbes is a promising sustainable strategy to enhance plant fitness and nutrient acquisition. However, effectiveness can vary due to environmental factors, microbial competition, and methodological challenges, while their precise modes of action remain uncertain. This underscores the need for further research to optimize inoculation strategies for consistent agricultural benefits.<br><br>RESULTS: Using a comprehensive, multidisciplinary approach, we investigate the effects of a consortium of beneficial microbes (BMc) (Pseudomonas sp. RU47, Bacillus atrophaeus ABi03, Trichoderma harzianum OMG16) on maize (Zea mays cv. Benedictio) through an inoculation experiment conducted within a long-term field trial across intensive and extensive farming practices. Additionally, an unexpected early drought stress emerged as a climatic variable, offering further insight into the effectiveness of the microbial consortium. Our findings demonstrate that BMc root inoculation primarily enhanced plant growth and fitness, particularly by increasing iron uptake, which is crucial for drought adaptation. Inoculated maize plants show improved shoot growth and fitness compared to non-inoculated plants, regardless of farming practices. Specifically, BMc modulate plant hormonal balance, enhance the detoxification of reactive oxygen species, and increase root exudation of iron-chelating metabolites. Amplicon sequencing reveals shifts in rhizosphere bacterial and fungal communities mediated by the consortium. Metagenomic shotgun sequencing indicates enrichment of genes related to antimicrobial lipopeptides and siderophores.<br><br>CONCLUSIONS: Our findings highlight the multifaceted benefits of BMc inoculation on plant fitness, significantly influencing metabolism, stress responses, and the rhizosphere microbiome. These improvements are crucial for advancing sustainable agricultural practices by enhancing plant resilience and productivity.}, }
@article {pmid40451466, year = {2025}, author = {Osogo, AK and Muyekho, F and Were, H and Okoth, P}, title = {Deciphering common bean (Phaseolus Vulgaris L.) microbiome assemblages reveal mechanistic insights into host-pathogen-microbiome interactions.}, journal = {Genomics}, volume = {}, number = {}, pages = {111064}, doi = {10.1016/j.ygeno.2025.111064}, pmid = {40451466}, issn = {1089-8646}, abstract = {Common bean (Phaseolus vulgaris L.) is the primary source of proteins and nutrients in most households in sub-Saharan Africa. However, production of this crop is constrained by several biotic factors. While research on common bean plant-pathogen interactions has predominantly focused on binary relationships, the diversity of microbes naturally inhabiting plant tissues and their interactions has often been overlooked. Recent findings, however, show that these resident microbes actively contribute to plant defense mechanisms, rather than merely acting as passive bystanders. This study aimed to document and explore potential interactions within the common bean microbiome assemblages through field investigations in selected locations across the western regions of Kenya. Common bean leaf samples were collected from farmer's fields along motorable roads 3-5 km apart. Shotgun metagenomic analysis identified a diverse range of microorganisms, including bacteria, fungi, yeast, phytoplasmas, viruses, and bacteriophages, across multiple taxonomic levels-spanning 4 Kingdoms, 136 Phyla, 168 Classes, 360 Orders, 792 Families, 2039 Genera, and 6130 Species-both epiphytic and endophytic, and pathogenic or non-pathogenic. Pseudomonadota consistently showed the highest taxonomic annotation for antimicrobial-resistant organisms, highlighting its central role in resistance across the studied area. The sequences obtained were mapped to the EggNOG, CAZy, and KEGG databases to explore, assign, and predict gene functions. The EggNOG database emphasized the importance of "Replication, recombination, and repair" processes in maintaining genomic stability, along with amino acid transport, energy production, and metabolism. CAZy analysis revealed a significant presence of glycosyltransferases, particularly from GT1 and GT32 families, and noted the role of enzymes like Glycoside Hydrolases in plant defense against pathogens. KEGG pathway analysis underscored the central role of metabolic processes such as energy metabolism, translation, and carbohydrate metabolism. Key pathways linked to plant defense and resilience, including 2-oxocarboxylic acid metabolism, amino acid biosynthesis, and secondary metabolite biosynthesis, were identified. These findings underscore the role of metabolic and enzymatic processes in strengthening plant defenses and stress tolerance while laying the groundwork for multidisciplinary research to advance sustainable agriculture and food safety.}, }
@article {pmid40451005, year = {2025}, author = {Su, X and Liu, J and Chang, L and Hu, W and Fang, Y and Li, J and Huang, L and Shu, W and Dong, H}, title = {Viral insights into the acidification of sulfidic mine tailings.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138754}, doi = {10.1016/j.jhazmat.2025.138754}, pmid = {40451005}, issn = {1873-3336}, abstract = {The acidification of sulfidic mine tailings, driven primarily by sulfur- and iron-oxidizing microorganisms, can lead to severe environmental pollution and imperil human health. The role of viruses in this process and its underlying mechanisms yet remain poorly understood. In this study, we recovered 623 species-level viral genomes and 322 prokaryotic genomes from seven metagenomes of mine tailings with pH values ranging from 7.51 to 2.13. We observed that acidification drastically altered geochemical properties and degraded environmental quality, characterized by significant decreases in carbon/nitrogen ratio and heavy metal levels. The structure and function of viral communities were significantly correlated with pH and prokaryotic diversity, showing distinct dynamics across different acidification stages, similar to patterns observed in the prokaryotic community. Notably, potential sulfur-oxidizing prokaryotes increased in relative abundance as pH declined, while their virus-host abundance ratio exhibited a significant positive correlation with pH. Results indicated that viral "top-down" predation on sulfur-oxidizing prokaryotes was likely suppressed during acidification, providing a survival advantage to these organisms over iron-oxidizing counterparts. Moreover, viruses likely reprogrammed the sulfur and iron metabolism of prokaryotic hosts and enhanced their adaptability to environmental stressors through auxiliary metabolic genes. Additionally, a pH- and lifestyle-dependent evolutionary scenario for viruses revealed that frequent recombination and the accumulation of synonymous mutations in lytic viruses and chronic Inoviridae, likely increased their intrapopulation diversity and resilience. These findings provide new insights into the multifaceted roles of viruses in mine tailings acidification, deepening understanding of the underlying mechanisms and advancing potential strategies to mitigate associated environmental risks.}, }
@article {pmid40450941, year = {2025}, author = {Wu, L and Wang, J and Jin, T and Zhou, X and Wang, L}, title = {Lignin-enhanced fungal-bacterial consortium for degradation of petroleum hydrocarbon contaminants.}, journal = {Journal of environmental management}, volume = {388}, number = {}, pages = {125973}, doi = {10.1016/j.jenvman.2025.125973}, pmid = {40450941}, issn = {1095-8630}, abstract = {A lignin-enhanced fungal-bacterial consortium strategy (Bau_Lignin) was proposed to promote the biodegradation of petroleum hydrocarbon contaminants (PHCs), with pyrene and n-docosane selected as representative compounds. Optimal performance was achieved by co-inoculating fungi and bacteria at a 5:5 ratio. Within 12 days, the pyrene removal efficiency of Bau_Lignin was 2.23 times and 1.67 times higher than that of the bacterial consortium (XH40) and the fungal-bacterial consortium (Bau), respectively. Lignin addition enhanced enzyme activities (e.g., ligninolytic enzymes, dioxygenases, dehydrogenases) and increased the abundance of key functional genera (e.g., Pseudomonas, Achromobacter, Stenotrophomonas). Metagenomic sequencing further revealed an enrichment of genes associated with biosurfactant production and oxygenase activity in Bau_Lignin, facilitating mass transfer, hydroxylation, and ring-cleavage processes. Thus, a potential reinforcement mechanism was proposed, highlighting the synergistic interactions among enzyme activities, functional genera, and key functional genes across multiple pathways.}, }
@article {pmid40450938, year = {2025}, author = {Hou, Y and Jia, R and Zhou, L and Zhang, L and Wei, S and Li, B and Zhu, J}, title = {Alterations in microbial-mediated methane, nitrogen, sulfur, and phosphorus cycling within paddy soil induced by integrated rice-fish farming.}, journal = {Journal of environmental management}, volume = {388}, number = {}, pages = {126056}, doi = {10.1016/j.jenvman.2025.126056}, pmid = {40450938}, issn = {1095-8630}, abstract = {Rice paddies are crucial ecosystems, supporting dense microbial populations and playing a significant role in global food security. Integrated rice-fish farming has been recognized as an important agricultural production pattern to enhance agro-ecosystem stability and food productivity. Using metagenomic sequencing, we compared the microbial-mediated soil CH4, N, S, and P cycles in integrated rice-fish farming versus traditional rice monoculture, exploring their potential coupling mechanisms within microbes. Integrated rice-fish farming has significantly impacted these microbial-mediated cycles in paddy soil, altering the overall functional diversity, sum abundance, and microbial host diversity for the CH4, N, S, and P cycling genes. Specifically, it suppressed the denitrification, assimilatory nitrate reduction (ANR), assimilatory sulfate reduction (ASR), thiosulfate oxidation, organic phosphoester hydrolysis, and two-component system pathways and most of their associated functional genes, while enhanced the acetoclastic methanogenesis and the reduction of tetrathionate to thiosulfate processes. Compared to traditional rice monoculture, integrated rice-fish farming resulted in metagenome-assembled genomes (MAGs) with fewer and more isolated biogeochemical cycling genes, lacking potential couplings among multi-element cycles. Additionally, this farming approach increased the soil nutrient levels including the total carbon (TC), total organic carbon (TOC), total nitrogen (TN), total sulfur (TS), and total phosphorus (TP) concentrations, which have been identified as the most crucial factors driving the alterations in microbial functional genes/pathways involved in biogeochemical cycling processes in our study. Overall, integrated rice-fish farming dynamically altered the microbial-mediated CH4, N, S, and P cycles and their potential couplings within microbes through promoting the soil nutrient levels, which could favor rice growth, thus maintaining food security and providing refined knowledge for maintaining soil sustainability.}, }
@article {pmid40450783, year = {2025}, author = {Rajput, V and Pramanik, R and Nannaware, K and Shah, P and Bhalerao, A and Jain, N and Shashidhara, LS and Kamble, S and Dastager, S and Dharne, M}, title = {Metagenomics based longitudinal monitoring of antibiotic resistome and microbiome in the inlets of wastewater treatment plants in an Indian megacity.}, journal = {The Science of the total environment}, volume = {986}, number = {}, pages = {179691}, doi = {10.1016/j.scitotenv.2025.179691}, pmid = {40450783}, issn = {1879-1026}, abstract = {The growing threat of antimicrobial resistance (AMR) poses a significant global challenge, undermining advancements in healthcare, agriculture, and life expectancy. Despite its critical importance, data on population-level AMR trends, including seasonal and temporal variations, remain scarce. In this study, we conducted metagenomic analysis on 190 wastewater samples collected monthly from December 2022 to December 2023 in Pune, India, to assess the diversity, dynamics, and co-occurrence of AMR determinants. Using nanopore shotgun sequencing, we generated 87.86 Gbp of data, enabling the taxonomic classification of 157 bacterial phyla and 3291 genera. Proteobacteria dominated the microbial community, with notable seasonal shifts, including increased Streptococcus abundance correlating with SARS-CoV-2 viral surges in March 2023. We identified 637 distinct antimicrobial resistance genes (ARGs) associated with 29 antibiotic classes, with multidrug, macrolide-lincosamide-streptogramin, beta-lactams, and tetracyclines genes being the most prevalent, particularly within WHO priority pathogens such as Enterobacteriaceae and Pseudomonas. Temporal normalization of ARG abundance revealed significant seasonal variability, peaking during winter, potentially driven by increased antibiotic use for respiratory infections. The integration of viral load data with AMR trends highlighted complex interactions between viral outbreaks and AMR dissemination. This study demonstrates the potential of wastewater surveillance as an early warning system for AMR, providing valuable insights into environmental and community resistance dynamics. Our results underscore the importance of integrated AMR surveillance to inform public health strategies aimed at mitigating the global AMR threat.}, }
@article {pmid40450775, year = {2025}, author = {Han, M and Li, S and Li, Z and Wang, A and Ren, N and Ho, SH}, title = {Layer-specific photo-metabolic specialization of encapsulated microalgae: A strategy for synchronous multi-nitrogen elimination from wastewater.}, journal = {Water research}, volume = {282}, number = {}, pages = {123926}, doi = {10.1016/j.watres.2025.123926}, pmid = {40450775}, issn = {1879-2448}, abstract = {Conventional wastewater treatment (WWT) systems face persistent challenges in simultaneous ammonium (NH4[+]-N) and nitrate (NO3[-]-N) removal due to substrate competition and energy-intensive multi-stage processes. This study presents an innovative strategy leveraging encapsulated microalgal systems to achieve synchronous 94.45 % NH4[+]-N and 98.47 % NO3[-]-N removal within a single reactor through spatial reprogramming of photosynthetic energy allocation. By exploiting the structural heterogeneity within alginate-encapsulated beads, depth-stratified metabolic zones were created that challenge the long-held dogma of microalgae's inherent NH4[+]-N preference. Multidimensional analyses, including spatial distribution mapping, molecular dynamics simulations, metagenomic profiling and photosynthetic regulation, further revealed that light-modulated oxygen gradients, polymer-mediated solute transport, and stratified photo-metabolic specialization synergistically reprogramed microalgal nitrogen metabolism, enabling co-utilization of NH4[+]-N and NO3[-]-N. The system demonstrated robust dual-nitrogen assimilation efficiencies under varying environmental conditions, transcending conventional substrate utilization hierarchies. This transformative approach not only resolves the dilemma of mixed nitrogen pollution but also advances sustainable WWT by integrating pollutant removal with biomass valorization. The findings provide mechanistic insights into microalgal metabolic plasticity and offer a scalable, energy-efficient solution to upgrade traditional denitrification technologies, aligning with urgent demands for circular economy in water resource management.}, }
@article {pmid40450375, year = {2025}, author = {Kuhar, U and Krapež, U and Slavec, B and Račnik, J and Šenica Kavčič, P and Jamnikar-Ciglenecki, U}, title = {Virome analysis suggests deltacoronaviruses and picornaviruses as a probable cause of severe intestinal disease on three quail farms.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {54}, pmid = {40450375}, issn = {2524-4671}, support = {research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; }, abstract = {BACKGROUND: Quail farming is increasingly popular mainly due to higher market interest in meat and eggs. However, quails are susceptible to several common poultry viral infections, especially in intensive farming systems. Enteric viruses in poultry can cause significant economic losses, particularly in young birds. Mixed viral infections often exacerbate disease severity. Gamma and deltacoronaviruses are known causes of enteritis in quails, although infections with coronaviruses as well as picornaviruses may be also asymptomatic. Advanced diagnostic tools like next-generation sequencing (NGS) and metagenomics have improved understanding of these infections, yet knowledge gaps persist, and new viruses are continually being identified.<br><br>RESULTS: Three outbreaks of enteritis with high mortality in quail farms were investigated using NGS with a metagenomic approach. We found that coronaviruses, picornaviruses (anativiruses) and parvoviruses were highly abundant in samples from investigated outbreaks. Viruses belonging to the families Adenoviridae, Astroviridae and Flaviviridae were less abundant and not present in all samples. Coronaviruses and picornaviruses were detected in all outbreaks, while parvovirus was detected only in one. The complete genomes of three quail deltacoronaviruses, three quail anativiruses and one quail chaphamaparvovirus were determined by NGS. Phylogenetic analysis revealed that the coronavirus and anativirus strains from this study were closely related to the other relevant quail virus strains. As for chaphamaparvovirus, this is the first report of this virus in quails.<br><br>CONCLUSIONS: The data from this study indicates the presence of numerous viruses in samples from quails with enteritis that have been overlooked by standard diagnostic approaches but could have played a role in the development of enteritis. These results may support further analysis of virome in healthy quails and in those with different clinical signs.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00428-6.}, }
@article {pmid40450182, year = {2025}, author = {Wang, C and Dong, T and Rong, X and Yang, Y and Mou, J and Li, J and Ge, J and Mu, X and Jiang, J}, title = {Microbiome in prostate cancer: pathogenic mechanisms, multi-omics diagnostics, and synergistic therapies.}, journal = {Journal of cancer research and clinical oncology}, volume = {151}, number = {6}, pages = {178}, pmid = {40450182}, issn = {1432-1335}, support = {82172230//the National Natural Science Foundation of China/ ; 21ZGY29//the Changchun Scientific and Technological Development Program/ ; 3R218FM83430//Life Spring AKY Pharmaceuticals/ ; 20240205001YY//the Jilin Scientific and Technological Development Program/ ; 2017F014//the Jilin Health Service Capacity Improvement Program/ ; }, mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/diagnosis/pathology ; Male ; *Microbiota ; Metagenomics/methods ; Multiomics ; }, abstract = {BACKGROUND: Prostate cancer (PCa) is a leading cause of cancer-related deaths in men, with the microbiome emerging as a significant factor in its development and progression. Understanding the microbiome's role could provide new insights into PCa pathogenesis and treatment.<br><br>OBJECTIVE: This review aims to explore the interactions between the microbiome and PCa, focusing on microbial imbalances and their effects on immune responses, inflammation, and hormone levels. It also discusses advanced research techniques and the potential for microbiome modulation in PCa management.<br><br>METHODS: The review synthesizes current literature on the microbiome's role in PCa, highlighting differences in microbial composition between cancerous and healthy prostate tissues. It examines techniques such as high-throughput sequencing and metagenomics and explores the mechanisms through which the microbiome influences PCa.<br><br>CONCLUSIONS: The review reveals substantial microbial differences in prostate tissues of PCa patients compared to healthy individuals, indicating a potential link between microbiome alterations and disease progression. It highlights the promise of microbiome-based strategies for diagnosis and treatment and underscores the need for further research into personalized, microbiome-centric approaches for PCa management.}, }
@article {pmid40450127, year = {2025}, author = {Yan, P and Zhu, J and Ji, Q and Hou, G and Liang, G and Liu, X and Liu, R}, title = {Significant impact of bleaching treatment on phage-host interaction dynamics in a full-scale wastewater treatment plant.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19165}, pmid = {40450127}, issn = {2045-2322}, support = {No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; }, mesh = {*Bacteriophages/genetics/physiology ; *Wastewater/microbiology/virology ; Sewage/microbiology/virology ; *Bacteria/genetics/virology ; *Water Purification/methods ; Genome, Viral ; Metagenomics ; *Host Microbial Interactions ; }, abstract = {The temporal dynamics of phage-host interactions within full-scale biological wastewater treatment (BWT) plants remain inadequately characterized. Here, we provide an in-depth investigation of viral and bacterial dynamics over a nine-year period in an activated sludge BWT plant, where bleach addition was applied to control sludge foaming. By conducting bioinformatic analyses on 98 metagenomic time-series samples, we reconstructed 3,486 bacterial genomes and 2,435 complete or near-complete viral genomes, which were classified into 361 bacterial and 889 viral clusters, respectively. Our results demonstrate that the primary bleaching event induced significant shifts in both bacterial and viral communities, as well as in virus-host interactions, as evidenced by alterations in bacteria-virus interaction networks and virus-to-host ratio dynamics. Following bleaching, the bacteria-virus network became less interconnected but more compartmentalized. Viral communities mirrored bacterial dynamics, indicating a strong coupling in phage-host interactions. Among the identified virus-host pairs, many exhibited a decelerating rise in viral abundance relative to host abundance, with virus-to-host ratios generally displaying a negative correlation with host abundance. This trend was particularly pronounced in virus-host pairs where viruses harbored integrase genes, indicative of temperate dynamics resembling a "Piggyback-the-Winner" model. Notably, the bleaching intervention appeared to induce a transition from lysogeny to lysis in viruses associated with some foaming-related bacterial species, suggesting a potential virus-involved indirect mechanism by which bleaching mitigates sludge foaming.}, }
@article {pmid40450092, year = {2025}, author = {Nesti, DR and Hayashida, K and Sugi, T and Artama, WT and Wijayanto, H and Kawai, N and Yamagishi, J}, title = {Development of a semicomprehensive detection method for paramyxoviruses and its validation using Indonesian bats.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19154}, pmid = {40450092}, issn = {2045-2322}, support = {0953/E4/KS.00/2021//Ministry of Higher Education, Science and Technology, Indonesia/ ; 0953/E4/KS.00/2021//Ministry of Higher Education, Science and Technology, Indonesia/ ; 0953/E4/KS.00/2021//Ministry of Higher Education, Science and Technology, Indonesia/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; 24wm0125008h0005//Japan Agency of Medical Research and Development (AMED)/ ; 24wm0125008h0005//Japan Agency of Medical Research and Development (AMED)/ ; 24wm0125008h0005//Japan Agency of Medical Research and Development (AMED)/ ; }, mesh = {*Chiroptera/virology ; Animals ; Indonesia ; *Paramyxoviridae Infections/virology/veterinary/diagnosis ; *Paramyxoviridae/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Genome, Viral ; Zoonoses/virology ; }, abstract = {An outbreak of zoonotic diseases is one of the worldwide threats. Bats were reported as important reservoir hosts for many emerging zoonotic diseases. To mitigate the risk, understanding bat virome and their distribution is indispensable. Universal detection methods that can simultaneously identify multiple viruses are some of the most promising approaches. Here, we developed a semicomprehensive detection method integrating group-wide RT-PCR for paramyxoviruses and multiplex next-generation sequencing. The RT-PCR consists of three sets of degenerative primers covering viruses from Paramyxoviridae, including Pneumoviridae, which have now been reclassified into a distinct family. Index nucleotides were added to the primers to enable cost-effective multiplex sequencing, and the length of index was optimized to increase sensitivity. The method was applied to tracheal and rectal swabs from 135 bats captured in Indonesia. A conventional RT-PCR test validated the NGS results. Collectively, seven sequences of novel paramyxovirus-like similar to Pararubulavirus, Orthorubulavirus, and Henipavirus were successfully identified from seven bat samples. Furthermore, sequences between the two different target locations detected by NGS in the virus genomes were verified by RT-PCR. The similarity of the obtained sequences to the known paramyxoviruses sequences was relatively low, ranging from 70.88 to 82.44%. It suggests that the obtained sequences from novel viruses and the zoonotic risk of those novel viruses remain unknown. This cost-affordable, semi-comprehensive, pan-paramyxovirus test can be applied to other samples for viral genome surveillance, and the same strategy can be implemented to other pathogens for zoonosis control.}, }
@article {pmid40450052, year = {2025}, author = {Kundral, S and Giang, PD and Grundon, LR and Supper, JM and Khare, SK and Bernhardt, PV and Evans, P and Bell, SG and De Voss, JJ}, title = {Characterisation of the thermophilic P450 CYP116B305 identified using metagenomics-derived sequence data from an Australian hot spring.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {133}, pmid = {40450052}, issn = {1432-0614}, support = {FT210100812//Australian Research Council/ ; DP240101500//Australian Research Council/ ; DP240101500//Australian Research Council/ ; }, mesh = {*Cytochrome P-450 Enzyme System/genetics/metabolism/chemistry/isolation &amp; purification ; *Hot Springs/microbiology ; Escherichia coli/genetics/metabolism ; Metagenomics ; Enzyme Stability ; Oxidation-Reduction ; Heme/metabolism ; Recombinant Proteins/genetics/metabolism/chemistry/isolation &amp; purification ; Hot Temperature ; Australia ; Queensland ; }, abstract = {Cytochrome P450 enzymes (P450s) have gained significant attention due to their remarkable ability to oxidise unactivated C-H bonds with high regio- and stereoselectivity. Their industrial utility is often limited by challenges such as low stability, poor expression, and dependence on elusive redox partners. These issues have driven the search for more robust P450s, especially those that are inherently stable under extreme conditions typical of industrial processes. "Self-sufficient P450s" in which the P450 heme domain is naturally fused to redox domains in a single polypeptide chain eliminates the need to identify and separately express required redox partners. Furthermore, P450s from thermophilic organisms are more temperature tolerant with fewer stability issues. This study presents a self-sufficient P450, CYP116B305, identified from metagenomically assembled genomes from Innot Hot Springs (71 °C), located in North Queensland, Australia. CYP116B305 was heterologously expressed in Escherichia coli and purified using standard protocols. Investigation of the thermal stability of CYP116B305 revealed a robust heme domain with a [15]T50 value of 56.9 ± 0.1 °C, while the reductase domain exhibited slightly lower stability, with a [15]T50 value of 52.5 ± 0.5 °C. Further characterisation revealed that CYP116B305 efficiently bound to and hydroxylated 2-hydroxyphenylacetic acid (2-HPA) at the C-5 position, yielding homogentisic acid. The catalytic parameters, including the coupling efficiency and rate of electron transfer from the NADPH cofactor to the P450 heme, were shown to improve at an elevated temperature (45 °C) compared to 25 °C. The combination of the self-sufficiency and improved stability makes CYP116B305 a promising platform for biotechnological applications and biocatalyst engineering. KEY POINTS: • Hot spring metagenomics reveals thermostable P450s of biocatalytic value. • CYP116B305 shows enhanced catalytic activity at elevated temperature (45 °C). • CYP116B305 is a promising platform enzyme for diverse biotechnological use.}, }
@article {pmid40449763, year = {2025}, author = {Liu, W and Chen, S and Yang, J and Chen, Y and Yang, Q and Lu, L and Li, J and Yang, T and Zhang, G and Hu, J}, title = {Characterization of blood and urine microbiome temporal variability in patients with acute myeloid leukemia.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107734}, doi = {10.1016/j.micpath.2025.107734}, pmid = {40449763}, issn = {1096-1208}, abstract = {BACKGROUND: Investigating the microbiota of blood and urine from acute myeloid leukemia (AML) patients is essential to unravel the complex role of microbiota in systemic host-microbe interactions and implications.<br><br>METHODS: We conducted a longitudinal observational study to characterize the temporal dynamics of blood and urine microbiota in 27 AML patients, utilizing metagenomic analysis pipeline for microbial identification to identify disease-associated microbial signatures.<br><br>RESULTS: The composition of blood and urine microbiota of AML was dominated by Proteobacteria phylum in blood, Firmicutes phylum in urine. The species and diversity of blood and urine microbiota did not have difference between AML patients and healthy controls. Restitution of alpha and beta diversity of blood microbiota and urine microbiota to resemble that of healthy controls occurred after cessation of treatment. Temporal variation of urine microbiome was higher than blood after treatment which was closely related to pathogenic bacteria and beneficial bacteria measured by coefficient of variation (CV) of alpha diversity. The temporal variability of urine microbiota was significantly correlated with platelet and exposure of levofloxacin. The variation of microbiome of AML patients with infection was found that the relative abundance of Burkholderia significantly enriched in blood and urine which had high accuracy and sensitivity. The correlation between blood microbiota and serum amino acid metabolites was similar to that between gut microbiota and serum metabolites.<br><br>CONCLUSION: This study represents the first comprehensive investigation to quantify the longitudinal variability of blood and urine microbiota in AML patients, revealing distinct patterns compared to gut microbiota and associations with adverse clinical outcomes. Our findings highlight the potential of leveraging stabilizing taxa as a target for microbiome restoration.}, }
@article {pmid40449445, year = {2025}, author = {Zheng, Z and Gustavsson, DJI and Zheng, D and Holmin, F and Falås, P and Wilén, BM and Modin, O and Persson, F}, title = {Genome-centric metagenomics reveals the effect of organic carbon source on one-stage partial denitrification-anammox in biofilm reactors.}, journal = {Journal of environmental management}, volume = {388}, number = {}, pages = {125972}, doi = {10.1016/j.jenvman.2025.125972}, pmid = {40449445}, issn = {1095-8630}, abstract = {Nitrogen removal from wastewater with anammox saves energy and resources. Partial denitrification-anammox (PDA) is a promising process alternative for municipal wastewater treatment, given that the understanding about how to control the microbiome and its activity reach sufficient level. Here, two moving bed biofilm reactors were fed with either acetate or propionate to study the role of organic carbon type for microbiome composition and nitrogen turnover during development of PDA. With acetate, 87 % of the removed nitrogen was converted via anammox during stable operation at a rate of 0.52 g N/(m[2]·d). With propionate, the anammox contribution was considerably lower (41 %), as was the rate of nitrogen removal (0.27 g N/(m[2]·d)). The microbiome composition in the acetate- and propionate-fed reactors was however similar, with an enrichment of metagenome assembled genomes (MAGs) having genes for nitrate reduction (narG, napA). A large fraction of these MAGs had the potential to accumulate nitrite since they lacked genes for nitrite reduction (nirS, nirK, nrfA). Genes for acetate utilization were common among these MAGs, but the necessary genes for propionate conversion were rare, suggesting that the genetic make-up of the individual denitrifiers had major influence on the nitrogen turnover. One anammox MAG (Ca. Brocadia sapporoensis), harboring genes for organic carbon utilization, prevailed in the PDA reactors. Another three anammox MAGs (Ca. B. fulgida, Ca. B. pituitae and a potentially new species within Ca. Brocadia), lacking genes for organic carbon utilization, decreased in abundance in the reactors, indicating the importance of metabolic versatility for anammox bacteria in PDA.}, }
@article {pmid40449443, year = {2025}, author = {Hou, M and Gu, X and Lai, W and Fan, Y and Sun, S and Yan, P and Zhang, Y and Zheng, X and He, S}, title = {Sulfur-iron interactions forming activated FexSy pool in-situ to synergistically improve nitrogen removal in denitrification system.}, journal = {Journal of environmental management}, volume = {388}, number = {}, pages = {126047}, doi = {10.1016/j.jenvman.2025.126047}, pmid = {40449443}, issn = {1095-8630}, abstract = {Sulfur-iron coupling has received increasing attention for improving nitrogen removal. However, the boosting mechanisms of denitrification in sulfur-iron coupling biological system are still ambiguous, and no reasonable explanation has been given for the mismatch between the amount of S[0] loss and the amount of SO4[2-] produced in the coupling system. Therefore, this study established sulfur-iron coupling denitrification systems, and investigated the nitrogen removal performances and coupling mechanisms of the systems. The research results showed that the TN removal efficiencies of the sulfur-iron coupling systems were 122.73-149.27 % higher than those of the single electron donor systems. In the process of nitrogen removal, about 26.03-35.32 % of the more leached S[0] and Fe[0] in the coupling systems co-precipitated to form activated FexSy pool in-situ, contributing about 25.41 % of the nitrogen removal and allowing the systems to remove 76.32-100 % of TN without external electron donors; moreover, the oxidation process of S[2-] provided electrons for the reduction of Fe (Ⅲ) to Fe (Ⅱ), generating more electron donors. Metagenomic sequencing results showed significant increases in the richness and diversity of functional microorganisms associated with sulfur and iron autotrophic denitrification in the coupling systems, and their contributions to the key genes in the denitrification, sulfur transformation and iron cycle processes increased substantially. In general, this study offered deeper understanding for assessing the nitrogen removal potential of the sulfur-iron coupling system, as well as investigating the interactions between S[0] and Fe[0] and elucidating nitrogen removal pathways within the system.}, }
@article {pmid40449312, year = {2025}, author = {Xia, Z and Ng, HY and Bae, S}, title = {Synergistic microalgal-bacterial interactions enhance nitrogen removal in membrane-aerated biofilm photoreactors treating aquaculture wastewater under salt stress: Insights from metagenomic analysis.}, journal = {Water research}, volume = {283}, number = {}, pages = {123878}, doi = {10.1016/j.watres.2025.123878}, pmid = {40449312}, issn = {1879-2448}, abstract = {This study investigates the membrane-aerated biofilm photoreactor (MABPR) for treating aquaculture effluents with low C/N ratio and elevated salinity (0.5%-3.2%). The MABPR integrated biofilm reactors with microalgal-bacterial consortia, achieving superior total inorganic nitrogen (TIN) removal by leveraging counter-diffusional biofilm properties, bubbleless aeration, and enhanced microalgal productivity. The system consistently outperformed conventional reactors, achieving 84.7 ± 1.9% TIN removal at 3.2% salinity with TIN removal flux increasing from 0.82 ± 0.04 to 1.22 ± 0.07 g/m[2] d. The MABPR promoted microalgal proliferation (Chl-a/VSS: 8.08-15.04 mg/g) and higher biomass productivity (1.83 g/m[2] d) compared to SBBPR and MABR. Elevated salinity stimulated extracellular polymeric substance (EPS) production, reinforcing biofilm stability and microbial resilience. The MABPR demonstrated 22%-65% higher nitrogen removal efficiency than controls at the highest salinity. Canonical nitrification-denitrification remained the primary nitrogen removal pathway, with short-cut nitrification-denitrification contributing under salt stress. Metagenomic analysis revealed bidirectional adaptation between microalgae and bacteria, with enriched nitrogen assimilation (GS/GOGAT pathway) compensating for bacterial deficits. Microalgae facilitated pollutant removal through ammonia uptake and dissolved organic matter release, supporting denitrification. At 3.2% salinity, Nitrosomonas and Nitrobacter abundance increased by 42.6% and 35.8%, while denitrifiers Denitromonas and Hoeflea dominated, comprising 59.4% and 35.9% of the population. The MABPR further promoted the synthesis of growth cofactors (vitamins, phytohormones), enhancing microalgal productivity and stress resilience. These synergistic microalgal-bacterial interactions supported pollutant removal, showcasing the MABPR as a robust, sustainable solution for aquaculture wastewater treatment and resource recovery under salt stress.}, }
@article {pmid40449097, year = {2025}, author = {Cañete-Reyes, &#xc1; and González, JG and Alteio, LV and Rodríguez-Lázaro, D and Hernández, M}, title = {Aetiology and environmental factors of the Watery Mouth Disease associated with neonatal diarrhoea in lambs.}, journal = {Veterinary microbiology}, volume = {306}, number = {}, pages = {110542}, doi = {10.1016/j.vetmic.2025.110542}, pmid = {40449097}, issn = {1873-2542}, abstract = {Watery Mouth Disease is the main disease in neonatal lambs, causing great economic losses. Despite this, the cause of the condition remains poorly understood. Therefore, we have analysed the main bacteria found in sick animals, their intestinal and temporal distribution, as well as the main sources of contamination. Twelve different farms were sampled, from which 331 samples were taken in total. From these samples, 184 environments were analyzed using 16S rRNA amplicon sequencing, 164 isolates were identified by whole genome sequencing and 35 bacterial counts were performed. The dominant bacterial groups at the rectal level were Escherichia-Shigella (36 %) and Clostridium (29 %), with a homogeneous distribution along the digestive tract and a maximum abundance ranging between 12 and 24 hours of lamb life. Within Escherichia-Shigella: Escherichia coli and Escherichia fergusonii and within Clostridium: Clostridium perfringens, Clostridium cadaveris, Clostridium tertium and Clostridium paraputricum were identified as the main isolates present in sick animals. The high presence of Clostridium strains, especially potentially pathogenic species like C. perfringens in sick animals, point out Clostridium as a new important protagonist of watery mouth disease and the need of their inclusion in future studies. In particular, bedding was established as the main microbial contaminating factor, reaching the highest increase 48 hours after removal and cleaning of the lambing area (i.e. 8.03 ×10[8], 1.88 ×10[6], 3.88 ×10[6], 4.85 ×10[7] and 4.00 ×10[5] CFU/g for mesophilic aerobes, coliforms, E. coli, mesophilic anaerobes and sporulates, respectively). These results highlight the need to increase cleanliness in bedding to reduce the presence of these bacteria.}, }
@article {pmid40448586, year = {2025}, author = {Jones, LM and El Aidy, S}, title = {Electroactive ecosystem insights from corrosion microbiomes inform gut microbiome modulation.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf112}, pmid = {40448586}, issn = {1751-7370}, abstract = {Electroactive microorganisms influence environmental and host-associated ecosystems through their ability to mediate extracellular electron transfer. This review explores parallels between EAM-driven microbiologically influenced corrosion systems and the human gut microbiome. In corrosion, EAMs contribute to biofilm formation, redox cycling, and material degradation through mechanisms such as direct electron transfer and syntrophic interactions. Similarly, gut-associated EAMs regulate redox balance, drive short-chain fatty acid production, and shape host-microbe interactions. Despite differing contexts, both systems share traits like anoxic niches, biofilm formation, and metabolic adaptability. Insights from well-characterized corrosion microbiomes offer valuable frameworks to understand microbial resilience, electron transfer strategies, and interspecies cooperation in the gut. Bridging knowledge between these systems can inform microbiome engineering approaches aimed at promoting gut health, highlighting the need for further functional metagenomics and exploration of archaeal contributions to biofilm stability and redox modulation.}, }
@article {pmid40448221, year = {2025}, author = {Fan, KC and Lin, CC and Chiu, YL and Koh, SH and Liu, YC and Chuang, YF}, title = {Compositional and functional gut microbiota alterations in mild cognitive impairment: links to Alzheimer's disease pathology.}, journal = {Alzheimer's research &amp; therapy}, volume = {17}, number = {1}, pages = {122}, pmid = {40448221}, issn = {1758-9193}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/microbiology/pathology/metabolism ; *Alzheimer Disease/microbiology/pathology/metabolism ; Male ; Female ; Aged ; Feces/microbiology ; Biomarkers ; Brain/pathology/metabolism ; Aged, 80 and over ; Dysbiosis ; tau Proteins ; Middle Aged ; }, abstract = {BACKGROUND: Emerging evidence highlights the bidirectional communication between the gut microbiota and the brain, suggesting a potential role for gut dysbiosis in Alzheimer's disease (AD) pathology and cognitive decline. Existing literature on gut microbiota lacks species-level insights. This study investigates gut microbiota alterations in mild cognitive impairment (MCI), focusing on their association with comprehensive AD biomarkers, including amyloid burden, tau pathology, neurodegeneration, and cognitive performance.<br><br>METHODS: We analyzed fecal samples from 119 individuals with MCI and 320 cognitively normal controls enrolled in the Taiwan Precision Medicine Initiative on Cognitive Impairment and Dementia cohort. Shotgun metagenomic sequencing was conducted with taxonomic profiling using MetaPhlAn4. Amyloid burden and plasma pTau181 were quantified via PET imaging and Simoa assays, respectively, while APOE genotyping was performed using TaqMan assays. Microbial diversity, differential abundance analysis, and correlation mapping with neuropsychological and neuroimaging measures were conducted to identify gut microbiota species signatures associated with MCI and AD biomarkers.<br><br>RESULTS: We identified 59 key microbial species linked to MCI and AD biomarkers. Notably, species within the same genera, such as Bacteroides and Ruminococcus, showed opposing effects, while Akkermansia muciniphila correlated with reduced amyloid burden, suggesting a protective role. Functional profiling revealed microbial pathways contributing to energy metabolism and neuroinflammation, mediating the relationship between gut microbes and brain health. Co-occurrence network analyses demonstrated complex microbial interactions, indicating that the collective influence of gut microbiota on neurodegeneration.<br><br>CONCLUSIONS: Our findings challenge genus-level microbiome analyses, revealing species-specific modulators of AD pathology. This study highlights gut microbial activity as a potential therapeutic target to mitigate cognitive decline and neurodegeneration.}, }
@article {pmid40447717, year = {2025}, author = {Lai, LM and Dai, QB and Cao, ML and Liu, Y and Zhao, R and Yuan, L}, title = {Clinical utility of metagenomic next-generation sequencing in pathogen detection for lower respiratory tract infections.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19039}, pmid = {40447717}, issn = {2045-2322}, support = {2024B1362//the Science and Technology Plan of Jiangxi Provincial Health Commission/ ; 202510284//the Science and Technology Plan of Jiangxi Provincial Health Commission/ ; 20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; }, mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; *Metagenomics/methods ; Middle Aged ; Retrospective Studies ; Aged ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; }, abstract = {Identifying pathogens in patients with lower respiratory tract infections (LRTIs) has always been a major challenge. Metagenomic next-generation sequencing (mNGS) technology is a new diagnostic tool that can assist clinicians in the etiological diagnosis of LRTIs. This study focuses on the clinical value of mNGS in the diagnosis of suspected LRTIs. A total of 400 patients with suspected LRTIs admitted at the First Affiliated Hospital of Nanchang University from July 2020 to February 2023 were enrolled in this retrospective study. Bronchoalveolar lavage fluid (BALF) samples were analyzed using both mNGS and culture methods. The diagnostic accuracy of two approaches was systematically compared against the final clinical diagnosis, which served as the gold-standard reference. Of the 400 enrolled cases, 82.3% (329/400) were diagnosed with LRTIs. From these cases, mNGS identified 76.8% (307/400) truepositive cases, 8.0% (32/400) falsepositive cases, 9.8% (39/400) truenegative cases, and 5.5% (22/400) falsenegative cases. mNGS demonstrated significantly higher sensitivity [93.3% (307/329) vs. 55.6(183/329)%] alongside greater negative predictive values [63.9% (39/61) vs.25.9%(51/197)], whereas culture offered higher specificity [54.9%(39/71) vs. 71.8%(51/71)]. The area under the receiver-operating curve (AUC) of mNGS[0.744(95%CI: 0.67-0.82)]was significantly higher than that of cultures[0.636(95%CI: 0.57-0.71)]. Specifically, mNGS detected more Streptococcus pneumoniae (7.0% vs. 0%), Haemophilus influenzae (6.7% vs. 0%), Aspergillus (9.4% vs. 3.5%), Pneumocystis jirovecii (11.9% vs. 0%) and other intracellular pathogens. Of the 329 patients with LRTIs, antibiotic treatment was modified based on the mNGS results in more than half of the patients(50.5%,166/329), including 20 cases of adjusted antimicrobial regimens, 70 cases de-escalated the empirical antibiotic treatment, and 76 patients escalated the treatment by increasing dosage or medication. 60.8%(101/166) of patients responded to modified antibiotic treatment. Significant benefits of mNGS have been shown in pathogen identification and antimicrobial treatment stewardship in patients with LRTIs. For those with suboptimal therapeutic responses, physicians should be alert to some emerging intracellular pathogens, including Chlamydia psittaci, Mycobacterium tuberculosis, and Pneumocystis jirovecii.}, }
@article {pmid40447596, year = {2025}, author = {Wang, X and Jiang, Q and Tian, X and Chen, W and Mai, J and Lin, G and Huo, Y and Zheng, H and Yan, D and Wang, X and Li, T and Gao, Y and Mou, X and Zhao, W}, title = {Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {92}, pmid = {40447596}, issn = {2055-5008}, mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Metagenomics/methods ; China ; *Lactobacillus/genetics/isolation &amp; purification/classification/physiology ; Adult ; Gardnerella vaginalis/growth &amp; development ; Microbiota ; Vaginosis, Bacterial/microbiology ; Biofilms/growth &amp; development ; Asian People ; Pregnant People ; Young Adult ; }, abstract = {This study investigated the relationship between vaginal microbiota and women's health conditions in 95 Chinese pregnant women in their third trimester. We conducted vaginal metagenomic analysis, examining species, functional pathways, and genes, and utilized correlation and LEfSe analyses to link microbiota to health conditions. Results revealed that healthy participants exhibited higher levels of Lactobacillus iners, with its abundance associated with tetrahydrofolate biosynthesis pathways. They also possessed more glycosyltransferase and ErmB antibiotic resistance genes compared to women with diagnosed conditions. Comparative genomics demonstrated that L. iners strains linked to bacterial vaginosis (BV) possessed more genes encoding biofilm-associated YhgE/Pip domain-containing proteins than healthy-associated strains. Notably, three BV-associated L. iners strains exhibited stronger biofilm formation abilities than four healthy-associated strains isolated in this study. Also, four out of seven L. iners strains inhibited the growth of Gardnerella vaginalis. Overall, L. iners may help maintain vaginal ecosystem stability in Chinese pregnant women.}, }
@article {pmid40447587, year = {2025}, author = {Paluoja, P and Vaher, M and Teder, H and Krjutškov, K and Salumets, A and Raime, K}, title = {Honey bulk DNA metagenomic analysis to identify honey biological composition and monitor honey bee pathogens.}, journal = {NPJ science of food}, volume = {9}, number = {1}, pages = {91}, pmid = {40447587}, issn = {2396-8370}, support = {616219790085//European Agricultural Fund for Rural Development/ ; 616219790085//European Agricultural Fund for Rural Development/ ; 616219790085//European Agricultural Fund for Rural Development/ ; }, abstract = {Honey's DNA mixture originates from various organisms like plants, arthropods, fungi, bacteria, and viruses. Conventional methods like melissopalynological analysis and targeted honey DNA metabarcoding offer a limited view of honey's biological composition. We conducted a honey bulk DNA metagenomic analysis to characterize the honey's taxonomic composition and identify honey bee-related pathogens and parasites based on 266 Estonian and 103 foreign honey samples. 70.4% of the DNA in Estonian honey was derived from green plant families like Brassicaceae, Rosaceae, Fabaceae, and Pinaceae. Geographical distribution analysis revealed distinct botanical compositions between Estonian mainland and island samples. The bacterial family Lactobacillaceae was prevalent overall, reflecting the honey bee microbiota in honey. We detected 12 honey bee pathogens and parasites, including Paenibacillus larvae, Nosema ceranae, Varroa destructor, and Aethina tumida. In conclusion, the study underscores the potential of bulk DNA-based non-targeted metagenomic approaches for monitoring honey bee health, environment, and honey composition, origin, and authenticity.}, }
@article {pmid40447574, year = {2025}, author = {Rodríguez Del Río, &#xc1; and Scheu, S and Rillig, MC}, title = {Soil microbial responses to multiple global change factors as assessed by metagenomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5058}, pmid = {40447574}, issn = {2041-1723}, mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects ; Metagenome ; Soil/chemistry ; Droughts ; Microbiota/genetics ; Salinity ; *Climate Change ; Global Warming ; }, abstract = {Anthropogenic activities impose multiple concurrent pressures on soils globally, but responses of soil microbes to multiple global change factors are poorly understood. Here, we apply 10 treatments (warming, drought, nitrogen deposition, salinity, heavy metal, microplastics, antibiotics, fungicides, herbicides and insecticides) individually and in combinations of 8 factors to soil samples, and monitor their bacterial and viral composition by metagenomic analysis. We recover 742 mostly unknown bacterial and 1865 viral Metagenome-Assembled Genomes (MAGs), and leverage them to describe microbial populations under different treatment conditions. The application of multiple factors selects for prokaryotic and viral communities different from any individual factor, favouring the proliferation of potentially pathogenic mycobacteria and novel phages, which apparently play a role in shaping prokaryote communities. We also build a 25 M gene catalog to show that multiple factors select for metabolically diverse, sessile and non-biofilm-forming bacteria with a high load of antibiotic resistance genes. Finally, we show that novel genes are relevant for understanding microbial response to global change. Our study indicates that multiple factors impose selective pressures on soil prokaryotes and viruses not observed at the individual factor level, and emphasizes the need of studying the effect of concurrent global change treatments.}, }
@article {pmid40446767, year = {2025}, author = {Adyari, B and Liao, X and Yan, X and Qiu, Y and Grossart, HP and Li, L and Yu, T and Mao, G and Liu, K and Su, J and Liu, Y and Hu, A}, title = {Anthropogenic gene dissemination in Tibetan Plateau rivers: sewage-driven spread, environmental selection, and microeukaryotic inter-trophic driving factors.}, journal = {Water research}, volume = {284}, number = {}, pages = {123887}, doi = {10.1016/j.watres.2025.123887}, pmid = {40446767}, issn = {1879-2448}, abstract = {The spread of anthropogenic genes, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs), and antibiotic-resistant bacteria (ARBs), is a growing public health concern. However, the role of anthropogenic activities in the dissemination of these genes and bacteria in Tibetan Plateau rivers is still unclear. In this study, we analyzed 138 metagenomic samples from water and sediment across nine Tibetan rivers, along with sewage samples from 21 wastewater treatment plants (WWTPs), at both the gene and contig levels, to investigate the spread of the sewage-enriched genes and their bacterial hosts (contigs) in Tibetan rivers. Overall, sewage input was positively correlated with increased the abundance of an average 56 % and 17 % of detected genes in water and sediment, respectively. However, FEAST source tracking analysis revealed that the overall contribution of sewage across all rivers was significantly lower than that of water and sediment. Additionally, sewage's impact varied across rivers, with the Yarlung Zangbo, the largest river, exhibiting limited influence despite receiving inputs from smaller rivers and WWTPs. Neutral community model (NCM) suggested that neutral processes and negative selection predominantly governed the spread of majority of highly abundant sewage-enriched genes and contigs, suggesting restricted environmental spread. In contrast, a subset of genes over-represented relative to neutral expectations (above-neutral prediction) showed lower overall abundance but higher richness, potentially reflecting selection that favor their retention in certain downstream environments. Furthermore, sewage-enriched genes and contigs in water, regardless of their community assembly processes, were linked to microbial interaction modules dominated by microeukaryotic groups associated with sewage, including consumer protists (ciliate), human parasites (e.g., Naegleria), algae, and fungi. These interactions may facilitate the dissemination of antimicrobial resistance in aquatic environments, though this pattern was less pronounced in sediment.}, }
@article {pmid40446617, year = {2025}, author = {Rono, JK and Zhang, Q and He, Y and Zhao, L and Wang, S and Lyu, Y and Li, C and Ngigi, AN and Yang, ZM and Feng, Z}, title = {Identification and characterization of halotolerant multifunctional GH6 endoglucanases ZFEG1605 and ZFEG1663 from Mt. Everest soil metagenome.}, journal = {Carbohydrate research}, volume = {554}, number = {}, pages = {109549}, doi = {10.1016/j.carres.2025.109549}, pmid = {40446617}, issn = {1873-426X}, abstract = {Environmental microorganisms express enzymes with unique hydrolytic activity, stability, and kinetic parameters, which are of great interest for biotechnological applications. In this study, two novel endoglucanases, ZFEG1605 and ZFEG1663, were cloned from Mt. Everest soil metagenomic library, heterologously expressed in E. coli BL21(DE3), and characterized. Both enzymes exhibited high activity on konjac glucommanan (KG) and sodium carboxymethylcellulose (CMC), while ZFEG1605 also exhibited activity towards guar gum (GG). The optimal pH for both enzymes was slightly shifted toward acidic range (pH 5/6). The optimal reaction temperatures for ZFEG1605 and ZFEG1663 were 50 and 40 °C, respectively. ZFEG1605 was more thermostable than ZFEG1663 as it remained stable up to 50 °C, compared to 40 °C for ZFEG1663. Both enzymes showed broad pH stability, although they retained more mannanase activity than CMCase activity within the same pH range. The endoglucanases exhibited remarkable salt tolerance, retaining over 70 % of their enzymatic activity in the presence of 2.5 M NaCl. The purified enzymes hydrolyzed alkali-pretreated rice straw to release reducing sugars, demonstrating their potential usage for biomass saccharification.}, }
@article {pmid40445840, year = {2025}, author = {Ricci, L and Selma-Royo, M and Golzato, D and Servais, C and Nabinejad, A and Marchi, P and Punčochář, M and Trenti, F and Garcia-Aloy, M and Armanini, F and Marconi, R and Asnicar, F and Pinto, F and Guella, G and Tamburini, S and Segata, N}, title = {Description of Catenibacterium mitsuokai subsp. tridentinum subsp. nov., an anaerobic bacterium isolated from human faeces, and emended description of C. mitsuokai.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.006798}, pmid = {40445840}, issn = {1466-5034}, mesh = {*Phylogeny ; *Feces/microbiology ; Humans ; Base Composition ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Genome, Bacterial ; Adult ; Fatty Acids/analysis ; Phospholipids/analysis ; }, abstract = {A recent metagenomic survey has revealed an unknown bacterial clade within the Catenibacterium mitsuokai species to be significantly more prevalent in non-urbanized populations, compared to urbanized ones. We isolated and characterized a strain of this clade from the stool of a healthy adult volunteer. Strain CMD8551[T] is strictly anaerobic, appears as long chains of Gram-positive rods and produces acetate in the presence of glucose. The lipidomic profile showed a higher proportion of saturated lipid species amongst the detected phospholipids. The whole genome is 2,320,430 bp long and has a G+C content of 33.7 mol% with 2,239 CDSs. A phylogenetic analysis comparing the sequences of the strain CMD8551[T] with publicly available reference genomes from the Catenibacterium genus revealed that the CMD8551[T] isolate, together with other isolate genomes, forms a distinct subspecies of C. mitsuokai and has an average nucleotide identity lower than 94% with respect to the previously described C. mitsuokai subsp. mitsuokai. Given the phenotypic, chemotaxonomic and phylogenetic characteristics of the newly isolated CMD8551[T] (=DSM 118469[T]=LMG 33725[T]=CIP 112509[T]) that clearly differ from those of the C. mitsuokai subsp. mitsuokai type strain RCA14-39[T], we propose it as the type strain of a novel subspecies of C. mitsuokai, with the name C. mitsuokai subsp. tridentinum subsp. nov.}, }
@article {pmid40445833, year = {2025}, author = {Li, W and Huang, B and Guo, M and Zeng, Z and Cai, T and Feng, L and Zhang, X and Guo, L and Jiang, X and Yin, Y and Wang, E and Huang, X and Zheng, J}, title = {Unveiling the evolution of antimicrobial peptides in gut microbes via foundation-model-powered framework.}, journal = {Cell reports}, volume = {44}, number = {6}, pages = {115773}, doi = {10.1016/j.celrep.2025.115773}, pmid = {40445833}, issn = {2211-1247}, abstract = {Antimicrobial resistance poses a major threat to public health, prompting the development of alternative therapies such as antimicrobial peptides (AMPs). Protein language models (PLMs) have advanced protein structure and function predictions, facilitating AMP discovery. We developed antimicrobial peptide structural evolution miner (AMP-SEMiner), an AI-driven framework that integrates PLMs, structural clustering, and evolutionary analysis to systematically identify AMPs encoded by small open reading frames and AMP-containing proteins in metagenome-assembled genomes. AMP-SEMiner identified over 1.6 million AMP candidates across diverse environments. Experimental validation showed antimicrobial activity in 9 of the 20 tested candidates, with 5 surpassing antibiotic effectiveness; variant peptides derived from these candidates similarly demonstrated strong antimicrobial efficacy. AMPs from human gut microbiomes revealed both conserved and adaptive evolutionary strategies, reflecting their dynamic ecological roles. AMP-SEMiner thus represents a valuable tool for expanding AMP discovery and has significant potential to inform the development of alternative antimicrobial treatments.}, }
@article {pmid40445752, year = {2025}, author = {Xing, Y and Hernandez Santos, HJ and Qiu, L and Ritter, SR and Zulk, JJ and Lahowetz, R and Patras, KA and Terwilliger, AL and Maresso, AW}, title = {Phage-induced protection against lethal bacterial reinfection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {22}, pages = {e2423286122}, doi = {10.1073/pnas.2423286122}, pmid = {40445752}, issn = {1091-6490}, support = {U19AI157981//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U19AI144297//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 5F31DK136201//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; 5359//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation (Kleberg Foundation)/ ; }, mesh = {*Phage Therapy/methods ; Animals ; *Bacteriophages/physiology ; *Reinfection/prevention &amp; control/therapy/microbiology ; Mice ; *Bacterial Infections/therapy/prevention &amp; control ; }, abstract = {Bacteriophages, or phages, are viruses that target and infect bacteria. Due to a worldwide rise in antimicrobial resistance (AMR), phages have been proposed as a promising alternative to antibiotics for the treatment of resistant bacterial infections. Up to this point in history, phage use in preclinical animal studies, clinical trials, and emergency-use compassionate care cases has centered around the original observation from 1915 showing phage as lytic agent, and thus a treatment that kills bacteria. Here, we describe an activity associated with phage therapy that extends beyond lytic activity that results in long-term protection against reinfection. This activity is potent, providing almost complete protection against a second lethal infection for animals treated with phage therapy. The activity also reduced infection burden an astounding billion-fold over the control. Reinfection protection requires phage lytic killing of its target bacterium but is independent of additional phage therapy. The effect is not driven by phage alone, lingering phage resistors, or a sublethal inoculum. In vitro phage-lysed bacteria provide partial protection, suggesting a combination of phage-induced lytic activity and immune stimulation by phage treatment is responsible for the effect. These observations imply certain phages may induce host adaptive responses following the lysis of the infecting bacteria. This work suggests phage therapy may contain a dual-action effect, an initial treatment efficacy followed by a long-term protection against reoccurring infection, a therapeutic-vaccination mechanism of action.}, }
@article {pmid40445195, year = {2025}, author = {Schuele, L and Masirika, LM and Cassidy, H and Clausen, PTLC and Zaeck, LM and Boter, M and Ndishimye, P and Udahemuka, JC and de Vries, RD and Otani, S and Molenkamp, R and Nieuwenhuijse, DF and Mbiribindi, JB and Siangoli, FB and Koopmans, M and Aarestrup, FM and Oude Munnink, BB}, title = {Metagenomic sequencing of mpox virus clade Ib lesions identifies possible bacterial and viral co-infections in hospitalized patients in eastern DRC.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0051225}, doi = {10.1128/spectrum.00512-25}, pmid = {40445195}, issn = {2165-0497}, abstract = {Mpox is an emerging zoonotic disease that caused two public health emergencies of international concern within two years. Less is known about the interplay of microbial organisms in mpox lesions which could result in superinfections that exacerbate outcomes or delay recovery. We utilized a unified metagenomic sequencing approach involving slow-speed centrifugation and differential lysis on 19 mpox lesion swabs of hospitalized patients in South Kivu province (eastern DRC) to characterize bacteria, antimicrobial resistance genes, mpox virus (MPXV), and viral co-infections. High-quality MPXV whole-genome sequences were obtained until a Ct value of 27. Furthermore, co-infections with other clinically relevant viruses, such as varicella zoster virus and herpes simplex virus-2, were detected and confirmed by real-time PCR. In addition, metagenomic sequence analysis of the bacterial content showed the presence of bacteria associated with skin and soft tissue infection in 10 of the 19 samples analyzed. These bacteria had a high abundance of resistance genes, with possible implications for antimicrobial treatment based on the predicted antimicrobial resistance. In conclusion, we report the presence of bacterial and viral pathogens in mpox lesions and detection of widespread resistance genes to the standard antibiotic treatment. The possibility of a co-infection, including antimicrobial resistance, should be considered when discussing treatment options, along with the determination of the case-fatality ratio.IMPORTANCEThe mpox virus clade Ib lineage emerged in the eastern Democratic Republic of the Congo owing to continuous human-to-human transmission in a vulnerable patient population. A major challenge of this ongoing outbreak is its occurrence in regions with severely limited healthcare infrastructure. As a result, less is known about co-infections in affected patients. Identifying and characterizing pathogens, including their antimicrobial resistance, is crucial for reducing infection-related complications and improving antimicrobial stewardship. In this study, we applied a unified metagenomics approach to detect and characterize bacterial and viral co-infections in mpox lesions of hospitalized mpox patients in the eastern DRC.}, }
@article {pmid40445192, year = {2025}, author = {Mullinax, SR and Darby, AM and Gupta, A and Chan, P and Smith, BR and Unckless, RL}, title = {A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {40445192}, issn = {2050-084X}, support = {AI139154/NH/NIH HHS/United States ; 2330095//National Science Foundation/ ; CMADP COBRE P20-GM103638/NH/NIH HHS/United States ; }, mesh = {Animals ; *Alleles ; Female ; Male ; *Drosophila Proteins/genetics/immunology ; *Selection, Genetic ; Providencia/immunology ; *Drosophila/genetics/immunology/microbiology ; Gastrointestinal Microbiome ; *Drosophila melanogaster/genetics/immunology/microbiology ; *Antimicrobial Peptides/genetics/immunology ; }, abstract = {The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales, multiple alleles are maintained in populations. In this study, we focus on the Drosophila AMP Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab-reared and wild-caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous for one allele of diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general have a shorter lifespans after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.}, }
@article {pmid40445060, year = {2025}, author = {Gao, H and Guo, Z and Xu, R and He, X and Fernio, JU and Li, S and Liu, X and Liu, H and Xue, W}, title = {Chemolithoautotrophic Antimonite Oxidation Coupled Nitrogen Fixation in the Rhizosphere of Local Plant in Antimony Tailing Area.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c03872}, pmid = {40445060}, issn = {1520-5851}, abstract = {Antimony (Sb) tailings pose a significant environmental challenge. N-fixing microorganisms are essential for nutrient accumulation and plant colonization in degraded habitats. However, the oligotrophic conditions of tailings often inhibit the energy-intensive N-fixing process. This study identified a chemolithoautotrophic Sb(III) oxidation-coupled nitrogen fixation (SbNF) pathway in the rhizosphere of local plants. SbNF integrates biological detoxification and nutrient accumulation, enabling plant colonization and ecological restoration of degraded habitats. Multi-omic analyses reveal that Sb content strongly shapes the composition of Sb-oxidizing and N-fixing bacterial communities in the rhizosphere. Abundant marker genes for carbon fixation (cbbL), Sb(III) oxidase (aioAB/anoA), and nitrogenase (nifH) were consistently detected in SbNF metagenome-assembled genomes. Positive correlations between gene abundances associated with autotrophic potential (aioA-cbbL) and coupling potential (aioA-nifH) were observed in the rhizoplane but not in the endosphere. In addition to genetic potentials, high-throughput cultivation of native SbNF-isolates (e.g., Pseudomonas, Arthrobacter, and Sphingomonas) confirmed their rapid Sb(III) oxidation coupling autotrophic growth and nitrogen fixation. Isolates also exhibited plant growth-promoting traits, including indole-3-acetic acid production, phosphate solubilization, and siderophore secretion, providing multiple benefits to host plants. Co-cultivation of these isolates revealed minimal antagonism, suggesting the potential for designing synthetic microbial communities for sustainable phytoremediation. Cross-validation further suggests that SbNF is widespread in the rhizosphere of various local plants. These findings uncover a novel biogeochemical process in the rhizosphere, linking mineral oxidation, autotrophic growth, and nitrogen fixation, highlighting its importance for the ecological restoration of degraded tailing area.}, }
@article {pmid40445001, year = {2025}, author = {Andréani, J and Smiljkovic, M and Lametery, E and Khedimallah, S and Court, N and Jardin, H and Arata-Bardet, J and Truffot, A and Germi, R and Morand, P and Cappy, P and Rodriguez, C and Lupo, J and Larrat, S}, title = {Metagenomics Diagnosis of a Parvovirus B19-Associated Encephalomyelitis in an Epidemic Context.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, doi = {10.1097/INF.0000000000004780}, pmid = {40445001}, issn = {1532-0987}, abstract = {In the context of increasing parvovirus B19 (B19V) infections, we describe a case of B19V encephalomyelitis without any usually associated clinical features. Etiology was identified by metagenomics and confirmed by PCR and whole-genome sequencing. This case highlights the need to consider the diagnosis of B19V infection in patients presenting with neurological symptoms.}, }
@article {pmid40444981, year = {2025}, author = {Harrison, K and Rapp, JZ and Jaffe, AL and Deming, JW and Young, J}, title = {Chemoautotrophy in subzero environments and the potential for cold-adapted Rubisco.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0060425}, doi = {10.1128/aem.00604-25}, pmid = {40444981}, issn = {1098-5336}, abstract = {The act of fixing inorganic carbon into the biosphere is largely facilitated by one enzyme, Rubisco. Beyond well-studied plants and cyanobacteria, many bacteria use Rubisco for chemolithoautotrophy in extreme environments on Earth. Here, we characterized the diversity of autotrophic pathways and chemolithoautotrophic Rubiscos from two distinct subzero, hypersaline Arctic environments: 40-kyr relic marine brines encased within permafrost (cryopeg brines) and first-year sea ice. The Calvin-Benson-Bassham (CBB) cycle was widely found in both environments, although with different predominant Rubisco forms. From cryopeg brine, reconstructions of metagenome-assembled genomes (MAGs) uncovered four MAGs with the potential for chemolithoautotrophy, of which the CBB-containing genus Thiomicrorhabdus was most abundant. A broader survey of Thiomicrorhabdus genomes from diverse environments identified a core complement of three Rubisco forms (II, IAc, IAq) with a complex pattern of gain and loss, with form II constitutively present in genomes from subzero environments. Using representative kinetic data, we modeled carboxylation rates of Rubisco forms II, IAc, and IAq across CO2, O2, and temperature conditions. We found that form II outcompetes form I at low O2, but cold temperatures minimize this advantage. Inspection of form II from genomes from cold environments identified signals of potential thermal adaptation due to key amino acid substitutions, which resulted in a more exposed active site. We argue that subzero form II from Thiomicrorhabdus warrants further study as it may have unique kinetics or thermal stability. This work can help address the limits of autotrophic functionality in extreme environments on Earth and other planetary bodies.IMPORTANCEAutotrophy, or the fixation of inorganic carbon to biomass, is a key factor in life's ability to thrive on Earth. Research on autotrophy has focused on plants and algae, but many bacteria are also autotrophic and can survive and thrive under more extreme conditions. These bacteria are a window to past autotrophy on Earth, as well as potential autotrophy in extreme environments elsewhere in the universe. Our study focused on dark, cold, saline environments, which are likely to be found on Enceladus and Europa, as well as in the Martian subsurface. We found evidence for potential cold adaptation in a key autotrophic enzyme, Rubisco, which could expand the known boundaries of autotrophy in rapidly disappearing icy environments on Earth. We also present a novel model framework that can be used to probe the limits of autotrophy not only on Earth but also on key astrobiological targets like Enceladus and Europa.}, }
@article {pmid40444423, year = {2025}, author = {Yi, H and Zhang, S and Wang, J and Xu, C and Yang, D and Lin, Q and Wang, X and Feng, S}, title = {CT Features for Prognostic Assessment of Pulmonary Mucormycosis in Patients With Hematological Diseases.}, journal = {Journal of thoracic imaging}, volume = {}, number = {}, pages = {}, doi = {10.1097/RTI.0000000000000832}, pmid = {40444423}, issn = {1536-0237}, support = {2021-I2M-1-017 and 2023-I2M-2-007//Chinese Academy of Medical Science Innovation Fund for Medical Sciences/ ; }, abstract = {PURPOSE: To explore the CT features in prognostic evaluations for pulmonary mucormycosis in patients with hematological diseases.<br><br>MATERIALS AND METHODS: A retrospective analysis of clinical data and chest CT features of 53 HD patients with PM was conducted. Univariate and multivariate logistic regression analyses were used to determine the risk factors for death. The Cox regression model was used to analyze the factors affecting the survival rate.<br><br>RESULTS: A total of 30 patients with proven PM and 23 with probable PM were included. All 30 patients with proven PM underwent bronchoscopy-guided biopsy, among which 9 cases underwent surgical resection. Of the 23 patients with probable PM, 5 cases had positive results in sputum smear microscopy, 4 cases in sputum culture, 13 cases in bronchoalveolar lavage fluid (BALF) microscopy, and 1 case in BALF culture. All identification of pathogen genera and partial species was conducted by metagenomic next-generation sequencing (mNGS) testing. In the multivariate regression analysis, the CT feature of multiple lesions (&#x2265;2) on the initial CT scan was an independent risk factor for mortality (P=0.019). Cox survival analysis demonstrated a significantly lower survival rate (P=0.043) in patients exhibiting the CT feature of multiple lesions on the initial CT scan.<br><br>CONCLUSIONS: The CT feature of multiple lesions (&#x2265;2) on the initial CT may serve as an independent risk factor for mortality in patients with hematologic disorders with pulmonary mucormycosis.}, }
@article {pmid40444400, year = {2025}, author = {Burdon, I and Bouras, G and Fenix, K and Yeo, K and Connell, J and Cooksley, C and Barry, E and Vreugde, S and Wormald, PJ and Psaltis, AJ}, title = {Metagenomics or Metataxonomics: Best Practice Methods to Uncover the Sinus Microbiome.}, journal = {International forum of allergy &amp; rhinology}, volume = {}, number = {}, pages = {e23617}, doi = {10.1002/alr.23617}, pmid = {40444400}, issn = {2042-6984}, support = {//Garnett Passe and Rodney Williams Memorial Foundation/ ; APP1196832//National Health and Medical Research Council/ ; }, }
@article {pmid40444000, year = {2025}, author = {Pacheco-Dorantes, C and Tovar-Pedraza, JM and Ochoa-Martínez, DL and González-Garza, R and Diaz-Lara, A}, title = {Unleashing the potential of high-throughput sequencing for plant virus and viroid detection in Mexico.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1603010}, pmid = {40444000}, issn = {1664-302X}, abstract = {High-throughput sequencing (HTS) has revolutionized plant virology in Mexico by enhancing the detection and characterization of plant viruses and viroids. This technology has contributed to identifying previously neglected pathogens affecting key crops such as corn, beans, and tomato. The use of HTS has also revealed the presence of mixed viral infections, highlighting the complexity of plant viromes within agricultural ecosystems. Furthermore, metagenomic studies have demonstrated the role of water sources as reservoirs for plant viruses, underscoring the urgent need for improved management strategies. Despite its advantages, the widespread adoption of HTS faces challenges, including high costs, the need for bioinformatics expertise, and infrastructure limitations. Supporting collaborations between research institutions and regulatory agencies is crucial to integrating HTS into routine phytosanitary programs. Future research should aim to expand HTS applications to include epidemiological monitoring, resistance breeding, and the development of sustainable management strategies to mitigate the impact of emerging plant viruses in Mexico.}, }
@article {pmid40443674, year = {2025}, author = {Wang, Y and Ma, X and Ma, C and Sun, T and Zhao, D and Li, H and Yan, Y and Guo, J}, title = {Case Report: Anti-NMDAR encephalitis associated with neurobrucellosis: causality or coexistence?.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1536740}, pmid = {40443674}, issn = {1664-3224}, mesh = {Humans ; Male ; *Brucellosis/complications/diagnosis/immunology/drug therapy/microbiology ; Adult ; *Anti-N-Methyl-D-Aspartate Receptor Encephalitis/diagnosis/etiology/immunology/drug therapy ; *Brucella melitensis/immunology ; Autoantibodies/immunology ; }, abstract = {Human brucellosis, caused by Brucella, is an infectious disease with specific endemic regions, especially in pastoral areas, and may affect multiple organ systems. Neurological involvement, namely neurobrucellosis, occurs in very few of these patients. Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is the most frequent type of autoimmune encephalitis and is usually associated with tumors or herpes simplex virus infections. However, the link between the two disease entities is unknown. In this report, we present a rare case of a 29-year-old Chinese man with anti-NMDAR encephalitis associated with neurobrucellosis, with the detection of anti-NMDAR antibodies by cell-based assay and Brucella melitensis by metagenomic next-generation sequencing in his cerebrospinal fluid sample. The patient improved after antimicrobial treatment and immunotherapies, including steroids and intravenous immunoglobulin. This case implicates Brucella infection as a possible trigger for the production of anti-NMDAR antibodies, and prospective studies should reveal whether there is a casual relationship between brucellosis and anti-NMDAR antibodies.}, }
@article {pmid40443669, year = {2025}, author = {Zhang, C and Xu, Y and Zhang, M and Li, J and Sun, Z and Wang, Y and Lin, P}, title = {An exploratory study on the metagenomic and proteomic characterization of hypothyroidism in the first half of pregnancy and correlation with Th1/Th2 balance.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1500866}, pmid = {40443669}, issn = {1664-3224}, mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/immunology/microbiology/metabolism ; Adult ; Proteomics/methods ; *Th2 Cells/immunology/metabolism ; *Th1 Cells/immunology/metabolism ; Metagenomics/methods ; *Gastrointestinal Microbiome/immunology ; *Pregnancy Complications/immunology/metabolism/microbiology ; *Proteome ; Cytokines/metabolism ; }, abstract = {OBJECTIVE: To explore the gut microbiota and proteomic characteristics of hypothyroidism in the first half of pregnancy (referred to as hypothyroidism in the first half of pregnancy) and its association with Th (T helper cells, Th)1/Th2 balance using metagenomics combined with proteomics.<br><br>METHODS: Stool and blood samples were collected from 20 hypothyroid (hypothyroidism group) and normal pregnant women (normal group) in the first half of pregnancy. Flora and proteomic characteristics were analyzed using metagenomics sequencing and 4D-DIA proteomics. Th1 and Th2 cells were quantified, and cytokine levels were measured using cellular micro-bead arra. The enzyme-linked immunosorbent test (ELISA) was utilized to assess differential proteins.<br><br>RESULTS: (1) Metagenomic sequencing revealed distinct microbial profiles: The &#x3b2;-diversity of gut microbiota was diminished in the hypothyroidism group (p < 0.05). LEfSe analysis identified Phocaeicola vulgatus and Bacteroides fragilis enriched in the hypothyroidism group (p<0.05), and Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis showed significant enrichment in pathways related to peptidoglycan biosynthesis and glycerol ester metabolism.(2) Proteomic analysis demonstrated downregulation of Diacylglycerol Kinase Kappa (DGKK) and P05109|S10A8(S10A8) proteins in the hypothyroidism group, with marked enrichment in the KEGG pathways for vascular smooth muscle contraction and phosphatidylinositol signaling. (3) ELISA validation confirmed that the proteins DGKK and S10A8 were downregulated in pregnant women in the hypothyroidism group.<br><br>CONCLUSION: Increased P. vulgatus and B. fragilis, decreased DGKK and S10A8 proteins, and a left shift in the Th1/Th2 balance in patients with hypothyroidism in the first half of pregnancy may be associated with the development of the disease.}, }
@article {pmid40442718, year = {2025}, author = {Pivrncova, E and Bohm, J and Barton, V and Klanova, J and Borilova Linhartova, P}, title = {Viable bacterial communities in freshly pumped human milk and their changes during cold storage conditions.}, journal = {International breastfeeding journal}, volume = {20}, number = {1}, pages = {44}, pmid = {40442718}, issn = {1746-4358}, support = {LM2023069//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; 857560//Horizon 2020 Framework Programme/ ; }, mesh = {Humans ; *Milk, Human/microbiology ; Female ; *Bacteria/isolation &amp; purification/genetics/classification ; *Food Storage/methods ; Adult ; RNA, Ribosomal, 16S ; *Microbiota ; Freezing ; Refrigeration ; Azides ; Propidium/analogs &amp; derivatives ; }, abstract = {BACKGROUND: Human milk harbors diverse bacterial communities that contribute to infant health. Although pumping and storing milk is a common practice, the viable bacterial composition of pumped milk and the impact of storage practice on these bacteria remains under-explored. This metagenomic observational study aimed to characterize viable bacterial communities in freshly pumped human milk and its changes under different storage conditions.<br><br>METHODS: In 2023, twelve lactating mothers from the CELSPAC: TNG cohort (Czech Republic) provided freshly pumped milk samples. These samples were stored under various conditions (refrigeration for 24&#xa0;h, 48&#xa0;h, or freezing for six weeks) and treated with propidium monoazide (PMA) to selectively identify viable cells. The DNA extracted from individual samples was subsequently analyzed using 16S rRNA amplicon sequencing on the Illumina platform.<br><br>RESULTS: The genera Streptococcus, Staphylococcus, Diaphorobacter, Cutibacterium, and Corynebacterium were the most common viable bacteria in fresh human milk. The median sequencing depth and Shannon index of fresh human milk samples treated with PMA (+&#x2009;PMA) were significantly lower than in untreated (-PMA) samples (p&#x2009;<&#x2009;0.05 for all), which was true also for each time point. Also, significant changes in these parameters were observed between fresh human milk samples and their paired frozen samples (p&#x2009;<&#x2009;0.05), while no differences were found between fresh human milk samples and those refrigerated for up to 48&#xa0;h (p&#x2009;>&#x2009;0.05). Of specific genera, only&#x2009;+&#x2009;PMA frozen human milk samples showed a significant decrease in the central log-ratio transformed relative abundances of the genera Diaphorobacter and Cutibacterium (p&#x2009;<&#x2009;0.05) in comparison to&#x2009;+&#x2009;PMA fresh human milk samples.<br><br>CONCLUSIONS: The study demonstrated that the bacterial profiles significantly differed between human milk samples treated with PMA, which represent only viable bacteria, and those untreated. While storage at 4&#xa0;&#xb0;C for up to 48&#xa0;h did not significantly alter the overall diversity and composition of viable bacteria in human milk, freezing notably affected both the viability and relative abundances of some bacterial genera.}, }
@article {pmid40442502, year = {2025}, author = {Tzlil, G and Marín, MDC and Matsuzaki, Y and Nag, P and Itakura, S and Mizuno, Y and Murakoshi, S and Tanaka, T and Larom, S and Konno, M and Abe-Yoshizumi, R and Molina-Márquez, A and Bárcenas-Pérez, D and Cheel, J and Koblížek, M and León, R and Katayama, K and Kandori, H and Schapiro, I and Shihoya, W and Nureki, O and Inoue, K and Rozenberg, A and Chazan, A and Béjà, O}, title = {Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40442502}, issn = {2058-5276}, support = {3131/20//Israel Science Foundation (ISF)/ ; JPMXP1323015482//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMXP1323015482//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {Aquatic bacterial rhodopsin proton pumps harvest light energy for photoheterotrophic growth and are known to contain hydroxylated carotenoids that expand the wavelengths of light utilized, but these have not been characterized in marine archaea. Here, by combining a marine chromophore extract with purified archaeal rhodopsins identified in marine metagenomes, we show light energy transfer from diverse hydroxylated carotenoids to heimdallarchaeial rhodopsins (HeimdallRs) from uncultured marine planktonic members of 'Candidatus Kariarchaeaceae' ('Candidatus Asgardarchaeota'). These light-harvesting antennas absorb in the blue-light range and transfer energy to the green-light-absorbing retinal chromophore within HeimdallRs, enabling the use of light that is otherwise unavailable to the rhodopsin. Furthermore, we show elevated proton pumping by the antennas in HeimdallRs under white-light illumination, which better simulates the light conditions encountered by these archaea in their natural habitats. Our results indicate that light-harvesting antennas in microbial rhodopsins exist in families beyond xanthorhodopsins and proteorhodopsins and are present in both marine bacteria and archaea.}, }
@article {pmid40442233, year = {2025}, author = {Li, X and Tang, C and Zhou, M and Mi, J and Liu, J and Han, L and Yu, X and Zhang, X}, title = {Characteristics of SARS-CoV-2 variants and potential co-infected pathogens in hospitalized patients based on metagenomic next-generation sequencing.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18923}, pmid = {40442233}, issn = {2045-2322}, support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; 23DX1900300//Shanghai Targeted Biomedical Emergency Project/ ; }, mesh = {Humans ; *COVID-19/virology/epidemiology ; *SARS-CoV-2/genetics/isolation &amp; purification/classification ; Aged ; Female ; Male ; *Coinfection/virology/microbiology/epidemiology ; Middle Aged ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Phylogeny ; Retrospective Studies ; Hospitalization ; Adult ; Aged, 80 and over ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is widely used to diagnose complex infections in hospitalized patients, particularly those associated with COVID-19 which has garnered significant concern over the past five years. To investigate the molecular epidemic of the viral variant and the potential co-infection pathogens, we conducted retrospective mNGS analysis of 254 SARS-CoV-2-positive specimens collected from 200 hospitalized patients between March and September 2023. Phylogenetic analysis of the identified Omicron subvariants showed minimal evolutionary divergence, with no association between sub-lineages and pneumonia severity. Notably, mNGS demonstrated enhanced detection of polymicrobial coinfections, identifying bacterial, fungal, and viral co-pathogens in 92.5% (185/200) of cases. Pneumonia severity was associated with advanced age (proportion of elderly patients: 61.1 vs 78.3%; p = 0.032) and comorbid conditions, particularly diabetes mellitus (OR 2.03, 95% CI 1.03-4.02, p = 0.041), but showed no correlation with SARS-CoV-2 sub-lineages or coinfecting pathogens. While mNGS enhances coinfection diagnosis, COVID-19 outcomes are predominantly driven by host factors rather than Omicron subvariant evolution. Prioritized monitoring of elderly and comorbid individuals remained critical for severe pneumonia management.}, }
@article {pmid40442154, year = {2025}, author = {Seong, HJ and Park, YM and Kim, BS and Yoo, HJ and Kim, T and Yoon, SM and Kim, JH and Lee, SY and Lee, YK and Lee, DW and Nam, MH and Hong, SJ}, title = {Integrated multi-omics reveals different host crosstalk of atopic dermatitis-enriched Bifidobacterium longum Strains.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {91}, pmid = {40442154}, issn = {2055-5008}, mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *Gastrointestinal Microbiome ; Infant ; *Bifidobacterium longum/genetics/isolation &amp; purification/classification/metabolism ; Female ; Male ; Metabolomics ; Metagenomics/methods ; Feces/microbiology ; *Host Microbial Interactions ; Clostridium/genetics/isolation &amp; purification ; Transcriptome ; Multiomics ; }, abstract = {The infant gut microbiome is essential for long-term health and is linked to atopic dermatitis (AD), although the underlying mechanisms are not fully understood. This study investigated gut microbiome-host interactions in 31 infants with AD and 29 healthy controls using multi-omics approaches, including metagenomic, host transcriptomic, and metabolomic analyses. Microbial diversity was significantly altered in AD, with Bifidobacterium longum and Clostridium innocuum associated with these changes. At the strain-level, only B. longum differed significantly between groups, with pangenome analyses identifying genetic variations potentially affecting amino acid and lipid metabolites. Notably, B. longum subclade I, which was more prevalent in healthy controls, correlated with host transcriptomic pathways involved in phosphatidylinositol 3-kinase-AKT signaling and neuroactive ligand-receptor pathways, as well as specific metabolites, including tetrahydrocortisol and ornithine. These findings highlight the role of B. longum strain-level variation in infants, offering new insights into microbiome-host interactions related to AD.}, }
@article {pmid40441146, year = {2025}, author = {Yang, Y and Duan, Y and Lang, S and Fondevila, MF and Schöler, D and Harberts, A and Cabré, N and Chen, S and Shao, Y and Vervier, K and Miyamoto, Y and Zhang, X and Chu, H and Yang, L and Tan, C and Eckmann, L and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Bataller, R and Stärkel, P and Lawley, TD and Schnabl, B}, title = {Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2025.05.003}, pmid = {40441146}, issn = {1934-6069}, abstract = {Alcohol-associated liver disease poses a global health burden with high mortality. Imbalances in the gut microbiota are important for disease progression. Using metagenomic sequencing of fecal samples from a multicenter, international cohort of patients with alcohol-associated hepatitis, we found that the presence of virulence factor KpsM, encoded in the genome of Escherichia coli (E. coli), correlated with patient mortality. Functional studies using gnotobiotic mouse models and genetic manipulation of bacteria demonstrated that kpsM-positive E. coli exacerbate ethanol-induced liver disease. The kpsM gene mediates the translocation of capsular polysaccharides to the cell surface. This enables kpsM-positive E. coli to evade phagocytosis by the scavenger receptor Marco on Kupffer cells in the liver, leading to bacterial spread. Importantly, inhibiting kpsM-dependent capsules with the small molecule 2-(4-phenylphenyl)benzo[g]quinoline-4-carboxylic acid (C7) attenuated ethanol-induced liver disease in mice. We show that precision targeting of the virulence factor KpsM is a promising approach to improve outcomes of patients with alcohol-associated hepatitis.}, }
@article {pmid40440847, year = {2025}, author = {Shirai, T and Motooka, D and Ushikai, Y and Komano, J and Shioda, T and Iida, T and Sakon, N}, title = {Molecular epidemiology of human sapovirus based on the surveillance of wastewater and patients with acute gastroenteritis in Osaka, Japan.}, journal = {The Science of the total environment}, volume = {985}, number = {}, pages = {179622}, doi = {10.1016/j.scitotenv.2025.179622}, pmid = {40440847}, issn = {1879-1026}, abstract = {Wastewater-based epidemiology has recently emerged as a promising tool for determining the prevalence of infectious diseases in a community. In the present study, human sapoviruses (HuSaVs) detected in wastewater collected weekly from January 2023 to March 2024 were analyzed using qPCR and next-generation sequencing (NGS), and the results were compared with those from clinical surveillance samples obtained from patients with acute gastroenteritis (AGE) in Osaka Prefecture, Japan. The detection trend of HuSaV in wastewater agreed with the clinical surveillance data in that HuSaV genomes increased in the cold season. In wastewater surveillance, five genotypes were detected, including GI.1, GI.2, GII.3, GII.5, and GV.1. GI.2 was not detected in the clinical surveillance. In the phylogenetic analysis, VP1 gene sequences obtained from wastewater were positioned in close proximity to those obtained from clinical samples. It is suggested that the results of wastewater surveillance reflect the status of ongoing HuSaV infection in a community. Interestingly, GV.1 was detected less frequently than GI.1 in clinical surveillance samples, but was predominantly detected in wastewater at nearly all time points, accounting for up to 94.5 % of all reads in November 2023. In particular, in November 2023, most gastroenteritis outbreaks and pediatric AGE cases were attributable to GI.1, but GV.1 was present at a higher proportion in the wastewater surveillance than GI.1. Wastewater surveillance was shown to complement clinical surveillance in that the former might be able to cover asymptomatic carriers. Our results demonstrate the importance of systematic clinical and wastewater surveillance in epidemiological analyses of HuSaV.}, }
@article {pmid40440727, year = {2025}, author = {Ning, J and Du, Y and Wang, J and Liu, W and Deng, Y and Gan, Y and Wang, Y}, title = {Contribution of Microbial Metabolism to Geogenic Phosphorus Enrichment in Groundwater: Insights from Metagenomic Sequencing and Organic Molecular Characterization.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c02169}, pmid = {40440727}, issn = {1520-5851}, abstract = {Microbial mediation in the enrichment of geogenic phosphorus (P) is often mentioned but rarely explored, especially in P enrichment processes through the mineralization of dissolved organic matter (DOM) containing natural P. To bridge the theoretical gap, this study investigated the mechanisms of P enrichment through microbially mediated mineralization of natural P-containing DOM by adopting an approach combining comprehensive field investigation with hydrochemical and molecular biological analyses. The co-analysis of the dominant microbial community compositions and genomics revealed that the microbial metabolism pathways involved in the biodegradation of P-containing DOM were associated with the enrichment level of dissolved inorganic phosphorus (DIP). Specifically, dephosphorylation was more pronounced under conditions of limited DIP, while C-P bond cleavage was the primary metabolic pathway under sufficient DIP. Co-occurrence network analysis further indicated that the substrates for DIP enrichment differed between dephosphorylation and C-P bond cleavage, namely CHONSP1 compounds in the region of highly unsaturated-low O compounds (AI ≤ 0.5, H/C < 1.5, and O/C < 0.4) and CHOP1 compounds in the region of highly unsaturated-high O compounds (AI ≤ 0.5, H/C < 1.5, and O/C ≥ 0.4), respectively. These findings provide new insights into geogenic P enrichment in groundwater from the perspective of microbial metabolism and have potential implications for the bioremediation of P-contaminated groundwater at different contamination levels.}, }
@article {pmid40440710, year = {2025}, author = {Zhu, Y and Sun, M and Chen, B and Liu, X and Yang, G and Li, X}, title = {Diagnostic Value of Cerebrospinal Fluid Metagenomics Next-generation Sequencing in Neurobrucellosis in Children.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, doi = {10.1097/INF.0000000000004845}, pmid = {40440710}, issn = {1532-0987}, support = {No. 2021GG0209//Science and Technology Project of the Inner Mongolia Department of Science and Technology/ ; }, abstract = {OBJECTIVE: To explore the clinical characteristics of neurobrucellosis in children and the diagnostic value of metagenomics next-generation sequencing (mNGS) of cerebrospinal fluid and traditional microbial detection methods.<br><br>METHODS: Three patients in the pediatrics department from April 2022 to October 2023 were diagnosed with brucellosis, and 5&#x2009;mL of cerebrospinal fluid was taken and sent for routine biochemical, bacterial Gram-stained smear, antacid-stained smear, ink staining, bacterial culture and second-generation sequencing of the microgeneration of the cerebrospinal fluid, respectively (Beijing AJiAn Genetics Medical Laboratory). Cranial magnetic resonance imaging, blood culture and blood Brucella antibody test were also performed to summarize the clinical features and pathogenic analysis.<br><br>RESULTS: The chief presentations were fever, headache, vomiting, somnolence and positive signs of meningeal irritation in all patients. Case 3: persistent hemiparesis of the left limb and cerebral infarction. Brucella was detected by cerebrospinal fluid mNGS in all cases, with sequence numbers of 5252, 162 and 59 Brucella and relative abundances of 80.26%, 6.14% and 1.06%, respectively. Cerebrospinal fluid cultures were negative, and blood cultures were positive in case 3.<br><br>CONCLUSIONS: The clinical characteristics of neurobrucellosis in children are variable, and meningoencephalitis is common. Traditional microbiological tests are difficult to detect Brucella, whereas cerebrospinal fluid mNGS can provide a precise diagnosis.}, }
@article {pmid40440092, year = {2025}, author = {Lawniczak, MKN and Kocot, KM and Astrin, JJ and Blaxter, M and Sotero-Caio, CG and Barker, KB and Childers, AK and Coddington, J and Davis, P and Howe, K and Johnson, WE and McKenna, DD and Wideman, JG and Pettersson, OV and Ras, V and Santos, BF and , }, title = {Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40440092}, issn = {2047-217X}, support = {//Science for Life Laboratory/ ; //Swedish Research Council/ ; 1846174//National Science Foundation/ ; 2138994//National Science Foundation/ ; 2321308//National Science Foundation/ ; 2001303//National Science Foundation/ ; 2110053//National Science Foundation/ ; 1937815//National Science Foundation/ ; DBI-2119963//National Science Foundation/ ; U24HG006941/HG/NHGRI NIH HHS/United States ; /NH/NIH HHS/United States ; //Agricultural Research Service/ ; }, mesh = {*Genome ; *Genomics/standards/methods ; *Metagenomics/standards/methods ; Earth, Planet ; *Specimen Handling/standards/methods ; }, abstract = {The Earth BioGenome Project has the extremely ambitious goal of generating, at scale, high-quality reference genomes across the entire Tree of Life. Currently in its first phase, the project is targeting family-level representatives and is progressing rapidly. Here we outline recommended standards and considerations in sample acquisition and processing for those involved in biodiverse reference genome creation. These standards and recommendations will evolve with advances in related processes. Additionally, we discuss the challenges raised by the ambitions for later phases of the project, highlighting topics related to sample collection and processing that require further development.}, }
@article {pmid40439988, year = {2025}, author = {Davidson, IM and Nikbakht, E and Haupt, LM and Dunn, PJ}, title = {Toward accurate vaginal microbiome profiling: protocol, bioinformatics, and core microbiota characterisation.}, journal = {Journal of assisted reproduction and genetics}, volume = {}, number = {}, pages = {}, pmid = {40439988}, issn = {1573-7330}, abstract = {PURPOSE: Rising demand for assisted reproductive technologies (ART) with limited improvements in success rates has driven interest in the impact of the vaginal microbiome on fertility outcomes. In order to fully examine the relationship between the vaginal microbiome and fertility outcomes, methodologies and technological developments must be standardised and benchmarked to provide the most accurate assessment of microbial population representation.<br><br>METHODS: This study sought to investigate the utility of 16S sequencing and bioinformatic approaches using nanopore sequencing to characterize core vaginal microbiota in a healthy Australian cohort of reproductive-age women.<br><br>RESULTS: Optimisation and comparison of different PCR strategies for whole 16S amplification was undertaken, along with the generation of bioinformatic analysis strategies. Initial qPCR identified the 27F-YM (MIX) primer as the most sensitive for C. trachomatis. However, nanopore sequencing revealed no detectable C. trachomatis across all six samples. Among the bioinformatic tools, Porechop with NanoCLUST most accurately identified microbial presence. Community state type (CST) I-characterised by Lactobacillus crispatus dominance-was identified as the most common CST (66%), aligning with patterns of a healthy vaginal microbiome.<br><br>CONCLUSION: The findings highlight a Lactobacillus-rich microbiome as the most common among healthy females; however, further refinement-potentially through a metagenomics approach-is recommended to address 16S rRNA primer limitations to enable improved accuracy of microbial detection for the vaginal microbiome.}, }
@article {pmid40439829, year = {2025}, author = {Wu, C and Han, X and Yang, F and Zhang, G and Zhao, C}, title = {Misdiagnosis of autoimmune glial fibrillary acidic protein astrocytopathy as infectious meningitis: a case report.}, journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology}, volume = {}, number = {}, pages = {}, pmid = {40439829}, issn = {1590-3478}, abstract = {BACKGROUND: Autoimmune glial fibrillary acidic protein astrocytopathy (A-GFAP-A) is a rare autoimmune central nervous system disorder associated with anti-GFAP IgG, presenting with meningoencephalitis or myelitis. Differential diagnosis from infectious causes, such as tuberculous meningitis (TBM), is challenging due to overlapping clinical and radiological features.<br><br>CASE PRESENTATION: A 24-year-old Chinese female presented with acute headache, fever, and vomiting. The cerebrospinal fluid (CSF) analysis showed lymphocytic pleocytosis, elevated protein and decreased glucose level. Brain magnetic resonance imaging (MRI) showed diffuse leptomeningeal enhancement. She was initially diagnosed with infectious meningitis and emperically treated with antibiotics and anti-tuberculosis therapy. However, her symptoms progressed with seizures, urinary retention, and tremor. Subsequent MRI revealed the involvement of the whole spinal cord. CSF analysis identified anti-GFAP IgG (titer 1:32). Bacterial, viral and tuberculous infection were excluded through bacterial culturing, metagenomic next-generation sequencing and Xpert MTB/RIF assay. The patient responded well to intravenous immunoglobulin and corticosteroids, achieving full remission. Finally, the diagnosis of A-GFAP-A was confirmed.<br><br>CONCLUSION: A-GFAP-A mimics infectious meningitis such as TBM due to similar CSF abnormalities and neuroimaging findings. This case underscores the importance of GFAP-IgG testing in differential diagnosis of patients with meningitis who have negative microbiological studies and atypical symptoms such as urinary retention and tremor.}, }
@article {pmid40439813, year = {2025}, author = {Biktasheva, L and Galitskaya, P and Kuryntseva, P and Shipaeva, M and Selivanovskaya, S}, title = {Challenges and distortions in microbial community analysis of oil reservoirs: a case study with heavy crude oil from the Romashkino field.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40439813}, issn = {1618-1905}, support = {075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-299//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {The study of the microbial community of wells is a methodologically complex, but urgent problem. In the course of our work, five samples of oil wells were selected from one deposit of the Romashkino field. The samples were subjected to nucleic acid extraction using three methods-direct DNA extraction, and after enrichment using aerobic and anaerobic cultivation methods. In three samples from wells W1-W3, extraction after anaerobic enrichment was successful. Effective aerobic cultivation was possible in all five samples. All three of these samples represented the aqueous part of the produced fluid; samples from wells W4 and W5, where extraction was difficult, represented the oil part. During the analysis of the microbial community in enrichment cultures from wells W1-W3, exogenous microorganisms such as Desulfovibrio, Acetobacterium, Bacillus, and Georgenia were discovered, which can be explained by the long-term exploitation of this section of the field. In one sample from well W1, community information was obtained using direct extraction and anaerobic enrichment. It was found that the microbial community changed significantly after enrichment, and its diversity decreased. At the same time, however, the functional profile of microorganisms has not changed, and sulfate-reducing microorganisms dominate in both samples. Thus, the results of the work allow us to make an assumption about the physicochemical parameters of samples in which the study of the microbial community is possible. In addition, it became known that well W1 needs to control the process of biological acidification and has a high risk of equipment corrosion.}, }
@article {pmid40439791, year = {2025}, author = {Gigliucci, F and Barbieri, G and Veyrunes, M and Chiani, P and Marra, M and Carollo, M and Knijn, A and Brambilla, G and Morabito, S}, title = {Characterization of the resistome and antibiotic-resistant bacteria in top soil improvers and irrigation waters devoted to food production: a case study from Italy.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {40439791}, issn = {1614-7499}, support = {RF-2019-12369714//Ministero della Salute/ ; }, abstract = {Biosolids and reclaimed waters are valuable resources for reintroducing organic matter into agricultural soils and reducing the water footprint of intensive agricultural food system. While the circular economy is a sustainable practice, it may introduce vulnerabilities in the food chain, by exposing crops to zoonotic agents and antimicrobial resistance determinants. This option is far from being a speculation and evidence start to accumulate indicating that the risk is tangible. This study provides further evidence that the circular economy practices of reusing biomass and reclaimed waters in agricultural setting may be vectors for the spreading of antibiotic resistance genes (ARGs) targeting molecules used to treat human bacterial infections. We screened biosolid and water samples for ARGs presence using shotgun metagenomic sequencing. We demonstrated that the identified ARGs are present in live bacterial organisms, harbouring multidrug-resistant gene clusters, confirmed through phenotypic testing and whole-genome sequencing of isolated bacteria. Additionally, we observed that most of the antibiotic-resistant bacteria identified belonged to environmentally widespread species, which were not expected to be exposed to the antimicrobials, suggesting that inter-species transfer of resistance genes.}, }
@article {pmid40439580, year = {2025}, author = {Bondeelle, L and Cheng, GS and Bergeron, A}, title = {What's new in the management of pulmonary complications in allogeneic stem cell transplantation?.}, journal = {Expert review of respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1080/17476348.2025.2513519}, pmid = {40439580}, issn = {1747-6356}, abstract = {INTRODUCTION: As survival increases after allogeneic hematopoietic stem cell transplantation (allo-HCT), several organ complications have emerged, including those involving the lung, which require a multidisciplinary management approach. The constant evolution of allo-HCT procedures, advances in diagnostic tools for infections and pulmonary disease, as well as new treatment approaches, require frequent updating of knowledge in this field.<br><br>AREAS COVERED: We review the multiple infectious and noninfectious lung complications that occur both early and late after allo-HCT. This includes an updated description of these complications, risk factors, diagnostic approach and outcome. A literature search was performed using PubMed-indexed journals.<br><br>EXPERT OPINION: The diagnosis of pulmonary complications after allo-HCT remains challenging, further complicated by the frequent association of co-infections and/or links between infection and noninfectious complications. The development of metagenomic next-generation sequencing (mNGS) should enhance the diagnostic yield of bronchoalveolar lavage but its clinical relevance remains to be evaluated. A better understanding of the pathophysiology of the lung chronic graft-versus-host disease (GVHD) and improved phenotyping are essential for advancing its diagnostic and therapeutic management. This requires a revision of diagnostic criteria and the identification of new biomarkers of early disease.}, }
@article {pmid40439559, year = {2025}, author = {Rouse, N and Buttler, J and Pabilonia, K and Weller, C and Respicio-Kingry, L and Dietrich, E and Petersen, J and Kovalenko, G and Bortz, E and Huntington, KB}, title = {Francisella tularensis Subspecies holarctica in Stranded Beluga Whales, Cook Inlet, Alaska, USA.}, journal = {Emerging infectious diseases}, volume = {31}, number = {6}, pages = {1247-1250}, doi = {10.3201/eid3106.250033}, pmid = {40439559}, issn = {1080-6059}, mesh = {Animals ; *Francisella tularensis/genetics/classification/isolation &amp; purification ; Alaska/epidemiology ; *Tularemia/veterinary/microbiology/epidemiology/diagnosis ; *Beluga Whale/microbiology ; Multilocus Sequence Typing ; Phylogeny ; }, abstract = {We report fatal tularemia in stranded beluga whales in Cook Inlet, Alaska, USA. Francisella tularensis was detected by nanopore metagenomics, confirmed by quantitative PCR and immunohistochemistry, and characterized as F. tularensis subspecies holarctica by multilocus sequence typing. Our findings should be considered when assessing biosecurity and marine mammal health in the North Pacific.}, }
@article {pmid40439405, year = {2025}, author = {Scribano, FJ and Gebert, JT and Engevik, KA and Hayes, NM and Villanueva, J and Pham, S and Kaundal, S and Dave, JJ and Prasad, BVV and Estes, MK and Ramani, S and Hyser, JM}, title = {BTP2 restricts Tulane virus and human norovirus replication independent of store-operated calcium entry.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0044425}, doi = {10.1128/jvi.00444-25}, pmid = {40439405}, issn = {1098-5514}, abstract = {Human norovirus is the leading cause of viral gastroenteritis across all age groups. While there is a need for human norovirus antivirals, therapeutic development has been hindered by a lack of cell culture systems and animal models of infection. Surrogate viruses, such as Tulane virus (TV), have provided tractable systems to screen potential antiviral compounds. Our previous work demonstrated that TV encodes a viral ion channel, which dysregulates cytosolic calcium signaling. We set out to investigate whether host pathways triggered by viral ion channel activity, including store-operated calcium entry (SOCE), play a role in virus replication. Using pharmacologic inhibitors and genetically engineered cell lines, we establish that the SOCE inhibitor, BTP2, reduces TV replication in an SOCE-independent manner. We observed a significant reduction in TV replication, protein expression, and RNA synthesis in cells with both pre- and post-infection BTP2 treatment. By serial passage and plaque isolation, we demonstrate that TV quasi-species have mixed susceptibility and resistance to BTP2. Sequence comparison of the quasi-species revealed that amino acid changes in the structural proteins were associated with drug resistance. We utilized reverse genetics to generate TV with the resistance-associated VP1 and VP2 amino acid changes and found that amino acid changes in both proteins conferred BTP2 resistance. Together, this supports that TV structural proteins are the targets of BTP2. Finally, using human intestinal organoids, we demonstrate that BTP2 significantly reduces human norovirus replication.IMPORTANCEOur work identifies BTP2 as a potential human norovirus antiviral pharmacophore and highlights the utility of targeting calicivirus structural proteins to restrict viral replication. Furthermore, we establish a system whereby Tulane virus (TV) can be used to screen novel antiviral candidates and establish their mechanism of action. Together, this will facilitate rapid preclinical validation of other novel human norovirus therapeutics.}, }
@article {pmid40439403, year = {2025}, author = {Pang, Y and Qiu, J and Yang, H and Zhang, J and Mo, J and Huang, W and Zeng, C and Xu, P}, title = {Application value of metagenomic next-generation sequencing based on protective bronchoalveolar lavage in nonresponding pneumonia.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0313824}, doi = {10.1128/spectrum.03138-24}, pmid = {40439403}, issn = {2165-0497}, abstract = {This study aims to explore the application value of metagenomic next-generation sequencing (mNGS) of protective bronchoalveolar lavage fluid in the differential diagnosis and pathogenetic identification of nonresponding pneumonia. This study analyzed patient symptoms, auxiliary examinations including pathogen detection, and treatment response to identify the reasons for the lack of response to initial treatment and the pathogenetic diagnosis of pulmonary infections. The diagnostic efficacy of pathogen culture and mNGS was statistically analyzed and compared based on the clinical diagnosis criteria. (1) The two most common reasons for the ineffectiveness of initial treatment in nonresponding pneumonia cases are that (i) the initial treatment did not cover the pathogenic bacteria in pulmonary infection cases and that (ii) non-infectious pulmonary diseases were responsible. The most common pathogens in pulmonary infection cases of nonresponding pneumonia are Mycobacterium tuberculosis (MTB), Pneumocystis jirovecii, Aspergillus, and Pseudomonas aeruginosa. (2) In pulmonary infectious cases, mNGS demonstrated a higher detection sensitivity for pathogenic bacteria than pathogen cultures. mNGS combined with protective bronchoalveolar lavage has good clinical application value in the accurate diagnosis of pathogens and identification of non-infectious diseases.IMPORTANCEThe combination of mNGS and the protective BAL technique demonstrates significant utility in accurately diagnosing pathogens and identifying non-infectious diseases. Misdiagnosis of non-infectious lung diseases as infectious lung diseases is a common factor contributing to the lack of response to initial treatment in nonresponding pneumonia patients. The most common pathogens in pulmonary infection cases of nonresponding pneumonia are MTB, Pneumocystis jirovecii, Aspergillus, and Pseudomonas aeruginosa.}, }
@article {pmid40439232, year = {2025}, author = {McGivern, BB and Ellenbogen, JB and Hoyt, DW and Bouranis, JA and Stemple, BP and Daly, RA and Bosman, SH and Sullivan, MB and Hagerman, AE and Chanton, JP and Tfaily, MM and Wrighton, KC}, title = {Polyphenol rewiring of the microbiome reduces methane emissions.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf108}, pmid = {40439232}, issn = {1751-7370}, abstract = {Methane mitigation is regarded as a critical strategy to combat the scale of global warming. Currently, about 40% of methane emissions originate from microbial sources, which is causing strategies to suppress methanogens-either through direct toxic effects or by diverting their substrates and energy-to gain traction. Problematically, current microbial methane mitigation knowledge lacks detailed microbiome-centered insights, limiting translation across conditions and ecosystems. Here we utilize genome-resolved metatranscriptomes and metabolomes to assess the impact of a proposed methane inhibitor, catechin, on greenhouse gas emissions for high-methane-emitting peatlands. In microcosms, catechin drastically reduced methane emissions by 72-84% compared to controls. Longitudinal sampling allowed for reconstruction of a catechin degradation pathway involving Actinomycetota and Clostridium, which break down catechin into smaller phenolic compounds within the first 21 days, followed by degradation of phenolic compounds by Pseudomonas_E from days 21 to 35. These genomes co-expressed hydrogen-uptake genes, suggesting hydrogenases may act as a hydrogen sink during catechin degradation and consequently reduce hydrogen availability to methanogens. In support of this idea, there was decreased gene expression by hydrogenotrophic and hydrogen-dependent methylotrophic methanogens under catechin treatment. There was also reduced gene expression from genomes inferred to be functioning syntrophically with hydrogen-utilizing methanogens. We propose that catechin metabolic redirection effectively starves hydrogen-utilizing methanogens, offering a potent avenue for curbing methane emissions across diverse environments including ruminants, landfills, and constructed or managed wetlands.}, }
@article {pmid40438915, year = {2025}, author = {Rivas-Santisteban, J and Martínez, JM and Escudero, C and Hernández-Antolín, R and Cid-Barrio, L and Ellis, GJ and Domingo, E and Sánchez, C and Sobrino, F and Amils, R}, title = {Metagenomic analysis of heavy water-adapted bacterial communities.}, journal = {Microbial genomics}, volume = {11}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001414}, pmid = {40438915}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; *Water Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Metagenome ; DNA Transposable Elements ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Micro-organisms can survive and thrive in unusual and extreme environments. Here, we present a metagenomic analysis of living bacteria found in highly pure, deleterious heavy water (>99% D2O), stored in sealed plastic containers for more than 30 years, without any external supply. Deep DNA sequencing analyses have revealed that the most abundant genetic signatures were primarily associated with Pseudomonadota and Bacteroidota. These bacteria exhibited shorter gene lengths and depletion of polar and metabolically costly amino acids compared to the related species from light water environments. Genes related to DNA transposition, repair and modification were notably abundant, particularly mutant forms of the IS3 transposable elements family. We also explore potential carbon and energy sources and discuss the evolutionary implications of bacteria capable of surviving in such an extreme human-made environment.}, }
@article {pmid40438350, year = {2025}, author = {Peng, H and Fu, J}, title = {Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis.}, journal = {National science review}, volume = {12}, number = {6}, pages = {nwaf128}, pmid = {40438350}, issn = {2053-714X}, }
@article {pmid40438301, year = {2025}, author = {Marra, PS and Marra, AR and Chen, E and Kobayashi, T and Celeghini, PD and Gutfreund, MC and Pardo, I and Lopes, GOV and Hsieh, MK and Boodhoo, NA and Fu, D and Torres-Espinosa, MA and Li, Y and Deliberato, RO and Algain, SMA and Salinas, JL and Edmond, MB and Amgarten, DE and de Mello Malta, F and Dos Santos, NV and Pinho, JRR and Louine, M and Wilson, MR}, title = {Metagenomic Next-generation Sequencing in Patients With Infectious Meningoencephalitis: A Comprehensive Systematic Literature Review and Meta-analysis.}, journal = {Open forum infectious diseases}, volume = {12}, number = {5}, pages = {ofaf274}, pmid = {40438301}, issn = {2328-8957}, abstract = {BACKGROUND: We aimed to assess the accuracy, clinical efficacy, and limitations of metagenomic next-generation sequencing (mNGS) for diagnosing infectious meningoencephalitis.<br><br>METHODS: We performed a systematic literature review and meta-analysis of studies that evaluated the performance of mNGS to determine the cause of infectious meningoencephalitis. We explored PubMed, Cumulative Index to Nursing and Allied Health, Embase, Cochrane Central Register of Controlled Trials, ClinicalTrials.gov, and Web of Science up to 12 November 2024. To perform a meta-analysis, we calculated the pooled diagnostic odds ratio (DOR) for mNGS and for conventional microbiological tests (CMTs) compared to the clinical diagnosis.<br><br>RESULTS: Thirty-four studies met the inclusion criteria, with mNGS-positive rates ranging from 43.5% to 93.5% for infectious meningoencephalitis. The meta-analysis included 23 studies with 1660 patients. The pooled sensitivity was 0.70 (95% confidence interval [CI], .67-.72), and its specificity was 0.93 (95% CI, .92-.94). The DOR for mNGS was 26.7 (95% CI, 10.4-68.8), compared to 12.2 (95% CI, 3.2-47.0) for CMTs. For tuberculosis meningoencephalitis, mNGS demonstrated a pooled sensitivity of 0.67 (95% CI, .61-.72) and specificity of 0.97 (95% CI, .95-.99), with a DOR of 43.5 (95% CI, 7.4-256.6).<br><br>CONCLUSIONS: Our review indicates that mNGS can be a valuable diagnostic tool for infectious meningoencephalitis, offering high sensitivity and specificity. mNGS's superior DOR compared to that of CMTs highlights its potential for more accurate diagnoses and targeted interventions. Further research is needed to optimize which patients and at what point in the diagnostic process mNGS should be used.}, }
@article {pmid40438215, year = {2025}, author = {Hanna, A and Abbas, H and Yassine, F and AlBush, A and Bilen, M}, title = {Systematic review of gut microbiota composition, metabolic alterations, and the effects of treatments on PCOS and gut microbiota across human and animal studies.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1549499}, pmid = {40438215}, issn = {1664-302X}, abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is an endocrine disorder affecting around 12% of women globally, associated with infertility and various comorbidities. Emerging evidence suggests a crucial role of gut microbiota in PCOS pathophysiology, prompting research to investigate alterations in gut microbial composition in patients with PCOS.<br><br>METHODS: This systematic review aims to analyze human and animal studies that compare gut microbiota composition, gut-derived metabolites, and treatment interventions in PCOS patients versus healthy controls. A comprehensive literature search was conducted using PubMed, Scopus, and Web of Science, yielding studies examining gut microbiota, metabolomic shifts, and treatment responses in PCOS models and human populations.<br><br>RESULTS: Our analysis revealed decreases in alpha diversity in PCOS patients, with more pronounced changes in beta diversity in animal models. Specific bacterial taxa, such as Bacteroides vulgatus, Escherichia-Shigella and Lactobacillus, showed implication in PCOS pathogenesis, suggesting potential microbial markers. Furthermore, discrepancies between human and animal studies show the need for humanized mouse models to bridge this gap. Interventions like probiotics and fecal microbiota transplantation (FMT) showed varying levels of efficacy, with FMT emerging as a more promising but invasive option, offering live bacteriotherapy as a potential therapeutic alternative. Alterations in gut-derived metabolites, including short-chain fatty acids and bile acids, highlighted the multifaceted nature of PCOS, with implications extending to metabolic, hormonal, and gut-brain axis disruptions.<br><br>DISCUSSION: In conclusion, PCOS exhibits complex interactions between gut microbiota and metabolic pathways, necessitating further research with standardized methods and larger sample sizes to elucidate the microbiome's role in PCOS.}, }
@article {pmid40438118, year = {2025}, author = {Diallo, D and Sun, S and Somboro, AM and Baya, B and Koné, A and Diarra, B and Nantoumé, M and Koloma, I and Diakite, M and Holl, J and Maiga, AI and Seydi, M and Theron, G and Hou, L and Fodor, A and Maiga, M}, title = {Metabolic and immune consequences of antibiotic related microbiome alterations during first-line tuberculosis treatment in Bamako, Mali.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1561459}, pmid = {40438118}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Adult ; Mali ; *Dysbiosis/chemically induced/immunology ; Middle Aged ; *Tuberculosis/drug therapy/microbiology/immunology/metabolism ; Cytokines/blood ; Longitudinal Studies ; *Antitubercular Agents/therapeutic use/adverse effects ; Young Adult ; Metabolomics ; }, abstract = {BACKGROUND: Individuals with a history of tuberculosis (TB) treatment are at a higher risk of experiencing a recurrent episode of the disease. Previous cross-sectional studies identified a connection between dysbiosis (alterations) in the gut microbiota composition and the administration of first-line TB antibiotics. However, these studies have not successfully elucidated this dysbiosis's resulting metabolic and immune consequences.<br><br>METHODS: In a longitudinal assessment, we studied the antituberculosis drug-related changes in the gut microbiota's composition and the resulting functional consequences. Sputum for TB culture, peripheral blood for metabolomics and cytokines analysis, and stool for shotgun metagenomics were collected from TB participants at Month-0, Month-2, Month-6 of treatment, and 9 Months after treatment (Month-15). Healthy controls were sampled at Month-0 and Month-6.<br><br>FINDINGS: We found notable differences in gut microbiota between individuals with TB and healthy controls. While gut microbiota tended to resemble healthy controls at the end of TB treatment, significant differences for many taxa persisted up to Month-15. Concurrently, disturbances in plasma metabolites, including tryptophan, tricarboxylic acids, and cytokine levels were observed. Certain fatty acids associated with inflammation pathways negatively correlated with the abundance of several taxa.<br><br>CONCLUSION: We observed alterations in the gut microbiota composition and function during treatment and at Month-15. Numerous changes in bacterial taxa abundances and inflammation-linked metabolites did not reverse at Month-15. This study suggests potential influences of anti-TB drugs and the gut microbiome on the disease outcome, response to treatment, and resistance to future TB infections.}, }
@article {pmid40437943, year = {2025}, author = {Franzin, M and Lagatolla, C and Forgiarini, SS and Haag, M and Neef, SK and Comar, M and Schaeffeler, E and Bellich, B and Bramuzzo, M and Decorti, G and Lucafò, M and Hofmann, U and Schwab, M and Stocco, G}, title = {Klebsiella pneumoniae contributes to altered cytotoxicity of thiopurines in vitro: Possible implications of biotransformation and bacterial metabolism.}, journal = {British journal of pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1111/bph.70089}, pmid = {40437943}, issn = {1476-5381}, support = {RC 07/22//Italian Ministry of Health, through the contribution given to the Institute for Maternal and Child Health IRCCS Burlo Garofolo/ ; //Robert Bosch Stiftung/ ; }, abstract = {BACKGROUND AND PURPOSE: Thiopurines are used in paediatric inflammatory bowel disease (IBD), but some patients do not respond. Because the gut microbiota influences drug efficacy and IBD-patient microbiota presents increased bacterial abundance, we investigated the impact of candidate Enterobacteriaceae on drug cytotoxicity, metabolism and efficacy.<br><br>EXPERIMENTAL APPROACH: Thiopurines were exposed in vitro to bacteria for 4&#x2009;h at 37&#xb0;C and drug concentrations measured by UV spectrophotometry. Cytotoxic effects and drug metabolite concentrations on NALM6 and JURKAT cells were determined after treatment with thiopurines exposed or not to bacteria. Drugs were measured in Klebsiella pneumoniae lysates and bacterial conditioned media were used for metabolomic analyses. Shotgun metagenomic sequencing was performed on eight IBD-patient faecal stools.<br><br>KEY RESULTS: Incubation of thiopurines with K. pneumoniae, but not Escherichia coli and Salmonella enterica, reduced thiopurine concentrations and cytotoxicity on NALM6 and JURKAT cells. Thiopurine metabolites were lower in cells treated with drugs previously exposed to K. pneumoniae. Internalisation of drugs was demonstrated by their detection in lysates after bacterial incubation. Untargeted metabolomics revealed biotransformation of thiopurines by K. pneumoniae, as reactions of deconjugation, reduction, glycosylation, acetylation or conjugation with propionic acid. Incubation with thiopurines led to changes in the secretion of endogenous bacterial metabolites. K. pneumoniae faecal abundance was associated with lower thiopurine metabolite concentrations in erythrocytes of paediatric IBD-patients.<br><br>CONCLUSIONS AND IMPLICATIONS: K. pneumoniae decreases the cytotoxicity of thiopurines through internalisation of MP and TG. We revealed potential bacterial drug biotransformation, as well as negative correlations between bacterial abundance and drug metabolites.}, }
@article {pmid40437611, year = {2025}, author = {Zhang, P and Tuo, X and Jiang, J and Zhang, Y and Zhao, J and Deng, C and Zhao, G and Cheng, Y and Song, L and Yang, Y and Guo, R and Zhang, H and Zhao, H and Ma, S and Li, L and Shi, H}, title = {Characteristics of the gut virome in patients with premalignant colorectal adenoma.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {597}, pmid = {40437611}, issn = {1479-5876}, support = {No.S2024-JC-QN-1554//Natural Science Basic Research Program of Shaanxi Province/ ; }, mesh = {Humans ; *Virome ; *Colorectal Neoplasms/virology/microbiology ; *Adenoma/virology/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Precancerous Conditions/virology/microbiology ; Case-Control Studies ; Aged ; Reproducibility of Results ; }, abstract = {BACKGROUND: The multi-kingdom gut microbiota (e.g., bacteriome, mycobiome, and virome) characteristics of colorectal cancer have been extensively studied, yet there is still an insufficient description of the microbiota features in its early-stage, colorectal adenoma, particularly in the gut virome aspect.<br><br>METHODS: Based on the Metagenomic Gut Virus catalogue (MGV) containing 54,118 non-redundant gut viral genomes, this study characterized the virome composition and diversity using publicly available metagenomic sequencing data from 419 individuals with premalignant colorectal adenoma and 552 healthy controls. Furthermore, we identified and assessed the reliability and classification performance of adenoma-associated microbial signatures through comparative analysis and the random forest model.<br><br>RESULTS: Our results revealed a notable shift in the gut virome structure of patients compared to healthy controls, characterized by a significant increase in viral families such as Microviridae, Podoviridae_crAss-like, and Quimbyviridae. At the viral operational taxonomic unit (vOTU) level, we identified 479 vOTU signatures showing significant differences in relative abundances between patients and controls, including some patient-enriched vOTUs tending to infect Bacteroidaceae and Lachnospiraceae. Correlation network analysis revealed specific bacterial species correlated with adenoma-associated viruses, suggesting frequent interactions between them. Moreover, random forest models trained on gut viral and bacterial signatures demonstrated area under the curve (AUC) scores of 0.68, 0.82, and 0.76 for classifying healthy individuals versus patients with tubular adenomas, patients with sessile serrated adenomas, and patients with both conditions, respectively. In three independent validation cohorts, the classification performance achieved AUC scores ranging from 0.61 to 0.65.<br><br>CONCLUSIONS: Our study provides insights into the gut virome in premalignant colorectal adenoma, highlighting its potential role in disease development and diagnosis. Further investigations are warranted to elucidate the underlying mechanisms of gut virus-bacteria interactions and validate diagnostic models in larger populations.}, }
@article {pmid40437401, year = {2025}, author = {Unrug-Bielawska, K and Sandowska-Markiewicz, Z and Pyśniak, K and Piątkowska, M and Czarnowski, P and Goryca, K and Mróz, A and Żeber-Lubecka, N and Wójcik-Trechcińska, U and Bałabas, A and Dąbrowska, M and Surynt, P and Radkiewicz, M and Mikula, M and Ostrowski, J}, title = {Western Diet and fecal microbiota transplantation alter phenotypic, liver fatty acids, and gut metagenomics and metabolomics in Mtarc2 knockout mice.}, journal = {Genes &amp; nutrition}, volume = {20}, number = {1}, pages = {13}, pmid = {40437401}, issn = {1555-8932}, support = {2018/29/B/NZ7/00809//Narodowe Centrum Nauki/ ; }, }
@article {pmid40436871, year = {2025}, author = {Zeng, L and Yu, B and Zeng, P and Duoji, Z and Zuo, H and Lian, J and Yang, T and Dai, Y and Feng, Y and Yu, P and Yang, J and Yang, S and Dou, Q}, title = {Mediation effect and metabolic pathways of gut microbiota in the associations between lifestyles and dyslipidemia.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {90}, pmid = {40436871}, issn = {2055-5008}, support = {723B2017//National Natural Science Foundation of China/ ; XZ202201ZD0001G//Science and Technology Major Project of Tibetan Autonomous Region of China/ ; XZ202303ZY0007G//Science and Technology Plan Projects of Tibet Autonomous Region/ ; CQFYJB01005//Chongqing Maternal and Child Health Hospital/ ; 2023YFC3604702//National Key Research and Development Program of China/ ; 2023YFC3604701; 2020YFC2008005; 2018YFC2002405//National Key Research and Development Program of China/ ; 2023YFS0251//Key R&amp;D Project of Sichuan Province/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dyslipidemias/microbiology/epidemiology ; Male ; Cross-Sectional Studies ; Female ; *Life Style ; Middle Aged ; Adult ; *Metabolic Networks and Pathways ; Feces/microbiology/chemistry ; China ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metagenome ; Metabolomics ; Triglycerides/blood ; Aged ; }, abstract = {Whether the role of gut microbial features lies in the pathways from lifestyles to dyslipidemia remains unclear. In this cross-sectional study, we conducted a metagenome-wide association analysis and fecal metabolomic profiling in 994 adults from the China Multi-Ethnic cohort. A total of 26 microbial species were identified as mediators between lifestyle factors and risk for dyslipidemia. Specifically, the abundance of [Ruminococcus] gnavus mediated the associations between lifestyles and risks for dyslipidemia, elevated low-density lipoprotein cholesterol, elevated total cholesterol, and elevated triglycerides. [Ruminococcus] gnavus, Alistipes shahii, and Lachnospira eligens were replicated to be associated with dyslipidemia in an external validation cohort. The potential metabolic pathways included arachidonic acid, bile acid, and aromatic amino-acid metabolism.}, }
@article {pmid40436643, year = {2025}, author = {Li, J and Wu, Y and Yang, Y and Chen, L and He, C and Zhou, S and Huang, S and Zhang, X and Wang, Y and Gui, Q and Lu, H and Zhang, Q and Yang, Y}, title = {Metagenomics reveals an increased proportion of an Escherichia coli-dominated enterotype in elderly Chinese people.}, journal = {Journal of Zhejiang University. Science. B}, volume = {26}, number = {5}, pages = {477-492}, doi = {10.1631/jzus.B2400341}, pmid = {40436643}, issn = {1862-1783}, support = {82101665, 82271588, 82200665 and 82100795//the National Natural Science Foundation of China/ ; LY22H030009//the Zhejiang Provincial Natural Science Foundation of China/ ; 2023ZL480//the Zhejiang Provincial Science and Technology Program of Traditional Chinese Medicine/ ; 2023RC153//the Medical and Health Research Project of Zhejiang Province/ ; }, mesh = {Aged ; Aged, 80 and over ; Female ; Humans ; Male ; Middle Aged ; Bacteroides ; China ; Diabetes Mellitus, Type 2/microbiology ; *Escherichia coli/genetics/isolation &amp; purification/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; East Asian People ; }, abstract = {Gut microbial communities are likely remodeled in tandem with accumulated physiological decline during aging, yet there is limited understanding of gut microbiome variation in advanced age. Here, we performed a metagenomics-based enterotype analysis in a geographically homogeneous cohort of 367 enrolled Chinese individuals between the ages of 60 and 94 years, with the goal of characterizing the gut microbiome of elderly individuals and identifying factors linked to enterotype variations. In addition to two adult-like enterotypes dominated by Bacteroides (ET-Bacteroides) and Prevotella (ET-Prevotella), we identified a novel enterotype dominated by Escherichia (ET-Escherichia), whose prevalence increased in advanced age. Our data demonstrated that age explained more of the variance in the gut microbiome than previously identified factors such as type 2 diabetes mellitus (T2DM) or diet. We characterized the distinct taxonomic and functional profiles of ET-Escherichia, and found the strongest cohesion and highest robustness of the microbial co-occurrence network in this enterotype, as well as the lowest species diversity. In addition, we carried out a series of correlation analyses and co-abundance network analyses, which showed that several factors were likely linked to the overabundance of Escherichia members, including advanced age, vegetable intake, and fruit intake. Overall, our data revealed an enterotype variation characterized by Escherichia enrichment in the elderly population. Considering the different age distribution of each enterotype, these findings provide new insights into the changes that occur in the gut microbiome with age and highlight the importance of microbiome-based stratification of elderly individuals.}, }
@article {pmid40436596, year = {2025}, author = {Tan, G and Lin, K and Hu, M and Wang, Y and Li, X and Li, X and Chen, S and Zhang, Q and Zheng, Z}, title = {Uncovering the resistome and mobilome across different types of ready-to-eat fermented foods.}, journal = {Food research international (Ottawa, Ont.)}, volume = {213}, number = {}, pages = {116577}, doi = {10.1016/j.foodres.2025.116577}, pmid = {40436596}, issn = {1873-7145}, mesh = {*Fermented Foods/microbiology ; *Food Microbiology ; *Fast Foods/microbiology ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Dairy Products/microbiology ; Vegetables/microbiology ; }, abstract = {Antimicrobial resistance in food poses a significant threat to public health, and the persistence of antibiotic resistance genes (ARGs) in ready-to-eat fermented foods (RTE-FFs) is a growing concern. However, information on the diversity, origins, and transferability of ARGs in RTE-FFs is limited. This study investigated the distribution of ARGs and mobile genetic elements (MGEs) in four types of RTE-FFs: soybean, dairy, meat, and vegetable products. Using whole metagenomic sequencing, we identified significant variations in the bacterial diversity, ARG profiles, and MGE profiles among these food types. Bean-based RTE-FFs exhibited the highest diversity of ARGs and MGEs, while dairy products showed the lowest diversity (p < 0.05). Eight types of ARGs were significantly more prevalent in bean-based foods than in the other food categories (p < 0.05). Several ARGs were highly abundant in the RTE-FFs, including aphA2, blaTEM-116, PBP1a, PBP1b, OqxA, OqxBgb, lsa(A), tet(34), and tet(58). Plasmids carried the highest number of ARGs among all MGEs, particularly those associated with beta-lactam, macrolide-lincosamide-streptogramin, tetracycline, and aminoglycoside resistance, suggesting a higher risk with plasmid-mediated transfer, especially in bean-based RTE-FFs. Metagenomic binning analysis recovered 76 high-quality metagenome-assembled genomes (MAGs), including four novel species. A total of 13 types of ARGs, encompassing 95 subtypes, were identified across the MAGs; Bacillus paranthracis, Enterococcus casseliflavus, and Enterococcus gallinarum had the most ARGs (16, 12, and 14, respectively). Dairy RTE-FFs (yogurt and cheese) contained a high abundance of Streptococcus thermophilus resistant to beta-lactams (PBP1b) and tetracycline (tetB(60)), raising concerns about ARG transfer in these food products. Bean RTE-FFs (sufu) harbored two pathogenic Acinetobacter species carrying carbapenem resistance genes (blaOXA-180, blaOXA-211, and blaOXA-230). No ARGs were found in the MGEs (prophages, insertion sequences, or transposons) within the MAGs. Overall, our results provide valuable insights into the antibiotic resistome and mobilome of various RTE-FFs to inform food production and management practices.}, }
@article {pmid40436373, year = {2025}, author = {Vosough, M and Drees, F and Sieber, G and Stach, TL and Beisser, D and Probst, AJ and Boenigk, J and Schmidt, TC}, title = {Integrative Analysis of Nontargeted LC-HRMS and High-Throughput Metabarcoding Data for Aquatic Environmental Studies Using Combined Multivariate Statistical Approaches.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.5c00539}, pmid = {40436373}, issn = {1520-6882}, abstract = {Significant progress in high-throughput analytical techniques has paved the way for novel approaches to integrating data sets from different compartments. This study leverages nontarget screening (NTS) via liquid chromatography-high-resolution mass spectrometry (LC-HRMS), a crucial technique for analyzing organic micropollutants and their transformation products, in combination with biological indicators. We propose a combined multivariate data processing framework that integrates LC-HRMS-based NTS data with other high-throughput data sets, exemplified here by 18S V9 rRNA and full-length 16S rRNA gene metabarcoding data sets. The power of data fusion is demonstrated by systematically evaluating the impact of treated wastewater (TWW) over time on an aquatic ecosystem through a controlled mesocosm experiment. Highly compressed NTS data were compiled through the implementation of the region of interest-multivariate curve resolution-alternating least-squares (MCR-ALS) method, known as ROIMCR. By integrating ANOVA-simultaneous component analysis with structural learning and integrative decomposition (SLIDE), the innovative SLIDE-ASCA approach enables the decomposition of global and partial common, as well as distinct variation sources arising from experimental factors and their possible interactions. SLIDE-ASCA results indicate that temporal variability explains a much larger portion of the variance (74.6%) than the treatment effect, with both contributing to global shared space variation (41%). Design structure benefits include enhanced interpretability, improved detection of key features, and a more accurate representation of complex interactions between chemical and biological data. This approach offers a greater understanding of the natural and wastewater-influenced temporal patterns for each data source, as well as reveals associations between chemical and biological markers in an exemplified perturbed aquatic ecosystem.}, }
@article {pmid40435904, year = {2025}, author = {Liu, Z and Yan, K and Li, J and Zhang, C and Xu, D and Wang, Y and Xie, X and Li, H and Qie, J and Li, J and Dong, X and Dong, L and Cui, H}, title = {Acute appendicitis in children: Two microbial states associated with clinical indicators and severity.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {2}, pages = {116925}, doi = {10.1016/j.diagmicrobio.2025.116925}, pmid = {40435904}, issn = {1879-0070}, abstract = {BACKGROUND: Acute appendicitis (AA) is one of the most common abdominal emergencies worldwide. It is associated with dysbiosis and is usually classified clinically as either simple appendicitis (SA) or complicated appendicitis (CA) . The etiology and pathogenesis of AA remain incompletely understood.<br><br>METHODS: A total of 74 pediatric intra-abdominal pus samples from appendectomy cases (aged 3-15) were collected for AA at Tianjin Children's Hospital (Feb 2022-Sep 2023). The samples were categorised into two groups based on pathological findings: SA (n = 27) and CA (n = 47). Metagenomic profiling was employed to characterized the microbial composition and function in both groups. Additionally, clinical parameters associated with the microbiota were analysed.<br><br>RESULTS: The SA group exhibited higher levels of Burkholderia, Mycobacterium, and Klebsiella, while the CA group demonstrated higher levels of Porphyromonas, Bacteroides, Fusobacterium, Prevotella, and Tannerella. Additionaly, there were significant differences in clinical parameters, including C-reactive protein (CRP), procalcitonin (PCT), fibrinogen, sodium, potassium, phosphorus, complement C3, and chloride, between two groups. Furthermore, functional profiling revealed alterations in microbial metabolism and antibiotic resistance, highlighting the complex interplay between microbial communities and host inflammatory responses in appendicitis.<br><br>CONCLUSIONS: This study identifies unique microbial and serum biomarkers and their correlates in varying severities of acute appendicitis, highlighting the role of the microbiome in the aetiology of acute appendicitis.}, }
@article {pmid40435848, year = {2025}, author = {Jung, H and Park, S and Park, SA and Kim, H and Lee, M and Park, CH and Jegal, J and Shin, G and Kim, HJ}, title = {FDA-hydrolysis activity: A pre-screening tool for optimizing compost selection in standardized plastic biodegradation testing.}, journal = {Waste management (New York, N.Y.)}, volume = {204}, number = {}, pages = {114907}, doi = {10.1016/j.wasman.2025.114907}, pmid = {40435848}, issn = {1879-2456}, abstract = {Current ISO 14855-1 standards for assessing plastic biodegradability under composting conditions rely on physicochemical parameters, such as pH and volatile solids, to select compost inocula. However, these indicators do not directly reflect microbial activity, which is central to biodegradation processes. This study proposes fluorescein diacetate hydrolase (FDA-H) activity as a rapid, integrative biological indicator to pre-screen composts before standardized biodegradation testing. FDA-H activity was measured in five composts and showed a strong correlation with early CO2 evolution (r = 0.93), reflecting initial microbial metabolic potential. Moderate correlations were also observed with final biodegradation rates of cellulose and polybutylene succinate (PBS), suggesting that microbial community shifts and substrate-specific adaptation influence long-term outcomes. Metagenomic analysis supported this by revealing distinct microbial succession patterns during degradation, especially for synthetic polymers. We also compared FDA-H with standardized microbial activity assays, including respiration and dehydrogenase activity. Unlike these methods, FDA-H captures extracellular hydrolytic enzyme activity relevant to polymer breakdown and offers advantages in speed and operational simplicity. While FDA-H does not replace ISO/OECD biodegradation standards, it complements them by providing early-stage insight into compost suitability. Integrating FDA-H into existing testing frameworks could enhance the reliability, efficiency, and biological relevance of compost selection, ultimately improving standardized biodegradation assessments.}, }
@article {pmid40435563, year = {2025}, author = {García-Pérez, P and Tomas, M and Giuberti, G and Capanoglu, E and Callegari, ML and Lucini, L and Patrone, V}, title = {Brassica microgreens shape gut microbiota and functional metabolite profiles in a species-related manner: A multi-omics approach following in vitro gastrointestinal digestion and large intestine fermentation.}, journal = {Microbiological research}, volume = {298}, number = {}, pages = {128226}, doi = {10.1016/j.micres.2025.128226}, pmid = {40435563}, issn = {1618-0623}, abstract = {Brassicaceae microgreens constitute a novel and promising source of bioactive compounds, such as polyphenols and glucosinolates. In this work, an integrative computational approach was performed to decipher the interaction between bioaccessible microgreen metabolites and human gut bacteria. To this end, in vitro gastrointestinal digestion and large intestine fermentation were performed on eight different microgreens, which were further subjected to a dual high-throughput approach that combined fecal metagenomics and untargeted metabolomics. Data reveal a significant correlation between Parabacteroides merdae and two isothiocyanates in arugula fermentates, suggesting a high bioaccessibility of these bioactive compounds. Meanwhile, two species of Roseburia were correlated with pseudooxynicotine, an anti-inflammatory catabolite of nicotine in Brassica oleracea fermentates (such as broccoli, Brussels sprouts, and red cabbage), coupled with an increase in short-chain fatty acid production. These findings confer evidence on the nutritional impact of microgreens consumption, revealing the most bioaccessible metabolites with associated health-promoting properties together with their participation in the shaping of gut microbial populations, possibly leading to prebiotic effects.}, }
@article {pmid40434915, year = {2025}, author = {Kuntz, TM and Liu, L and Wang, K and Everett, C and Eliassen, AH and Willett, WC and Sinha, R and Chan, AT and Rimm, EB and Garrett, WS and Segata, N and Piccinno, G and Huttenhower, C and Morgan, X and Song, M}, title = {Comparing the metagenomic performance of stools collected from custom cards and 95% ethanol in epidemiologic studies.}, journal = {Cancer epidemiology, biomarkers &amp; prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {}, number = {}, pages = {}, doi = {10.1158/1055-9965.EPI-25-0157}, pmid = {40434915}, issn = {1538-7755}, abstract = {Background Stool cards have been used for microbiome assessment in epidemiological studies. Methods We compared shotgun metagenomic sequencing from 32 participants who self-collected stool samples from the same bowel movement using a custom stool card vs. a collection tube with 95% ethanol fixative in the Nurses' Health Study II. We evaluated the agreement between methods at both the whole-community and individual species levels. To contextualize the comparison for disease association studies, we assessed the performance of the two collection methods for differentiating colorectal cancer-associated taxa. Results Overall, metagenomes from cards and 95% ethanol were highly correlated within individuals. No difference was found in alpha diversity and only ~1% of variation in beta diversity was explained by the collection method. At the species level, while the relative abundances were highly correlated between card and ethanol sample pairs (Spearman rho = 0.96), 10 (out of 239) species showed a differential abundance in paired samples, including overrepresentation of Escherichia coli and underrepresentation of three Streptococcus species in cards compared with ethanol. Among a set of 99 colorectal cancer-associated species, 4 showed differential abundances between collection methods; however, this number was consistent with what would be expected by chance. Conclusions Metagenomic sequencing using stool samples self-collected using stool cards or 95% ethanol yielded largely consistent results, although differential abundances were observed for a small number of individual species. Impact Stool cards can be a cost-effective alternative to collect stool samples for metagenomic sequencing in epidemiologic studies but warrant additional considerations for data analysis.}, }
@article {pmid40434822, year = {2025}, author = {Berelson, MFG and Heavens, D and Nicholson, P and Clark, MD and Leggett, RM}, title = {From air to insight: the evolution of airborne DNA sequencing technologies.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {5}, pages = {}, doi = {10.1099/mic.0.001564}, pmid = {40434822}, issn = {1465-2080}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Sequence Analysis, DNA/methods ; *DNA, Environmental/genetics/analysis/isolation &amp; purification ; Humans ; Environmental Monitoring/methods ; Computational Biology/methods ; Biodiversity ; }, abstract = {Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.}, }
@article {pmid40434093, year = {2025}, author = {Koldaş, SS and Sezerman, OU and Timuçin, E}, title = {Exploring the role of microbiome in cystic fibrosis clinical outcomes through a mediation analysis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019625}, doi = {10.1128/msystems.00196-25}, pmid = {40434093}, issn = {2379-5077}, abstract = {UNLABELLED: Human microbiome plays a crucial role in host health and disease by mediating the impact of environmental factors on clinical outcomes. Mediation analysis is a valuable tool for dissecting these complex relationships. However, existing approaches are primarily designed for cross-sectional studies. Modern clinical research increasingly utilizes long follow-up periods, leading to complex data structures, particularly in metagenomic studies. To address this limitation, we introduce a novel mediation framework based on structural equation modeling that leverages linear mixed-effects models using penalized quasi-likelihood estimation with a debiased lasso. We applied this framework to a 16S rRNA sputum microbiome data set collected from patients with cystic fibrosis over 10 years to investigate the mediating role of the microbiome in the relationship between clinical states, disease aggressiveness phenotypes, and lung function. We identified richness as a key mediator of lung function. Specifically, Streptococcus was found to be significantly associated with mediating the decline in lung function on treatment compared to exacerbation, while Gemella was associated with the decline in lung function on recovery. This approach offers a powerful new tool for understanding the complex interplay between microbiome and clinical outcomes in longitudinal studies, facilitating targeted microbiome-based interventions.<br><br>IMPORTANCE: Understanding the mechanisms by which the microbiome influences clinical outcomes is paramount for realizing the full potential of microbiome-based medicine, including diagnostics and therapeutics. Identifying specific microbial mediators not only reveals potential targets for novel therapies and drug repurposing but also offers a more precise approach to patient stratification and personalized interventions. While traditional mediation analyses are ill-equipped to address the complexities of longitudinal metagenomic data, our framework directly addresses this gap, enabling robust investigation of these increasingly common study designs. By applying this framework to a decade-long cystic fibrosis study, we have begun to unravel the intricate relationships between the sputum microbiome and lung function decline across different clinical states, yielding insights that were previously unknown.}, }
@article {pmid40434086, year = {2025}, author = {Nieves-Morales, R and Paez-Diaz, JA and Rodriguez-Carrio, SM and Melendez Martinez, G and Rivera-Lopez, EO and Rodríguez-Ramos, J and García-Arrarás, JE and Rios-Velazquez, C}, title = {Intestinal microbiome profile of the brown rock sea cucumber (Holothuria glaberrima) using ITS and 16S rDNA amplicons from direct mechanical, enzymatic, and chemical metagenomic extraction.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0029325}, doi = {10.1128/mra.00293-25}, pmid = {40434086}, issn = {2576-098X}, abstract = {Using direct mechanical, enzymatic, and chemical extraction methods, the intestinal microbiome of the marine invertebrate Holothuria glaberrima was obtained. ITS and 16S rDNA regions were sequenced to enrich and investigate the prokaryotic and fungal diversity profiles from different anatomical regions within the sea cucumber's intestinal biology.}, }
@article {pmid40434078, year = {2025}, author = {Weisse, L and Martin, L and Moumen, B and Héchard, Y and Delafont, V}, title = {Environmental diversity of Candidatus Babelota and their relationships with protists.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0026125}, doi = {10.1128/msystems.00261-25}, pmid = {40434078}, issn = {2379-5077}, abstract = {Ca. Babelota is a phylum of strictly intracellular bacteria whose representatives are commonly detected in various environments through metagenomics, though their presence, ecology, and biology have never been addressed so far. As a group of strict intracellular, we hypothesize that their presence, occurrence, and abundance heavily depend on their hosts, which are known as heterotrophic protists, based on few described isolates. Here, we conducted a sampling campaign allowing to characterize protists and associated bacterial communities, using high-throughput sequencing. In parallel, a systematic enrichment of protists from samples was performed to attempt characterization and isolation of new Ca. Babelota within native hosts. We found that Ca. Babelota are among the most widespread phylum among the rare ones. Protist enrichments are allowed in certain cases to enrich as well for Ca. Babelota, which could be visualized in vivo infecting protist cells. Though cosmopolitan, Ca. Babelota diversity was highly site-specific. Cooccurrence analyses allowed to retrieve well-known as well as new putative associations involving numerous protists of various trophic regimes. The combination of approaches developed in this study enhances our understanding of Ca. Babelota ecology and biology, while paving the way for future isolation of new members of this elusive phylum, which could have huge impact on protists-and ecosystems-functioning.IMPORTANCEOur understanding of microbial diversity surrounding us and colonizing the environment has been dramatically impacted by the advent of DNA-based analyses. Such progress helped shine a new light on numerous lineages of yet-to-be-characterized microbes, whose ecology and biology are basically unknown. Among those uncharacterized clades is the Candidatus Babelota, a bacterial phylum for which parasitism seems to be an ancestral trait. All known Ca. Babelota thrive by infecting phagotrophic protist hosts, thereby impacting this basal link of the trophic chain. The Ca. Babelota constitutes a model that stands out, as phylum-wide conserved parasitism has only been described in one previous occurrence for Bacteria, with the Chlamydiota. Thus, exploring the intricate interplay between Ca. Babelota and their protist hosts will advance our knowledge of bacterial diversity, their ecology, and global impact on ecosystem functioning.}, }
@article {pmid40434009, year = {2025}, author = {Chen, ZY and Gao, FZ and Bai, H and Zhang, M and He, LY and Liu, YS and Ying, GG}, title = {Key Contribution and Risk of Airborne Antibiotic Resistance: Total Suspended Particles or Settled Dust?.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c11038}, pmid = {40434009}, issn = {1520-5851}, abstract = {The atmosphere is an important environmental medium in spreading antimicrobial resistance (AMR) in animal farming systems, yet the exposure risks associated with airborne pathways remain underexplored. This study employed metagenomic sequencing to investigate the airborne transmission of AMR in chicken farms (i.e., chicken feces, total suspended particles (TSP), and dust) and its exposure risks on the gut and nasal cavities of workers, office staff, and nearby villagers. Results revealed that TSP exhibited greater abundance, diversity, and transfer potential of antibiotic resistance genes (ARGs) compared to dust. The abundance of airborne resistome decreased with distance from the chicken house, and ARGs were estimated to spread up to 9.48 km within 1 h. While the gut resistome of workers and villagers showed limited differences, emerging tet(X) variants and high-risk dfrA remain future concerns. More nasal resistome was attributable to TSP compared to dust. Workers faced significantly higher inhalable exposures to antibiotic-resistant bacteria (ARB) and human pathogenic antibiotic-resistant bacteria (HPARB), exceeding those of office staff and villagers by an order of magnitude. We also compiled lists of high-risk and potential-risk airborne ARGs to inform monitoring. These findings highlight the need for regular air disinfection in animal farms and better protective measures for workers.}, }
@article {pmid40433987, year = {2025}, author = {Zhou, Z and Yang, M and Fang, H and Zhang, B and Ma, Y and Li, Y and Liu, Y and Cheng, Z and Zhao, Y and Si, Z and Zhu, H and Chen, P}, title = {Tailoring a Functional Synthetic Microbial Community Alleviates Fusobacterium nucleatum-infected Colorectal Cancer via Ecological Control.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e14232}, doi = {10.1002/advs.202414232}, pmid = {40433987}, issn = {2198-3844}, support = {24ZDFA001//Gansu Provincial Science and Technology Major Project/ ; 2024-8-27//Lanzhou Municipal Science and Technology Program/ ; 2024-8-30//Lanzhou Municipal Science and Technology Program/ ; 2024-4-2//Lanzhou Municipal Science and Technology Program/ ; 20250260006//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; 20250260016//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; 20250260020//College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; }, abstract = {Polymorphic microbiomes play important roles in colorectal cancer (CRC) occurrence and development. In particular, Fusobacterium nucleatum (F. nucleatum) is prevalent in patients with CRC, and eliminating it is beneficial for treatment. Here, multiple metagenomic sequencing cohorts are combined with multiomics to analyze the microbiome and related functional alterations. Furthermore, local human metagenome and metabolomics are used to discover commensal consortia. A synthetic microbial community (SynCom) is then designed by metabolic network reconstruction, and its performance is validated using coculture experiments and an AOM-DSS induced mouse CRC model. The sequencing result shows that F. nucleatum is more abundant in both the feces and tumor tissues of CRC patients. It causes alterations through various pathways, including microbial dysbiosis, lipid metabolism, amino acid metabolism, and bile acid metabolism disorders. The designed SynCom contains seven species with low competition interrelationship. Furthermore, the SynCom successfully inhibits F. nucleatum growth in vitro and achieves colonization in vivo. Additionally, it promotes F. nucleatum decolonization, and enhances tryptophan metabolism and secondary bile acid conversion, leading to reduced lipid accumulation, decreased inflammatory reaction, and enhanced tumor inhibition effect. Overall, the bottom-up designed SynCom is a controllable and promising approach for treating F. nucleatum-positive CRC.}, }
@article {pmid40433668, year = {2025}, author = {von Ameln Lovison, O and Zempulski Volpato, FC and Weber, LG and Barth, AL and Simon Coitinho, A and Martins, AF}, title = {Unveiling the role of the upper respiratory tract microbiome in susceptibility and severity to COVID-19.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1531084}, pmid = {40433668}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/microbiology/pathology/virology ; Cross-Sectional Studies ; Disease Susceptibility ; *Microbiota ; SARS-CoV-2 ; Female ; Male ; Severity of Illness Index ; Middle Aged ; *Respiratory System/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Biomarkers ; Aged ; }, abstract = {It is argued that commensal bacteria in the upper respiratory tract (URT) protect against pathogen colonization and infection, including respiratory viruses. Given that the microbiome can mediate immune modulation, a link between the URT microbiome (URTM) and COVID-19 susceptibility and severity is expected. This 16S metagenomics cross-sectional study assessed URTM composition, metabolic prediction, and association with laboratory biomarkers in non-COVID-19 pneumonia (NO-CoV), moderate (M-CoV), severe (S-CoV) COVID-19 patients, as well as COVID-19-negative, asymptomatic (NC) patients. The S-CoV group exhibited reduced URTM diversity, primarily due to a decreased abundance of eubiotic taxa. Some of these taxa (e.g., Haemophilus sp., Neisseria sp.) were also associated with inflammatory biomarkers. Multiple metabolic pathways (e.g., short-chain fatty acids, vitamin B12) linked to immune response, antiviral activity, and host susceptibility showed decreased abundance in S-CoV. These pathways could suggest potential alternatives for the therapeutic arsenal against COVID-19, providing reassurance about the progress in understanding and treating this disease.}, }
@article {pmid40433443, year = {2025}, author = {Dahal, U and Bansal, A}, title = {Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.}, journal = {Current genomics}, volume = {26}, number = {2}, pages = {81-94}, pmid = {40433443}, issn = {1389-2029}, abstract = {Analyzing prokaryotic codon usage trends has become a crucial topic of study with significant ramifications for comprehending microbial genetics, classification, evolution, and the control of gene expression. This review study explores the numerous facets of prokaryotic codon usage patterns, looking at different parameters like habitat and lifestyle across broad groups of prokaryotes by emphasizing the role of codon reprogramming in adaptive strategies and its integration into systems biology. We also explored the numerous variables driving codon usage bias, including natural selection, mutation, horizontal gene transfer, codon-anticodon interaction, and genomic composition in prokaryotes through a thorough study of current literature. Furthermore, a special session on codon usage on pathogenic prokaryotes and the role of codon usage in the phylogeny of prokaryotes has been discussed. We also looked at the various software and indices that have been recently applied to prokaryotic genomes. The promising directions that lay ahead to map the future of codon usage research on prokaryotes have been emphasized. Codon usage variations across prokaryotic communities could be better understood by combining environmental, metagenomic, and system biology approaches.}, }
@article {pmid40432811, year = {2025}, author = {Wang, H and Zhao, J and Wang, X and Li, M and Hu, T and Xu, H and Dong, M and He, W and Che, Z}, title = {Diagnostic Performance of Clinical Metagenomic Next-Generation Sequencing for Suspected Central Nervous System Infections in a Municipal Hospital: A Retrospective Study in China.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {2637-2652}, pmid = {40432811}, issn = {1178-6973}, abstract = {PURPOSE: Cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) has the potential to identify the majority of pathogens in a single test. Accurate pathogen identification is vital for central nervous system infection (CNSi). However, there are few related studies investigating in a municipal hospital.<br><br>PATIENTS AND METHODS: A total of 52 suspected CNSi patients were retrospectively recruited in Xinxiang central hospital between July 2019 and April 2023. The diagnostic performance of CSF mNGS, conventional microbiological tests (CMT), and the combination of CSF mNGS and CMT were evaluated by comparing to the final diagnosis.<br><br>RESULTS: Among 52 suspected CNSi patients, 35 were diagnosed as CNSi. In comparison to the final diagnosis, the area under curves (AUC) for CSF CMT, CSF mNGS, and the combination of CMT and mNGS for the diagnosis of CNSi were 0.56 (95% CI 0.4-0.72), 0.74 (95% CI 0.61-0.84), and 0.76 (95% CI 0.63-0.88), respectively. The sensitivities were 11.43% (95% CI 4.54%-25.95%), 48.57% (95% CI 32.99%-64.43%), and 51.43% (95% CI 35.57%-67.01%), respectively. The accuracy was 40.38 (95% CI 27.01%-54.90%), 65.38% (95% CI 50.91%-78.03%), and 67.31% (95% CI 52.89%-79.67%), respectively. Furthermore, based on CSF mNGS results, seven patients confirmed initial treatment, two escalated, and one de-escalated. Additionally, we identified the optimal cutoff values as 1.75 U/L for CSF adenosine deaminase (ADA), 75.44 U/L for CSF protein, and 185 mmH2O for CSF pressure, when these values were exceeded, CSF mNGS tended to yield positive results.<br><br>CONCLUSION: CSF mNGS showed superior diagnostic performance in CNSi and hence could serve as a complementary tool to CMT and conjunctively guide the precision therapy. Additionally, the values for CSF ADA, protein and pressure could assist in predicting mNGS positive result. With technical improvements for mNGS sample processing to increase throughput and reduce costs, clinicians may use mNGS more widely in municipal hospital laboratories.}, }
@article {pmid40431707, year = {2025}, author = {Fougere, GC and Xu, D and Gaiero, JR and McCreary, C and Marchand, G and Despres, C and Wang, A and Fall, ML and Griffiths, JS}, title = {Genomic Diversity of Tomato Brown Rugose Fruit Virus in Canadian Greenhouse Production Systems.}, journal = {Viruses}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/v17050696}, pmid = {40431707}, issn = {1999-4915}, support = {J-003395//Agriculture and Agri-Food Canada/ ; J-002497//Agriculture and Agri-Food Canada/ ; }, mesh = {*Solanum lycopersicum/virology ; *Plant Diseases/virology ; Phylogeny ; *Genome, Viral ; Canada ; *Genetic Variation ; *Tobamovirus/genetics/classification ; Genomics ; }, abstract = {Tomato brown rugose fruit virus (ToBRFV) is a recently emerged viral pathogen in the Tobamovirus genus first observed in 2014 in the Middle East that has since spread worldwide, causing significant losses in greenhouse tomato production. ToBRFV is easily mechanically transmitted and can escape the durable Tm-2[2] resistance gene, facilitating its global spread. Seed companies have identified novel sources of resistance and introduced these resistance traits into commercial cultivars. The identity, number, and mechanisms of these putative novel resistance genes are largely unknown but could be exerting selective pressures on ToBRFV. Here, we report 15 new ToBRFV genomic sequences from Canadian greenhouse production systems in susceptible and novel resistant or tolerant cultivars collected since 2023. We combined these sequences with five other Canadian ToBRFV genomes previously deposited in Genbank and a further five consensus sequences derived from metagenomic-based wastewater monitoring sequence data and conducted phylogenetic analysis. Most Canadian sequences grouped together when compared with 332 publicly available international sequences, but several isolates appeared distantly related, suggesting multiple introductions to Canadian production systems. High sequence identity between samples suggest movement of ToBRFV between independent greenhouses, highlighting areas where biosecurity can be improved. Several novel non-synonymous polymorphisms identified in the p126 and movement protein (MP) open reading frames (ORFs) were unique to Canadian sequences and associated with infection of novel resistant tomato cultivars. Many polymorphisms in the p126 ORF are located in a region of the protein associated with Tm-1 resistance-breaking isolates of tomato mosaic virus and ToBRFV, but have not been previously reported. Four novel polymorphisms in MP were also identified and do not appear to be associated with sites previously identified as interacting with Tm-2[2] and could be related to other unknown resistance genes. Together, these results confirm the difficulties in preventing the transmission of ToBRFV, identify putative adaptations to novel and existing resistance genes, and emphasize the urgent need for the cloning and characterization of these new sources of resistance to ToBRFV.}, }
@article {pmid40431691, year = {2025}, author = {Penzes, JJ and Kaelber, JT}, title = {Capsid Structure of the Fish Pathogen Syngnathus Scovelli Chapparvovirus Offers a New Perspective on Parvovirus Structural Biology.}, journal = {Viruses}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/v17050679}, pmid = {40431691}, issn = {1999-4915}, mesh = {Animals ; *Capsid/chemistry/ultrastructure ; *Capsid Proteins/chemistry/genetics ; *Parvovirus/ultrastructure/genetics/chemistry ; *Parvoviridae Infections/veterinary/virology ; *Fish Diseases/virology ; Models, Molecular ; Cryoelectron Microscopy ; Phylogeny ; }, abstract = {Chapparvoviruses (ChPVs) comprise a divergent lineage of the Parvoviridae ssDNA virus family and evolved to infect vertebrate animals independently from the Parvovirinae subfamily. Despite being pathogenic and widespread in environmental samples and metagenomic assemblies, their structural characterization has proven challenging. Here, we report the first structural analysis of a ChPV, represented by the fish pathogen, Syngnathus scovelli chapparvovirus (SsChPV). We show through the SsChPV structure that the lineage harbors a surface morphology, subunit structure, and multimer interactions that are unique among parvoviruses. The SsChPV capsid evolved a threefold-related depression of α-helices that is analogous to the β-annulus pore of denso- and hamaparvoviruses and may play a role in monomer oligomerization during assembly. As interacting β-strands are absent from the twofold symmetry axis, the viral particle lacks the typical stability and resilience of parvovirus capsids. Although all parvoviruses thus far rely on the threading of large, flexible N-terminal domains to the capsid surface for their intracellular trafficking, our results show that ChPVs completely lack any such N-terminal sequences. This led to the subsequent degradation of their fivefold channel, the site of N-terminus externalization. These findings suggest that ChPVs harbor an infectious pathway that significantly deviates from the rest of the Parvoviridae.}, }
@article {pmid40431505, year = {2025}, author = {Zhang, R and Hu, W and Zhong, S and Chen, W and Chen, M and Yu, Q}, title = {Impact of Enterococcus faecium Kimate-X on Reducing Stress in Dogs Through Gut Microbiota Modulation.}, journal = {Veterinary sciences}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/vetsci12050412}, pmid = {40431505}, issn = {2306-7381}, abstract = {Stress in dog breeding leads to significant physiological and psychological burdens, including anxiety, reduced appetite, weakened immune function, gut microbiota imbalance, and even death. Currently, there are various pharmacological interventions for stress management, but few focus on gut health. This study evaluates the potential of a novel strain, Enterococcus faecium Kimate-X, in alleviating transport stress and improving gut health in dogs, providing an alternative to traditional pharmacological treatments. In vitro experiments showed that Kimate-X significantly enhanced the activities of superoxide dismutase (SOD) and catalase (CAT) while reducing the levels of malondialdehyde (MDA) and tumor necrosis factor-α (TNF-α) in RAW 264.7 macrophage cells. In vivo, dogs supplemented with Kimate-X exhibited significantly lower cortisol levels after transport, indicating reduced stress. Metagenomic analysis revealed increased gut microbiota diversity and higher concentrations of short-chain fatty acids (acetate, propionate, and butyrate) in fecal samples. This study systematically uncovers the mechanism by which Enterococcus faecium Kimate-X alleviates transport stress through modulation of the gut microbiota. These findings provide new scientific evidence supporting the use of probiotics as a novel approach to stress management in animals.}, }
@article {pmid40431358, year = {2025}, author = {Yue, Y and Yang, HJ and Li, C and Ryu, MS and Seo, JW and Jeong, DY and Park, S}, title = {Beneficial Effects of Traditional Fermented Soybean Sauce (Kanjang) on Memory Function, Body Water, and Glucose Metabolism: Roles of Gut Microbiota and Neuroinflammation.}, journal = {Nutrients}, volume = {17}, number = {10}, pages = {}, doi = {10.3390/nu17101617}, pmid = {40431358}, issn = {2072-6643}, support = {2023-3//functional research of fermented soybean food (safety monitoring)" under the Ministry of Agriculture, Food and Rural Affairs/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Male ; Rats, Sprague-Dawley ; *Soy Foods/microbiology ; Rats ; *Memory/drug effects ; *Neuroinflammatory Diseases ; *Glucose/metabolism ; Scopolamine ; *Fermented Foods ; Water/metabolism ; Neuroprotective Agents/pharmacology ; *Glycine max ; Fermentation ; }, abstract = {Background: Traditional fermented soybean foods, acting as potential synbiotics, may help mitigate cognitive impairment associated with amnesia. This study investigated the neuroprotective effects of four kanjang (Korean fermented soy sauce) varieties and their underlying mechanisms. Methods: Male Sprague Dawley rats (n = 70) were divided into seven groups: normal control, scopolamine control, positive control (1 mg/kg bw/day of donepezil), and four scopolamine-treated groups receiving different kanjang varieties (0.5% in high-fat diet). Based on their Bacillus content, the kanjang samples were categorized as traditionally made kanjang (TMK) with high Bacillus (SS-HB), TMK with medium Bacillus (SS-MB), TMK with low Bacillus (SS-LB), and factory-made kanjang (SS-FM). Results: Scopolamine administration disrupted energy, glucose, and water metabolism and impaired memory function (p < 0.05). All kanjang treatments improved insulin sensitivity, reduced inflammation, enhanced glucose tolerance, and decreased visceral fat. SS-MB, SS-HB, and SS-FM increased skeletal muscle mass. They maintained body water homeostasis by suppressing the renin-angiotensin-aldosterone system. Kanjang treatments improved memory function, with SS-FM showing the least significant effects. The treatments reduced neuronal cell death in the hippocampal CA1 region, decreased acetylcholinesterase activity, and increased brain-derived neurotrophic factor mRNA expression. Gut microbiota analysis revealed that kanjang treatments increased Lactobacillaceae and decreased Lachnospiraceae, with SS-HB and SS-LB specifically elevating Ligilactobacillus. Metagenomic analysis demonstrated enhanced glycolysis/gluconeogenesis pathways and enhanced butanoate metabolism while reducing lipopolysaccharide biosynthesis and pro-inflammatory signaling. SS-MB and SS-LB increased intestinal goblet cell counts and the serum butyrate concentration. Conclusions: These findings suggest that kanjang consumption, particularly SS-HB and SS-LB varieties, can ameliorate memory impairment in this murine model through multiple mechanisms: metabolic improvements, enhanced neurotrophic signaling, gut microbiota modulation, and reduced neuroinflammation via gut-brain axis activation. Human clinical trials are warranted to determine if these promising neuroprotective effects translate to clinical applications.}, }
@article {pmid40431314, year = {2025}, author = {Li, B and Gesang, Q and Sun, Y and Wang, Y and Nan, J and Xu, J}, title = {Soil Microbial Adaptation and Biogeochemical Feedback in Degraded Alpine Meadows of the Qinghai-Tibetan Plateau.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13051142}, pmid = {40431314}, issn = {2076-2607}, support = {XZ202401YD0026//Science and Technology Projects of Xizang Autonomous Region, China/ ; }, abstract = {Alpine meadows on the Qinghai-Tibetan Plateau are experiencing rapid degradation due to climate change and anthropogenic disturbances, leading to severe ecological consequences. In this study, we investigated the response of soil microbial communities and their metabolic functions across a degradation gradient using metagenomic sequencing and comprehensive soil physicochemical analysis in the city of Lhasa, China. Results showed that soil pH increased with degradation, while most nutrients, including different forms of nitrogen, phosphorus, and potassium, declined. pH, ammonium nitrogen, and organic matter were identified as key factors driving degradation dynamics. Microbial community composition shifted markedly, with distinct biomarker taxa emerging at different degradation levels. Network analysis revealed a progressive loss of microbial connectivity, with Actinobacteria dominance increasing in heavily degraded soils, while cross-phylum interactions weakened. Functional analysis of biogeochemical cycling genes showed that carbon, nitrogen, and phosphorus cycling were all disrupted by degradation, but each exhibited unique response patterns. These findings will extend our understanding of microbial-mediated soil processes under degradation and provide a scientific foundation for ecosystem management, conservation, and targeted restoration strategies in alpine meadows.}, }
@article {pmid40431310, year = {2025}, author = {Castaño-Jiménez, PA and Baltazar-Díaz, TA and González-Hernández, LA and García-Salcido, R and Klimov-Kravtchenko, K and Andrade-Villanueva, JF and Arellano-Arteaga, KJ and Padilla-Sánchez, MP and Del Toro-Arreola, S and Bueno-Topete, MR}, title = {Deciphering the Language of Intestinal Microbiota Associated with Sepsis, Organ Failure, and Mortality in Patients with Alcohol-Related Acute-on-Chronic Liver Failure (ACLF): A Pioneer Study in Latin America.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13051138}, pmid = {40431310}, issn = {2076-2607}, support = {P3E 277752-2024//Universidad de Guadalajara/ ; }, abstract = {ACLF is a severe stage of liver cirrhosis, characterized by multiple organ failure, systemic inflammation, and high short-term mortality. The intestinal microbiota (IM) influences its pathophysiology; however, there are currently no studies in Latin American populations. Therefore, we analyzed IM and its relationships with sepsis, organ failure, and mortality. In parallel, we quantified serum lipopolysaccharides as a marker of bacterial translocation. Fecal samples from 33 patients and 20 healthy controls (HCs) were obtained. The IMs were characterized by 16S-rRNA amplicon sequencing, the metagenomic functional predictive profiles were analyzed by PICRUSt2, and LPS quantification was performed by ELISA. Patients with ACLF showed significant alterations in alpha and beta diversity compared to the HCs. A strong dominance index accurately predicted 28-day and 90-day mortalities. The IMs showed a polarization toward Proteobacteria associated with increased LPS. The LPS correlated with clinical severity, organ dysfunction, and higher pathogenic taxa. The Klebsiella/Faecalibacterium ratio showed good performance in identifying sepsis (AUROC = 0.83). Furthermore, Morganella, Proteus, and Klebsiella were enriched in patients with multiorgan failure. Lactobacillus, Escherichia/Shigella, Veillonella, and Ruminococcus gnavus exhibited potential in predicting 28- and 90-day mortalities. The IM alterations in ACLF may be useful as clinical biomarkers of poor prognosis, primarily for mortality and sepsis. These findings are representative of western Mexico.}, }
@article {pmid40431283, year = {2025}, author = {Huang, J and Sheng, Y and Jia, X and Qian, W and Li, Z}, title = {Comparative Analysis of Microbial-Short-Chain Fatty Acids-Epithelial Transport Axis in the Rumen Ecosystem Between Tarim Wapiti (Cervus elaphus yarkandensis) and Karakul Sheep (Ovis aries).}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13051111}, pmid = {40431283}, issn = {2076-2607}, abstract = {Under long-term ecological stress, the Tarim wapiti (Cervus elaphus yarkandensis) has evolved unique adaptations in digestive physiology and energy metabolism. A multi-omics comparison of three Tarim wapiti and five Karakul sheep was used to examine the synergistic mechanism between rumen bacteria, short-chain fatty acids, and host epithelial regulation in order to clarify the mechanism of high roughage digestion efficiency in Tarim wapiti. Metagenomic sequencing (Illumina NovaSeq 6000) and gas chromatography revealed that Tarim wapiti exhibited significantly higher acetate and total VFA (TVFA) concentrations compared to Karakul sheep (p < 0.01), accompanied by lower ruminal pH and propionate levels. Core microbiota analysis identified Bacteroidetes (relative abundance: 52.3% vs. 48.1%), Prevotellaceae (22.7% vs. 19.4%), and Prevotella (18.9% vs. 15.6%) as dominant taxa in both species, with significant enrichment of Bacteroidetes in wapiti (p < 0.01). Functional annotation (PICRUSt2) demonstrated enhanced glycan biosynthesis (KEGG ko00511), DNA replication/repair (ko03430), and glycoside hydrolases (GH20, GH33, GH92, GH97) in wapiti (FDR < 0.05). Transcriptomic profiling (RNA-Seq) of rumen epithelium showed upregulated expression of SCFA transporters (PAT1: 2.1-fold, DRA: 1.8-fold, AE2: 2.3-fold; p < 0.01) and pH regulators (Na[+]/K[+] ATPase: 1.7-fold; p < 0.05) in wapiti. Integrated analysis revealed coordinated microbial-host interactions through three key modules: (1) Bacteroidetes-driven polysaccharide degradation, (2) GHs-mediated fiber fermentation, and (3) epithelial transporters facilitating short-chain fatty acids absorption. These evolutionary adaptations, particularly the Bacteroidetes-short-chain fatty acids-transporter axis, likely underpin the wapiti's superior roughage utilization efficiency, providing molecular insights for improving ruminant feeding strategies in an arid environment.}, }
@article {pmid40431261, year = {2025}, author = {Mendes Silva Cruz, A and Cardoso, JF and Pinheiro, KC and Ferreira, JA and Barbagelata, LS and Silva, SP and Chagas Junior, WD and Lobo, PS and Teixeira, DM and André Junior, W and Ordenes Silva, I and Santos, MC and Soares Farias, LS and Sousa, MS and Neto Tavares, F}, title = {Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13051088}, pmid = {40431261}, issn = {2076-2607}, support = {4648 MPT/IEC/FADESP//Public Ministry of Labor through the Research Support and Development Foudation/ ; 159996/2021-0//National Council for Scientific and Technological Development/ ; NU2GGH002174/CC/CDC HHS/United States ; NU2GGH002174//Funda&#xe7;&#xe3;o Oswaldo Cruz/ ; }, abstract = {It is important to understand which bacterial taxa are most abundant during SARS-CoV-2 infection and to promote mitigation strategies for conditions subsequent to infection. Nasopharyngeal swab samples were collected from patients infected with SARS-CoV-2 and their family contacts (uninfected and asymptomatic) during the outbreak of the P.1 variant of SARS-CoV-2 in Parintins, Amazonas-Brazil, in March 2021. The samples were investigated by a shotgun sequencing metagenomic approach using the NextSeq 500 Illumina® system. The samples were stratified according to the presence or absence of SARS-CoV-2, household group, sex, and age. Of the total of 63 individuals, 37 (58.73%) were positive for SARS-CoV-2 and 26 (41.27%) were negative for SARS-CoV-2 and other respiratory viruses (FLU, AdV, HBoV, HCoV, HMPV, RSV, PIV, HRV). The alpha diversity indexes Chao1, species observed, Simpson, and Inv Simpson demonstrated a significant difference (p < 0.05) in both the diversity of observed species and the abundance of some taxa between positive and negative individuals. We also observed an abundance of opportunists such as Klebsiella pneumoniae, Staphylococcus spp, and Shigella sonnei, previously associated with the severity of COVID-19. Our results suggest that SARS-CoV-2 infection causes changes in the microenvironment of the nasopharyngeal region, allowing greater proliferation of opportunistic bacteria and decreased abundance of commensal bacteria.}, }
@article {pmid40431220, year = {2025}, author = {Goldiș, A and Dragomir, R and Mercioni, MA and Goldiș, C and Sirca, D and Enătescu, I and Olariu, L and Belei, O}, title = {Personalized Microbiome Modulation to Improve Clinical Outcomes in Pediatric Inflammatory Bowel Disease: A Multi-Omics and Interventional Approach.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13051047}, pmid = {40431220}, issn = {2076-2607}, support = {Without a Grant Number//"Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania; without a Grant Number/ ; }, abstract = {Inflammatory bowel disease (IBD) is a complex disorder influenced by genetic, environmental, and microbial factors, with emerging evidence highlighting the gut microbiome's role in disease pathogenesis. This study investigates the impact of microbiome-targeted interventions in pediatric IBD by integrating multi-omics analysis, including metagenomics, metabolomics, transcriptomics, and clinical biomarkers, to identify microbial dysbiosis patterns and potential therapeutic targets. A cohort of pediatric IBD patients underwent a personalized intervention involving dietary modifications, probiotic supplementation, and selective antibiotic therapy. Microbiome composition, inflammatory markers (fecal calprotectin, CRP), and disease activity scores (PCDAI/PUCAI) were assessed before and after treatment. At the 3-month follow-up, patients showed significant clinical improvement, with reduced stool frequency (p = 0.004) and improved stool consistency (p < 0.001). Symptoms such as bloating and abdominal pain decreased, while energy levels increased (p < 0.001). Dietary changes included higher fruit, meat, and dairy intake, and lower fast-food and sweets consumption (p < 0.001). Physician assessments classified 90% as "improved", reinforcing the effectiveness of personalized microbiome interventions. Microbiome-targeted interventions (diet, probiotics, and selective antibiotics) improved pediatric IBD outcomes by reducing pathogenic bacteria and increasing short-chain fatty acid (SCFA)-producing species, lowering inflammation and symptoms. Early-life factors (cesarean birth, and formula feeding) influence IBD risk. Personalized diets enhanced microbial balance. Integrating multi-omics supports precision medicine, offering microbiome-based biomarkers and reducing immunosuppressive reliance.}, }
@article {pmid40431204, year = {2025}, author = {Han, H and Chen, P and Zhao, W and Li, S and Zhang, K}, title = {Acclimation Time Enhances Adaptation of Heterotrophic Nitrifying-Aerobic Denitrifying Microflora to Linear Anionic Surfactant Stress.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13051031}, pmid = {40431204}, issn = {2076-2607}, support = {22YFZCSN00170//Tianjin Science and technology planning project fund/ ; 2022YFD1601104//the National Key R&amp;D Program of China during the 14th Five-Year Plan period/ ; CAAS-ZDRW202306//the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences, and the Major Scientific Research Task of the Agricultural Science and Technology Innovation Program of CAAS/ ; }, abstract = {Linear anionic surfactants (LAS) pose significant stress to microbial denitrification in wastewater treatment. This study investigated the performance and adaptation mechanisms of heterotrophic nitrification-aerobic denitrification (HN-AD) microbial consortia under LAS exposure after short-term (SCM, 2 months) and long-term (LCM, 6 months) acclimation. Results showed a dose-dependent inhibition of total nitrogen (TN) removal, with LCM achieving 97.40% TN removal under 300 mg/L LAS, which was 16.89% higher than SCM. Biochemical assays indicated that LCM exhibited lower reactive oxygen species (ROS) levels, a higher ATP content, and reduced LDH release, suggesting enhanced oxidative stress resistance and membrane stability. EPS secretion also increased in LCM, contributing to environmental tolerance. Metagenomic analysis revealed that long-term acclimation enriched key genera including Pseudomonas, Aeromonas, and Stutzerimonas, which maintained higher expression of denitrification (e.g., nosZ, nirS) and ammonium assimilation genes (glnA, gltB). Although high LAS concentrations reduced overall community diversity and led to convergence between SCM and LCM structures, LCM retained greater functional capacity and stress resistance. These findings underscore the importance of acclimation in sustaining denitrification performance under surfactant pressure and offer valuable insights for engineering robust microbial consortia in complex wastewater environments.}, }
@article {pmid40431180, year = {2025}, author = {Wang, R and Yang, S and Zhao, W}, title = {Microbial Community Responses and Nitrogen Cycling in the Nitrogen-Polluted Urban Shi River Revealed by Metagenomics.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13051007}, pmid = {40431180}, issn = {2076-2607}, support = {LH2022C098//Research Grants of Nature Scientific Foundation of Heilongjiang Province/ ; ES202217//the 2022 Open Fund of National Key Laboratory of Urban Water Resources and Water Environ-ment/ ; 2023-KYYWF-1495//Basic Research Business Fees for Provincial Higher Education Institutions in Heilongjiang Prov-ince/ ; }, abstract = {Nitrogen pollution in urban rivers, exacerbated by rapid urbanization, poses a growing threat to water quality. Microbial communities are essential in mediating nitrogen cycling and mitigating pollution in these ecosystems. This study integrated three-year (2021-2023) water quality monitoring with metagenomic sequencing to investigate microbial community dynamics, nitrogen cycling processes, and their responses to nitrogen pollution in the Shi River, Qinhuangdao, China. Nitrogen pollution was predominantly derived from industrial discharges from enterprises in the Shi River Reservoir upstream (e.g., coolant and chemical effluents), agricultural runoff, untreated domestic sewage (particularly from catering and waste in Pantao Valley), and livestock farming effluents. Total nitrogen (TN) concentrations ranged from 2.22 to 6.44 mg/L, exceeding China's Class V water standard (2.0 mg/L, GB 3838-2002), with the highest level at the urbanized W4 site (6.44 mg/L). Nitrate nitrogen (NO3-N) accounted for 60-80% of TN. Metagenomic analysis revealed Fragilaria, Microcystis, and Flavobacterium thriving (up to 15% relative abundance) under nitrogen stress, with nitrogen metabolism genes (narG, nifH, nirK) enriched at polluted sites (W2, W4), narG reaching 26% at W1. Dissolved oxygen positively correlated with nitrate reductase gene abundance, while ammonia nitrogen inhibited it. Burkholderiales and Limnohabitans dominated denitrification, offering insights into sustainable urban river management.}, }
@article {pmid40431168, year = {2025}, author = {Mameda, R and Bono, H}, title = {Optimization of Mapping Tools and Investigation of Ribosomal RNA Influence for Data-Driven Gene Expression Analysis in Complex Microbiomes.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13050995}, pmid = {40431168}, issn = {2076-2607}, support = {JPMJPF2010//Japan Science and Technology Agency/ ; }, abstract = {For gene expression analysis in complex microbiomes, utilizing both metagenomic and metatranscriptomic reads from the same sample enables advanced functional analysis. Due to their diversity, metagenomic contigs are often used as reference sequences instead of complete genomes. However, studies optimizing mapping strategies for both read types remain limited. In addition, although transcripts per million (TPM) is commonly used for normalization, few studies have evaluated the influence of ribosomal RNA (rRNA) in metatranscriptomic reads. This study compared Burrows-Wheeler Aligner-Maximal Exact Match (BWA-MEM) and Bowtie2 as mapping tools for metagenomic contigs. Even after optimizing Bowtie2 parameters, BWA-MEM showed higher efficiency in mapping both metagenomic and metatranscriptomic reads. Further analysis revealed that rRNA sequences contaminate predicted protein-coding regions in metagenomic contigs. When comparing TPM values across samples, contamination by rRNA led to an overestimation of TPM changes. This effect was more pronounced when the difference in rRNA content between samples was larger. These findings suggest that metatranscriptomic reads mapped to rRNA should be excluded before TPM calculations. This study highlights key factors influencing read mapping and quantification in gene expression analysis of complex microbiomes. The findings provide insights for improving analytical accuracy and advancing functional studies using both metagenomic and metatranscriptomic data.}, }
@article {pmid40431158, year = {2025}, author = {Mirete, S and Sánchez-Costa, M and Díaz-Rullo, J and González de Figueras, C and Martínez-Rodríguez, P and González-Pastor, JE}, title = {Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13050985}, pmid = {40431158}, issn = {2076-2607}, support = {PID2021-126114NB-C43//Spanish Ministry of Science and Innovation which also included European Regional Development Fund (FEDER)/ ; }, abstract = {Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations. MAG-based studies have identified microbial lineages form Archaea and Bacteria responsible for methane oxidation, carbon sequestration in marine sediments, ammonia oxidation, and sulfur metabolism, highlighting their critical roles in ecosystem stability. From a sustainability perspective, MAGs provide essential insights for climate change mitigation, sustainable agriculture, and bioremediation. The ability to characterize microbial communities in diverse environments, including soil, aquatic ecosystems, and extreme habitats, enhances biodiversity conservation and supports the development of microbial-based environmental management strategies. Despite these advancements, challenges such as assembly biases, incomplete metabolic reconstructions, and taxonomic uncertainties persist. Continued improvements in sequencing technologies, hybrid assembly approaches, and multi-omics integration will further refine MAG-based analyses. As methodologies advance, MAGs will remain a cornerstone for understanding microbial contributions to global biogeochemical processes and developing sustainable interventions for environmental resilience.}, }
@article {pmid40431157, year = {2025}, author = {Coates, N and John, DA and Jordan, S and Storey, M and Thornton, CA and Garaiova, I and Wang, D and Allen, SJ and Michael, DR and Plummer, SF and Facey, PD}, title = {The Impact of Probiotic Supplementation on the Development of the Infant Gut Microbiota: An Exploratory Follow-Up of a Randomised Controlled Trial.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13050984}, pmid = {40431157}, issn = {2076-2607}, support = {Collaborative Industrial Research (Project No. HE09 COL 1002)//Knowledge Exploitation Fund/ ; Accelerate Programme (Project code: PR-0228)//European Regional Development Fund (ERDF)/ ; N/A//Cultech Ltd/ ; }, abstract = {Early-life establishment of the gut microbiota plays a role in lifelong health, with disruptions linked to heightened risks of metabolic and immune disorders. Probiotic supplementation may be used to modulate the infant gut microbiome to promote favourable development. Here, we evaluate how Lab4B probiotic supplementation shapes the development of the infant gut microbiome over the first 6 months. Faecal samples collected from infants enrolled in PROBAT (ISRCTN26287422), a randomised, double-blind, placebo-controlled trial, were analysed using culture-dependent and -independent (16S rDNA and metagenomic shotgun sequencing) techniques to examine the composition, diversity, and metabolic capabilities of the microbiome, as well as the abundance of antimicrobial resistance genes (ARGs). Probiotic supplementation encouraged the development of a microbiome with a distinct composition characterised by elevated abundances of Bifidobacteriaceae in the first 6 weeks (p = 0.006) and Lactobacillaceae throughout the first 6 months (p < 0.05 at every 6-week time point), accelerated microbial diversification, reduced abundance of beta-lactam- and cephalosporin-resistance genes, and differences in predicted metabolic capabilities at the start and end points. Supplementation of this neonatal population, which is at high risk of atopy, with the Lab4B probiotic significantly influenced the development of the infant gut microbiota during the first 6 months.}, }
@article {pmid40431145, year = {2025}, author = {Jiang, K and Ye, L and Cao, C and Che, G and Wang, Y and Hong, Y}, title = {Multi-Metagenome Analysis Unravels Community Collapse After Sampling and Hints the Cultivation Strategy of CPR Bacteria in Groundwater.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/microorganisms13050972}, pmid = {40431145}, issn = {2076-2607}, support = {32360005//National Natural Science Foundation of China/ ; 2022JBQN091//Fundamental Research Funds for the Inner Mongolia Normal University/ ; 2022JBTD010//Fundamental Research Funds for the Inner Mongolia Normal University/ ; }, abstract = {Groundwater harbors phylogenetically diverse Candidate Phyla Radiation (CPR) bacteria, representing an ideal ecosystem for studying this microbial dark matter. However, no CPR strains have been successfully isolated from groundwater, severely limiting further research. This study employed a multi-metagenome approach, integrating time-resolved sampling, antibiotic/nutrient interventions, and microbial correlation networks to unravel CPR ecological roles in groundwater and provide insights into their subsequent cultivation. Through 36 metagenomes from a groundwater system containing at least 68 CPR phyla, we revealed the time-sensitive collapse of CPR communities: total abundance plummeted from 7.9% to 0.15% within 48 h post-sampling, driven by competition with rapidly dividing non-CPR bacteria, such as members of Pseudomonadota. Ampicillin (100 mg/L) stabilized CPR communities by suppressing competitors, whereas low-nutrient conditions paradoxically reversed this effect. Long-term enrichment (14 months) recovered 63 CPR phyla (0.35% abundance), revealing their survival resilience despite nutrient deprivation. Correlation networks prioritized Actinomyces, a novel Acidimicrobiaceae genus, Aestuariivirga, Baekduia and Caedimonadaceae as potential CPR partners, providing actionable targets for co-culture trials. Here, we propose actionable recommendations spanning groundwater sampling, activation status, identification of CPR symbiotic partners, and optimization of culture conditions, which bypass traditional blind cultivation and are critical for future efforts to cultivate CPR bacterial strains from groundwater. Cultivating CPR bacteria will contribute to clarifying their diversity, ecological roles, evolutionary mechanisms, metabolic pathways, and genetic potential.}, }
@article {pmid40431076, year = {2025}, author = {Mendybayeva, A and Makhambetov, A and Yanin, K and Taskuzhina, A and Khusnitdinova, M and Gritsenko, D}, title = {Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/plants14101511}, pmid = {40431076}, issn = {2223-7747}, support = {BR21882269//The Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {Kazakhstan's rich biodiversity includes diverse apple populations, notably the wild apple tree (Malus sieversii) prized for traits like disease resistance and adaptability, potentially aiding breeding programs. Analyzing their microbiomes offers insights into bacterial diversity and how it influences apple tree development, making it a reliable method for understanding ecological interactions. In this research, 334 apple tree samples were collected from different mountain ranges in southeastern Kazakhstan. An analysis using nanopore-based 16S rRNA sequencing showed a distinct similarity in the microbiome compositions of samples from the Zhongar and Ile Alatau mountain ranges, with a predominance of Pseudomonadaceae, Enterobacteriaceae, and Microbacteriaceae. In contrast, samples from Ketmen ridge showed a higher prevalence of Enterobacteriaceae. Alongside the less represented Pseudomonadaceae family, in the Ketmen ridge region, bacteria of the Xanthomonadaceae, Alcaligenaceae, and Brucellaceae families were also present. Across all regions, beneficial plant-associated bacteria were identified, such as Pseudomonas veronii, Stenotrophomonas geniculata, and Kocuria rhizophila, potentially enhancing plant resilience. However, opportunistic phytopathogens were also detected, including Pseudomonas viridiflava and Serratia marcescens, particularly in the Ile Alatau region. These findings highlight the complex microbial interactions in M. sieversii, thus offering key insights into host-microbe relationships that can inform apple breeding and ecological preservation efforts.}, }
@article {pmid40430824, year = {2025}, author = {Mwendwa, K and Mutuku, F and Wambua, S and Nzaro, M and Ndenga, BA and Agoi, K and LaBeaud, AD and Bosire, C}, title = {Temporal Variation and Human Host Predominance in Aedes aegypti from Coastal and Western Kenya: Insights from Pooled Blood Meal Metagenomics.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/pathogens14050505}, pmid = {40430824}, issn = {2076-0817}, support = {NIH R01 AI102918/NH/NIH HHS/United States ; }, mesh = {Animals ; *Aedes/physiology/genetics/virology ; Kenya ; Humans ; *Mosquito Vectors/virology/physiology/genetics ; *Metagenomics/methods ; Feeding Behavior ; Seasons ; Cattle ; }, abstract = {Aedes aegypti is the primary vector of arboviral diseases such as dengue, chikungunya, yellow fever, and Zika, posing significant global health and economic challenges. The effective control of this mosquito species requires understanding its seasonality, feeding behavior, and ecological dynamics. Modern molecular techniques, such as amplicon metagenomic sequencing, provide insights into vector-host interactions and feeding patterns. This study investigated the temporal variation of Ae. aegypti abundance and its blood meal sources in coastal and western Kenya over 16 months. A total of 64,360 mosquitoes were collected, with Ae. aegypti comprising 10.9% (7035/64,360). Coastal sites had a higher proportion (64.7%) of Ae. aegypti than western Kenya. Seasonal variation in abundance was observed, with peaks during the long rainy season and decline during the dry season. Blood meal analysis identified 15 vertebrate hosts, with humans being the primary source (86.6-95.9%). Other hosts included domestic animals such as turkey, sheep, cow, goat, and chicken. These findings highlight the role of rainfall in arboviral disease transmission and Ae. aegypti's strong preference for human hosts. Additionally, this study demonstrates the cost-effectiveness of group testing for identifying blood meal sources, with implications for public health interventions.}, }
@article {pmid40430785, year = {2025}, author = {Tóth, AG and Solymosi, N and Tenk, M and Káldy, Z and Németh, T}, title = {First Animal Source Metagenome Assembly of Lawsonella clevelandensis from Canine External Otitis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/pathogens14050465}, pmid = {40430785}, issn = {2076-0817}, support = {SRF-001//University of Veterinary Medicine Budapest/ ; 874735 (VEO)//European Union's Horizon 2020 research and innovation program/ ; MILAB//European Union project RRF-2.3.1-21-2022-00004/ ; }, mesh = {Animals ; Dogs ; *Dog Diseases/microbiology ; Female ; *Otitis Externa/microbiology/veterinary ; *Metagenome ; Genome, Bacterial ; Nanopore Sequencing ; High-Throughput Nucleotide Sequencing ; }, abstract = {External otitis is one of the most common conditions in dogs to be presented to the veterinarian. Moreover, the disorder is often challenging to manage. The range and role of microorganisms involved in the pathogenesis are currently not fully understood. Therefore, the condition has been studied using third-generation sequencing (Oxford Nanopore Technology) to gain a more complete picture of the pathogens involved. Throughout the metagenome assembly of a sample from the ear canal of an 11-year-old female Yorkshire terrier suffering from chronic external otitis, a genome of Lawsonella clevelandensis was compiled. To our knowledge, this result is the first of its type of animal origin. The outcome of the assembly is a single circular chromosome with a length of 1,909,339 bp and 1727 predicted genes. One open reading frame associated with antimicrobial resistance could have been identified. Comparing all available genomes, the species can be associated with three main genome clusters. The finding contributes to the extending knowledge bank about this often-overlooked pathogen and raises attention to the role of nanopore sequencing by the identification and characterization of microorganisms that are difficult to culture.}, }
@article {pmid40430233, year = {2025}, author = {Rivera-Martínez, A and Laredo-Tiscareño, SV and Adame-Gallegos, JR and Luna-Santillana, EJ and Rodríguez-Alarcón, CA and García-Rejón, JE and Casas-Martínez, M and Garza-Hernández, JA}, title = {Viruses in Simuliidae: An Updated Systematic Review of Arboviral Diversity and Vector Potential.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/life15050807}, pmid = {40430233}, issn = {2075-1729}, support = {419-24-23//Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n (Secihti) of Mexico/ ; 740742, 769056, and 842817//The Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n (Secihti) of Mexico/ ; RIPI2019ICB45//RIPI2019ICB45/ ; 4034275//The Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n (Secihti) of Mexico/ ; }, abstract = {Black flies (Diptera: Simuliidae) are important vectors of pathogens, including filarial nematodes, protozoans, and arboviruses, which significantly impact human and animal health. Although their role in arbovirus transmission has not been as thoroughly studied as that of mosquitoes and ticks, advances in molecular tools, particularly metagenomics, have enabled the identification of non-cultivable viruses, significantly enhancing our understanding of black-fly-borne viral diversity and their public and veterinary health implications. However, these methods can also detect insect-specific viruses (i.e., viruses that are unable to replicate in vertebrate hosts), which may lead to the incorrect classification of black flies as potential vectors. This underscores the need for further research into their ecological and epidemiological roles. This systematic review, conducted following the PRISMA protocol, compiled and analyzed evidence on arbovirus detection in Simuliidae from scientific databases. Several arboviruses were identified in these insects, including vesicular stomatitis virus New Jersey serotype (VSVNJ), Venezuelan equine encephalitis virus (VEEV), and Rift Valley fever virus. Additionally, in vitro studies evaluating the vector competence of Simuliidae for arboviruses such as dengue virus, Murray Valley encephalitis virus, and Sindbis virus were reviewed. These findings provide critical insights into the potential role of black flies in arbovirus transmission cycles, emphasizing their importance as vectors in both public and veterinary health contexts.}, }
@article {pmid40430189, year = {2025}, author = {Escorcia Mora, P and Valbuena, D and Diez-Juan, A}, title = {The Role of the Gut Microbiota in Female Reproductive and Gynecological Health: Insights into Endometrial Signaling Pathways.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/life15050762}, pmid = {40430189}, issn = {2075-1729}, abstract = {Fertility is a dynamic, multifactorial process governed by hormonal, immune, metabolic, and environmental factors. Recent evidence highlights the gut microbiota as a key systemic regulator of reproductive health, with notable impacts on endometrial function, implantation, pregnancy maintenance, and the timing of birth. This review examines the gut-endometrial axis, focusing on how gut microbial communities influence reproductive biology through molecular signaling pathways. We discuss the modulatory roles of microbial-derived metabolites-including short-chain fatty acids, bile acids, and tryptophan catabolites-in shaping immune tolerance, estrogen metabolism, and epithelial integrity at the uterine interface. Emphasis is placed on shared mechanisms such as β-glucuronidase-mediated estrogen recycling, Toll-like receptor (TLR)-driven inflammation, Th17/Treg cell imbalance, and microbial translocation, which collectively implicate dysbiosis in the etiology of gynecological disorders including endometriosis, polycystic ovary syndrome (PCOS), recurrent implantation failure (RIF), preeclampsia (PE), and preterm birth (PTB). Although most current evidence remains correlational, emerging insights from metagenomic and metabolomic profiling, along with microbiota-depletion models and Mendelian randomization studies, underscore the biological significance of gut-reproductive crosstalk. By integrating concepts from microbiology, immunology, and reproductive molecular biology, this review offers a systems-level perspective on host-microbiota interactions in female fertility.}, }
@article {pmid40429958, year = {2025}, author = {San-Martin, MI and Chamizo-Ampudia, A and Sanchiz, &#xc1; and Ferrero, M&#xc1; and Martínez-Blanco, H and Rodríguez-Aparicio, LB and Navasa, N}, title = {Microbiome Markers in Gastrointestinal Disorders: Inflammatory Bowel Disease, Colorectal Cancer, and Celiac Disease.}, journal = {International journal of molecular sciences}, volume = {26}, number = {10}, pages = {}, doi = {10.3390/ijms26104818}, pmid = {40429958}, issn = {1422-0067}, mesh = {Humans ; *Celiac Disease/microbiology/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; Biomarkers/metabolism ; *Colorectal Neoplasms/microbiology/metabolism ; Animals ; Metagenomics/methods ; }, abstract = {Intestinal microbiota and the host's immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, likely contributing to the dramatic increase in inflammatory diseases in the last few decades. Recent advances in DNA sequencing technologies have tremendously helped to characterize the microbiome associated with disease, both in identifying global alterations and discovering specific biomarkers that potentially contribute to disease pathogenesis, as evidenced by animal studies. Beyond bacterial alterations, non-bacterial components such as fungi, viruses, and microbial metabolites have been implicated in these diseases, influencing immune responses and gut homeostasis. Multi-omics approaches integrating metagenomics, metabolomics, and transcriptomics offer a more comprehensive understanding of the microbiome's role in disease pathogenesis, paving the way for innovative diagnostic and therapeutic strategies. Unraveling the metagenomic profiles associated with disease may facilitate earlier diagnosis and intervention, as well as the development of more personalized and effective therapeutic strategies. This review synthesizes recent and relevant microbiome research studies aimed at characterizing the microbial signatures associated with inflammatory bowel disease, colorectal cancer, and celiac disease.}, }
@article {pmid40429402, year = {2025}, author = {Tar, I and Krisztina, S and Martos, R and Kiss, C and Márton, I}, title = {Effects of Comorbid Disease Improvement on Oral Lichen Planus (OLP) and Oral Leukoplakia (OL) Lesions: A Retrospective Longitudinal Study.}, journal = {Journal of clinical medicine}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/jcm14103408}, pmid = {40429402}, issn = {2077-0383}, abstract = {Background: Previous attempts to treat oral potentially malignant disorders OPMDs) effectively have failed. Longitudinal studies investigating the effects of comorbid diseases improvement on OPMDs are not yet available. Therefore, the current study examined the effects of comorbid disease improvement on OPMDs healing, both in oral lichen planus (OLP) and oral leukoplakia (OL) patients. Methods: The data from 197 consecutive patients (144 females and 53 males, age ± SD: 55.19 ± 12.37 years, with ages ranging from 23 to 91 years), with oral lesions considered OLP and OL, were processed and evaluated. The frequency of comorbid diseases and the presence of HPV (here, subtypes were not evaluated) in the lesions in OLP and OL patient groups were evaluated and compared to the results of controls (n = 139). Risk models for OLP and OL lesions were established. High-risk models for erosive-atrophic OLP and non-homogeneous OLP were also described. The influence of comorbid disease improvement was also evaluated. Lesions were scored at the first and last visit (full recovery = 0, improvement = 1, and no improvement = 2). Results: One hundred and ninety-seven patients (144 OLP + 53 OL) were followed up for an average of 47.66 months (min-max: 1-203 months, SD: 54.19). Based on the established models, HPV infection, iron deficiency, diabetes, and thyroid function disorders seem to act as risk factors for OLP and may also affect OL formation. The improvement in comorbid diseases can cause significant improvement in OLP and OL lesions. Conclusions: By meticulous follow-up of comorbid diseases, improvement in OLP and OL lesions can be achieved.}, }
@article {pmid40429337, year = {2025}, author = {Brożek-Mądry, E and Ziuzia-Januszewska, L and Misztal, O and Burska, Z and Sosnowska-Turek, E and Sierdziński, J}, title = {Nasal Rinsing with Probiotics-Microbiome Evaluation in Patients with Inflammatory Diseases of the Nasal Mucosa.}, journal = {Journal of clinical medicine}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/jcm14103341}, pmid = {40429337}, issn = {2077-0383}, support = {RPWM.01.02.01-28-0027/18-00//European Regional Development Fund, European Social Fund, Regional Operational Program of the Warmian-Masurian Voivodeship - Research at Probios/ ; }, abstract = {Background/Objectives: The evidence regarding the efficacy of probiotics in chronic rhinosinusitis (CRS) is very limited, prompting the EPOS2020 steering group to advise against their use in CRS treatment. Therefore, further research to evaluate the impact of probiotics on microbial communities is particularly important. This study aimed to assess the influence of probiotic nasal rinses on nasal microbiota profiles in patients with primary CRS, granulomatosis with polyangiitis (GPA), and nasal septal perforation (NSP) using 16S rRNA sequencing. Methods: Thirty-six patients with nasal mucosal diseases, including sixteen with primary CRS, eleven with GPA, and nine with NSP, were randomly assigned to either a study group receiving nasal rinses with probiotics containing Lactobacillus plantarum and Bifidobacterium animalis, or a control group using nasal rinses with saline. Metagenomic analysis targeting the V3-V4 hypervariable region of the 16S rRNA gene was performed to characterize bacterial and archaeal populations. Results: At the genus level, the most abundant co-colonizers included Staphylococcus, Streptococcus, and Haemophilus. After one month of probiotic rinsing, a decrease in abundance of the genera Finegoldia (p = 0.010), Haemophilus (p = 0.020), Streptococcus (p = 0.027), Staphylococcus (p = 0.033), Micrococcus (p = 0.035), Corynebacterium (p = 0.049), Gemella (p = 0.055), Rubrobacter (p = 0.055), and Pseudonocardia (p = 0.058) was observed. Conversely, the abundance of probiotic species Lactobacillus plantarum and Bifidobacterium animalis increased. Moreover, increases in the genera Dolosigranulum and Stenotrophomonas were observed, although they did not reach statistical significance. Conclusions: Probiotic nasal rinses may contribute to restoring microbial homeostasis by reducing genera associated with inflammatory dysbiosis in nasal inflammatory diseases, warranting further research on their clinical benefits.}, }
@article {pmid40429183, year = {2025}, author = {Zhou, J and Qin, W and Zeng, Y and Huang, X and Yuan, J and Yin, Y and Xu, P and Fan, X and Zhang, R and Li, G and Zhang, Y}, title = {Effects of Colony Breeding System and Nest Architecture on Soil Microbiome and Fertility in the Fungus-Growing Termite Macrotermes barneyi Light.}, journal = {Insects}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/insects16050470}, pmid = {40429183}, issn = {2075-4450}, support = {31601891//National Natural Science Foundation of China/ ; 2023AFB1005//Natural Science Foundation of Hubei Province of China/ ; IWHR-2024TE003//Open Research Fund of Key Laboratory of Termite Control of Ministry of Water Resources, China Institute of Water Resources and Hydropower Research/ ; EWPL202408//Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization/ ; }, abstract = {Macrotermes barneyi is a typical fungus-growing termite that forms both monogynous (single queen) and polygynous (multiple queen) colonies in nature. This species influences the local soil fertility in part by redistributing nutrients across the landscape in its habitats. However, how the colony structure of M. barneyi affects nutrient cycling and microbial communities within the nest is not well understood. In this study, we compared the physicochemical properties and microbial communities across nest parts between monogynous and polygynous colonies of M. barneyi. Our results showed that the fungus garden is the most nutrient-rich part of the nest, with higher soil moisture, organic matter, ammonium nitrogen, nitrate nitrogen, available sulfur, available potassium, available silicon, and available boron than other nest parts. Notably, the fungus garden in monogynous colonies had higher nitrate nitrogen, available sulfur, and available silicon than those in the polygynous colonies. The microbial α-diversity in the fungus garden was lower than that in other parts of the nest. β-diversity analysis revealed a clear separation of microbial communities between monogynous and polygynous colonies across nest parts. Furthermore, the relative abundance of functional genes associated with "cell cycle control, cell division, and chromosome partitioning" was higher in the fungus garden of polygynous colonies compared to monogynous colonies. Our results suggest that the fungus garden plays a crucial role in maintaining colony stability in M. barneyi colonies. The rapid depletion of nutrients in the fungus garden to sustain the larger population in polygynous colonies likely influences microbial community dynamics and nutrient cycling.}, }
@article {pmid40428846, year = {2025}, author = {Torraco, A and Di Nicolantonio, S and Cardisciani, M and Ortu, E and Pietropaoli, D and Altamura, S and Del Pinto, R}, title = {Meta-Analysis of 16S rRNA Sequencing Reveals Altered Fecal but Not Vaginal Microbial Composition and Function in Women with Endometriosis.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {61}, number = {5}, pages = {}, doi = {10.3390/medicina61050888}, pmid = {40428846}, issn = {1648-9144}, support = {SRA-882725/CCF/CCF/United States ; }, mesh = {Humans ; Female ; *Endometriosis/microbiology/physiopathology ; *Feces/microbiology ; *Vagina/microbiology ; *RNA, Ribosomal, 16S/analysis/genetics ; Dysbiosis/microbiology ; Adult ; Gastrointestinal Microbiome ; Metagenomics/methods ; }, abstract = {Background and Objectives: Dysbiosis of the oral-gut axis is related to several extraintestinal inflammatory diseases, including endometriosis. This study aims to assess the microbial landscape and pathogenic potential of distinct biological niches during endometriosis. Materials and Methods: A microbiome meta-analysis was conducted on 182 metagenomic sequences (79 of fecal and 103 of vaginal origin) from women with and without endometriosis. Fecal and vaginal microbial diversity, differential abundance, and functional analysis based on disease status were assessed. Random forest, gradient boosting, and generalized linear modeling were used to predict endometriosis based on differentially enriched bacteria. Results: Only intestinal microbes displayed distinctive taxonomic and functional characteristics in women with endometriosis compared to control women. Taxonomic differences were quantified using the microbial endometriosis index (MEI), which effectively distinguished between individuals with and without the disease. The observed functional enrichment pointed to proinflammatory pathways previously related to endometriosis development. Conclusions: Dysbiosis in the oral-gut microbial community appears to play a prevalent role in endometriosis. Our findings pave the ground for future studies exploring the potential mechanistic involvement of the oral-gut axis in disease pathogenesis.}, }
@article {pmid40428471, year = {2025}, author = {Detcharoen, M and Khrueakaew, P and Benjakul, S and Romyasamit, C and Suyapoh, W and Saetang, J}, title = {Surveillance of Antimicrobial Resistance in the Asian Seabass (Lates calcarifer) Supply Chain Using Nanopore Sequencing.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/foods14101691}, pmid = {40428471}, issn = {2304-8158}, support = {SEAOHUN/2024-SC218-0105-3009//the United States Agency for International Development (USAID) through SEAOHUN 2024 One Health Research &amp; Training (OHRT) Awards/ ; }, abstract = {Intensive fish farming worldwide has increased reliance on antibiotics to control bacterial pathogens, raising concerns about antimicrobial resistance (AMR) in aquaculture. These resistant bacteria can persist and pass through the food supply chain, from farms to consumers. Despite this risk, antimicrobial resistance genes (ARGs) in aquaculture environments and fish products have not been elucidated. This study aimed to detect ARGs found in the Asian seabass (Lates calcarifer), an economically important fish in Thailand, collected from farms, fish container vehicles, and markets, using Nanopore metagenomic sequencing. We detected multiple ARGs in all sample types. Water samples harbored the rpsL gene conferring streptomycin resistance. Container samples exhibited the highest diversity of ARGs, including multiple beta-lactamases and the rsmA gene, conferring resistance to fluoroquinolones, diaminopyrimidines, and phenicol antibiotics. Fish samples generally lacked ARGs, except for one sample harboring rsmA. Non-metric multidimensional scaling revealed distinct microbial communities in water, compared with those found in container and fish samples, indicating potential cross-contamination during handling or storage. Our findings emphasize that containers could be critical control points for minimizing AMR spread. Overall, this study highlights the interconnection between environmental, fish, and human health, highlighting the importance of integrated AMR surveillance and management in aquaculture systems.}, }
@article {pmid40428372, year = {2025}, author = {Dimitrova, L and Ilieva, Y and Gouliamova, D and Kussovski, V and Hubenov, V and Georgiev, Y and Bratanova, T and Kaleva, M and Zaharieva, MM and Najdenski, H}, title = {Isolation, Enrichment and Analysis of Aerobic, Anaerobic, Pathogen-Free and Non-Resistant Cellulose-Degrading Microbial Populations from Methanogenic Bioreactor.}, journal = {Genes}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/genes16050551}, pmid = {40428372}, issn = {2073-4425}, support = {&#x41a;P-06-N71/8 from 08.12.2023//National Fund for Scientific Research, Republic of Bulgaria/ ; }, mesh = {*Cellulose/metabolism ; *Bioreactors/microbiology ; Anaerobiosis ; *Microbial Consortia/genetics ; Biodegradation, Environmental ; Bacteria/genetics/isolation &amp; purification/metabolism ; Aerobiosis ; *Bacteria, Anaerobic/genetics/isolation &amp; purification/metabolism ; Methane/metabolism ; Biofuels ; }, abstract = {Background: Nowadays, the microbial degradation of cellulose represents a new perspective for reducing cellulose waste from industry and households and at the same time obtaining energy sources. Methods: We isolated and enriched two aerobic (at 37 °C and 50 °C) and one anaerobic microbial consortium from an anaerobic bioreactor for biogas production by continuous subculturing on peptone cellulose solution (PCS) medium supplemented with 0.3% treated or untreated Whatman filter paper under static conditions. Samples were taken every 7 days until day 21 to determine the percentage of cellulose biodegradation. We determined the antimicrobial resistance of aerobic and anaerobic consortia and some single colonies by disc diffusion method, against 42 clinically applied antibiotics. PCR analyses were performed to search for the presence of eight genes for cellulolytic activity and nine genes for antibiotic resistance. By metagenomics analysis, the bacterial and fungal genus distributions in the studied populations were determined. Results: Aerobes cultured at 50 °C degraded cellulose to the greatest extent (47%), followed by anaerobes (24-38%) and aerobes (8%) cultured at 37 °C. The bacterial sequence analysis showed that the dominant phyla are Bacillota and Bacteroidetes and genera-Paraclostridium, Defluvitalea, Anaerobacillus, Acetivibrio, Lysinibacillus, Paenibacillus, Romboutsia, Terrisporobacter, Clostridium, Sporanaerobacter, Lentimicrobium, etc. in a different ratio depending on the cultivation conditions and the stage of the process. Some of these representatives are cellulolytic and hemicellulolytic microorganisms. We performed lyophilization and proved that it is suitable for long-term storage of the most active consortium, which degrades even after the 10th re-inoculation for a period of one year. We proved the presence of ssrA, ssrA BS and blaTEM genes. Conclusions: Our findings demonstrated the potential utility of the microbial consortium of anaerobes in the degradation of waste lignocellulose biomass.}, }
@article {pmid40428326, year = {2025}, author = {Sun, YF and Han, ZX and Yao, XK and Meng, J and Ren, WL and Wang, CK and Yuan, XX and Zeng, YQ and Wang, YF and Sun, ZW and Wang, JW}, title = {Effects of Different Stages of Training on the Intestinal Microbes of Yili Horses Analyzed Using Metagenomics.}, journal = {Genes}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/genes16050504}, pmid = {40428326}, issn = {2073-4425}, mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Feces/microbiology ; *Physical Conditioning, Animal ; *Bacteria/genetics/classification/isolation &amp; purification ; }, abstract = {Objectives: The aim of this study was to investigate the effects of different stages of training on the intestinal microbial abundance of Yili horses. Methods: Ten Yili horses, all aged 2 years old and weighing 305 ± 20 kg, were selected and divided into a training group and an untrained group. The training group performed riding training 6 days a week, and the untrained group moved freely in the activity circle every day. Fecal samples were collected on days 30 and 60, and the intestinal microorganisms were detected and analyzed using metagenomics. Results: Compared with the 30-day untrained group, the relative abundances of Bacteroidetes were significantly increased in the 30-day training group (p < 0.01). Conversely, the abundances of Clostridiaceae, Clostridium, and Ruminococcus were significantly decreased (p < 0.01), whereas those of Prevotella, Bacteroideaceae, and Bacteroidetes were significantly increased (p < 0.05). Additionally, the relative abundances of Firmicutes and Actinomycetes were significantly decreased (p < 0.05). Compared with the 60-day untrained group, no significant differences in the phyla Bacteriaceae and Bacteriae of the 60-day training group (p > 0.05) were observed. In the linear discriminant analysis effect size analysis, seven significantly different bacteria were detected in the fecal flora of horses in the 30-day training group versus the untrained 30-day group, but only one significantly different bacterium was detected after 60 days. The Kyoto Encyclopedia of Genes and Genomes analysis showed that the differentially expressed genes were related to metabolism and the environmental information processing pathway, carbohydrate metabolism, and membrane transport pathways. Conclusions: Therefore, training seems to affect the diversity and composition of the gut microbiota of Yili horses, especially during the first 30 days of training.}, }
@article {pmid40428305, year = {2025}, author = {Guo, Q and Zhang, W and Xu, C and Li, X and Wang, B and Xiong, C and Duan, W and Luo, T and Wang, W and Zhou, J}, title = {Comparative Analysis of Gut Microbiome Community Structures in Different Populations of Asian Elephants in China and Their Correlation with Diet.}, journal = {Genes}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/genes16050483}, pmid = {40428305}, issn = {2073-4425}, support = {202501AS070053//Key Project of Yunnan Basic Research Program/ ; }, mesh = {Animals ; *Elephants/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Diet ; China ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: The interaction and co-evolution between the gut microbiome and the host play important roles in the host's physiology, nutrition, and health. Diet is considered an important driver of differences in the gut microbiota; however, research on the relationship between the gut microbiota and diet in Asian elephants remains limited.<br><br>METHODS: In this study, we explored the gut microbiota structure and its relationship with diet in different populations of Asian elephants through metagenomic sequencing, combined with previously published dietary data.<br><br>RESULTS: This study found that the dominant gut microbiota of Asian elephants includes the phyla Bacillota (29.85% in BP, 22.79% in RC, 21.89% in SM, 31.67% in ML, and 33.00% in NGH), Bacteroidota (25.25% in BP, 31.44% in RC, 16.44% in SM, 25.73% in ML, and 23.74% in NGH), and Spirochaetota (3.49% in BP, 6.18% in RC, 1.71% in SM, 2.69% in ML, and 3.52% in NGH), with significant differences in the gut microbiota among different populations. Correlation analysis between the gut microbiota and diet revealed that dietary diversity did not directly affect the alpha diversity of the gut microbiota. However, specific food types might play a key role in shaping the gut microbiota structure by regulating the abundance of certain microbiota.<br><br>CONCLUSIONS: This study reveals significant differences in the gut microbiota structure among different populations of Asian elephants and explores the impact of diet on the structure. The results provide foundational data for a deeper understanding of the gut microbiota structure of Asian elephants and offer important references for the scientific conservation and precise management strategies of this species.}, }
@article {pmid40427823, year = {2025}, author = {Santos, AFB and Nunes, M and Filipa-Silva, A and Pimentel, V and Pingarilho, M and Abrantes, P and Miranda, MNS and Crespo, MTB and Abecasis, AB and Parreira, R and Seabra, SG}, title = {Wastewater Metavirome Diversity: Exploring Replicate Inconsistencies and Bioinformatic Tool Disparities.}, journal = {International journal of environmental research and public health}, volume = {22}, number = {5}, pages = {}, doi = {10.3390/ijerph22050707}, pmid = {40427823}, issn = {1660-4601}, support = {PTDC/CTA AMB/29586/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia, Portugal 568 through projects AgriWWAter/ ; 706, Internalproject IBETXplore 2017//VirusFreeWater/ ; GHTM- UID/04413/2020//Internal exploratory Project WasteWaterVir/ ; LA/P/0117/2020//LA-REAL/ ; }, mesh = {*Wastewater/virology ; *Computational Biology/methods ; *Virome ; Portugal ; *Metagenomics/methods ; *Viruses/classification/isolation &amp; purification/genetics ; }, abstract = {This study investigates viral composition in wastewater through metagenomic analysis, evaluating the performance of four bioinformatic tools-Genome Detective, CZ.ID, INSaFLU-TELEVIR and Trimmomatic + Kraken2-on samples collected from four sites in each of two wastewater treatment plants (WWTPs) in Lisbon, Portugal in April 2019. From each site, we collected and processed separately three replicates and one pool of nucleic acids extracted from the replicates. A total of 32 samples were processed using sequence-independent single-primer amplification (SISPA) and sequenced on an Illumina MiSeq platform. Across the 128 sample-tool combinations, viral read counts varied widely, from 3 to 288,464. There was a lack of consistency between replicates and their pools in terms of viral abundance and diversity, revealing the heterogeneity of the wastewater matrix and the variability in sequencing effort. There was also a difference between software tools highlighting the impact of tool selection on community profiling. A positive correlation between crAssphage and human pathogens was found, supporting crAssphage as a proxy for public health surveillance. A custom Python pipeline automated viral identification report processing, taxonomic assignments and diversity calculations, streamlining analysis and ensuring reproducibility. These findings emphasize the importance of sequencing depth, software tool selection and standardized pipelines in advancing wastewater-based epidemiology.}, }
@article {pmid40427639, year = {2025}, author = {DeSantis, AH and Buss, K and Coker, KM and Pasternak, BA and Chi, J and Patterson, JS and Gu, H and Jurutka, PW and Sandrin, TR}, title = {Multiomics-Based Profiling of the Fecal Microbiome Reveals Potential Disease-Specific Signatures in Pediatric IBD (PIBD).}, journal = {Biomolecules}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/biom15050746}, pmid = {40427639}, issn = {2218-273X}, support = {GR39923//Phoenix Children's Hospital Foundation Leadership Grant/ ; }, mesh = {Humans ; Child ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Metagenomics/methods ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Metabolomics/methods ; Adolescent ; *Colitis, Ulcerative/microbiology/genetics/metabolism ; *Crohn Disease/microbiology/genetics/metabolism ; Biomarkers/metabolism ; Transcriptome ; Multiomics ; }, abstract = {Inflammatory bowel disease (IBD), which includes Crohn's Disease (CD) and Ulcerative Colitis (UC), is a chronic gastrointestinal (GI) disorder affecting 1 in 100 people in the United States. Pediatric IBD (PIBD) is estimated to impact 15 per 100,000 children in North America. Factors such as the gut microbiome (GM), genetic predisposition to the disease, and certain environmental factors are thought to be involved in pathogenesis. However, the pathophysiology of IBD is incompletely understood, and diagnostic biomarkers and effective treatments, particularly for PIBD, are limited. Recent work suggests that these factors may interact to influence disease development, and multiomic approaches have emerged as promising tools to elucidate the pathophysiology. We employed metagenomics, metabolomics- and metatranscriptomics-based approaches to examine the microbiome, its genetic potential, and its activity to identify factors associated with PIBD. Metagenomics-based analyses revealed pathways such as octane oxidation and glycolysis that were differentially expressed in UC patients. Additionally, metatranscriptomics-based analyses suggested enrichment of glycan degradation and two component systems in UC samples as well as protein processing in the endoplasmic reticulum, ribosome, and protein export in CD and UC samples. In addition, metabolomics-based approaches revealed patterns of differentially abundant metabolites between healthy and PIBD individuals. Interestingly, overall microbiome community composition (as measured by alpha and beta diversity indices) did not appear to be associated with PIBD. However, we observed a small number of differentially abundant taxa in UC versus healthy controls, including members of the Classes Gammaproteobacteria and Clostridia as well as members of the Family Rikenellaceae. Accordingly, when identifying potential biomarkers for PIBD, our results suggest that multiomics-based approaches afford enhanced potential to detect putative biomarkers for PIBD compared to microbiome community composition sequence data alone.}, }
@article {pmid40427376, year = {2025}, author = {Tang, J and Dong, L and Tang, M and Arif, A and Zhang, H and Zhang, G and Zhang, T and Xie, K and Su, S and Zhao, Z and Dai, G}, title = {Metagenomic Analysis Reveals the Characteristics of Cecal Microbiota in Chickens with Different Levels of Resistance During Recovery from Eimeria tenella Infection.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/ani15101500}, pmid = {40427376}, issn = {2076-2615}, support = {(JATS [2023]447)//Jiangsu Agricultural Industry Technology System/ ; }, abstract = {Coccidiosis, caused by Eimeria protozoa, is a severe intestinal parasitic disease that results in substantial economic losses to the global poultry industry annually. The gut microbiota plays a crucial role in host health, metabolism, immune function, and nutrient absorption in chickens. Recent studies have focused on the effects of Eimeria tenella's (E. tenella) acute infection period on host health. However, recovery conditions, cecal microbiota composition, and functional differences in the ceca of chickens with varying resistance to E. tenella remain poorly understood during the recovery period after infection. This study aimed to compare growth performance, cecal histopathology, and the cecal microbiota characteristics in control (R_JC), resistant (R_JR), and susceptible (R_JS) chickens during recovery, using metagenomic sequencing. The results revealed significant differences in both cecal tissue structure and growth performance between the different groups during recovery. Although no significant differences were observed in microbial alpha diversity among the groups, sequencing analysis highlighted notable changes in microbial composition and abundance. Bacteroidetes, Firmicutes, and Proteobacteria were the predominant phyla in chicken cecal contents; however, Firmicutes abundance was lower in the R_JS group than in the R_JC and R_JR groups. Further analysis, combining linear discriminant analysis effect size (LEfSe) and differential heatmap analysis, identified Bacteroides_fluxus, Ruminococcus_flavefaciens, and Bacteroides_sp_CACC_737 as dominant microorganisms in the R_JR group (p < 0.05) compared to both the R_JC and R_JS groups. In contrast, Sutterella_sp_AM11-39, Bacteroides_sp_43_108, Mycobacterium, Mycoplasma_arginini, and Chlamydia dominated in the R_JS group, while Butyricimonas, Butyricimonas_sp_Marseille-P3923, and Flavonifractor_plautii were significantly reduced in the R_JS group (p < 0.05). Additionally, beneficial cecal microorganisms such as Flavonifractor_sp__An10, Pseudoflavonifractor, and Faecalicoccus were significantly decreased in both the R_JR and R_JS groups (p < 0.05) compared to the R_JC group. Predictive functional analysis using the KEGG and CAZy databases further indicated that the cecal microbiota in the R_JR group exhibited enhanced metabolism-related pathways, whereas these pathways were significantly diminished in the R_JS group, potentially influencing the recovery process from coccidial infection. These findings provide valuable insights into the cecal microbiota's role during recovery from E. tenella infection and deepen our understanding of the impact of coccidial infections on host health.}, }
@article {pmid40427319, year = {2025}, author = {Xu, C and Guo, X and Li, L}, title = {Metagenomic Comparison of Gut Microbes of Lemur catta in Captive and Semi-Free-Range Environments.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/ani15101442}, pmid = {40427319}, issn = {2076-2615}, abstract = {In order to protect endangered species, many zoos adopt diverse rearing models to achieve optimal conservation outcomes. This study employed metagenomic approaches to assess differences in the fecal microbiome of captive and semi-free-ranging ring-tailed lemurs (Lemur catta). The results show that captivity significantly altered the microbial community structure. The inter-individual variability in the microbial community within the captive-bred (CB) group was lower than that in the semi-free-ranging (FR) group, yet these individuals harbored a higher abundance of potential pathogens (Treponema_D). In contrast, microbial genera associated with fiber degradation and short-chain fatty acid production in the FR group were significantly elevated (Faecalibacterium, Roseburia, and Megamonas) as compared to the CB group. Environmental variations between the two rearing systems led to distinct profiles in microbial functions and carbohydrate-active enzyme gene composition. Notably, the FR group of lemurs exhibited an increased abundance of enzyme genes associated with the degradation of complex polysaccharides (cellulose, hemicellulose, and pectin), suggesting that their diet, rich in natural plant fibers, enhances the capacity of their gut microbiota to extract essential energy and nutrients. Conversely, the CB group displayed a more homogeneous microbial community with a higher prevalence of potential pathogens, implying that a captive lifestyle may negatively impact gastrointestinal health. These findings offer valuable insights into the influence of rearing conditions on gut microbial ecology and its potential implications for the health management of ring-tailed lemurs.}, }
@article {pmid40426565, year = {2025}, author = {Wang, L and He, J and Feng, H and Li, Q and Song, M and Gou, H and He, Y and Zhu, K}, title = {Antifungal Effects of the Phloroglucinol Derivative DPPG Against Pathogenic Aspergillus fumigatus.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/antibiotics14050499}, pmid = {40426565}, issn = {2079-6382}, support = {32230106//National Natural Science Foundation of China/ ; }, abstract = {Background: Fungal infections pose an increasingly predominant threat to human and animal health. Modified compounds derived from chemo-diverse natural products offer enhanced therapeutic efficacies and promising approaches to combat life-threatening fungal pathogens. Methods: We performed biosynthetic gene clusters analysis of 2,4-diacetylchloroglucoside (DAPG) in 4292 shotgun metagenomes samples from the healthy and diseased skin. Then, we assessed the antifungal activity of DAPG and the derivative 2,4-diproylphloroglucinol (DPPG) against pathogenic fungi by minimum inhibitory concentrations. The inhibitory effects of DPPG were measured using hyphal growth assay and spore germination assay. Concurrently, the mechanism of DPPG on Aspergillus fumigatus was investigated in membrane permeability and fluidity. The therapeutic efficacy was evaluated in a Galleria mellonella infection model. Results: We observed a significantly higher abundance of bacteria harboring DAPG biosynthetic clusters on healthy skin compared to diseased skin. Further, we designed and synthesized a series of phloroglucinol derivatives based on DAPG and obtained an antifungal candidate DPPG. DPPG not only exhibited robust antifungal activity against Aspergillus spp. and Candida spp. but also impaired hyphal growth and spore germination of A. fumigatus in vitro. A mechanism study showed that DPPG reduced membrane fluidity and increased the leakage of cellular contents, resulting in membrane perturbation and fungal death. Lastly, the therapeutic efficacy of DPPG was confirmed in a G. mellonella infection model. Conclusions: Our study demonstrates that DPPG is a potent scaffold to combat invasive fungal infections.}, }
@article {pmid40426556, year = {2025}, author = {Starkova, D and Egorova, S and Suzhaeva, L and Nguyen, TQ and Kaftyreva, L and Makarova, M and Zhamborova, S and Polev, D and Saitova, A and Nguyen, VH and Vo, TK and Nguyen, LT}, title = {Antimicrobial Resistance and Phylogenetic Analysis of Multidrug-Resistant Non-Typhoidal Salmonella Isolates from Different Sources in Southern Vietnam.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/antibiotics14050489}, pmid = {40426556}, issn = {2079-6382}, abstract = {Background/Objectives: Non-typhoidal Salmonella (NTS) is one of the most common causative agents of food poisoning in Vietnam, and contaminated livestock meat poses a major risk to human health. The present study aims to provide the genetic characteristics of NTS with a particular focus on antimicrobial resistance and determine phylogenetic relationships between isolates from different sources in Southern Vietnam based on whole-genome sequencing (WGS) data. Methods: A total of 49 NTS isolates from pork/broiler meat, pigs, chickens, and humans were collected in Ho Chi Minh City and four provinces of Southern Vietnam. Phenotypic antimicrobial susceptibility testing (AST) and WGS for all isolates were performed. Results: As a result, 14 different serotypes were identified, among which S. Typhimurium and its monophasic variant were the dominant serotypes for human and pig sources. All chicken samples belonged to S. Indiana, whereas S. Infantis predominated in broiler meat. AST results revealed that 98% of isolates were multidrug resistant. NTS strains isolated from poultry and pigs exhibited resistance to the highest priority antimicrobials-quinolones and polymyxin, as well as to β-lactams, aminoglycosides, tetracycline, and sulfonamide, which are considered to be critical for the treatment of severe diseases. Conclusions: The results highlight the utmost importance of issues related to the selection, spreading, and transmission of multi-resistant strains from animals to humans.}, }
@article {pmid40426541, year = {2025}, author = {Buzgó, L and Kiss, Z and Göbhardter, D and Lesinszki, V and Ungvári, E and Rádai, Z and Laczkó, L and Damjanova, I and Kardos, G and Tóth, &#xc1;}, title = {High Prevalence of Cefiderocol Resistance Among New Delhi Metallo-β-Lactamase Producing Klebsiella pneumoniae High-Risk Clones in Hungary.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/antibiotics14050475}, pmid = {40426541}, issn = {2079-6382}, abstract = {BACKGROUND/OBJECTIVES: The global spread of carbapenemase-producing K. pneumoniae (CPKP) strains represent a severe public health threat due to very limited choice of antibacterial therapy. Cefiderocol, a novel siderophore-cephalosporin, may represent a new therapeutic option but resistance is increasingly being described. Our aim was to investigate in vitro cefiderocol susceptibility among CPKP strains in Hungary and assess correlations between resistance, carbapenemase types, and clonal lineages.<br><br>METHODS: The study was performed on 420 CPKP strains from 34 Hungarian healthcare institutes (HCIs) submitted to the National Reference Laboratory of Antimicrobial Resistance (March 2021 to April 2023). The disk diffusion method (Liofilchem, Via Scozia, Italy) was used for in vitro cefiderocol susceptibility testing (according to EUCAST guidelines). For molecular epidemiologic investigation, we used whole genome sequencing (Illumina MiSeq, 150 bp paired-end) and pulsed-field gel electrophoresis (PFGE). Carbapenemase gene type was determined by multiplex PCR. Statistical analysis was performed in R (v.4.2.0).<br><br>RESULTS: Dominant high-risk clones (ST147, ST395, ST258) exhibited regional distribution, with ST147/NDM-1 strains showing the highest cefiderocol resistance (75%). Overall resistance was 65%. Carbapenemase gene types occurred as follows: 35 blaVIM, 53 blaKPC, 57 blaOXA-48-like, 153 blaNDM, and 122 blaOXA-48-like+blaNDM. Cefiderocol resistance rates by carbapenemase type were 20%, 44%, 70%, and 75% in the case of blaVIM, blaOXA-48-like, blaKPC, blaNDM, and blaOXA-48-like+blaNDM.<br><br>CONCLUSIONS: The results show a high prevalence of cefiderocol resistance in CPKP in Hungary, with different rates of resistance in different carbapenemase gene-carrying high-risk clones, highlighting the growing challenge in treating these infections.}, }
@article {pmid40426528, year = {2025}, author = {Yi, L and Ren, Z and Feng, Y and Zhang, Y and Liu, J and Yuan, X and Kuang, Q and Deng, H and Yang, B and Yu, D}, title = {Chronic Heat Stress Can Induce Conjugation of a Novel ermB-Containing ICEFZMF, Increasing Resistance to Erythromycin Among Enterococcus Strains in Diverse Intestinal Segments in the Mouse Model.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/antibiotics14050460}, pmid = {40426528}, issn = {2079-6382}, support = {No. 32302922//Natural Science Foundation of China/ ; No. 2024J08038//Natural Science foundation of Fujian province/ ; JAT220060//Education Research Fund for Young Academic of Fujian Province/ ; }, abstract = {BACKGROUND: The impact of heat stress on intestinal bacterial antimicrobial resistance (AMR) and its underlying mechanisms is not fully understood. This study aims to explore how heat stress influences AMR in the gut and the mechanisms involved.<br><br>METHODS: A Specific-Pathogen-Free (SPF) mouse model was used, divided into a control group (maintained at 25 &#xb0;C) and a heat stress group (exposed to 42 &#xb0;C for 30 min twice daily for 55 days). The effectiveness of the model was verified by RT-qPCR and histopathological analysis. Antibiotic susceptibility testing and clonal analysis (ERIC-PCR) were performed. Colonization assays were conducted to determine the accumulation of resistant strains in the gut. Metagenomic sequencing was conducted to investigated microbial composition.<br><br>RESULTS: RT-qPCR and Histopathological analysis revealed intestinal damage and significant upregulation of genes related to stress response, intestinal barrier integrity and inflammation, indicating successful model establishment and physiological alterations. Antibiotic susceptibility testing revealed increased resistance to erythromycin, chloramphenicol, and tetracycline among Enterococcus strains. Clonal analysis demonstrated that these resistant strains were clonally unrelated. Sequencing identified a novel ermB-carrying integrative and conjugative element (ICEFZMF) among four erythromycin-resistant strains. The rectum harbored a higher proportion of erythromycin-resistant Enterococcus strains with elevated minimum inhibitory concentrations (MICs) after 25 days of heat stress exposure. Colonization assays confirmed that heat stress led to the accumulation of erythromycin-resistant Enterococcus in the rectum. Metagenomic sequencing revealed significant changes in microbial composition, favoring anaerobic metabolism.<br><br>CONCLUSIONS: This study suggests that chronic heat stress can promote the emergence of antibiotic-resistant strains through ICE transfer, providing insight for environmental safety.}, }
@article {pmid40426500, year = {2025}, author = {Tóth, AG and Tóth, DL and Remport, L and Tóth, I and Németh, T and Dubecz, A and Patai, &#xc1;V and Wagenhoffer, Z and Makrai, L and Solymosi, N}, title = {A One Health Approach Metagenomic Study on Antimicrobial Resistance Traits of Canine Saliva.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/antibiotics14050433}, pmid = {40426500}, issn = {2079-6382}, support = {SRF-001//University of Veterinary Medicine Budapest/ ; 874735 (VEO)//European Union's Horizon 2020/ ; 2024-2.1.2-EK&#xd6;P-2024-00018//Ministry of Culture and Innovation of Hungary/ ; }, abstract = {Background: According to the One Health concept, the physical proximity between pets and their owners facilitates the interspecies spread of bacteria including those that may harbor numerous antimicrobial resistance genes (ARGs). Methods: A shotgun sequencing metagenomic data-based bacteriome and resistome study of 1830 canine saliva samples was conducted considering the subsets of ARGs with higher public health risk, ESKAPE pathogen relatedness (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), and survey results on the physical and behavioral characteristics of the participating dogs. Results: A total of 318 ARG types achieved sufficiently high detection rates. These ARGs can affect 31 antibiotic drug classes through various resistance mechanisms. ARGs against tetracyclines, cephalosporins, and, interestingly, peptides appeared in the highest number of samples. Other Critically Important Antimicrobials (CIAs, WHO), such as aminoglycosides, fluoroquinolones, or macrolides, were among the drug classes most frequently affected by ARGs of higher public health risk and ESKAPE pathogen-related ARGs of higher public health risk. Several characteristics, including coat color, sterilization status, size, activity, or aggressiveness, were associated with statistically significant differences in ARG occurrence rates (p < 0.0500). Conclusions: Although the oral microbiome of pet owners is unknown, the One Health and public health implications of the close human-pet bonds and the factors potentially underlying the increase in salivary ARG numbers should be considered, particularly in light of the presence of ARGs affecting critically important drugs for human medicine.}, }
@article {pmid40426336, year = {2025}, author = {Wang, Y and Zhou, K and Zhang, Y and Li, C and Zhang, Y and Ren, X and Mi, C and Ma, L and Duan, Y and Liu, M and Ping, G and Tian, X and Song, Z}, title = {The Systemic Impact of Helicobacter pylori Infection on the Microbiome of Whole Digestive Tract Based on Mucosal, Gastric Juice, and Fecal Specimens.}, journal = {Helicobacter}, volume = {30}, number = {3}, pages = {e70047}, doi = {10.1111/hel.70047}, pmid = {40426336}, issn = {1523-5378}, support = {82170562//National Natural Science Foundation of China/ ; 7232199//Beijing Natural Science Foundation/ ; BYSYZD2023008//Key Clinical Projects of Peking University Third Hospital/ ; }, mesh = {Humans ; *Feces/microbiology ; Cross-Sectional Studies ; *Helicobacter Infections/microbiology ; Male ; Middle Aged ; Female ; *Gastric Juice/microbiology ; Adult ; *Helicobacter pylori/physiology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; *Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Metagenomics ; }, abstract = {BACKGROUND: Recent studies have found that in addition to directly impacting the gastric microbiome, Helicobacter pylori (H. pylori) infection may cause intestinal microbial dysbiosis. However, most existing studies on the influence of H. pylori infection on the intestinal microbiome used fecal specimens with inconsistent conclusions. Only one limited study on 8 H. pylori-infected patients has previously assessed the impact of H. pylori infection on the microbiome of the entire gastrointestinal tract, finding no significant effect on the bacterial composition of the lower gastrointestinal tract.<br><br>METHODS: This single-center cross-sectional study collected mucosa of the esophagus, stomach, small intestine, and colon, as well as gastric juice and feces from 120 participants of the H. pylori-infected group (HIG) and 30 of the healthy control group (HCG). 16S rRNA sequencing was applied to analyze the bacterial composition and functional pathways, and metagenomics was adopted to assess the composition of viruses, eukaryotes, and archaea in the feces, as well as the antibiotic resistance gene (ARG) and virulence factors of bacteria (VF).<br><br>RESULTS: Compared with the HCG, the alpha and beta diversity of bacteria in the mucosa of the whole digestive tract and the gastric juice of the HIG showed significant changes, with increased microbial dysbiosis index and significantly different compositions at the phylum and genus levels. Functional pathway analysis revealed that the metabolic characteristics of the flora changed in the HIG, with site-specific differences. Fecal specimens demonstrated no significant differences in the above indicators between the two groups. In addition, feces-based metagenomic analysis revealed that only eukaryotes had higher diversity in the HIG, whereas viruses and archaea showed no significant changes; the Shannon index of ARG increased; and VF showed no significant change.<br><br>CONCLUSIONS: This study revealed that H. pylori infection significantly influenced the diversity, composition, and metabolic functional pathway of bacteria in different parts of the digestive tract and the gastric juice. Moreover, fecal microbial composition may not fully represent the mucosal microbial composition of the gastrointestinal tract.<br><br>TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR2300073419.}, }
@article {pmid40426239, year = {2025}, author = {Dehon, E and Vrchovecká, S and Mathieu, A and Favre-Bonté, S and Wacławek, S and Droit, A and Vogel, TM and Sanchez-Cid, C}, title = {Impact of fluoroquinolone and heavy metal pollution on antibiotic resistance maintenance in aquatic ecosystems.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {58}, pmid = {40426239}, issn = {2524-6372}, support = {JPI AMR SARA//Agence Nationale de la Recherche/ ; JPI AMR SARA//Agence Nationale de la Recherche/ ; }, abstract = {BACKGROUND: Freshwater pollution with compounds used during anthropogenic activities could be a major driver of antibiotic resistance emergence and dissemination in environmental settings. Fluoroquinolones and heavy metals are two widely used aquatic pollutants that show a high stability in the environment and have well-known effects on antibiotic resistance selection. However, the impact of these compounds on antibiotic resistance maintenance in aquatic ecosystems remains unknown. In this study, we used a microcosm approach to determine the persistence of two fluoroquinolones (ciprofloxacin, ofloxacin) and two heavy metals (copper and zinc) in the Rhône river over 27 days. In addition, we established links between antibiotic and metal pollution, alone and in combination, and the composition of freshwater bacterial communities, the selection of specific members and the selection and maintenance of antibiotic and metal resistance genes (ARGs and MRGs) using a metagenomics approach.<br><br>RESULTS: Whereas ofloxacin was detected at higher levels in freshwater after 27 days, copper had the strongest influence on bacterial communities and antibiotic and metal resistance gene selection. In addition, heavy metal exposure selected for some ARG-harboring bacteria that contained MRGs. Our research shows a heavy metal-driven transient co-selection for fluoroquinolone resistance in an aquatic ecosystem that could be largely explained by the short-term selection of Pseudomonas subpopulations harboring both fluoroquinolone efflux pumps and copper resistance genes.<br><br>CONCLUSION: This research highlights the complexity and compound-specificity of dose-response relationships in freshwater ecosystems and provides new insights into the medium-term community structure modifications induced by overall sub-inhibitory levels of antibiotic and heavy metal pollution that may lead to the selection and maintenance of antibiotic resistance in low-impacted ecosystems exposed to multiple pollutants.}, }
@article {pmid40426218, year = {2025}, author = {Liwinski, T and Auer, MK and Schröder, J and Pieknik, I and Casar, C and Schwinge, D and Henze, L and Stalla, GK and Lang, UE and von Klitzing, A and Briken, P and Hildebrandt, T and Desbuleux, JC and Biedermann, SV and Holterhus, PM and Bang, C and Schramm, C and Fuss, J}, title = {Correction: Gender-affirming hormonal therapy induces a gender-concordant fecal metagenome transition in transgender individuals.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {295}, pmid = {40426218}, issn = {1741-7015}, }
@article {pmid40426166, year = {2025}, author = {He, J and Yang, L and Niu, C}, title = {Human pegivirus detected in patient with reversible severe encephalitis and axillary lymphadenopathy: a case report.}, journal = {Diagnostic pathology}, volume = {20}, number = {1}, pages = {66}, pmid = {40426166}, issn = {1746-1596}, mesh = {Humans ; Female ; Middle Aged ; *Lymphadenopathy/virology/diagnosis ; *Flaviviridae Infections/diagnosis/virology/drug therapy/complications ; *Flaviviridae/isolation &amp; purification/genetics ; *Encephalitis, Viral/virology/diagnosis/drug therapy ; Antiviral Agents/therapeutic use ; Treatment Outcome ; }, abstract = {Human pegivirus (HPgV) has been postulated as a potential etiological factor in encephalomyelitis and exhibits lymphotropic characteristics. However, the co-occurrence of encephalitis and lymphadenopathy with HPgV detected has never been reported. Herein, we report a case of a 48-year-old woman admitted with fever followed by sudden loss of consciousness. Radiological imaging demonstrated encephalitis and lymphadenopathy. Initial analysis of blood and cerebrospinal fluid (CSF) failed to reveal specific etiology. The only pathogen found in CSF was later determined to be HPgV using metagenomic next-generation sequencing (mNGS). After receiving treatment with acyclovir, meropenem, and ceftriaxone sodium, the patient fully recovered. This case contributes additional evidence in support of the hypothesis regarding the pathogenic potential of HPgV and highlights the diagnostic utility of mNGS in detecting rare pathogens.}, }
@article {pmid40426027, year = {2025}, author = {Bilton, TP and Alemu, SW and Dodds, KG and Henry, H and Hess, MK and Jordan, R and Booker, F and Hickey, SM and Amyes, N and Knowler, K and Sandoval, E and Peers-Adams, J and van Stijn, TC and Baird, H and Watson, T and Bain, W and Veenvliet, B and Pile, G and Bryson, B and Clarke, SM and Johnson, PL and McEwan, JC and Rowe, SJ}, title = {Rumen metagenome profiles are heritable and rank the New Zealand national sheep flock for enteric methane emissions.}, journal = {Genetics, selection, evolution : GSE}, volume = {57}, number = {1}, pages = {25}, pmid = {40426027}, issn = {1297-9686}, support = {C10X1807//Ministry of Business, Innovation and Employment/ ; }, mesh = {Animals ; *Methane/metabolism/analysis ; *Rumen/microbiology/metabolism ; *Metagenome ; Sheep/genetics/metabolism/microbiology ; New Zealand ; Female ; Male ; Carbon Dioxide/metabolism ; }, abstract = {BACKGROUND: Global targets to reduce greenhouse gas emissions to meet international climate change commitments have driven the livestock industry to develop solutions to reduce methane emission in ruminants while maintaining production. Research has shown that selective breeding for low methane emitting ruminants using genomic selection is one viable solution to meet methane targets at a national level. However, this requires obtaining sufficient measures of methane on individual animals across the national herd. In sheep, one affordable method for measuring methane on-farm to rank animals on their methane emissions is portable accumulation chambers (PAC), although this method is not without its challenges. An alternative is to use a proxy trait that is genetically correlated with PAC methane measures. One such trait that has shown promise is rumen metagenome community (RMC) profiles. In this study, we investigate the potential of using RMC profiles as a proxy trait for methane emissions from PAC using a large sheep dataset consisting of 4585 mixed-sex lambs from several flocks and years across New Zealand.<br><br>RESULTS: RMC profiles were generated from rumen samples collected on the animals immediately after being measured through PAC using restriction enzyme-reduced representation sequencing. We predicted methane (CH4) and carbon dioxide (CO2) emissions (grams per day), as well as the ratio CH4/(CO2&#x2009;+&#x2009;CH4) (CH4Ratio), from the RMC profiles and SNP-array genotype data. Heritability and microbiability estimates were similar to values found in the literature for all traits. The correlation of PAC methane with predicted methane was 1.9- to 2.3-fold (CH4) and 1.2- to 1.5-fold (CH4Ratio) greater for RMC profiles compared to host genomics only. The genetic correlation between methane predicted from RMC profiles and PAC methane was 0.75&#x2009;&#xb1;&#x2009;0.12 for CH4 and 0.64&#x2009;&#xb1;&#x2009;0.11 for CH4Ratio when using a validation set consisting of the animals with the most recent year of birth in the dataset.<br><br>CONCLUSIONS: RMC profiles are predictive of, and genetically correlated, with PAC methane measures. Therefore, RMC profiles are a suitable proxy trait for determining the genetic merit of an animal's methane emissions and could be incorporated into existing breeding programs to facilitate selective breeding for low methane emitting sheep.}, }
@article {pmid40425565, year = {2025}, author = {Mezhibovsky, E and Wu, G and Wu, Y and Ning, Z and Bacalia, K and Sadangi, S and Patel, R and Poulev, A and Duran, RM and Macor, M and Coyle, S and Lam, YY and Raskin, I and Figeys, D and Zhao, L and Roopchand, DE}, title = {Grape polyphenols reduce fasting glucose and increase hyocholic acid in healthy humans: a meta-omics study.}, journal = {NPJ science of food}, volume = {9}, number = {1}, pages = {87}, pmid = {40425565}, issn = {2396-8370}, support = {R01 AT010242/NH/NIH HHS/United States ; }, abstract = {Grape polyphenols (GPs) are rich in B-type proanthocyanidins, which promote metabolic resilience. Longitudinal metabolomic, metagenomic, and metaproteomic changes were measured in 27 healthy subjects supplemented with soy protein isolate (SPI, 40 g per day) for 5 days followed by GPs complexed to SPI (GP-SPI standardized to 5% GPs, 40 g per day) for 10 days. Fecal, urine, and/or fasting blood samples were collected before supplementation (day -5), after 5 days of SPI (day 0), and after 2, 4 and 10 days of GP-SPI. Most multi-omic changes observed after 2 and/or 4 days of GP-SPI intake were temporary, returning to pre-supplementation profiles by day 10. Shotgun metagenomics sequencing provided insights that could not be captured with 16S rRNA amplicon sequencing. Notably, 10 days of GP-SPI decreased fasting blood glucose and increased serum hyocholic acid (HCA), a glucoregulatory bile acid, which negatively correlated with one gut bacterial guild. In conclusion, GP-induced suppression of a bacterial guild may lead to higher HCA and lower fasting blood glucose.}, }
@article {pmid40425088, year = {2025}, author = {Ma, X and Zhang, Q and Tan, X and Lu, Y and Wang, H and Zhu, G}, title = {Biological co-reduction of Perchlorate and Nitrate in wastewater: Insights into the Competitive Inhibition Mechanisms in UASB Reactors.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121950}, doi = {10.1016/j.envres.2025.121950}, pmid = {40425088}, issn = {1096-0953}, abstract = {The pollution caused by wastewater with high perchlorate concentrations should not be underestimated. Efficient biodegradation is a promising treatment method. Nitrate, which often coexists with perchlorate in wastewater, has a great influence on its degradation. Therefore, in-depth studies on the combined degradation mechanisms of perchlorate and nitrate under coexisting conditions are essential. This study developed two heterotrophic up-flow anaerobic sludge blanket (UASB) reactors. In R1, perchlorate was efficiently removed, with a load of 927 ± 7.72 gClO4[-]/(m[3]·d), and removal efficiency exceeded 99.4%. In R2, perchlorate and nitrate were removed simultaneously, with loadings of 927 ± 3.52 gClO4[-]/(m[3]·d) and 81 ± 7.25 gNO3[-]-N/(m[3]·d), respectively. Removal efficiencies were 95.9 ± 3.24% for perchlorate and 99.8 ± 0.09% for nitrate. A modified Monod competition model indicated that nitrate concentration exerts a more significant inhibitory effect at nitrate-to-perchlorate concentration ratios of 1:1 or higher. Batch experiments identified the optimal CH3COO[-]: ClO4[-]: NO3[-]-N molar ratio as 5.4:1:3.6 and the ideal environmental ORP as -200 ± 20 mV for co-removal of perchlorate and nitrate. Metagenomic analysis revealed the dynamics of microbial communities and functional genes associated with perchlorate and nitrate reduction. Nitrate presence regulates the abundance and activity of NapC and cyt c transporter enzymes, which indirectly weaken the perchlorate electron transport pathway and directly affect terminal electron receptor coupling efficiency. This study provided valuable insights for optimizing biological treatment strategies for wastewater contaminated with perchlorate and nitrate.}, }
@article {pmid40424901, year = {2025}, author = {Victor, MP and Øvreås, L and Marathe, NP}, title = {Characterization of known and novel clinically important antibiotic resistance genes and novel microbes from wastewater-impacted high Arctic fjord sediments.}, journal = {The Science of the total environment}, volume = {985}, number = {}, pages = {179699}, doi = {10.1016/j.scitotenv.2025.179699}, pmid = {40424901}, issn = {1879-1026}, abstract = {Arctic microbiota is enigmatic and highly underexplored. With the aim of understanding the resistome and microbiota of high-Arctic fjord sediments and the effect of wastewater discharge on sediment microbiota, we analyzed sediments from Advent fjord in Svalbard using metagenomics. We show the presence of 888 clinically relevant antibiotic resistance genes including genes coding resistance against last-resort antibiotics such as carbapenems, colistin, vancomycin, linezolid and tigecycline in the sediment microbiota. Using computational models, 478 novel β-lactamases belonging to 217 novel β-lactamase families were revealed in the sediment microbiota. Further, we identified hosts for 69 novel families and showed that these genes are widespread in the Arctic environment. We assembled 644 metagenome-assembled genomes (MAGs) from sediment metagenomes. Of these >97 % belonged to novel taxa with 89 bacterial MAGs representing seven putative novel phyla. These MAGs encoded important functions like nutrient cycling and methane metabolism etc. Our study demonstrated mixing of human associated bacteria and Arctic sediment microbiota. It provides the first comprehensive dataset of the distribution and diversity of novel microbes and β-lactamases in the wastewater-impacted high Arctic fjord sediments.}, }
@article {pmid40424445, year = {2025}, author = {Li, W and Cai, J and Chen, G and Liu, Y and Wu, X and Bai, Y and Wu, Y and Wang, T}, title = {Microbial community succession mediated by planting patterns in the Loess Plateau, China: Implications for ecological restoration.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0324786}, doi = {10.1371/journal.pone.0324786}, pmid = {40424445}, issn = {1932-6203}, mesh = {*Soil Microbiology ; China ; Soil/chemistry ; *Microbiota ; Forests ; Ecosystem ; *Environmental Restoration and Remediation ; }, abstract = {Microbial community succession plays a key role in restoring fragile ecosystems and mitigating ecological degradation. However, the mechanisms by which vegetation restoration promotes ecological restoration and microbial community reconstruction in degraded soils remain unclear. This study utilized metagenomic high-throughput sequencing technology to analyze microbial community dynamics in soil samples collected from eight different planting patterns in the ecologically degraded areas of the Chinese Loess Plateau. The results indicated significant effects of terrain location and restorative cropping patterns on soil microbial abundance and function. In particular, soil C and N nutrient abundance was highest in mixed forest soils, and the total number of microorganisms was highest and more diverse. Therefore, through vegetation restoration, mixed forests significantly enhanced regional ecological functions. Notably, creating mixed forests with both trees and shrubs resulted in optimal ecological functions, providing a valuable direction for vegetation construction and structural optimization in the region.}, }
@article {pmid40424276, year = {2025}, author = {Goldman, M and Zhao, C and Pollard, KS}, title = {Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM).}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1012277}, doi = {10.1371/journal.pcbi.1012277}, pmid = {40424276}, issn = {1553-7358}, abstract = {Microbiome association studies typically link host disease or other traits to summary statistics measured in metagenomics data, such as diversity or taxonomic composition. But identifying disease-associated species based on their relative abundance does not provide insight into why these microbes act as disease markers, and it overlooks cases where disease risk is related to specific strains with unique biological functions. To bridge this knowledge gap, we developed microSLAM, a mixed-effects model and an R package that performs association tests that connect host traits to the presence/absence of genes within each microbiome species, while accounting for strain genetic relatedness across hosts. Traits can be quantitative or binary (such as case/control). MicroSLAM is fit in three steps for each species. The first step estimates population structure across hosts. Step two calculates the association between population structure and the trait, enabling detection of species for which a subset of related strains confer risk. To identify specific genes whose presence/absence across diverse strains is associated with the trait, step three models the trait as a function of gene occurrence plus random effects estimated from step two. Applying microSLAM to 710 gut metagenomes from inflammatory bowel disease (IBD) samples, we discovered 56 species whose population structure correlates with IBD, meaning that different lineages are found in cases versus controls. After controlling for population structure, 20 species had genes significantly associated with IBD. Twenty-one of these genes were more common in IBD patients, while 32 genes were enriched in healthy controls, including a seven-gene operon in Faecalibacterium prausnitzii that is involved in utilization of fructoselysine from the gut environment. The vast majority of species detected by microSLAM were not significantly associated with IBD using standard relative abundance tests. These findings highlight the importance of accounting for within-species genetic variation in microbiome studies.}, }
@article {pmid40423879, year = {2025}, author = {Zhao, Y and Dai, Z and Lang, Y and Li, R and Zheng, H and Mi, J and He, X and Liu, J and Xiang, R and Mei, X and Liu, Y and Wang, Y and Guo, H and Yang, Q and Ren, K and Yang, T}, title = {Screening of Fecal Bacteroides Strains and Discovery of Bacteroides eggerthii S13-F8 with Protective Effects Against Chemotherapy-Induced Diarrhea.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40423879}, issn = {1867-1314}, support = {2024NSFSC0044//the Natural Science Foundation of Sichuan province/ ; No. 2024kjTzn04//CMC Excellent-talent Program/ ; }, abstract = {Chemotherapy-induced diarrhea (CID) is a frequent gastrointestinal side effect in cancer patients, particularly associated with the use of 5-fluorouracil (5-FU). This study aimed to isolate multiple Bacteroides strains from the feces of healthy individuals and identify Bacteroides eggerthii (B. eggerthii) S13-F8 as the optimal candidate for alleviating CID. Whole-genome sequencing of B. eggerthii S13-F8 was conducted to uncover its functional characteristics and explore the potential mechanisms underlying its protective effects against CID. The anti-CID efficacy of B. eggerthii S13-F8 was assessed using multiple parameters, including diarrhea severity, food intake, and body weight changes. Comprehensive analyses, including blood tests, intestinal histopathology, colon transcriptomics, and fecal metagenomics, were performed to elucidate its underlying mechanisms. In a 5-FU-induced mouse model, B. eggerthii S13-F8 significantly alleviated weight loss and diarrhea. Histological examination revealed that B. eggerthii S13-F8 preserved the villus height-to-crypt depth (V/C) ratio and protected goblet cells in colonic tissues. Gene expression analysis showed that B. eggerthii S13-F8 upregulated protective markers, such as Aqp8, Slc26a3, and mucin-related genes (TFF3, FCGBP, and Muc2), while downregulating pro-inflammatory mediators, including IL-1α, IL-22, and Cxcl2. Furthermore, B. eggerthii S13-F8 modulated gut microbiota composition by suppressing pathogenic bacteria (Pseudomonas aeruginosa, Salmonella, γ-Proteobacteria, and Shigella) and enriching beneficial taxa, such as Lactobacillus and Akkermansia muciniphila. In conclusion, B. eggerthii S13-F8 demonstrates significant potential in mitigating severe diarrhea caused by 5-FU chemotherapy, providing a strong foundation for its development as a live biotherapeutic for CID treatment.}, }
@article {pmid40423870, year = {2025}, author = {Zhang, M and Zhang, H and Hong, A and Huang, J and Yang, L and Long, Y and Yu, Z}, title = {Dynamic changes of dental plaque and saliva microbiota in OSCC progression.}, journal = {Clinical oral investigations}, volume = {29}, number = {6}, pages = {314}, pmid = {40423870}, issn = {1436-3771}, support = {32170071//This work was funded by the National Natural Science Foundation of China/ ; 82273466//This work was funded by the National Natural Science Foundation of China/ ; 2023ZJ1120//Hunan Provincial Science and Technology Department/ ; 2024JJ2039//Natural Science Foundation of Hunan Province/ ; 2024JJ8117//Natural Science Foundation of Hunan Province/ ; }, mesh = {Humans ; *Saliva/microbiology ; Disease Progression ; *Dental Plaque/microbiology ; *Mouth Neoplasms/microbiology/pathology ; *Carcinoma, Squamous Cell/microbiology/pathology ; Female ; *Microbiota ; Male ; Middle Aged ; Neoplasm Staging ; Metagenomics ; }, abstract = {OBJECTIVES: To elucidate the changes in microbial composition and genomics in saliva and dental plaque during the progression of Oral Squamous Cell Carcinoma (OSCC), and to identify virulence factors and pathways associated with tumor differentiation in OSCC patients.<br><br>MATERIALS AND METHODS: Using metagenomic sequencing, 64 saliva and dental plaque samples from OSCC patients at different stages of differentiation were examined.<br><br>RESULTS: The results showed notable differences in the microbial composition and genomic profiles across ecological regions and differentiation degrees. Notably, the relative abundance of specific microbes, such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Haemophilus parainfluenzae, increased in poorly differentiated OSCC. Microbial alpha diversity in dental plaque and saliva correlates with tumor T staging. Dental plaque microbiota shows higher specialization, especially in poorly differentiated tumors. Both microbiota types become more stable with advanced T staging. Genomic analysis reveals increased virulence factors in poorly differentiated stages.Subsequently, functional pathway analysis and tracing of pathogens reveal specific microbial mechanisms in oral cancer pathogenesis. Certain oral pathogens may promote tumorigenesis by secreting factors like GAPDH (glyceraldehyde-3-phosphate dehydrogenase), GspG (a gingipain precursor), and AllS (a lysine-specific gingipain precursor).<br><br>CONCLUSIONS: OSCC progression is associated with altered microbial composition, diversity, and genomic profiles in saliva and dental plaque. Poorly differentiated stages show higher abundance of pathogens and virulence factors, implicating them in tumorigenesis.<br><br>CLINICAL RELEVANCE: Understanding the microbial and genomic changes in saliva and dental plaque during OSCC progression could aid in developing new diagnostic biomarkers and targeted therapies, potentially enhancing early detection, treatment efficacy, and patient prognosis. Maintaining oral microbiota homeostasis may also help prevent oral cancer.}, }
@article {pmid40423743, year = {2025}, author = {Zhao, Z and Leng, S and Zou, Y and Xiang, L and Li, Y and Liu, Y and Wang, C and Yu, M}, title = {First report of Stemphylium lycopersici keratitis, a complex corneal infection case.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {15}, number = {1}, pages = {46}, pmid = {40423743}, issn = {1869-5760}, support = {82070928//National Natural Science Foundation of China/ ; 2022-YF05-01936-SN//Chengdu Municipal Science and Technology Program/ ; }, abstract = {Filamentous fungi are among the emerging causes of infections, although corneal infections caused by these fungi are rare, they can lead to severe clinical outcomes. In this report, we present the first documented case of keratitis caused by Stemphylium lycopersici, a filamentous hemipteran fungus of the Pleosporaceae family. A 66-year-old man presented conjunctival redness, irritation, and visual deterioration in his left eye, following a stone chip injury that occurred five months earlier. Despite multiple treatments, the causative pathogen remained unidentified, leading to worsening symptoms and significant vision loss. This deterioration led the patient to seek care at our hospital. An in vivo confocal microscopy (IVCM) examination suggested a fungal infection. Consequently, antifungal medications were administered, but the condition did not improve. Metagenomic next-generation sequencing (mNGS) examination of corneal scrapings revealed a mixed infection with S. lycopersici and human alphaherpesvirus 1. This definitive diagnosis facilitated the implementation of targeted therapy, leading to progressive symptomatic improvement. Early and rapid pathogen identification using mNGS analysis of corneal scrapings enables accurate management of infectious keratitis, contributing to visual recovery and reducing the risk of resistance to corneal pathogenic microbes.}, }
@article {pmid40422860, year = {2025}, author = {Zhang, Y and Ge, J and Wang, Y and Tang, Z and Ma, X and Liu, J and Wu, D and Wu, X}, title = {Clinical value of metagenomic next-generation sequencing in screening oropharyngeal colonization in patients undergoing allogeneic hematopoietic stem cell transplantation: a prospective observational study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0002825}, doi = {10.1128/spectrum.00028-25}, pmid = {40422860}, issn = {2165-0497}, abstract = {UNLABELLED: Screening for colonization is an essential procedure in allogeneic hematopoietic stem cell transplantation (allo-HSCT). Although metagenomic next-generation sequencing (mNGS) has played an important role in the diagnosis of complex and challenging infections, its effectiveness in screening oropharyngeal colonization is not yet fully assessed. We performed a prospective analysis (ChiCTR2300069450) involving 128 allo-HSCT patients between June 2022 and June 2023. Before the conditioning regimen, all patients underwent oropharyngeal and anal swab tests to detect colonizing pathogens. In addition to culture-based methods, we also analyzed oropharyngeal swab samples using mNGS. Among the allo-HSCT patients, the overall colonization rate from cultures was 15.6%, while mNGS identified an oropharyngeal colonization rate of 49.2%. Patients with oropharyngeal Enterobacteriaceae colonization had a higher incidence of post-transplant bloodstream infection (BSI) (39.1% vs 19.0%, P = 0.034) and thrombotic microangiopathy (17.4% vs 8.5%, P = 0.04). Multivariate analysis confirmed oropharyngeal Enterobacteriaceae colonization as an independent risk factor for non-relapse mortality (NRM), overall survival (OS), and progression-free survival (PFS) (P = 0.024, 0.030, and 0.021, respectively). The individuals with carbapenem-resistant Enterobacteriaceae (CRE) colonization experienced delayed platelet engraftment (P = 0.018). Moreover, they had significantly worse OS (P = 0.002), higher NRM (P = 0.00015), and poorer PFS (P = 0.00095). Screening for oropharyngeal colonization using mNGS provides critical clinical value in predicting transplant prognosis. Clinicians should closely monitor patients with oropharyngeal Enterobacteriaceae or CRE colonization.<br><br>IMPORTANCE: Screening for colonization is essential for predicting infection risk in allo-HSCT patients. Traditional microbiological testing methods, however, are time-consuming and have low sensitivity. In this paper, we examine the impact of oropharyngeal colonization on outcomes following allo-HSCT while also evaluating the utility of mNGS for detecting colonization. Our investigation reveals that screening for oropharyngeal colonization using mNGS provides critical clinical value in predicting transplant outcomes and prognosis. Additionally, not all colonization has clinical relevance, but oropharyngeal Enterobacteriaceae colonization has negative impacts on transplant prognosis. Colonization by CRE had particularly severe consequences, which warrants serious attention.<br><br>CLINICAL TRIALS: This study is registered as a single-center clinical trial (Registration No. ChiCTR2300069450).}, }
@article {pmid40422288, year = {2025}, author = {Nguyen, AT and Ratnasiri, K and Barratt Heitmann, G and Tazin, S and Anderson, C and Hanif, S and Yeamin, A and Shoab, AK and Shanta, IS and Jahan, F and Hossain, MS and Mahmud, ZH and Jubair, M and Rahman, M and Rahman, M and Ercumen, A and Benjamin-Chung, J}, title = {Potential pathogens and antimicrobial resistance genes in household environments: a study of soil floors and cow dung in rural Bangladesh.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0066925}, doi = {10.1128/aem.00669-25}, pmid = {40422288}, issn = {1098-5336}, abstract = {In low- and middle-income countries, living in homes with soil floors and animal cohabitation may expose children to fecal organisms, increasing the risk of enteric and antimicrobial-resistant infections. Our objective was to understand whether cow cohabitation in homes with soil floors in rural Bangladesh contributed to the presence and diversity of potential pathogens and antimicrobial resistance genes (ARGs) in the home. In 10 randomly selected households in rural Sirajganj District, we sampled floor soil and cow dung, which is commonly used as sealant in soil floors. We extracted DNA and performed shotgun metagenomic sequencing to explore potential pathogens and ARGs in each sample type. We detected 7 potential pathogens in soil only, 38 pathogens in cow dung only, and 182 pathogens in both soil and cow dung. Cow dung exhibited modestly higher potential pathogen genus richness compared to soil floors (Wilcoxon signed-rank test, P = 0.002). Using Bray-Curtis dissimilarity, potential pathogen species community composition differed between floors and cow dung (permutational multivariate analysis of variance, P < 0.001). All soil floor and cow dung samples contained ARGs; detected ARGs confer resistance to antibiotic classes including sulfonamides, rifamycin, aminoglycosides, lincosamides, and tetracycline. Paired floor and cow dung samples shared ARGs against rifamycin and glycopeptides, but otherwise, there was little overlap in resistomes between sample types. Our findings contribute to the growing literature on household soil and domestic animals as potentially important contributors to disease transmission and as reservoirs of antimicrobial resistance in low-income country settings.IMPORTANCEIn low-income countries, inadequate housing materials and animal cohabitation can lead to fecal contamination of rural homes. Contaminated soil floors are difficult to clean and may harbor organisms causing illness and antibiotic resistance, especially in young children, who frequently ingest soil. We sequenced soil floor and cow dung samples from households in Sirajganj district, Bangladesh, and identified potential pathogens and antibiotic resistance genes. We detected 182 potential pathogens in both soil and cow dung; organisms present in both sample types at the highest relative abundances were Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, and Pseudomonas aeruginosa. Antibiotic resistance genes were found in all samples. In cow dung, the most common genes conferred resistance to the antibiotics lincosamide, rifamycin, cephamycin, tetracycline, and multiple antibiotics. In soil floors, the most common genes conferred resistance to rifamycin, sulfonamides, and multiple antibiotics. Household soil and cow dung may be important reservoirs of pathogens and antimicrobial resistance in low-income country settings with high levels of animal cohabitation compared to settings with finished household floors and minimal animal cohabitation.}, }
@article {pmid40422085, year = {2025}, author = {Liu, L and Shi, J and Wang, H and Du, H and Yang, J and Wei, K and Zhou, Z and Li, M and Huang, S and Zhan, L and Li, G and Lv, Y and Shen, H and Cai, W}, title = {The characteristics of tissue microbiota in different anatomical locations and different tissue types of the colorectum in patients with colorectal cancer.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019825}, doi = {10.1128/msystems.00198-25}, pmid = {40422085}, issn = {2379-5077}, abstract = {The gut microbiota is intricately associated with the onset and progression of colorectal cancer (CRC), leading to significant interest in developing prevention and treatment strategies that leverage gut microbiota. In this study, we collected 57 samples from 19 CRC patients, comprising cancerous tissue, paracancerous tissue, and normal mucosa. Utilizing metagenomic sequencing and bioinformatics analysis, we identified differences in the microbiomes and their functional characteristics across the various tissue types. The results indicated that species such as Alistipes putredinis were predominantly found in normal tissues, while Pseudomonas putida was enriched in paracancerous tissue, and Malassezia restricta was prevalent in cancerous tissues. Furthermore, the microbial functions exhibited variability among the different tissue types. Random forest analysis suggested that Moraxella osloensis may be implicated in the onset and progression of colorectal cancer. We also classified the patients into three subgroups based on the anatomical location of the colorectum: right-sided colon, left-sided colon, and rectum. The subgroup analysis revealed that the microbiota enriched in normal mucosa and paracancerous tissue varied across different anatomical sites. These findings not only elucidate the characteristics of the microbiomes in the normal mucosa, paracancerous tissue, and cancerous tissues of CRC patients, thereby providing new potential targets for clinical diagnosis and treatment, but also contribute to the existing microbiome data pertinent to CRC research.IMPORTANCEThis study provides crucial insights into the relationship between gut microbiota and colorectal cancer (CRC) by analyzing microbial communities in different tissue types and anatomical locations of CRC patients. We identified distinct microbial signatures, such as Alistipes putredinis in normal tissues and Malassezia restricta in cancerous tissues, indicating location-specific microbiomes with unique functional attributes. These findings suggest potential new biomarkers or therapeutic targets for CRC. The observed microbiota variations among right-sided colon, left-sided colon, and rectum cancers underscore the heterogeneity of CRC, pointing toward more personalized treatment strategies. By enhancing our understanding of the microbiome's role in CRC, this research paves the way for innovative diagnostic tools and targeted therapies tailored to individual patient profiles. This work is essential for advancing clinical approaches to CRC management.}, }
@article {pmid40421996, year = {2025}, author = {Yang, H and Yang, Y and Cui, G and Xu, Y and Zhao, R and Le, G and Xie, Y and Li, P}, title = {Dietary methionine restriction ameliorates atherosclerosis by remodeling the gut microbiota in apolipoprotein E-knockout mice.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5fo00841g}, pmid = {40421996}, issn = {2042-650X}, abstract = {Dietary methionine restriction (MR) has been shown to reduce the risk of atherosclerosis, but the specific regulatory effects and mechanisms remain unclear. This research intends to investigate the effects of MR on atherosclerosis in apolipoprotein E-knockout (ApoE[-/-]) mice fed a high-fat, high-cholesterol, high-choline diet and their mechanisms. ApoE[-/-] mice were fed a normal diet (0.86% methionine + 4.5% fat + 0% cholesterol + 0.2% choline), a high-fat, high-cholesterol, high-choline diet (0.86% methionine + 20% fat + 1% cholesterol + 1% choline), or a high-fat, high-cholesterol, high-choline + MR diet (0.17% methionine + 20% fat + 1% cholesterol + 1% choline) for 8 consecutive weeks. The results show that MR reduced body weight, fat mass, fat deposition in the liver and adipocytes, and plasma lipid levels; improved the morphological structure of the aorta; and reduced the aortic lesion area and lipid levels. In addition, MR downregulated aortic pro-inflammatory cytokine levels, upregulated aortic anti-inflammatory cytokine levels, and improved aortic oxidative stress. Moreover, metagenomic sequencing results suggested that MR improved the gut microbiota composition, particularly through increased relative abundance of short-chain fatty acid (SCFA)-producing bacteria, and changed the relative abundance of inflammation-, lipid metabolism-, and bile acid metabolism-related bacteria at the species level. Furthermore, MR promoted SCFA production and bile acid metabolism, and reduced cell adhesion molecules and foam cell formation in the aorta. Thus, our findings indicated that MR improved the gut microbiota composition, especially increased SCFA production, and ameliorated oxidative stress and inflammation in the aorta, thereby preventing atherosclerosis.}, }
@article {pmid40421334, year = {2025}, author = {Ponce Alencastro, JA and Salinas Lucero, DA and Solis, RP and Herrera Giron, CG and Estrella López, AS and Anda Suárez, PX}, title = {Molecular Mechanisms and Emerging Precision Therapeutics in the Gut Microbiota-Cardiovascular Axis.}, journal = {Cureus}, volume = {17}, number = {4}, pages = {e83022}, pmid = {40421334}, issn = {2168-8184}, abstract = {A microbiome in the gut plays a significant role in cardiovascular health and disease. Dysbiosis is an imbalance in the gut microbiome, leading to multiple cardiovascular diseases (CVD) such as atherosclerosis, hypertension, and heart failure. Gut microbe-derived metabolites such as trimethylamine-N-oxide (TMAO) and short-chain fatty acids (SCFAs) are important mediators of the gut-heart axis. Evaluation of the relationship between the gut microbiome and host biomarkers with CVD requires the integration of metagenomics and metabolomics with meta-omics approaches. The literature review found that microbes and metabolic signatures are associated with the risk and progression of CVD. The development of precision therapeutic approaches for targeting gut microbiota includes preventing adverse microbial effects using probiotics, prebiotics, and the drug-as-bug approach to inhibit harmful metabolites of microbiomes, and fecal microbiota transplantation (FMT). However, the implication and practice of these findings in clinical settings face challenges due to the heterogeneity of study designs, difficulty in the determination of causality, and the impact of confounding factors such as diet, medication, and potential inter-individual gut microbiome variability. Future researchers are recommended to conduct longitudinal studies to further establish both gut microbiome associations with CVD and develop successful precision therapeutics approaches based on the microbiome for the treatment of CVD.}, }
@article {pmid40420833, year = {2025}, author = {Clasen, F and Yildirim, S and Arıkan, M and Garcia-Guevara, F and Hanoğlu, L and Yılmaz, NH and Şen, A and Celik, HK and Neslihan, AA and Demir, TK and Temel, Z and Mardinoglu, A and Moyes, DL and Uhlen, M and Shoaie, S}, title = {Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2506843}, doi = {10.1080/19490976.2025.2506843}, pmid = {40420833}, issn = {1949-0984}, mesh = {Humans ; *Parkinson Disease/microbiology/physiopathology ; *Cognitive Dysfunction/microbiology/physiopathology ; *Gastrointestinal Microbiome ; *Mouth/microbiology ; *Brain/physiopathology/microbiology ; Male ; Female ; Aged ; *Bacteria/genetics/classification/pathogenicity/isolation &amp; purification ; Metagenomics ; Virulence ; Virulence Factors/genetics/metabolism ; Saliva/microbiology/chemistry ; Middle Aged ; }, abstract = {The human microbiome is increasingly recognized for its crucial role in the development and progression of neurodegenerative diseases. While the gut-brain axis has been extensively studied, the contribution of the oral microbiome and gut-oral tropism in neurodegeneration has been largely overlooked. Cognitive impairment (CI) is common in neurodegenerative diseases and develops on a spectrum. In Parkinson's Disease (PD) patients, CI is one of the most common non-motor symptoms but its mechanistic development across the spectrum remains unclear, complicating early diagnosis of at-risk individuals. Here, we generated 228 shotgun metagenomics samples of the gut and oral microbiomes across PD patients with mild cognitive impairment (PD-MCI) or dementia (PDD), and a healthy cohort, to study the role of gut and oral microbiomes on CI in PD. In addition to revealing compositional and functional signatures, the role of pathobionts, and dysregulated metabolic pathways of the oral and gut microbiome in PD-MCI and PDD, we also revealed the importance of oral-gut translocation in increasing abundance of virulence factors in PD and CI. The oral-gut virulence was further integrated with saliva metaproteomics and demonstrated their potential role in dysfunction of host immunity and brain endothelial cells. Our findings highlight the significance of the oral-gut-brain axis and underscore its potential for discovering novel biomarkers for PD and CI.}, }
@article {pmid40420635, year = {2025}, author = {Ziegler, MJ and Loughrey, S and Bekele, S and Huang, E and Tolomeo, P and David, MZ and Lautenbach, E and Glaser, LJ and Kelly, BJ}, title = {Comparative performance of sponge versus flocked swabs for culture-based and metagenomic detection of microbial contamination in the healthcare environment.}, journal = {Infection control and hospital epidemiology}, volume = {}, number = {}, pages = {1-6}, doi = {10.1017/ice.2025.87}, pmid = {40420635}, issn = {1559-6834}, abstract = {BACKGROUND: Identifying optimal methods for sampling surfaces in the healthcare environment is critical for future research requiring the identification of multidrug-resistant organisms (MDROs) on surfaces.<br><br>METHODS: We compared 2 swabbing methods, use of a flocked swab versus a sponge-stick, for recovery of MDROs by both culture and recovery of bacterial DNA via quantitative 16S polymerase chain reaction (PCR). This comparison was conducted by assessing swab performance in a longitudinal survey of MDRO contamination in hospital rooms. Additionally, a laboratory-prepared surface was also used to compare the recovery of each swab type with a matching surface area.<br><br>RESULTS: Sponge-sticks were superior to flocked swabs for culture-based recovery of MDROs, with a sensitivity of 80% compared to 58%. Similarly, sponge-sticks demonstrated greater recovery of Staphylococcus aureus from laboratory-prepared surfaces, although the performance of flocked swabs improved when premoistened. In contrast, recovery of bacterial DNA via quantitative 16S PCR was greater with flocked swabs by an average of 3 log copies per specimen.<br><br>CONCLUSIONS: The optimal swabbing method of environmental surfaces differs by method of analysis. Sponge-sticks were superior to flocked swabs for culture-based detection of bacteria but inferior for recovery of bacterial DNA.}, }
@article {pmid40419960, year = {2025}, author = {Shen, Q and Fan, X and Sun, Y and Gao, H and Su, X}, title = {TaxaCal: enhancing species-level profiling accuracy of 16S amplicon data.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {136}, pmid = {40419960}, issn = {1471-2105}, support = {2021YFF0704500//National Key Research and Development Program of China/ ; 32070086//National Natural Science Foundation of China/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenomics/methods ; Algorithms ; Machine Learning ; Humans ; *Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: 16S rRNA amplicon sequencing is a widely used method for microbiome composition analysis due to its cost-effectiveness and lower data requirements compared to metagenomic whole-genome sequencing (WGS). However, inherent limitations in 16S-based approach often lead to profiling discrepancies, particularly at the species level, compromising the accuracy and reliability of findings.<br><br>RESULTS: To address this issue, we present TaxaCal (Taxonomic Calibrator), a machine learning algorithm designed to calibrate species-level taxonomy profiles in 16S amplicon data using a two-tier correction strategy. Validation on in-house produced and public datasets shows that TaxaCal effectively reduces biases in amplicon sequencing, mitigating discrepancies between microbial profiles derived from 16S and WGS. Moreover, TaxaCal enables seamless cross-platform comparisons between these two sequencing approaches, significantly improving disease detection in 16S-based microbiome data.<br><br>CONCLUSIONS: Therefore, TaxaCal offers a cost-effective solution for generating high-resolution microbiome species profiles that closely align with WGS results, enhancing the utility of 16S-based profiling in microbiome research. As microbiome-based diagnostics continue to evolve, TaxaCal has the potential to be a crucial tool in advancing the utility of 16S sequencing in clinical and research settings.}, }
@article {pmid40419911, year = {2025}, author = {Jiao, YN and Meng, JB}, title = {Veno-arterial extracorporeal membrane oxygenation in a patient with septic cardiomyopathy induced by severe community-acquired pneumonia due to Acinetobacter baumannii: A case report.}, journal = {Medicine}, volume = {104}, number = {21}, pages = {e42092}, doi = {10.1097/MD.0000000000042092}, pmid = {40419911}, issn = {1536-5964}, support = {2022KY700//Health Commission of Zhejiang Province of China/ ; 2024KY875//Health Commission of Zhejiang Province of China/ ; 2023ZL031//Zhejiang Provincial Administration of Traditional Chinese Medicine , China/ ; }, mesh = {Humans ; Male ; *Extracorporeal Membrane Oxygenation/methods ; Aged ; *Acinetobacter baumannii/isolation &amp; purification ; *Cardiomyopathies/therapy/etiology/microbiology ; Community-Acquired Infections/complications/microbiology ; *Shock, Septic/therapy/etiology/microbiology ; *Shock, Cardiogenic/therapy/etiology ; *Acinetobacter Infections/complications/therapy ; *Pneumonia, Bacterial/complications ; Community-Acquired Pneumonia ; }, abstract = {RATIONALE: Community-acquired pneumonia due to Acinetobacter baumannii (CAP-AB) is uncommon; however, its mortality is extremely high because of severe pneumonia, septic shock, and multiple organ dysfunction syndrome including septic cardiomyopathy and cardiogenic shock. Veno-arterial extracorporeal membrane oxygenation (VA-ECMO), an important component of treatment in the early stage of septic cardiomyopathy can affect the prognosis of similar patients.<br><br>PATIENT CONCERNS: A 65-year-old man presented to the fever clinic with fever, cough, and stuffiness for 1 day. On admission, he manifested hypoxemia and hypotension, and chest computed tomography showed pneumonia, and Acinetobacter baumannii (AB) was positive in bronchoalveolar lavage fluid tested by metagenomic next-generation sequencing (mNGS).<br><br>DIAGNOSES: Community-acquired pneumonia (CAP), respiratory failure, septic shock, septic cardiomyopathy, and cardiogenic shock.<br><br>INTERVENTIONS: As the diagnosis of septic shock, septic cardiomyopathy and cardiogenic shock induced by CAP-AB and respiratory failure were made, cefoperazone/sulbactam 3&#x2005;g q8h, moxifloxacin 400&#x2005;mg qd, inotropes and vasopressors and mechanical ventilation were initiated. However, although global end diastolic volume index was 744&#x2005;mL/m2, hypotension and tachycardia remained, the left ventricular ejection fraction was 30%, and circulatory failure (cardiogenic shock) did not improve. Hence, VA-ECMO was applied to assist circulation on the day of admission due to the involvement of septic cardiomyopathy and cardiogenic shock.<br><br>OUTCOMES: On day 2, tachycardia improved, left ventricular ejection fraction increased to 54%, and VA-ECMO was withdrawn on day 5. On day 10, mechanical ventilation was withdrawn and the tracheal cannula was removed. Subsequently, the patient was transferred to the respiratory department on day 14.<br><br>LESSONS: A patient with septic cardiomyopathy and cardiogenic shock induced by severe CAP-AB was treated with VA-ECMO in the early stage. Patients with CAP-induced septic cardiomyopathy may benefit from the introduction of VA-ECMO during the early stage. Further studies are required to evaluate the advantages and disadvantages of early VA-ECMO in patients with CAP-induced septic cardiomyopathy.}, }
@article {pmid40419790, year = {2025}, author = {Wang, D and Duan, Y and He, L and Jiang, J and Xian, J and Yuan, K and Zhang, R and Zhang, H and Wang, J and Li, N and Huang, M and Hu, C and Lu, S and Luo, Z and Deng, T and Zhang, Z and Chen, B and Li, W}, title = {Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {804}, pmid = {40419790}, issn = {2399-3642}, support = {82102301//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology/mortality ; Male ; Female ; Metagenomics/methods ; Middle Aged ; Severity of Illness Index ; *SARS-CoV-2/genetics ; *Microbiota ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Sputum/microbiology ; Adult ; Transcriptome ; *Respiratory System/microbiology ; }, abstract = {The interaction between gut and oropharyngeal microbiota plays a significant role in the viral infections like SARS-CoV-2, but role of the lower respiratory tract microbiota remains unclear. Our study utilized metatranscriptomics and metagenomics to analyze the microbial composition of bronchoalveolar lavage fluid and sputum samples from 116 COVID-19 patients, categorized into mild, severe, and critical groups. Our analysis revealed significant differences in viral genotypes across disease stages. As disease severity increased, the Chao index also rose. The mild group was predominantly dominated by Firmicutes, while the severe group showed an increase in Bacteroidetes. The critical group was characterized by a higher abundance of Actinobacteria and Proteobacteria. Notably, the abundance of Streptococcus and Rothia decreased as the disease progressed. Additionally, the Shannon index correlated with mortality risk, while the Chao index was associated with ICU admission, mechanical ventilation, and patient survival. These findings highlight the strong link between microbial composition and COVID-19 severity, providing valuable insights for assessing disease progression.}, }
@article {pmid40419614, year = {2025}, author = {Lu, W and Hua, J and Zhang, M and Yan, L and Zhao, H and Lv, X}, title = {Metagenomic sequencing reveals the taxonomic and functional characteristics of rumen microorganisms in Dongliu buffalo.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18398}, pmid = {40419614}, issn = {2045-2322}, support = {[2021]1146//Joint Research on Improved Beef Cattle Breeds in Anhui Province/ ; }, mesh = {Animals ; *Rumen/microbiology ; *Buffaloes/microbiology ; Female ; Male ; *Metagenomics/methods ; *Metagenome ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification ; Phylogeny ; *Microbiota ; }, abstract = {In this study, the composition of the rumen microbiota and its functional characteristics were investigated using a metagenomic approach in Dongliu buffalo. This study compared the rumen microbial communities of six female and four male Dongliu buffaloes of similar age, weight and lifestyle. Taxonomic analysis identified 964 genera across 52 phyla, dominated by Bacteroidota (47.54%) and Bacillota (28.20%). While alpha and beta diversity showed no sex differences (PERMANOVA P = 0.82), males exhibited higher Fibrobacter at the genus level (P = 0.02). Functional profiling revealed 429 KEGG pathways, with carbohydrate metabolism (11.17%) and amino acid metabolism (9.74%) as dominant processes. Males showed enrichment in cellulose-degrading enzymes (EC2.4.1.20, EC1.2.1.90, EC2.7.1.58) and CAZymes (GH94, GT35), while females had higher Bacteroides abundance (P = 0.01) and CAZymes like CBM47. Core cellulolytic genera (Prevotella, Ruminococcus) demonstrated male-biased GH/CBM activity, linked to enhanced fiber degradation. COG annotation highlighted carbohydrate metabolism as central, with sex-specific functional partitioning in replication (female-enriched) and secondary metabolism (male-enriched). Network analysis revealed Prevotella's dominance in CAZymeme contributions and functional specialization in lignocellulose degradation pathways, suggesting sex-driven microbial adaptation to dietary fiber utilization.}, }
@article {pmid40417475, year = {2024}, author = {Marini, S and Barquero, A and Wadhwani, AA and Bian, J and Ruiz, J and Boucher, C and Prosperi, M}, title = {OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier.}, journal = {AMIA ... Annual Symposium proceedings. AMIA Symposium}, volume = {2024}, number = {}, pages = {798-807}, pmid = {40417475}, issn = {1942-597X}, mesh = {*Metagenomics/methods ; *Software ; *Mobile Applications ; }, abstract = {Portable genomic sequencers such as Oxford Nanopore's MinION enable real-time applications in clinical and environmental health. However, there is a bottleneck in the downstream analytics when bioinformatics pipelines are unavailable, e.g., when cloud processing is unreachable due to absence of Internet connection, or only low-end computing devices can be carried on site. Here we present a platform-friendly software for portable metagenomic analysis of Nanopore data, the Oligomer-based Classifier of Taxonomic Operational and Pan-genome Units via Singletons (OCTOPUS). OCTOPUS is written in Java, reimplements several features of the popular Kraken2 and KrakenUniq software, with original components for improving metagenomics classification on incomplete/sampled reference databases, making it ideal for running on smartphones or tablets. OCTOPUS obtains sensitivity and precision comparable to Kraken2, while dramatically decreasing (4- to 16-fold) the false positive rate, and yielding high correlation on real-word data. OCTOPUS is available along with customized databases at https://github.com/DataIntellSystLab/OCTOPUS and https://github.com/Ruiz-HCI-Lab/OctopusMobile.}, }
@article {pmid40417422, year = {2025}, author = {Roothans, N and Pabst, M and van Diemen, M and Herrera Mexicano, C and Zandvoort, M and Abeel, T and van Loosdrecht, MCM and Laureni, M}, title = {Long-term multi-meta-omics resolves the ecophysiological controls of seasonal N2O emissions during wastewater treatment.}, journal = {Nature water}, volume = {3}, number = {5}, pages = {590-604}, pmid = {40417422}, issn = {2731-6084}, abstract = {Nitrous oxide (N2O) is the third most important greenhouse gas and originates primarily from natural and engineered microbiomes. Effective emission mitigations are currently hindered by the largely unresolved ecophysiological controls of coexisting N2O-converting metabolisms in complex communities. To address this, we used biological wastewater treatment as a model ecosystem and combined long-term metagenome-resolved metaproteomics with ex situ kinetic and full-scale operational characterization over nearly 2 years. By leveraging the evidence independently obtained at multiple ecophysiological levels, from individual genetic potential to actual metabolism and emergent community phenotype, the cascade of environmental and operational triggers driving seasonal N2O emissions has ultimately been resolved. We identified nitrifier denitrification as the dominant N2O-producing pathway and dissolved O2 as the prime operational parameter, paving the way to the design and fostering of robust emission control strategies. This work exemplifies the untapped potential of multi-meta-omics in the mechanistic understanding and ecological engineering of microbiomes towards reducing anthropogenic impacts and advancing sustainable biotechnological developments.}, }
@article {pmid40417222, year = {2025}, author = {Tian, C and Liu, J and Chen, Z and Li, L}, title = {Case report: Analysis of the efficacy and safety of anti-infectious treatment for brain abscess caused by oral anaerobes.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1506879}, pmid = {40417222}, issn = {1663-9812}, abstract = {Anaerobic meningitis is relatively rare, and the positivity rate of cerebrospinal fluid (CSF) cultures is exceedingly low, particularly in light of the limited research data regarding bacterial meningitis caused by oral anaerobes. This report presents a case involving a 24-year-old woman who developed fever and headache 32 days after undergoing a cesarean section. The symptoms persisted for 2 weeks, and enhanced nuclear magnetic resonance (NMR) scanning confirmed the suspicion of a brain abscess. Additionally, metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) identified several microbial species, including Porphyromonas gingivalis, Prevotella heparinolyticus, Fusobacterium nucleatum, Parvimonas micra and Filifactor alocis. Bacterial culture of CSF revealed the growth of Prevotella heparinolyticus. Following bilateral ventricular external drainage, intracranial lesion resection, and the implantation of an Ommaya reservoir in the right lateral ventricle, cranial decompression treatment was performed. Antimicrobial therapy administered successively over a period of 6 weeks, including vancomycin, meropenem, metronidazole, polymyxin B and ceftazidime, resulting in significant control of the infection. Clinical pharmacists engaged in comprehensive discussions with clinicians regarding the antimicrobial drug regimens and recommended a combined regimen of meropenem and metronidazole. An individualized anti-infective treatment protocol was developed based on therapeutic drug monitoring (TDM), which is anticipated to yield valuable insights for the management of brain abscesses resulting from oral anaerobic bacteria.}, }
@article {pmid40416301, year = {2025}, author = {Vatta, P and Cacciò, SM}, title = {Detection of parasites in food and water matrices by shotgun metagenomics: A narrative review.}, journal = {Food and waterborne parasitology}, volume = {39}, number = {}, pages = {e00265}, pmid = {40416301}, issn = {2405-6766}, abstract = {Many helminths and protozoa are transmitted to humans through the consumption of contaminated food or water, and this underlines the importance of methods for their detection in these matrices. Due to the difficulties in isolating parasites prior to their identification, indirect detection methods are used, mostly relying upon targeted amplification of nucleic acids via PCR and/or qPCR. With the development of high throughput sequencing technologies, an untargeted detection method, shotgun metagenomics, became available. By sequencing the total DNA extracted from a given source, and through bioinformatics analyses of the sequencing reads, shotgun metagenomics allows profiling the entire microbial community therein present, including eukaryotes and, therefore, parasites. In this article, we reviewed the studies that specifically addressed the detection of parasites in food (n = 2) and water matrices (n = 10) by shotgun metagenomics. Most studies focused on wastewater samples and reported the detection of many parasites of human and veterinary importance from various areas of the world, highlighting the potential of shotgun metagenomics to provide important data for parasitic pathogens surveillance. After examining the different analytical workflows employed in these studies, which were not developed for detection of eukaryotes (or parasites), we identified two aspects deserving attention. First, that assignment based on short reads matching ribosomal sequences may generate false positives due to high sequence conservation among eukaryotic organisms. Second, that reassessing the relatively small number of reads of eukaryotic origin by a BLAST search can confirm, or deny, identification of parasitic pathogens.}, }
@article {pmid40415958, year = {2025}, author = {Lin, L and Li, J and Zhang, C and Li, J and Wu, B and Huang, Z and Lv, J and Liu, M and Li, W and Zhang, W and Fang, X}, title = {Comprehensive analysis of culture-negative periprosthetic joint infection with metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1564488}, pmid = {40415958}, issn = {2235-2988}, mesh = {Humans ; *Prosthesis-Related Infections/microbiology/drug therapy ; Male ; Female ; Retrospective Studies ; Aged ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Metagenomics/methods ; Risk Factors ; *Bacteria/genetics/classification/isolation &amp; purification ; Aged, 80 and over ; Anti-Bacterial Agents/therapeutic use ; Coinfection/microbiology ; Adult ; }, abstract = {OBJECTIVE: This study aimed to identify the risk factors and microbial profiles of patients with culture-negative periprosthetic joint infection (PJI) using metagenomic next generation sequencing (mNGS) and to compare the clinical characteristics and treatment outcomes of culture-negative PJI (CN PJI) with culture-positive PJI (CP PJI).<br><br>METHODS: A retrospective analysis was conducted on 223 patients who met the International Consensus Meeting criteria for PJI and underwent surgical treatment at our hospital between February 2013 and January 2023. Clinical and follow-up data, including microbiological culture results and mNGS findings, were collected. Based on culture results, patients were divided into the CP PJI and CN PJI groups. Risk factors and microbial profiles of CN PJI patients were summarized with the aid of mNGS results. Differences in clinical characteristics and treatment outcomes between the two groups were also analyzed.<br><br>RESULTS: Among the 223 patients, 168 were in the CP PJI group, and 55 were in the CN PJI group. Risk factors for negative cultures included polymicrobial infections, infections caused by rare pathogens, and prolonged antibiotic use prior to sampling. In the CN PJI group, over a quarter of cases involved polymicrobial infections (25.5%) or rare pathogen infections (38.2%), with Mycoplasma sp. being the most frequently identified rare pathogen (7.2%). Compared to the CP PJI group, the CN PJI group exhibited distinctly longer hospital stays (P<0.001), extended antibiotic use (P=0.02), and a higher rate of antibiotic-related complications (P=0.026). However, no significant difference was noted in reinfection rates between the two groups (P=0.412).<br><br>CONCLUSION: CN PJI presents a unique microbial spectrum and distinct clinical therapeutic characteristics. mNGS offers a more comprehensive understanding of infecting microorganisms, particularly those often missed by conventional culture techniques. With advancements in sample collection, optimized culture methods, molecular diagnostic tools, and early targeted therapies, CN PJI may achieve clinical outcomes comparable to CP PJI.}, }
@article {pmid40415957, year = {2025}, author = {Zhang, S and Guo, Q and Gai, W and Guo, Y and Zheng, Y}, title = {A comprehensive evaluation of plasma metagenomics sequencing for the diagnosis of suspected infection in pediatric patients with hematologic diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1584214}, pmid = {40415957}, issn = {2235-2988}, mesh = {Humans ; Child, Preschool ; Male ; Child ; Female ; Retrospective Studies ; Infant ; *Hematologic Diseases/complications/microbiology ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adolescent ; Sensitivity and Specificity ; *Cell-Free Nucleic Acids/blood/genetics ; *Communicable Diseases/diagnosis ; }, abstract = {BACKGROUND: As a non-invasive technology, plasma cell-free DNA (cfDNA) next-generation sequencing (mNGS) has been widely used for clinical detection of a variety of infectious diseases. Infections are a major cause of poor prognosis in children with hematologic diseases. So far, there has been limited research on the use of plasma cfDNA mNGS in children with hematological disorders at high risk of infection.<br><br>METHODS: We retrospectively analyzed the clinical data of 73 children with hematological disorders suspected of early infection admitted to Anhui Children's Hospital between September 2023 and February 2024. The diagnostic performance and clinical implications of mNGS versus conventional microbiological testing (CMT) were evaluated.<br><br>RESULTS: The positive rate of mNGS was significantly higher than that of CMT (69.86% vs 31.51%, P < 0.001). When compared with the final clinical diagnosis, the sensitivity of mNGS was significantly higher than that of CMT (71.88% vs 35.94%, P < 0.001). There is a high degree of agreement between the positive results of the two assays (78.95%). A total of 46 pathogens were identified in children with hematologic diseases, of which 41 pathogens were detected by mNGS and only 12 pathogens were detected by CMT. In these patients, the most common bacteria detected were Klebsiella pneumoniae and Mycoplasma pneumoniae. Human betaherpesvirus 5 (CMV) was the most commonly detected virus. All fungi were detected only by mNGS. Overall, mNGS had a positive effect on the clinical treatment for 65.75% of patients in this study. Positive results are more likely to be obtained with mNGS when white blood cell counts, neutrophil counts, and lymphocyte counts are low.<br><br>CONCLUSIONS: Early plasma cfDNA mNGS improved the performance of pathogen detection in children with hematological diseases. Rapid identification of the pathogen followed by precise targeted antimicrobial therapy improves the prognosis of patients.}, }
@article {pmid40415955, year = {2025}, author = {Guo, Y and Lin, L and Zhang, M and Yu, Y and Wang, Y and Cao, J and Li, Y and Sun, X and Guan, M and Wen, S and Wang, X and Fang, Z and Duan, W and Duan, J and Huang, T and Xia, W and Guo, S and Wei, F and Zheng, D and Huang, X}, title = {Salivary mycobiome alterations in HIV-infected MSM: dominance of Pseudogymnoascus and functional shifts across disease stages.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1564891}, pmid = {40415955}, issn = {2235-2988}, mesh = {Humans ; Male ; *Saliva/microbiology ; Cross-Sectional Studies ; *HIV Infections/microbiology/complications ; *Mycobiome ; Adult ; *Homosexuality, Male ; Middle Aged ; CD4 Lymphocyte Count ; *Fungi/classification/genetics/isolation &amp; purification ; Disease Progression ; Metagenomics ; }, abstract = {BACKGROUND: Oral health is increasingly recognized as a crucial determinant of overall health in people living with HIV/AIDS (PLWHA). Specifically, the oral mycobiome may play a pivotal role in HIV-associated oral complications. However, the fungal species involved and their potential as biomarkers for HIV-related oral conditions remain poorly understood. This study investigates salivary fungal profiles in PLWHA who have sex with men (MSM), focusing on diversity, functional shifts, and correlations with disease progression.<br><br>METHODS: A cross-sectional study included 25 MSM participants divided into five groups: HIV-negative controls (n = 5) and four HIV-positive groups stratified by CD4 count: Stage 0 (HIV RNA-positive/antibody-negative; n = 5), Stage 1 (CD4 &#x2265;500 cells/&#x3bc;L; n = 5), Stage 2 (CD4 200-499 cells/&#x3bc;L; n = 5), and Stage 3 (CD4 <200 cells/&#x3bc;L or opportunistic infections; n = 5). Saliva samples were collected and analyzed using metagenomic sequencing (Illumina NovaSeq platform). Bioinformatic analyses included genome assembly (MEGAHIT), gene clustering (CD-HIT), gene abundance calculation (SOAPaligner), species annotation (BLASTP), and KEGG pathway annotation (KOBAS 2.0). Statistical analyses (Kruskal-Wallis tests, Spearman's correlation) assessed associations between fungal profiles, CD4 count, and viral loads.<br><br>RESULTS: A total of 51 fungal genera were identified, with Pseudogymnoascus being the most abundant. Functional analysis revealed 113 shared KEGG pathways, of which 69 were unique to Stage 3, primarily related to metabolic and disease-related processes. Notably, Auricularia exhibited a positive correlation with CD4 count (P &#x2264; 0.01), while Mucor showed a negative correlation (P = 0.0299).<br><br>CONCLUSIONS: Salivary mycobiome composition and function shift significantly across HIV stages, reflecting immune decline. Pseudogymnoascus dominance challenges conventional views of oral fungal ecology in immunocompromised hosts. These findings highlight the mycobiome's diagnostic potential for monitoring HIV-related oral health. Longitudinal studies are needed to validate clinical relevance.}, }
@article {pmid40415946, year = {2025}, author = {Leclercq, L and Debarre, S and Lloret, E and Taminiau, B and Daube, G and Rambaud, C and Drider, D and Siah, A and Desprez, B and Hilbert, JL and Lucau-Danila, A}, title = {Unveiling the hidden allies of industrial chicory-a metagenomic exploration of rhizosphere microbiota and their impact on productivity and plant health.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1509094}, pmid = {40415946}, issn = {1664-302X}, abstract = {BACKGROUND: As industrial chicory is significant for food, fodder, and medicinal purposes, its cultivation is increasingly crucial for producers. To enhance productivity, resistance, and the nutritional and functional values of this plant, we aimed to investigate its interactions with the microbial environment. We performed the first comprehensive taxonomic and functional characterization of the rhizosphere microbiota associated with industrial chicory, investigating how environmental factors influence its composition.<br><br>METHODS: Six different land plots were simultaneously cultivated with the same chicory genotype in northern France. Using soil analyses and metagenomic approaches, we characterized the diversity of bacterial and fungal communities in the soil microbiome associated with chicory plants and discussed their functional traits.<br><br>RESULTS: We observed significant taxonomic variability, influenced by soil composition and cultivation history across each plot. The presence of chicory plants distinctly shaped the microbial community. Specifically, chicory was found to recruit Streptomyces species that produce plant hormones and Penicillium species that facilitate phosphate solubilization and promote plant growth. Moreover, the plant demonstrated an ability to repel pathogens and adapt to local microbial communities by selectively favoring beneficial microorganisms according to local stresses and nutritional needs.<br><br>DISCUSSION: Our study represents a comprehensive taxonomic and functional analysis of the Cichorium intybus rhizosphere microbiome, underscoring the pivotal role of soil composition and land-use history. The specific microbial recruitment by chicory was also addressed.}, }
@article {pmid40415944, year = {2025}, author = {Zhu, W and Han, S and Cheng, Y and Yu, Z and Zhao, G and He, X}, title = {Root zone microbial communities of Artemisia ordosica Krasch. at different successional stages in Mu US Sandy Land: a metagenomic perspective with culturomics insights.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1585700}, pmid = {40415944}, issn = {1664-302X}, abstract = {Phytoremediation offers a promising strategy for addressing the global challenge of land desertification. In the Mu Us Sandy Land of China, Artemisia ordosica Krasch. has emerged as a key species for desertification control. Its root-associated microbial communities may enhance the plant's adaptability to sandy, nutrient-poor environments. Despite their ecological significance, comprehensive investigations of these microbial communities remain limited. In this study, microbial communities in the root zone (i.e., rhizosphere soil, non-rhizosphere soil, and root endosphere) of A. ordosica were analyzed via high-throughput sequencing and different isolation approaches across successional stages (moving dunes, semi-fixed dunes, and fixed dunes) in the Mu Us Sandy Land of northern China. Metagenomic analysis revealed that microbial diversity was significantly higher in the rhizosphere and non-rhizosphere soils than in the root endosphere; moving dunes exhibited lower diversity than semi-fixed and fixed dunes. Meanwhile, distinct microbial community structures across successional stages were revealed by principal coordinates analysis (PCoA), demonstrating substantial differences between the root endosphere and other zones. Environmental factors, including nitrate nitrogen (NO3 [-]-N), organic matter (OM), available potassium (AK), and total potassium (TK), significantly influenced microbial community composition. Moreover, dominant genera such as Arthrobacter and Paraphoma were identified, potentially contributing to A. ordosica growth. From a culturomics perspective, 93 bacterial isolates were obtained using conventional streak plate and colony pick methods, with Firmicutes (37.63%) and Bacillus (23.66%) identified as the dominant taxa. In parallel, 14 fungal strains were isolated, primarily belonging to Penicillium (35.71%) and Aspergillus (21.43%), both of which are well-documented for their stress tolerance in arid ecosystems. A high-throughput cultivation and identification method, tailored to recover rare and slow-growing bacteria, was employed and successfully broadened the cultured diversity to include Proteobacteria (46.43%) and representatives of the rarely cultivated Deinococcus-Thermus phylum. This study provides metagenomic with culturomics insights into the microbial communities associated with A. ordosica, enhancing the understanding of plant-microbe interactions in sandy land ecosystems.}, }
@article {pmid40415928, year = {2025}, author = {Karimianghadim, R and Satokari, R and Yeo, S and Arkkila, P and Kao, D and Pakpour, S}, title = {Prolonged effect of antibiotic therapy on the gut microbiota composition, functionality, and antibiotic resistance genes' profiles in healthy stool donors.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1589704}, pmid = {40415928}, issn = {1664-302X}, abstract = {INTRODUCTION: Fecal microbiota transplantation (FMT) is highly effective in preventing Clostridioides difficile recurrence by restoring gut microbiota composition and function. However, the impact of recent antibiotic use, a key exclusion criterion for stool donors, on gut microbiota recovery is poorly understood.<br><br>METHODS: We investigated microbial recovery dynamics following antibiotic use in three long-term stool donors from Canada and Finland. Using longitudinal stool sampling, metagenomic sequencing, and qPCR, we assessed changes in bacterial diversity, community composition, microbial functions, the gut phageome, and the risk of transmitting antibiotic-resistant genes (ARGs).<br><br>RESULTS: Antibiotics caused lasting disruption to bacterial communities, significantly reducing important taxa like Bifidobacterium bifidum, Blautia wexlerae, Akkermansia muciniphila, Eubacterium sp. CAG 180, and Eubacterium hallii, with effects persisting for months. Functional analyses revealed alterations in housekeeping genes critical for energy production and biosynthesis, with no direct links to key health-related pathways. Antibiotics also disrupted viral populations, decreasing diversity and increasing crAssphage abundance, reflecting disrupted host-bacteriophage dynamics. No significant increase in clinically important ARGs was detected.<br><br>DISCUSSION: These findings highlight the unpredictable and complex recovery of gut microbiota post-antibiotics. Individualized suspension periods in donor programs, guided by metagenomic analyses, are recommended to optimize FMT outcomes in various indications by considering antibiotic spectrum, duration, and host-specific factors.}, }
@article {pmid40415580, year = {2025}, author = {Bosquez, JM and Graf, EH}, title = {Reducing the Noise in Plasma Metagenomics to Further Define Clinical Utility.}, journal = {Clinical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/clinchem/hvaf065}, pmid = {40415580}, issn = {1530-8561}, }
@article {pmid40415184, year = {2025}, author = {Sheyn, U and Poff, KE and Eppley, JM and Leu, AO and Bryant, JA and Li, F and Romano, AE and Burger, A and Barone, B and DeLong, EF}, title = {Mesoscale eddies shape Prochlorococcuscommunity structure and dynamics in the oligotrophic open ocean.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf106}, pmid = {40415184}, issn = {1751-7370}, abstract = {Mesoscale eddies, horizontally rotating currents sometimes referred to as "ocean weather," influence open ocean macronutrient distributions, primary production, and microbial community structure. Such eddies impact ecosystems like the North Pacific Subtropical Gyre, where year-round thermal stratification limits the mixing of subsurface macronutrients with surface waters. Populations of the dominant primary producer Prochlorococcusin the North Pacific Subtropical Gyre consist of genetic variants with differential adaptive traits to light intensity, temperature, and macronutrient availability. How Prochlorococcuspopulation variants respond to transient, localized environmental changes, however, remains an open question. Leveraging microbial community phylogenetic, metagenomic, and metatranscriptomic data, we report here a consistent, specific enrichment of Prochlorococcushigh-light I ecotypes around the deep chlorophyll maximum in cyclonic eddies, but not adjacent anticyclonic eddies. The shallower deep chlorophyll maximum depths of cyclones had lower temperatures, higher light intensities, and elevated nutrient concentrations compared to adjacent anticyclones, which favored Prochlorococcushigh-light I ecotype proliferation. Prochlorococcushigh-light I ecotypes in the cyclone deep chlorophyll maximum exhibited unique genetic traits related to nitrogen metabolism and were enriched in gene transcripts associated with energy production, cell replication, and proliferation. Prochlorococcusgene transcripts involved in amino acid transport, metabolism, and biosynthesis were also elevated in the cyclone. These results suggest the potential importance of nitrogen metabolism in Prochlorococcushigh-light I ecotype proliferation in cyclonic eddies. Our findings demonstrate how mesoscale eddies shape microbial community structure in the oligotrophic ocean and how Prochlorococcuscommunities respond to short-term localized environmental variability.}, }
@article {pmid40415036, year = {2025}, author = {Rungsihiranrut, A and Muangchinda, C and Pinyakong, O}, title = {Metagenomic analysis reveals the roles of Actinobacteria in plasticizer-contaminated landfills and aids in identifying key degraders.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18157}, pmid = {40415036}, issn = {2045-2322}, support = {N41A660167//The National Research Council of Thailand (NRCT)/ ; }, mesh = {*Actinobacteria/genetics/metabolism/classification ; *Metagenomics/methods ; Biodegradation, Environmental ; *Plasticizers/metabolism ; Soil Microbiology ; Dibutyl Phthalate/metabolism ; Waste Disposal Facilities ; Diethylhexyl Phthalate/metabolism ; Metagenome ; *Soil Pollutants/metabolism ; }, abstract = {Phthalate ester (PAE) contamination, particularly from dibutyl phthalate (DBP) and di-2-ethylhexyl phthalate (DEHP), originating from landfills and released into the environment, poses a significant concern. Understanding PAE biodegradation is crucial for developing bioremediation strategies. This study used cover material from a 1-month-old landfill for soil microcosms. Indigenous microbes effectively removed 300 mg kg[-1] of DBP and DEHP as individual and mixed substrates, achieving complete DBP removal and 70% DEHP removal at room temperature (27-30 °C) and 37 °C. Actinobacteria were dominant, indicating potential active PAE-degraders. Shotgun metagenomic analysis revealed an increased abundance of potential PAE catabolic genes, such as those encoding esterase, lipase, and dioxygenase, under all conditions, mainly associated with Streptomyces, Saccharopolyspora, Nocardia, Nocardioides, and Amycolatopsis. The genes associated with Saccharopolyspora were abundant at 37 °C, while those related to Nocardia and Actinomadura were prevalent at room temperature, suggesting temperature preferences. The genera Saccharopolyspora and Actinomadura have not been linked to PAE degradation, indicating potential novel PAE degraders. Furthermore, PAE-degrading bacteria were isolated using media designed from metagenomic data and were categorized into Streptomyces, Amycolatopsis, and Nocardia. This work highlights the roles of rare taxa and provides insights into potential novel PAE degraders, emphasizing the need for further research into these organisms.}, }
@article {pmid40414991, year = {2025}, author = {Rashid, MH and Pascottini, OB and Xie, L and Niazi, M and Lietaer, L and Comlekcioglu, U and Opsomer, G}, title = {Shotgun metagenomic composition, microbial interactions and functional insights into the uterine microbiome of postpartum dairy cows with clinical and subclinical endometritis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18274}, pmid = {40414991}, issn = {2045-2322}, support = {2(3)/HRD/OSS-III/2022/HEC/83//Higher Education Commission, Pakistan/ ; KP 2020; FFB200048//Ghent University, Belgium/ ; BOF17/DOC/269//Ghent University, Belgium/ ; 12Y5220N//University of Antwerp, Belgium/ ; CSC; 202206300032//China Scholarship Council/ ; }, mesh = {Animals ; Cattle ; Female ; *Endometritis/microbiology/veterinary ; *Cattle Diseases/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; Postpartum Period ; *Uterus/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; *Microbial Interactions ; Metagenome ; }, abstract = {Clinical endometritis (CE) is associated with bacterial pathogens while the same has not been proved about subclinical endometritis (SCE). We aimed to use shotgun metagenomic sequencing to investigate the associations between potentially unidentified pathogens and SCE. Uterine cytobrush samples from multiparous Holstein cows (n = 23) were taken at 21 days in milk (DIM) and sequenced via the Illumina shotgun platform. At 36 DIM, the cows were diagnosed as CE (n = 7), SCE (n = 7), or healthy (n = 9). We did not find differences in the alpha and beta diversity of bacteria and eukaryotes among the health groups. Relative abundance of typical pathogens i.e. Fusobacterium, Peptoniphilus, Peptostreptococcus, and Trueperella was greater in CE than healthy controls. We did not find evidence of eukaryotic or viral association in infection, yet, distinct patterns of bacterial co-occurrence were observed among pathogenic and non-pathogenic bacteria. In CE cows, Wnt/catenin pathway had lower abundance than SCE or healthy cows. Our findings support that CE is characterized by domination of pathogenic bacteria that intercorrelate, whereas SCE is not associated with bacterial colonization.}, }
@article {pmid40414888, year = {2025}, author = {Xie, X and Yang, H and Zhao, X and Teng, L and Yang, Y and Luo, H}, title = {Potential role of key rumen microbes in regulating host health and growth performance in Hu sheep.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {51}, pmid = {40414888}, issn = {2524-4671}, abstract = {BACKGROUND: Average daily gain (ADG) is an important component affecting the profitability of sheep. However, research on the relationship between rumen microbes and sheep growth phenotype is still very lacking. Therefore, in this study, 16 Hu sheep were selected from a cohort of 318 sheep assigned to the same feeding and management conditions, and divided into high growth rate (HADG, n = 8) group and low growth rate (LADG, n = 8) group according to the extreme ADG value. Then, the differences in rumen microbes, rumen fermentation and animal immune parameters were further compared between groups to explore the potential role of rumen key microbes in regulating the health and growth performance of Hu sheep hosts.<br><br>RESULTS: The results showed that specific pathogenic bacteria associated with ADG, including Anaerotruncus, Sediminibacterium and Glaesserella, exhibited significant correlations with interleukin-6 (IL-6) and immunoglobulin G (IgG). These interactions disrupt immune homeostasis in the host, leading to a metabolic prioritization of energy resources toward immune responses, thereby impairing growth and development. Succinivibrio_dextrinosolvens was enriched in HADG sheep and exhibited a significant positive correlation with propionate levels. This promoted propionate production in the rumen, enhancing the metabolic activity of carbohydrate, amino acid and energy metabolism, ultimately contributing to higher ADG in sheep. Importantly, random forest analysis results showed that Succinivibrio_dextrinosolvens could classify sheep into HADG and LADG with a prediction accuracy of 81.2%. Additionally, we identified 34 bacteria belonged to connectors in the HADG co-occurrence network, including Alloprevotella, Phascolarctobacterium, Anaerovibrio, Butyricicoccus, Ruminococcaceae_noname, and Roseburia, etc., which play an important role in the degradation of carbohydrates and convert them into short-chain fatty acids (SCFAs), maintaining rumen health, and modulating inflammation.<br><br>CONCLUSIONS: In summary, key microbes in the rumen affect the overall healthy homeostasis and rumen fermentation of the host, leading to changes in energy utilization, which in turn affects the average daily gain of Hu sheep. Succinivibrio_dextrinosolvens is a promising biomarker for selecting high growth rate sheep in the future. This study provides a new method to manipulate rumen bacteria to improve growth performance in sheep.}, }
@article {pmid40414843, year = {2025}, author = {Thompson, TP and Rice, CJ and Athanasakis, E and Mawhinney, J and Gilmore, BF and Fitzgerald, P and Skvortsov, T and Kelly, SA}, title = {The effect of sample type and location on industrial workplace sink and hand dryer microbiomes.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {325}, pmid = {40414843}, issn = {1471-2180}, mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Humans ; Workplace ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Hand Disinfection ; Hand/microbiology ; Metagenomics ; }, abstract = {One major issue in tackling antimicrobial resistance (AMR) is the ability to effectively track resistance spread in environments where surveillance is limited. Such environments include those experiencing high volumes of hand washing and drying from multiple users. This study characterised the microbial populations and antimicrobial resistomes of two different sample types from a pharmaceutical industrial site as part of an AMR environmental surveillance programme. Paired samples were collected from hand dryers and adjacent sinks in distinct sampling locations: from toilets adjacent to 'wet' labs, and locations associated with 'dry' activities. Microbial populations in hand dryers were significantly different to those of sinks, whereas there was no significant difference based on sample location. The opposite effect was observed for resistomes, where profiles differed significantly based on sample location, but not sample type. When both sample type and location were considered together, differences in microbiomes were driven primarily by hand dryer profiles from different locations. Analysis of metagenomically-assembled genomes revealed the presence of many poorly characterised organisms, and suggested no specific families predominated in terms of ARG carriage. This study emphasises the impact of human activities in determining the resistome of commonly used appliances, and the need for continued AMR surveillance programmes.}, }
@article {pmid40414257, year = {2025}, author = {Bostanci, N and Manoil, D and Van Holm, W and Belibasakis, GN and Teughels, W}, title = {Microbial Markers for Diagnosis and Risk Assessment for Periodontal Diseases: A Systematic Literature Search and Narrative Synthesis.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.14183}, pmid = {40414257}, issn = {1600-051X}, support = {01-11-2021//Vetenskapsr&#xe5;det/ ; 01-11-2024//Vetenskapsr&#xe5;det/ ; //Funding for "Senior Clinical Associates" from the Faculty of Medicine of the University of Geneva/ ; FoUI-966140//Steering Group for Odontological Research/ ; FoUI-978687//Steering Group for Odontological Research/ ; }, abstract = {AIM: To examine the accuracy of microbiological biomarkers in diagnosing periodontal diseases, specifically addressing three focus questions: (FQ1) distinguishing health from disease; (FQ2) predicting disease progression; and (FQ3) assessing treatment outcomes.<br><br>MATERIALS AND METHODS: A PRISMA-guided search in MEDLINE, EMBAS and WEB OF SCIENCE included cross-sectional and longitudinal studies (e.g., randomised controlled trials, cohort studies) with &#x2265;&#x2009;20 participants per group. Eligible studies involved individuals diagnosed with periodontal health, gingivitis or periodontitis, based on well-defined clinical criteria, and utilised microbiological analyses of oral fluids and/or dental plaque. Diagnostic accuracy had to be evaluated using sensitivity, specificity or area under the receiver operating characteristic (ROC) curve (AUC), or alternatively, data for their computation had to be provided.<br><br>RESULTS: Thirty-one studies were included, mostly cross-sectional or case-control, with significant variability in sampling sites, microbial analyses and diagnostic definitions, complicating direct comparisons. Frequently investigated biomarkers included Aggregatibacter actinomycetemcomitans (JP2 genotype), Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola. The highest diagnostic accuracy (AUC >&#x2009;0.95) was achieved through composite microbiome-based metrics such as the subgingival microbial dysbiosis index. However, methodological heterogeneity and inconsistent criteria limited reliability.<br><br>CONCLUSION: Although microbiological biomarkers hold promise for periodontal disease diagnostics and monitoring, current evidence is insufficient for clinical implementation. Future research should standardise methodologies, sampling protocols and diagnostic criteria to ensure robust validation and facilitate integration into precision dentistry.}, }
@article {pmid40414102, year = {2025}, author = {Rubel, V and Filker, S and Lanzén, A and Abad, IL and Stoeck, T}, title = {Exploiting taxonomic information from metagenomes to infer bacterial bioindicators and environmental quality at salmon aquaculture installations.}, journal = {Marine pollution bulletin}, volume = {218}, number = {}, pages = {118173}, doi = {10.1016/j.marpolbul.2025.118173}, pmid = {40414102}, issn = {1879-3363}, abstract = {Environmental DNA (eDNA) metabarcoding has emerged as a powerful method for assessing the environmental impacts of marine Atlantic salmon aquaculture by identifying bacterial bioindicators and inferring biotic indices. However, because this approach relies on the PCR amplification of 16S rRNA gene fragments, it may introduce errors that compromise bioindicator reliability. In contrast, metagenomic analysis which captures the complete set of genetic material directly extracted from environmental samples circumvents biases inherent to PCR amplification. We hypothesized that metagenomic data could offer superior assessments of benthic environmental impacts associated with salmon aquaculture compared to metabarcoding. To test this, we compared bacterial community structures derived from both metabarcoding and metagenomic analyses of 68 sediment samples obtained from aquaculture installation sites characterized by varying degrees of benthic impact as determined by macroinvertebrate inventories. Bacterial bioindicators were identified from each dataset, and Random Forest models were used to predict the degrees of benthic impacts. Metagenomics identified a greater number of bioindicators at both the family and individual sequence variant levels, resulting in higher predictive accuracy for impact assessments. Notably, only a few bioindicators were common to both methods, suggesting that methodological limitations and distorted abundance patterns in metabarcoding data may lead to spurious indicators. These findings highlight both the challenges and potential advantages of employing metagenomics for reliable environmental impact assessments.}, }
@article {pmid40413948, year = {2025}, author = {Pholtaisong, J and Kongsinkaew, C and On-Mee, T and Chittapun, S and Pornpukdeewattana, S and Todhanakasem, T and Kunyanee, K and Panya, A and Phonsatta, N and Yingcharoen, P and Charoenrat, T}, title = {Natural versus Saccharomyces boulardii self-induced anaerobic coffee fermentation: Effects on physicochemical properties and microbial ecology, and their influence on volatile profiles and sensory attributes across roast levels.}, journal = {Food chemistry}, volume = {488}, number = {}, pages = {144871}, doi = {10.1016/j.foodchem.2025.144871}, pmid = {40413948}, issn = {1873-7072}, abstract = {This study investigates the effects of natural self-induced anaerobic fermentation (NSIAF) and Saccharomyces boulardii self-induced anaerobic fermentation (SSIAF) on Arabica coffee during wet processing. Over 24 h of fermentation, NSIAF exhibited greater microbial diversity, higher titratable acidity, and increased reducing sugar consumption, while SSIAF provided a more controlled microbial environment dominated by S. boulardii. Volatile compound analysis identified 207 compounds, with lighter roasts showing the greatest number of significantly different compounds between NSIAF and SSIAF treatments. Sensory evaluation revealed a higher cupping score for NSIAF at a light roast (82.08 ± 0.14) compared to SSIAF (81.58 ± 0.14), reflecting distinct flavor characteristics imparted by each fermentation process. Both methods achieved specialty coffee standards (≥80 points), highlighting the potential of NSIAF for complex and diverse profiles and the suitability of SSIAF for consistency and controlled fermentation.}, }
@article {pmid40413859, year = {2025}, author = {Merchant, M and Mande, SS and Sar, P}, title = {Microbial community enrichment and transition in landfill for the biotransformation of unpretreated low-density polyethylene (LDPE) under aerobic and anaerobic conditions.}, journal = {Chemosphere}, volume = {382}, number = {}, pages = {144429}, doi = {10.1016/j.chemosphere.2025.144429}, pmid = {40413859}, issn = {1879-1298}, abstract = {Low density polyethylene (LDPE), prevalent in single-use plastics, poses a significant environmental challenge due to its limited biodegradation. This study aims to enrich and characterize unpretreated LDPE degrading microorganisms from a nearly 50-year-old municipal landfill under aerobic and anaerobic conditions. Detailed analysis of the microbial communities through 16S rRNA gene based metataxonomy, whole genome metagenomics as well as thorough characterization of LDPE films exposed to the enriched microorganisms are done. Distinct shifts between plastisphere and bulk communities were observed. Shotgun metagenomics enabled reconstruction of thirty high-quality metagenome-assembled genomes (MAGs), revealing genes for plastic and hydrocarbon degradation, and biosurfactant production. Several plastic degradation-associated bacteria were identified, including Pseudomonas, Streptomyces, Burkholderia, Bacillus, Thermobifida, Saccharomonospora, Methylocaldum, Methylobacter, Ilumatobacter, Rubrivivax, and archaeal candidates like Methanosarcina and Nitrosarchaeum were observed. MAGs from Burkholderiales and Chlamydiales showed higher potential for LDPE degradation. Scanning electron microscopy showed biofilm formation on plastics, atomic force microscopy indicated surface topological changes, and Fourier transform infrared spectroscopy revealed increased carbonyl groups. Aerobic enrichments allowed up to 60% weight reduction of LDPE, with a degradation rate of 0.00766 mg/day and reaching half-life in nearly 90.49 days, confirming the biodegradation potential of the microbial community. From these observations, this study suggests two potential mechanisms of LDPE degradation under aerobic and anaerobic conditions by enriched communities. This study highlights role of landfill microbiomes in LDPE degradation, offering valuable insights into microbial succession of plastisphere and contributing to the development of effective plastic-degrading community. Future research could explore optimizing these for large-scale plastic waste management.}, }
@article {pmid40413728, year = {2025}, author = {Kousgaard, SJ and Dall, SM and Albertsen, M and Nielsen, HL and Thorlacius-Ussing, O}, title = {Fecal microbiota transplantation from a healthy pouch donor for chronic pouchitis: a proof-of-concept study.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2510464}, doi = {10.1080/19490976.2025.2510464}, pmid = {40413728}, issn = {1949-0984}, mesh = {Humans ; *Pouchitis/therapy/microbiology ; *Fecal Microbiota Transplantation/adverse effects/methods ; Male ; Female ; Adult ; Middle Aged ; Feces/microbiology ; Quality of Life ; Chronic Disease/therapy ; Gastrointestinal Microbiome ; Proof of Concept Study ; Treatment Outcome ; Tissue Donors ; Denmark ; }, abstract = {Chronic pouchitis is a common complication after ileal pouch-anal anastomosis (IPAA) with limited treatment options. In this case series, we aimed to investigate clinical and microbiome changes, as well as adverse events, associated with using fecal microbiota transplantation (FMT) from a donor with a normal functioning IPAA to induce remission in patients with chronic pouchitis. Methods The study was a case-series including a 4-week intervention period and 12-month follow-up. Patients with chronic pouchitis who met the inclusion criteria were recruited from the Department of Gastrointestinal Surgery at Aalborg University Hospital, Denmark. Participants received FMT derived from a donor with a normal functioning IPAA. Treatment was administered by enema daily for two weeks, then every other day for two more weeks. Disease severity and quality of life (QoL) were accessed at baseline and 30-day follow-up. Clinical remission was defined as Pouchitis Disease Activity Index (PDAI) <7. Fecal samples from participants, healthy donors, and the IPAA donor were analyzed using shotgun metagenomic sequencing. Results Three patients with chronic pouchitis were included and completed the treatment protocol and follow-up visits. At the 30-day follow-up, all participants achieved clinical remission with reduced endoscopic inflammation. The median total PDAI score decreased from 8 (range 10-8) at baseline to 6 (range 6-5) at 30 days. Two participants reported improved QoL, while one reported no change. Few mild, self-limited adverse events were reported by all participants during treatment, with no serious events. Principal component analysis of fecal samples distinguished two clusters: healthy donors and the IPAA donor, with participant samples forming a separate cluster Conclusion We observed that all participants achieved clinical remission with reduced endoscopic inflammation following a 4-week FMT intervention. Adverse events were mild and self-limited. Metagenomic analysis revealed distinct microbiome clusters between IPAA donor and recipients, both of which differed from those of healthy donors.}, }
@article {pmid40413726, year = {2025}, author = {Zhang, DY and Li, D and Chen, SJ and Zhang, LJ and Zhu, XL and Chen, FD and Chen, C and Wang, Q and Du, Y and Xiong, JX and Huang, SM and Zhang, XD and Lv, YT and Zeng, F and Chen, RX and Huang, X and Mao, F and Zhou, S and Yao, Q and Huang, Y and Chen, R and Mo, Y and Xie, Y and Jiang, YH and Chen, Z and Mo, CY and Chen, JJ and Bai, FH}, title = {Bacteroides uniformis-generated hexadecanedioic acid ameliorates metabolic-associated fatty liver disease.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2508433}, doi = {10.1080/19490976.2025.2508433}, pmid = {40413726}, issn = {1949-0984}, mesh = {Humans ; Gastrointestinal Microbiome ; Animals ; *Bacteroides/metabolism/genetics ; Mice ; Male ; Female ; Middle Aged ; Feces/microbiology ; Liver/metabolism ; *Fatty Liver/microbiology/metabolism ; Fecal Microbiota Transplantation ; Prospective Studies ; Adult ; Metabolomics ; Mice, Inbred C57BL ; }, abstract = {Gut microbiota exerts a pivotal influence on the development of Metabolic Associated Fatty Liver Disease (MAFLD), although the specific contributions of individual bacterial strains and their metabolites remain poorly defined. We conducted stool shotgun metagenomic sequencing and plasma untargeted metabolomics in a large prospective cohort comprising 120 MAFLD patients and 120 matched healthy controls. The mechanisms and microbial-derived metabolites involved in MAFLD were further investigated through multi-omics analyses in vitro and in vivo. Distinct differences were identified in both the microbial community structure and metabolomic profiles between MAFLD patients and healthy controls. Bacteroides uniformis (B. uniformis) was the most significantly depleted species in MAFLD and negatively correlated with hepatic steatosis and BMI. MAFLD was characterized by marked disruptions in fatty acid and amino acid metabolism. Combined analysis of metabolomic and metagenomic data achieved high diagnostic accuracy for MAFLD and hepatic steatosis severity (AUC = 0.93). Transplantation of fecal microbiota from MAFLD subjects into ABX mice led to the onset of MAFLD-like symptoms, whereas B. uniformis administration alleviate disease progression by inhibiting intestinal fat absorption, FFA from eWAT influx into liver via the gut-liver axis, and IRE1α-XBP1s-mediated flipogenesis and ferroptosis, as confirmed by hepatic transcriptomic and proteomic analyses. Hexadecanedioic acid (HDA), potentially identified as a key metabolite produced by B. uniformis, ameliorated MAFLD symptoms. Mechanistically, B. uniformis-derived HDA also inhibited fat absorption and transported, and entered the liver via the portal vein to suppress IRE1α-XBP1s-mediated flipogenesis and ferroptosis. B. uniformis and its potential putative metabolite HDA may contribute to MAFLD progression modulation, through regulation of the IRE1α-XBP1s axis. This study provides new insights into the gut-liver axis in MAFLD and offers promising therapeutic targets based on specific microbes and their metabolites.}, }
@article {pmid40413632, year = {2025}, author = {Begovic, K and Bryant, L and Glenn, K and Gamble, S}, title = {Clinical Application of Metagenomic Next-Generation Sequencing of Microbial Cell-free DNA in Ruling Out Invasive Fungal Infection in a Patient with Thermal Burn Wounds: A Case Report.}, journal = {Journal of burn care &amp; research : official publication of the American Burn Association}, volume = {}, number = {}, pages = {}, doi = {10.1093/jbcr/iraf094}, pmid = {40413632}, issn = {1559-0488}, abstract = {Patients with severe thermal burns are highly susceptible to invasive fungal infections due to compromised skin integrity, prolonged hospitalization, and immunosuppression. Traditional diagnostic methods, such as cultures and tissue biopsies with histopathology, have limitations. Metagenomic next-generation sequencing (mNGS) of microbial cell-free DNA in plasma is a rapid, non-invasive diagnostic tool for detecting fungal elements in the bloodstream. The aim of this report is to present the utility of this method to aid in ruling out an invasive fungal infection in a patient with burns. This case involves a middle-aged male with extensive thermal burns who developed sepsis, with concerns of invasive fungal infection after fungal elements were detected in wound cultures of skin grafts. However, β-D-glucan and galactomannan assays were negative, and metagenomic next-generation sequencing did not detect fungal DNA in plasma. Histopathological examination of tissue biopsies later confirmed the absence of angioinvasion, and blood cultures showed no evidence of fungemia. As a result, antifungal therapy was safely discontinued without clinical deterioration. While metagenomic next-generation sequencing has shown potential for negative predictive value in immunocompromised patients, its role in patients with burns warrants further investigation. Integrating metagenomic next-generation sequencing with conventional diagnostic methods may improve clinical decision-making, reduce unnecessary empirical antifungal treatment, and enhance patient outcomes.}, }
@article {pmid40413611, year = {2025}, author = {Ju, J and He, J and Ye, B and Li, S and Zhao, J and Chen, W and Zhang, Q and Zhao, W and Yang, J and Liu, L and Li, Y and Xia, M and Liu, Y}, title = {Microbial metabolism mediates the deteriorative effects of sedentary behaviour on insulin resistance.}, journal = {Clinical and translational medicine}, volume = {15}, number = {5}, pages = {e70348}, pmid = {40413611}, issn = {2001-1326}, support = {2023YFC3606300//National Key Research and Development Program of China/ ; 82330105//Key Project of National Natural Science Foundation of China/ ; Overseas//Distinguished Young Scholars of the National Natural Science Foundation of China/ ; 21HAA01094//Distinguished Young Scholars of the National Natural Science Foundation of China/ ; 2024A04J6477//Guangzhou Science and Technology Project/ ; }, mesh = {*Insulin Resistance/physiology ; Humans ; *Sedentary Behavior ; Male ; *Gastrointestinal Microbiome/physiology ; Adult ; }, abstract = {BACKGROUND: Prolonged sedentary time is a strong risk factor for insulin resistance. Recent evidence indicates that gut microbiota may influence the regulation of insulin sensitivity and demonstrates a distinct profile between sedentary and physically active individuals. However, whether and how microbial metabolism mediates the progression of insulin resistance induced by prolonged sedentary time remains unclear.<br><br>METHODS: 560 male participants without hypoglycaemic therapy were included, and insulin resistance was evaluated using the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR). The gut microbiota was identified through metagenomics, host genetic data were obtained using a genotyping array, and plasma metabolites were quantified by liquid chromatography mass spectrometry.<br><br>RESULTS: A panel of 15 sedentary-related species and 38 sedentary-associated metabolic capacities accounted for 31.68% and 21.48% of the sedentary time-related variation in HOMA-IR, respectively. Specifically, decreased Roseburia sp. CAG:471, Intestinibacter bartlettii, and Firmicutes bacterium CAG:83, but increased Bacteroides xylanisolvens related to longer sedentary time, were causally linked to the development of insulin resistance. Furthermore, integrative analysis with metabolomics identified reduced L-citrulline and L-serine, resulting from a suppression of arginine biosynthesis as key microbial effectors linking longer sedentary time to enhanced insulin resistance.<br><br>CONCLUSIONS: In summary, our findings provide insights into the mediating role of gut microbiota on the progression of insulin resistance induced by excessive sedentary time, and highlight the possibility of counteracting the detrimental effect of prolonged sedentary time on insulin resistance by microbiota-modifying interventions.<br><br>KEY POINTS: Prolonged sedentary time leads to a depletion of Roseburia sp. CAG:471 and Firmicutes bacterium CAG:83, and suppresses arginine biosynthesis. Decreased L-citrulline and L-serine function as key microbial effectors mediating the adverse effect of sedentary time on insulin sensitivity. Targeting gut microbiota holds promise to combat insulin resistance induced by excessive sedentary time.}, }
@article {pmid40413198, year = {2025}, author = {Brandão Gontijo, J and Huang, L and Levintal, E and Prieto García, C and Erikson, CB and Coyotl, A and Horwath, WR and Dahlke, HE and Mazza Rodrigues, JL}, title = {Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {858}, pmid = {40413198}, issn = {2052-4463}, support = {7975//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 2021-38420-34070//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; }, mesh = {*Soil Microbiology ; *Groundwater ; Agriculture ; *Metagenome ; Microbiota ; Bacteria/genetics/classification ; Metagenomics ; California ; Archaea/genetics ; Soil ; }, abstract = {Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.}, }
@article {pmid40412970, year = {2025}, author = {Mao, J and Chen, J and Yang, L and Wang, Q and Lin, H and Bai, Y}, title = {Combined impacts of chlorine and pharmaceutical discharge on river periphyton and zoobenthos.}, journal = {Journal of environmental sciences (China)}, volume = {156}, number = {}, pages = {725-734}, doi = {10.1016/j.jes.2024.10.020}, pmid = {40412970}, issn = {1001-0742}, mesh = {Rivers/chemistry/microbiology ; *Water Pollutants, Chemical/toxicity ; *Disinfectants/toxicity ; *Chlorine/toxicity ; Pharmaceutical Preparations/analysis ; Animals ; }, abstract = {Following the COVID-19 outbreak, a vast array of chlorine disinfectants was used to eliminate the virus, leading to inevitable discharge into aquatic ecosystems. These environments also contain various anthropogenic micropollutants, such as pharmaceuticals, which pose threats to the survival and activities of biological communities. Consequently, the presence of discharged chlorine disinfectants and pharmaceuticals can simultaneously impact the structure and function of aquatic ecosystems. To investigate the combined effects of chlorine disinfectants and pharmaceuticals on the periphyton and zoobenthos (Limnodrilus hoffmeisteri) community composition and function, we conducted a 12-flume reactor experiment using sodium hypochlorite and representative pharmaceuticals (abundant in the Yangtze River) as influents. Results demonstrated that the discharge of chlorine disinfectants further altered the composition of river prokaryotic communities. Eukaryotic organisms within the periphyton exhibited greater resilience to chlorine exposure compared to prokaryotic communities. Metagenomic analysis revealed that prokaryotic communities with different compositions can execute similar functions, while RNA sequencing indicated that co-exposure promoted biological processes such as focal adhesion and ribosome synthesis, but inhibited activities related to nitrogen metabolism and resistance to folate antimicrobials. Additionally, co-exposure induced oxidative stress in L. hoffmeisteri, leading to stronger environmental adaptation.}, }
@article {pmid40412963, year = {2025}, author = {Wang, C and Tian, Z and Luan, X and Zhang, H and Zhang, Y and Yang, M}, title = {Distribution of antibiotic resistance genes on chromosomes, plasmids and phages in aerobic biofilm microbiota under antibiotic pressure.}, journal = {Journal of environmental sciences (China)}, volume = {156}, number = {}, pages = {647-659}, doi = {10.1016/j.jes.2024.10.008}, pmid = {40412963}, issn = {1001-0742}, mesh = {*Biofilms/drug effects ; Plasmids/genetics ; *Anti-Bacterial Agents/pharmacology ; Bacteriophages/genetics ; *Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The objective of this study is to quantitatively reveal the main genetic carrier of antibiotic resistance genes (ARGs) for blocking their environmental dissemination. The distribution of ARGs in chromosomes, plasmids, and phages for understanding their respective contributions to the development of antimicrobial resistance in aerobic biofilm consortium under increasing stresses of oxytetracycline, streptomycin, and tigecycline were revealed based on metagenomics analysis. Results showed that the plasmids harbored 49.2 %-83.9 % of resistomes, which was higher (p < 0.001) than chromosomes (2.0 %-35.6 %), and no ARGs were detected in phage contigs under the strict alignment standard of over 80 % identity used in this study. Plasmids and chromosomes tended to encode different types of ARGs, whose abundances all increased with the hike of antibiotic concentrations, and the variety of ARGs encoded by plasmids (14 types and 64 subtypes) was higher than that (11 types and 27 subtypes) of chromosomes. The dosing of the three antibiotics facilitated the transposition and recombination of ARGs on plasmids, mediated by transposable and integrable transfer elements, which increased the co-occurrence of associated and unassociated ARGs. The results quantitatively proved that plasmids dominate the proliferation of ARGs in aerobic biofilm driven by antibiotic selection, which should be a key target for blocking ARG dissemination.}, }
@article {pmid40412639, year = {2025}, author = {Iriarte, J and Lundin, D and Martinez-Varela, A and Gónzalez, JM and Sánchez, P and Dachs, J and Vila-Costa, M}, title = {Entanglement of Hydrocarbon-Degrading Bacteria and Polycyclic Aromatic Hydrocarbons in the Ocean.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126512}, doi = {10.1016/j.envpol.2025.126512}, pmid = {40412639}, issn = {1873-6424}, abstract = {Knowledge of Earth's microbiomes capacity to degrade aromatic compounds is limited by the lack of precise tools for accurately targeting degrading genes and their associated taxa. Additionally, these estimates are hardly compared to in situ background concentrations of polycyclic aromatic hydrocarbons (PAHs), particularly in oceanic waters. This knowledge is important for assessing the persistence of the widespread and abundant PAHs in the environment, and their interactions with microbes. Here, we present a new tool to identify aromatic ring-hydroxylating dioxygenase α-subunit (arhdA) gene sequences by combining profile-based search with phylogenetic placement in a reference phylogeny. We identified arhdA-harboring taxa in both the Genome Taxonomy Database and the Malaspina Vertical Profiles Gene Database, a gene catalog derived from metagenomes collected during the Malaspina expedition. We found that multiple ubiquitous taxa in tropical and temperate oceans harbor arhdA. The comparison of arhdA gene abundances in seawater metagenomes with the field PAH concentrations showed that higher abundances of arhdA gene copies per cell were negatively correlated with 2-4 ring PAHs, consistent with the known degradation of lighter PAHs. Gene abundances were significantly higher in the particle-associated fraction than in the free-living fraction, suggesting particulate matter as a relevant reservoir of PAH degraders. Finally, we show that PAHs modulate, with other environmental variables, the structure of oceanic microbial communities.}, }
@article {pmid40412397, year = {2025}, author = {Klingenberg, C and Justine, M and Moyo, SJ and Löhr, IH and Gideon, J and Mdoe, P and Mduma, E and Manyahi, J and Bargheet, A and Pettersen, VK and Paschal, J and Syre, H and Bernhoff, E and Bukhay, R and Blomberg, B and Langeland, N}, title = {Home administration of a multistrain probiotic once per day for 4 weeks to newborn infants in Tanzania (ProRIDE): a double-blind, placebo-controlled randomised trial.}, journal = {The Lancet. Global health}, volume = {13}, number = {6}, pages = {e1082-e1090}, doi = {10.1016/S2214-109X(25)00064-6}, pmid = {40412397}, issn = {2214-109X}, mesh = {Humans ; *Probiotics/administration &amp; dosage ; Tanzania ; Double-Blind Method ; Infant, Newborn ; Female ; Male ; Infant ; }, abstract = {BACKGROUND: Probiotics are commonly given to preterm and term infants to reduce gut colonisation and prevent disease. Evidence for the beneficial effect of probiotic therapy is sparse, particularly in term infants from low-income and middle-income countries with high infant morbidity and mortality. This study aimed to assess whether a 4-week course of probiotic therapy might reduce death and hospitalisation up to age 6 months in healthy infants in Tanzania.<br><br>METHODS: In this investigator-initiated, single-site, double-blind, placebo-controlled randomised trial conducted at Haydom Lutheran Hospital and in the surrounding area in northeast Tanzania, we randomly assigned healthy infants born in the hospital, in other local health facilities, or at home who weighed 2 kg or more (1:1) to receive a multistrain probiotic mixture (including Lactobacillus acidophilus, Bifidobacterium bifidum, and Bifidobacterium longum subsps infantis) or placebo once per day for 4 weeks. Caregivers of study participants, investigators, study staff, hospital clinicians, and individuals involved in data management or analysis were masked to treatment allocation during all the data collection and management phases of the trial. Caregivers were shown how to give five drops (0&#xb7;2 mL) of allocated treatment solution orally to their infant and then requested to administer this treatment once per day for 4 weeks or until the bottle was empty. During scheduled study visits at ages 1 week, 6 weeks, and 6 months, trained field workers visited each participant's home and used a standardised questionnaire to obtain a history of recent illness, medication use, breastfeeding practice, and the current condition of the child. At the 6-week and 6-month follow-up visits, the participants' weights and lengths were measured, and stool samples were collected. Stool samples were used for analysis of extended-spectrum &#x3b2;-lactamase-producing Enterobacterales (to evaluate gut colonisation rates) and metagenomic sequencing. The primary outcome was a composite of death or hospitalisation during the first 6 months of life, assessed in three populations: a modified intention-to-treat population (mITT), which included all participants with a known primary outcome at 6 months of follow-up; the intention-to-treat population, which included all participants who were enrolled and randomly assigned to a treatment group; and the per-protocol population, which included only infants in the mITT whose caregivers reported having given them the study solution once per day during the 4-week intervention period. This trial is registered with ClinicalTrials.gov, NCT04172012, and is complete.<br><br>FINDINGS: Between Feb 1, 2022, and Jan 4, 2023, 2000 participants were enrolled and randomly assigned to the probiotic (n=1000) or placebo (n=1000) groups, with administration of the probiotic or placebo treatment beginning on median day 1 (IQR 1-2) of life. 6 months after inclusion, data for the primary outcome were available for 1945 (97&#xb7;3%) of the 2000 participants. By mITT, there was no statistically significant difference in the primary outcome between the two study groups. Hospitalisation or death occurred in 34 (3%) of 970 participants in the probiotic group and 31 (3%) of 975 participants in the placebo group (crude relative risk 1&#xb7;10, 95% CI 0&#xb7;68-1&#xb7;78). There were also no differences in the overall incidence of adverse events between the groups, but fewer caregiver-reported gastrointestinal events were reported in the probiotic group.<br><br>INTERPRETATION: Daily administration of a multistrain probiotic mixture in the first 4 weeks of life did not reduce the rate of death or hospitalisation up to age 6 months among infants in Tanzania and did not cause any short-term safety concerns.<br><br>FUNDING: Western and Northern Norway Regional Health Authorities, Trond Mohn Foundation, and Joint Programming Initiative on Antimicrobial Resistance.}, }
@article {pmid40412391, year = {2025}, author = {Breyer, E and Stix, C and Kilker, S and Roller, BRK and Panagou, F and Doebke, C and Amano, C and Saavedra, DEM and Coll-García, G and Steger-Mähnert, B and Dachs, J and Berrojalbiz, N and Vila-Costa, M and Sobrino, C and Fuentes-Lema, A and Berthiller, F and Polz, MF and Baltar, F}, title = {The contribution of pelagic fungi to ocean biomass.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.05.004}, pmid = {40412391}, issn = {1097-4172}, abstract = {Metagenomic analysis has recently unveiled the widespread presence of pelagic fungi in the global ocean, yet their quantitative contribution to carbon stocks remains elusive, hindering their incorporation into biogeochemical models. Here, we revealed the biomass of pelagic fungi in the open-ocean water column by combining ergosterol extraction, Calcofluor-White staining, catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and microfluidic mass sensor techniques. We compared fungal biomass with the biomass of other more studied microbial groups in the ocean such as archaea and bacteria. Globally, fungi contributed 0.32 Gt C (CI: 0.19-0.46), refining previous uncertainty estimates from two orders of magnitude to less than one. While fungal biomass was lower than that of bacteria, it exceeded that of the archaea (archaea:fungi:bacteria biomass ratio of 1:9:44). Collectively, our findings reveal the important contribution of fungi to open-ocean biomass and, consequently, the marine carbon cycle, emphasizing the need for their inclusion in biogeochemical models.}, }
@article {pmid40412032, year = {2025}, author = {Guruge, SK and Han, Z and Karunaratne, SHPP and Chandrajith, R and Cooray, T and Hu, C and Zhang, Y and Yang, M}, title = {Short- and long-read metagenomics uncover the mobile extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater in Sri Lanka.}, journal = {Water research}, volume = {283}, number = {}, pages = {123831}, doi = {10.1016/j.watres.2025.123831}, pmid = {40412032}, issn = {1879-2448}, abstract = {The antibiotic resistance issue in low- and middle-income countries has drawn global concern. This study presents the first metagenomic investigation of antibiotic resistance genes (ARGs) in hospital and municipal wastewater treatment plants (WWTPs) in Sri Lanka, using Illumina short-read and Nanopore long-read sequencing. Samples from three representative WWTPs receiving hospital and/or municipal wastewater (domestic generated) were collected from four districts in Sri Lanka, and as a comparison, wastewater directly discharged without treatment was also taken. ARG abundance was significantly higher in hospital wastewater (7.22 copies/cell) than in municipal wastewater (2.33 copies/cell), and greatly decreased by 82 % and 93 % after treatment processes, respectively. Similar trends were observed for mobile genetic elements. The prevalent subtypes of clinically relevant extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater were blaOXA, blaGES, blaVEB and blaTEM, whereas blaCTX-M and blaNDM were less dominant, which indicated the potential unique distribution pattern of ESBL and carbapenemase genes in Sri Lanka. Using long-read metagenomics, bacterial host range and genetic locations (plasmid or chromosome) of ARGs in sludge samples were predicted. Diverse pathogenic host taxa (Pseudomonas, Streptococcus, Salmonella and Escherichia) and a higher plasmid proportion were identified in the hospital WWTP (39.8 % vs. 21.5 % in the municipal WWTP). Detected mobile genetic contexts in this study, IS6100-sul1-blaOXA-329-blaGES-5-blaGES-5-intI1 and ISKpn6-blaKPC-2-ISKpn7-ISPsy42, were also common in antibiotic-resistant plasmids in Enterobacteriaceae from different countries. These data will serve to expand the inventory of global ARG epidemiology. Also, the finding emphasizes that the wastewater treatment projects, especially in healthcare facilities, are vital for reducing clinically relevant ARG discharge to the environment. Further monitoring using advanced meta-omics approaches is crucial to assess potential ARG risks and optimize control strategies for improving human and ecosystem health in Sri Lanka.}, }
@article {pmid40411710, year = {2025}, author = {Chen, L and Chen, C and Bai, Y and Li, C and Wei, C and Wei, R and Luo, R and Li, R and Ma, Q and Geng, Y}, title = {Evaluation of the effects of different formulations of protectants on the preservation of the microbiota in fecal microbiota transplantation.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40411710}, issn = {1618-1905}, abstract = {BACKGROUND: With the increasing indications for fecal microbiota transplantation for the treatment of diseases, there is a growing demand for the preparation of frozen or lyophilized fecal microbiota products that are viable and can stably colonize the recipient. The addition of protective agents plays an important role in the preparation. However, there has been no systematic evaluation of the protective agents used in fecal microbiota sample transplantation preparation for transplantation.<br><br>METHODS: We were used the donor bacterial flora containing 10 different formulations of protective agents were frozen, lyophilized, and stored. Plate counting, CCK8 assay, flow cytometry after LIVE/DEAD staining, and fluorescence intensity were used to assess viable bacteria in vitro. In addition, the donor bacterial flora samples containing different formulations protective agents were transplanted into antibiotic-treated SPF mice, with 3 mice in each group and a total of 5 groups. Fecal samples were collected for metagenomic sequencing to observe the colonization of the bacterial flora in the recipient mice.<br><br>RESULTS: The preliminary screening results showed that the survival rate of bacteria in the 5% trehalose (T) groups, and 5% sucrose, 5% inulin, and 1% cysteine hydrochloride (SI) groups was slightly higher than that in the other groups. SI groups tended to be more protective against anaerobes than T groups. The donor gut microbiota containing the SI groups protective agent exhibited the best colonization of the recipient mice. The protective effects of different formulations of protective agents on the colonized probiotic strains and the metabolic function of the bacterial flora in recipient mice were found to be species specific.<br><br>CONCLUSIONS: SI groups can not only better protect the activity of anaerobic bacteria in the intestine, but also effectively promote the effective colonization of donor intestinal bacteria in the recipient mice, and the effect of frozen storage method is less, and can be used at the same time as frozen and freeze-dried preparation. It can be used as a reference for the selection of protective agents in the preparation of fecal microbiota transplantation samples.}, }
@article {pmid40411603, year = {2025}, author = {Georgakis, N and Premetis, GE and Pantiora, P and Varotsou, C and Bodourian, CS and Labrou, NE}, title = {The impact of metagenomic analysis on the discovery of novel endolysins.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {126}, pmid = {40411603}, issn = {1432-0614}, support = {4036//HFRI/ ; }, mesh = {*Metagenomics/methods ; *Endopeptidases/genetics/isolation &amp; purification/pharmacology/metabolism ; Bacteriophages/enzymology/genetics ; Anti-Bacterial Agents/pharmacology ; Computational Biology ; Humans ; }, abstract = {Metagenomics has revolutionized enzyme discovery by enabling the study of genetic material directly from environmental samples, bypassing the need for microbial cultivation. This approach is particularly effective for identifying novel endolysins, phage-derived enzymes with antibacterial properties suited for therapeutic and industrial applications. Diverse ecosystems, such as biofilms, human microbiome, hot springs, and geothermal areas, serve as rich reservoirs for endolysins with traits like thermostability, broad-spectrum activity, specificity and resistance to harsh conditions. Functional metagenomics, complemented by bioinformatics, enables the discovery and annotation of previously uncharacterized endolysins. Examples of endolysins discovered from metagenomics analysis are discussed. Despite the challenges of analyzing complex microbial ecosystems and isolating target genes, metagenomics holds immense potential for uncovering innovative endolysins, paving the way for developing new biotechnological applications. KEY POINTS: • Endolysins offer antibacterial potential for therapeutic and industrial use. • Metagenomics enables discovery of novel endolysins from diverse ecosystems. • Advances in tools and methods have accelerated novel endolysins discovery.}, }
@article {pmid40410832, year = {2025}, author = {Chu, B and Ge, S and He, W and Sun, X and Ma, J and Yang, X and Lv, C and Xu, P and Zhao, X and Wu, K}, title = {Gut symbiotic bacteria enhance reproduction in Spodoptera frugiperda (J.E. Smith) by regulating juvenile hormone III and 20-hydroxyecdysone pathways.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {132}, pmid = {40410832}, issn = {2049-2618}, support = {2023FY100500//Chinese Science &amp;Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &amp;Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &amp;Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &amp;Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &amp;Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &amp;Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &amp;Technology Fundamental Resources Investigation Program/ ; 2023FY100500//Chinese Science &amp;Technology Fundamental Resources Investigation Program/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; CARS-02//National Modern Agricultural Industry Technology System Construction Fund of China/ ; }, mesh = {Animals ; *Spodoptera/microbiology/physiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Ecdysterone/metabolism ; *Symbiosis ; Female ; Reproduction ; Enterobacter/isolation &amp; purification/physiology ; Larva/microbiology ; Enterococcus/isolation &amp; purification/physiology/genetics ; Klebsiella/isolation &amp; purification/genetics/physiology ; Bacteria/classification/genetics ; *Juvenile Hormones/metabolism ; }, abstract = {BACKGROUND: The insect gut microbiota forms a complex, multifunctional system that significantly affects phenotypic traits linked to environmental adaptation. Strong reproductive potential underpins the migratory success, population growth and destructive impact of the fall armyworm, Spodoptera frugiperda (J.E. Smith). However, the precise role of gut bacteria in S. frugiperda reproductive processes, distribution and transmission dynamics remains unclear.<br><br>RESULTS: We examined the gut microbiota of S. frugiperda a major invasive agricultural pest, identifying Enterococcus, Enterobacter, and Klebsiella as core microorganisms present throughout its life cycle. These microbes showed heightened activity during the egg stage, early larval stages and pre-oviposition period in females. Using an axenic insect re-infection system, Enterococcus quebecensis FAW181, Klebsiella michiganensis FAW071 and Enterobacter hormaechei FAW049 were found to significantly enhance host fecundity, increasing egg production by 62.73%, 59.95%, and 56.71%, respectively. Metagenomic and haemolymph metabolomic analyses revealed a positive correlation between gut symbiotic bacteria and hormone metabolism in female S. frugiperda. Further analysis of metabolites in the insect hormone biosynthesis pathway, along with exogenous injection of juvenile hormone III and 20-hydroxyecdysone, revealed that gut microbes regulate these hormones, maintaining levels equivalent to those in control insects. This regulation supports improved fecundity in S. frugiperda, aiding rapid colonization and population expansion.<br><br>CONCLUSIONS: These findings emphasize the pivotal role of gut bacteria E. quebecensis FAW181, E. hormaechei FAW049, and K. michiganensis FAW071 in enhancing S. frugiperda reproduction by modulating JH III levels through JHAMT regulation and concurrently modulating the levels of 20E and its precursors via PHM. Our results provide novel insights into microbe-host symbiosis and pest management strategies for alien invasive species. Video Abstract.}, }
@article {pmid40410357, year = {2025}, author = {Rozday, TJ}, title = {Metagenomics distilled: new k-mer-based methods.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40410357}, issn = {1740-1534}, }
@article {pmid40410138, year = {2025}, author = {Chen, AS and Kim, H and Nzabarushimana, E and Shen, J and Williams, K and Gurung, J and McGoldrick, J and Burke, KE and Yarze, JC and Nguyen, LH and Staller, K and Chung, DC and Xavier, RJ and Khalili, H}, title = {Association of distinct microbial and metabolic signatures with microscopic colitis.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4644}, pmid = {40410138}, issn = {2041-1723}, support = {R01AG068390//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; P30DK043351//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Metabolome ; Feces/microbiology ; *Colitis, Microscopic/microbiology/metabolism ; Aged ; Adult ; Case-Control Studies ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Diarrhea/microbiology/metabolism ; Metabolomics ; Metagenomics ; Biomarkers/metabolism ; }, abstract = {Microscopic colitis (MC) is a chronic inflammatory disease of the large intestine that primarily affects older adults and presents with chronic diarrhea. The etiology is unknown and there are currently no FDA approved medications or biomarkers for treatment or monitoring of the disease. Emerging evidence have implicated the gut microbiome and metabolome disturbances in MC pathogenesis. We conduct a comprehensive analysis of gut microbial and metabolic changes in a cohort of 683 participants, including 131 patients with active MC, 159 with chronic diarrhea, and 393 age- and sex-matched controls without diarrhea. Stool microbiome and metabolome are profiled using whole-genome shotgun metagenomic sequencing and ultra-high performance liquid chromatography-mass spectrometry, respectively. Compared to controls, eight microbial species including pro-inflammatory oral-typical Veillonella dispar and Haemophilus parainfluenzae, and 11 species, including anti-inflammatory Blautia glucerasea and Bacteroides stercoris are enriched and depleted in MC, respectively. Pro-inflammatory metabolites, including lactosylceramides, ceramides, lysophospholipids, and lysoplasmalogens, are enriched in active MC. Multi-omics analyses reveal robust associations between microbial species, metabolic pathways, and metabolites, suggesting concordant disruptions in MC. Here, we show distinct shifts in gut microbiome and metabolome in MC that can inform the development of non-invasive biomarkers and novel therapeutics.}, }
@article {pmid40410126, year = {2025}, author = {Su, C and Zhou, H and Wang, Y and Duan, X and Jiang, T and Zhang, C and Gao, H and Kong, L and Wang, M and Guo, C}, title = {Contrasting Effects of Atmospheric Particulate Matter Deposition on Free-Living and Particle-Associated Bacteria in the South China Sea.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12533}, pmid = {40410126}, issn = {1520-5851}, abstract = {Atmospheric particulate matter (PM) deposition has become an important nutrient source in marine ecosystems, increasing particulate organic carbon and resource heterogeneity. However, their effects on marine bacterial communities remain unclear. In this study, by conducting on-board microcosm experiments with anthropogenic East Asian PM in the oligotrophic South China Sea, the response of particle-associated (PA) bacteria was investigated and compared with its free-living (FL) counterparts. Results showed that PM input increased nutrient heterogeneity, shifting bacterial community composition and lifestyle. Copiotrophic PA bacteria became more abundant and contributed a disproportionately higher percentage to total bacterial production despite a decline in total bacterial abundance. FL bacteria showed increased diversity, shifting from oligotrophs to copiotrophs, while PA bacteria displayed reduced diversity and nondirectional compositional changes, suggesting their distinct assembly mechanisms in response to external nutrient inputs. Metagenomic analysis further revealed that PM drives a shift toward a copiotrophic, particle-attached lifestyle with upregulated pathways for chemotaxis, motility, and biofilm formation. Notably, PM addition also increased the relative abundance of oil-degrading taxa. These findings reveal the complexity of microbial responses to environmental perturbations and underscore the need to consider unique ecological niches and bacterial lifestyles.}, }
@article {pmid40409349, year = {2025}, author = {Zhou, S and Wang, K and Huang, J and Xu, Z and Yuan, Q and Liu, L and Wang, Z and Miao, J and Wang, H and Wang, T and Guan, W and Ding, C}, title = {Indole-3-lactic acid suppresses colorectal cancer via metabolic reprogramming.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2508949}, doi = {10.1080/19490976.2025.2508949}, pmid = {40409349}, issn = {1949-0984}, mesh = {*Colorectal Neoplasms/metabolism/drug therapy/pathology/microbiology ; Humans ; Animals ; Gastrointestinal Microbiome/drug effects ; Mice ; *Indoles/metabolism/pharmacology/administration &amp; dosage ; STAT3 Transcription Factor/metabolism ; Cell Proliferation/drug effects ; Tryptophan/metabolism ; Cell Line, Tumor ; Male ; Female ; Receptors, Aryl Hydrocarbon/metabolism ; Cell Movement/drug effects ; Apoptosis/drug effects ; Metabolic Reprogramming ; }, abstract = {Research indicates that abnormal gut microbiota metabolism is linked to colorectal cancer (CRC) progression, but the role of microbiota-related tryptophan metabolism disruption remains unclear. Using metagenomic sequencing and targeted Trp metabolomics, our research identified that CRC patients had abnormal indole-3-lactic acid (ILA) levels, which were related to tumor malignancy. Exogenous ILA administration suppressed CRC development in AOM/DSS induced and xenograft mice models. Furthermore, in vitro experiments demonstrated that ILA inhibits tumor cell proliferation, migration, and anti-apoptotic capabilities. Mechanistically, ILA appears to directly occupy the phosphorylation sites of STAT3, leading to a reduction in intracellular phosphorylated STAT3 (p-STAT3) levels and the inhibition of the HK2 pathway, thereby downregulating glucose metabolism in cancer cells. Notably, this inhibition is independent of the aryl hydrocarbon receptor (AHR). In conclusion, our research findings demonstrate that alterations in tryptophan metabolism among CRC patients can influence tumor progression and reveal a novel mechanism through which ILA exerts its inhibitory effects on CRC. These findings offer new insights into the role of gut microbiota in CRC and identify potential clinical therapeutic targets.}, }
@article {pmid40409085, year = {2025}, author = {Xie, Y and Wang, T and Guo, C and Chu, C and Liu, Z and Jiang, L and Deng, Y and Yi, J}, title = {Metagenomic insights into the microorganisms responsible for producing amino acid nitrogen during sufu fermentation.}, journal = {Food chemistry}, volume = {487}, number = {}, pages = {144763}, doi = {10.1016/j.foodchem.2025.144763}, pmid = {40409085}, issn = {1873-7072}, abstract = {Amino acid nitrogen (AAN), a key contributor to umami taste, plays a central role in flavor development during sufu fermentation. Given the critical influence of microbial metabolism on flavor formation, this study employed metagenomic analysis to investigate the mechanisms of AAN generation. During sufu fermentation, the AAN content increased significantly, reaching a final concentration of 0.56 g/100 g. Metagenomic analysis revealed that both bacterial (e.g., Dysgonomonas macrotermitis, Lactococcus lactis) and fungal (e.g., Rhizopus arrhizus) species were the core microbiota driving AAN formation. These microorganisms encoded abundant proteases and amino acid hydrolases essential for AAN metabolism. Functional profiling highlighted carbohydrate and amino acid metabolism as the dominant pathways in flavor formation. Notably, glutamate synthesis was associated with pathways ko00220 and ko00250, mediated by glutamate synthetase (EC 1.4.1.13) and glutamine synthetase (EC 6.3.1.2). These findings elucidate the microbial enzymatic mechanisms-particularly amino acid transformations-underlying sufu's umami taste development during fermentation.}, }
@article {pmid40408992, year = {2025}, author = {Zhang, S and Li, J and Lai, J and Zhang, Q and Zhao, Z and Li, B}, title = {Transfer dynamics of intracellular and extracellular last-resort antibiotic resistome in hospital wastewater.}, journal = {Water research}, volume = {283}, number = {}, pages = {123833}, doi = {10.1016/j.watres.2025.123833}, pmid = {40408992}, issn = {1879-2448}, abstract = {The increasing prevalence of last-resort antibiotic resistance genes (LARGs) has posed severe public health hazards. Previous studies focused primarily on the profiles of intracellular LARGs (iLARGs) in hospital wastewater (HWW), while largely neglecting the expression patterns of iLARGs and the presence of extracellular LARGs (eLARGs). Currently, wastewater resistomes and transfer dynamics of LARGs are still poorly characterized. This study integrates Nanopore-metagenomic and metatranscriptomic sequencing to conduct the comprehensive longitudinal analysis of both iLARGs and eLARGs in HWW. Our study firstly revealed the distinct seasonal patterns of iLARGs and eLARGs. Specifically, iLARGs showed higher abundance during colder seasons, whereas eLARGs showed higher abundance in warm seasons. Both clinical pathogens and functional bacteria of wastewater treatments were identified as important hosts of LARGs, while clinical pathogens played predominant roles in the high expression levels of LARGs. Acinetobacter spp. was identified as major host of blaNDM-1 in HWW, which is unrestricted by plasmid host range compatibility. However, HWW treatments could not remove LARGs effectively and instead facilitated their transmission by enhancing the expression and horizontal transfer of mobile genetic element (MGE)-derived LARGs. Our study provides comprehensive insights for the atlas and transfer dynamics of LARGs in HWW for the development of control strategies under worldwide spread of antibiotic resistance.}, }
@article {pmid40408985, year = {2025}, author = {Liu, Y and Deng, Y and van Loosdrecht, MCM and Chen, G}, title = {Development of nitrification and elemental sulfur-based denitrification/anammox (NS[0]DA) process for mainstream nitrogen removal.}, journal = {Water research}, volume = {283}, number = {}, pages = {123836}, doi = {10.1016/j.watres.2025.123836}, pmid = {40408985}, issn = {1879-2448}, abstract = {The implementation of mainstream anaerobic ammonium oxidation (anammox) can facilitate the realization of carbon-neutral wastewater treatment. However, this technology remains challenging owing to the inability to stably provide nitrite. In this study, we developed a novel nitrification and elemental sulfur-based partial autotrophic denitrification/anammox (NS[0]DA) process for mainstream nitrogen removal. The NS[0]DA system consists of a nitrification reactor and a combined elemental sulfur-based denitrification and anammox (S[0]DA) reactor. Each reactor was independently initiated and optimized before being integrated. At mainstream nitrogen levels (48.5 ± 1.7 mg NH4[+]-N/L) and 25 °C, the NS[0]DA system achieved 89.1 ± 5.7 % total nitrogen (TN) removal efficiency, with an effluent TN concentration of 5.4 ± 2.8 mg N/L. The system exhibited a low N2O emission factor (0.23 %), significantly lower than other anammox-based systems. The S[0]DA reactor achieved a nitrogen removal rate of 0.53 kg N/(m[3]·d) with a short hydraulic retention time (2 h). Anammox accounted for 87.3 ± 7.0 % of the TN removal in the S[0]DA reactor. Isotope experiments and kinetic analysis revealed the cooperation between anammox and denitrification for nitrogen removal. Polysulfides formed in the S[0]DA reactor enhanced the utilization rate of elemental sulfur. High-throughput sequencing identified Thiobacillus and Candidatus Brocadia as the dominant genera of sulfur oxidation and anammox, respectively. The nitrogen and sulfur metabolic pathways were further verified through metagenomic analysis. Overall, the NS[0]DA process provides a stable and efficient nitrogen removal process, minimizing oxygen demand, eliminating organic carbon requirements, and reducing N2O emissions compared to conventional nitrification/denitrification. This approach offers a promising solution for mainstream nitrogen removal in wastewater treatment.}, }
@article {pmid40408861, year = {2025}, author = {Huo, W and Yu, J and Ye, R and Lin, Z and Zhang, R and Shen, Q}, title = {Enhanced ethanol-driven carboxylate chain elongation by MOF-808 from waste activated sludge: Process and mechanism.}, journal = {Journal of environmental management}, volume = {387}, number = {}, pages = {125886}, doi = {10.1016/j.jenvman.2025.125886}, pmid = {40408861}, issn = {1095-8630}, abstract = {Carboxylate chain elongation can create value-added bioproducts from waste activated sludge (WAS). The bioconversion of WAS during anaerobic fermentation is often constrained by inefficient hydrolysis. The addition of MOF-808 (200 mg MOF-808/g volatile solids (VS)) increased caproate production and selectivity by approximately 38.9 % and 28.9 %, respectively. MOF-808 significantly promoted the hydrolysis of WAS, accelerated the degradation of extracellular polymeric substances, and enhanced acetate accumulation. Absolute quantitative metagenomics conducted during the acidification and chain elongation phases demonstrated that MOF-808 markedly improved enzymatic hydrolysis. The absolute gene abundance of protease and α-glucosidase increased by 168.9 % and 191.2 %, respectively, compared to the control trial. Furthermore, the reverse β-oxidation (RBO) pathway, the primary route for chain elongation, exhibited a 19.2 %-76.1 % increase in gene abundance for enzymes involved in this pathway in the presence of MOF-808. Notably, the absolute gene abundance of electron-bifurcating enzyme complexes, including butyryl-CoA dehydrogenase-electron transferring flavoprotein complex (Bcd-EtfAB), proton-translocating NAD(P)[+] transhydrogenase, ATPase (subunits A-I), and NAD oxidoreductase (RnfA-E), was significantly elevated in the MOF-808 trial. These findings provide valuable insights into enhancing the efficiency of chain elongation fermentation of WAS using MOF-like materials.}, }
@article {pmid40407725, year = {2025}, author = {Liu, W and Su, M and Zhang, D and Liu, S and Zhang, Y and Yang, Z}, title = {Identification of Clonorchis sinensis in Bronchoalveolar Lavage Fluid and Peripheral Blood Using Next-Generation Sequencing in a Patient with Septic Shock: a Case Report and Literature Review.}, journal = {Emerging microbes &amp; infections}, volume = {}, number = {}, pages = {2511133}, doi = {10.1080/22221751.2025.2511133}, pmid = {40407725}, issn = {2222-1751}, abstract = {SummaryWe present a case report of a 59-year-old male diagnosed with pancreatic cancer with multiple abdominal metastases, in whom metagenomic next-generation sequencing unexpectedly identified Clonorchis sinensis genomic sequences in both bronchoalveolar lavage fluid and peripheral blood specimens. Subsequent examination further confirmed the presence of viable C. sinensis eggs in the stool samples. The findings underscore the prognostic significance of enhanced diagnostic protocols for parasitic infections in oncological cases. This investigation demonstrates the clinical utility of molecular diagnostic approaches and alternative biological specimens for detecting C. sinensis infection.}, }
@article {pmid40407371, year = {2025}, author = {Li, S and Wu, J and Wang, Q and Cao, H and Zhang, L}, title = {The landscape of bacterial contractile injection systems across large-scale metagenomes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0321324}, doi = {10.1128/spectrum.03213-24}, pmid = {40407371}, issn = {2165-0497}, abstract = {UNLABELLED: Bacterial contractile injection systems (CISs) have evolved as sophisticated mechanisms that enable bacteria to interact with and manipulate their hosts. Resembling bacteriophage tails, these systems inject effector proteins directly into target cells, facilitating complex bacterial-host interactions. Despite significant advances in understanding CISs, exploration has largely been constrained by the availability of completely sequenced microbial genomes, potentially underrepresenting their diversity in natural environments. In this study, we identified 1,129 CISs from metagenome-assembled genomes spanning 14 bacterial phyla and 1 archaeal phylum. Notably, CISs were identified in many uncultured microorganisms and were highly enriched in the phylum Bacteroidota. Structural gene composition varied across ecosystems, with Bacteroidetes injection systems (BISs) from the human digestive system lacking typical tail fiber proteins and Cis6. However, all BISs encoded homologs of Aasi_0556, suggesting functional similarities with T6SS[iv]. Furthermore, we identified a candidate CIS cargo protein, BDI_2459, containing the toxin-associated DUF4157 domain, which exhibited moderate toxin potential. We cloned and heterologously expressed BDI_2459 in Escherichia coli. The standalone BDI_2459 did not exhibit its activity. However, there was activity when fused with a periplasmic translocation tag.<br><br>IMPORTANCE: Overall, this study expands our understanding of the ecological diversity, evolutionary adaptations, and functional roles of contractile injection systems (CISs) in microbial communities. The findings particularly highlight their adaptations to human-associated microbiomes. In addition, we conducted preliminary functional studies targeting the cargo protein BDI_2459 in CIS from Parabacteroides distasonis (CIS[Pd]). These results provide new insights into CIS-mediated bacterial interactions and pave the way for future microbiome engineering and antibacterial strategies.}, }
@article {pmid40407311, year = {2025}, author = {Li, H and Wang, Z and He, S and Zhao, X and Wu, Q and Sun, Y and Fan, Y and Hu, X and Tian, Z and Zhang, S}, title = {Unraveling gut microbiome alterations and metabolic signatures in hereditary transthyretin amyloidosis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0230224}, doi = {10.1128/spectrum.02302-24}, pmid = {40407311}, issn = {2165-0497}, abstract = {UNLABELLED: Hereditary transthyretin amyloidosis (hATTR) is a rare, often fatal disease characterized by the abnormal aggregation of atypical transthyretin fibrils. Given the variability in the penetrance and clinical manifestations of hATTR, the role of nongenetic factors, particularly those related to the gut microbiota, warrants investigation. We conducted a cross-sectional study, examining the untargeted serum metabolome and gut metagenome in 13 patients with hATTR and 22 healthy controls. Significant disparities were observed in both the serum metabolome and gut microbiome of individuals with hATTR when compared to healthy controls. Notably, the serum levels of gamma-aminobutyric acid (GABA) and taurine were markedly decreased in the hATTR group, with the most pronounced reduction in those exhibiting hATTR-related cardiac amyloidosis. Additionally, commensals such as Bifidobacterium pseudocatenulatum, Lactobacillus rogosae, and Hungatella hathewayi were significantly diminished in hATTR patients and were positively correlated with the metabolite module containing GABA and taurine. Metagenomic and metabolomic pathway enrichment analyses collectively revealed disruptions in glutamate and taurine metabolism in hATTR. Our findings imply that patients with hATTR may exhibit metabolic irregularities in glutamate and taurine, potentially associated with an imbalance in the gut microbiota.<br><br>IMPORTANCE: Hereditary transthyretin amyloidosis (hATTR) is influenced not only by genetic factors but also by environmental or host factors during its onset and progression. Previous studies have independently examined the metabolome or gut microbiome in hATTR, but the interplay between the microbiota and metabolism under this condition remains largely unknown. Our cross-sectional study represents the first comprehensive integration of gut metagenome and serum metabolome analyses in hATTR patients. We observed disturbances in glutamate and taurine metabolism among these patients, which correlated with distinctive shifts in the gut microbiota. This study offers insights into the intricate dynamics among gut dysbiosis, metabolic imbalances, and the progression of hATTR, suggesting directions for future research into the underlying mechanisms and therapeutic strategies.}, }
@article {pmid40407237, year = {2025}, author = {Liu, M and Zhou, G and Zhang, C and Chen, L and Ma, D and Zhang, L and Jia, C and Ma, L and Zhang, J}, title = {Impact of Virus-Mediated Modifications in Bacterial Communities on the Accumulation of Soil Organic Carbon.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e06449}, doi = {10.1002/advs.202506449}, pmid = {40407237}, issn = {2198-3844}, support = {2022YFD1500401//National Key Research and Development Program of China/ ; 2023YFD1901001//National Key Research and Development Program of China/ ; CARS-03//Agriculture Research System of China/ ; CARS-52//Agriculture Research System of China/ ; 42277336//National Natural Science Foundation of China/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; }, abstract = {Microbial adaptations to resource availability are crucial to predict the responses of ecosystems to carbon (C) changes, yet viral roles in C cycling under varying levels of C remain elusive. Through metagenomic analysis of soils with contrasting C availability, a total of 24,789 viral contigs predominantly represent Microviridae and Siphoviridae. The soils with low C availability (straw removal) harbored 21% lysogenic viruses and enriched auxiliary metabolic genes (AMGs) related to C degradation (p < 0.05). Conversely, the soils with high C availability (straw returning) show 93% lytic viruses, stronger virus-bacteria symbiosis, and numerous host functional genes related to C cycling and viral AMGs linked to C fixation (p < 0.05). Furthermore, these findings show that the addition of viruses boosted microbial metabolic efficiency and recalcitrant C accumulation (p < 0.05), with lytic activity accelerating organic C turnover via nutrient release and necromass formation. Overall, this study demonstrates viruses as key regulators of sustainable sequestration of C through host-driven metabolic optimization.}, }
@article {pmid40407188, year = {2025}, author = {Batarseh, TN and Koskella, B}, title = {Distinguishing among evolutionary and ecological processes shaping microbiome dynamics.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf107}, pmid = {40407188}, issn = {1751-7370}, abstract = {Evolution is defined as the change in allele frequency over time as a result of either neutral processes, such as genetic drift, or as an adaptive process in response to selection. In contrast, ecological dynamics describe changes in population densities, species distributions, species interactions, and/or relative abundances within communities, all of which can also be the result of either stochastic or deterministic processes. Although the distinction between these patterns has long held for plants and animals, microbial community dynamics can blur the line between ecological and evolutionary processes, especially as they can occur on very similar timescales. Despite the importance of differentiating changes occurring within a population or strain from those occurring among populations, many common methodologies used to study microbiomes are not able to differentiate among them. In this review, we summarize the forces known to generate genetic diversity in bacterial genomes and describe the approaches used to study bacterial evolution from simple to more complex systems. We then explore how current methodologies and conceptual understanding can be applied to both understand and differentiate between the ecological and evolutionary processes in microbial communities. By highlighting lessons from longitudinal microbiome studies and experimental evolution, we explore the unique opportunities afforded by newer sequencing approaches and better sequencing resolution. Throughout, we identify the unique and outstanding challenges in studying these processes in microbiome systems and emphasize the great benefits in doing so to move forward our ability to better predict and manipulate microbiomes.}, }
@article {pmid40407096, year = {2025}, author = {Creskey, M and Silva Angulo, F and Wu, Q and Tamming, L and Fekete, EEF and Cheng, K and Ning, Z and Wang, A and Brito Rodrigues, P and de Rezende Rodovalho, V and Ramirez Vinolo, MA and Figeys, D and Li, X and Trottein, F and Zhang, X}, title = {Metaproteomics reveals age-specific alterations of gut microbiome in hamsters with SARS-CoV-2 infection.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2505117}, doi = {10.1080/19490976.2025.2505117}, pmid = {40407096}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/virology ; Cricetinae ; *Proteomics/methods ; SARS-CoV-2 ; Feces/microbiology ; Age Factors ; Metagenomics ; Disease Models, Animal ; Mesocricetus ; Male ; }, abstract = {The gut microbiome's pivotal role in health and disease is well established. SARS-CoV-2 infection often causes gastrointestinal symptoms and is associated with changes of the microbiome in both human and animal studies. While hamsters serve as important animal models for coronavirus research, there exists a notable void in the functional characterization of their microbiomes with metaproteomics. In this study, we present a workflow for analyzing the hamster gut microbiome, including a metagenomics-derived hamster gut microbial protein database and a data-independent acquisition metaproteomics method. Using this workflow, we identified 32,419 protein groups from the fecal microbiomes of young and old hamsters infected with SARS-CoV-2. We showed age-specific changes in the expressions of microbiome functions and host proteins associated with microbiomes, providing further functional insight into the interactions between the microbiome and host in SARS-CoV-2 infection. Altogether, this study established and demonstrated the capability of metaproteomics for the study of hamster microbiomes.}, }
@article {pmid40406519, year = {2025}, author = {Song, T and Yin, L and Zhou, X and Tao, X and Tie, D and Zhang, J and Jiang, L}, title = {Microbiota profiling from biopsied tissues in complex infections: a diagnostic and prognostic analysis through metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1567981}, pmid = {40406519}, issn = {2235-2988}, mesh = {Humans ; Male ; Retrospective Studies ; Female ; Middle Aged ; *Metagenomics/methods ; Prognosis ; *High-Throughput Nucleotide Sequencing/methods ; Biopsy ; Adult ; Aged ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Coinfection/microbiology/diagnosis ; Fungi/isolation &amp; purification/genetics/classification ; Viruses/isolation &amp; purification/genetics/classification ; Aged, 80 and over ; Sensitivity and Specificity ; *Communicable Diseases/diagnosis/microbiology ; }, abstract = {BACKGROUND: Infectious diseases that require tissue biopsy are usually more difficult to diagnose through conventional microbiological tests (CMT), and knowledge of the infection microbiota pattern from biopsied tissues remains incomplete. Our study aimed to investigate the diagnostic and prognostic value of metagenomic next-generation sequencing (mNGS), characterize the microbiota profile from biopsied tissues, and examine its relationship with clinical outcomes.<br><br>METHODS: This retrospective cohort study included 110 patients who underwent tissue biopsy and sent both mNGS and CMT due to suspected complex infection. Microbiota patterns were illustrated via unsupervised hierarchical clustering analysis. Multivariate regression analysis was used to investigate the effect measures.<br><br>RESULTS: The sensitivity of mNGS was significantly higher than that of CMT regarding bacteria (87.23% vs 40.43%, P=0.01), viruses (100% vs 5.56%, P<0.001), and fungi (87.5% vs 28.6%, P=0.04). Polymicrobial infection accounted for 45.2% (33/73) of the infection samples. In skeletal articular biopsied tissues, Staphylococcus presented the highest mean abundance among different species of bacteria (21.2% of all bacterial reads, standard deviation (SD) 38.9). Anaerobic bacteria (24.0%, SD 25.9) represented the most common bacteria in biopsied tissue from the lung or mediastinum. The presence of gram-negative bacteria (adjusted OR 5.21, 95% CI 1.39-19.43, P=0.01), Enterobacteriaceae (adjusted OR 5.71, 95% CI 1.17-28.03, P=0.03) and Staphylococcus (adjusted OR 8.64, 95% CI 1.95-38.34, P=0.005) was associated with an increased risk of treatment failure. Early mNGS sampling within 7 days after admission was associated with a significantly decreased risk of all-cause mortality (HR 0.18, 95% CI 0.04-0.94; P=0.04), treatment failure (OR 0.17, 95% CI 0.05-0.66; P=0.01), and increased probability of clinical resolution (OR 3.03, 95% CI 1.24-7.40; P=0.01).<br><br>CONCLUSION: mNGS demonstrates significant diagnostic and prognostic efficacy in patients undergoing tissue biopsy for suspected complex infections. The presence of Gram-negative bacteria, Enterobacteriaceae, and Staphylococcus is associated with a higher probability of treatment failure, which underscores the advantage of using mNGS to guide more aggressive antibiotic strategies.}, }
@article {pmid40406411, year = {2025}, author = {Wen, Z and Chen, M and Xia, C and Sun, Y and Zhang, Y}, title = {Acute transverse myelitis caused by Paragonimus infection: a case report and review of the literature.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1506201}, pmid = {40406411}, issn = {2296-858X}, abstract = {Acute transverse myelitis (ATM) is a rare but severe neurological disorder that can be triggered by infections, autoimmune conditions, or other factors. While the association between parasitic infections and ATM is uncommon, Paragonimus infection can cause significant neurological damage, posing a diagnostic challenge. We report the case of a 65-year-old male patient who developed acute limb weakness, sensory loss, and fever following abdominal pain. Initial diagnostic tests were inconclusive; however, advanced imaging and metagenomic sequencing of cerebrospinal fluid ultimately confirmed an Paragonimus infection. After treatment with praziquantel, the patient successfully regained substantial motor function. This case highlights the need to consider parasitic infections in endemic areas and demonstrates the critical role of advanced diagnostic tools, such as metagenomic sequencing, in achieving timely diagnosis and treatment, ultimately improving the patient's prognosis.}, }
@article {pmid40405248, year = {2025}, author = {Cornejo-Granados, F and Gallardo-Becerra, L and Romero-Hidalgo, S and Lopez-Zavala, AA and Cota-Huízar, A and Cervantes-Echeverría, M and Sotelo-Mundo, RR and Ochoa-Leyva, A}, title = {Host genome drives the microbiota enrichment of beneficial microbes in shrimp: exploring the hologenome perspective.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {50}, pmid = {40405248}, issn = {2524-4671}, support = {Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; }, abstract = {BACKGROUND: Pacific Whiteleg shrimp (Litopenaeus vannamei) is an important model for breeding programs to improve global aquaculture productivity. However, the interaction between host genetics and microbiota in enhancing productivity remains poorly understood. We investigated the effect of two shrimp genetic lines, Fast-Growth (Gen1) and Disease-Resistant (Gen2), on the microbiota of L. vannamei.<br><br>RESULTS: Using genome-wide SNP microarray analysis, we confirmed that Gen1 and Gen2 represented distinct genetic populations. After confirming that&#xa0;the rearing pond did not significantly influence the microbiota composition, we determined that genetic differences explained 15.8% of the microbiota variability, with a stronger selective pressure in the hepatopancreas than in the intestine. Gen1, which exhibited better farm productivity, fostered a microbiota with greater richness, diversity, and resilience than Gen2, along with a higher abundance of beneficial microbes. Further, we demonstrated that a higher abundance of beneficial microbes was associated with healthier shrimp vs. diseased specimens, suggesting that Gen1 could improve shrimp's health and productivity by promoting beneficial microbes. Finally, we determined that the microbiota of both genetic lines was significantly different from their wild-type counterparts, suggesting farm environments and selective breeding programs strongly alter the natural microbiome.<br><br>CONCLUSIONS: This study highlights the importance of exploring the hologenome perspective, where integrating host genetics and microbiome composition can enhance breeding programs and farming practices.}, }
@article {pmid40405096, year = {2025}, author = {Yasmin, A and Rahman, MS and Kador, SM and Ahmed, MM and Moon, MEK and Akhter, H and Sultana, M and Begum, A}, title = {Metagenomic insights into microbial diversity and potential pathogenic transmission in poultry farm environments of Bangladesh.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {318}, pmid = {40405096}, issn = {1471-2180}, mesh = {Bangladesh ; Animals ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects/pathogenicity ; RNA, Ribosomal, 16S/genetics ; Farms ; *Poultry/microbiology ; *Microbiota/genetics ; *Metagenomics ; *Poultry Diseases/transmission/microbiology ; Biodiversity ; Soil Microbiology ; DNA, Bacterial/genetics ; }, abstract = {The microbiome plays a critical role in poultry health and productivity, influencing growth, immunity, and the overall farm ecosystem. This study investigated microbial diversity, antibiotic resistance pathways, and functional potential across various components of poultry ecosystems-cloacal swabs, droppings, feed, hand swabs, soil, and water-in different districts of Bangladesh. Using 16S rRNA gene amplicon sequencing, we identified 2,745 Operational Taxonomic Units (OTUs) and analyzed microbial richness, community structure, and functional pathways. Alpha diversity metrics revealed that droppings exhibited the highest microbial richness (726 OTUs in Noakhali), while feed samples showed the lowest diversity (211 OTUs). Beta diversity analysis indicated significant differences in microbial composition across sample sources, with PERMANOVA confirming that sample origin accounted for 51.45% of the variability (p < 0.001). Proteobacteria dominated the microbial communities (48.36%), followed by Firmicutes (19.83%) and Cyanobacteria (12.02%). Key genera of concern, such as Enterobacter (26.62% in hand swabs), Acinetobacter (30.87% in cloacal swabs), and Shigella (22.89% in cloacal swabs), were identified, highlighting potential contamination and zoonotic risks. Conversely, beneficial genera like Lactobacillus (36.89% in feed) and Enterococcus (10.78% in droppings) were prevalent, suggesting roles in gut health and nutrient cycling. Functional pathway analysis (KEGG) revealed that carbohydrate and amino acid metabolism were highly active in droppings and feed, reflecting nutrient utilization. Antimicrobial resistance (AMR) pathways, such as 23S rRNA-methyltransferase and multidrug efflux pumps, were widespread, with pathogenic genera (Enterobacter, Acinetobacter, Shigella, Pseudomonas) showing strong positive correlations with AMR pathways. These findings underscore the influence of environmental factors on microbial diversity and functional potential in poultry farming. The study highlights the need for improved management practices and biosecurity measures to mitigate risks associated with microbial pathogens and antimicrobial resistance, ultimately supporting healthier and more sustainable poultry production in Bangladesh.}, }
@article {pmid40405076, year = {2025}, author = {Li, J and Chen, Z and Yan, X and Chen, Q and Chen, C and Liu, H and Shen, J}, title = {Effects of USP25 knockout on the gut microbial diversity and composition in mice.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {315}, pmid = {40405076}, issn = {1471-2180}, support = {2022J011443//Natural Science Foundation of Fujian Province/ ; 2024J011450//Natural Science Foundation of Fujian Province/ ; 2024112//Medical Research Foundation of Putian University/ ; 2024104//Medical Research Foundation of Putian University/ ; 82301785//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice, Knockout ; Mice ; Mice, Inbred C57BL ; *Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Ubiquitin Thiolesterase/genetics/deficiency ; Biodiversity ; Male ; }, abstract = {BACKGROUND: The gut microbiota plays a crucial role in host health. Recent study revealed that ubiquitin-specific protease 25 (USP25) deficiency affected colonic immune responses and resistance to certain bacterial infection. This study aimed to investigate the impact of USP25 gene deletion on the gut microbiota of mice, utilizing 16 S rRNA amplicon sequencing and metagenomic sequencing to provide a comprehensive analysis of microbial diversity, composition and functional characteristics.<br><br>METHODS: We collected fecal samples from 10 wild type (WT) C57BL/6J mice and 10 USP25[-/-] mice (C57BL/6J-Usp25[em1]cyagen) for 16&#xa0;S rRNA amplicon sequencing. Subsequently, the 6 of the 20 samples underwent further analysis using metagenomic sequencing.<br><br>RESULTS: Our results revealed significant differences in the gut microbiota between USP25 knockout (KO) mice and wild-type (WT) controls, with KO mice exhibiting 1,858 unique amplicon sequence variants (ASVs) compared to 1,723 in WT mice. Notably, the KO group displayed a higher tendency for biofilm formation and a greater proportion of gram-negative bacteria, while the WT group demonstrated enhanced stress tolerance and a higher presence of gram-positive bacteria. Functional prediction analyses indicated an increase in antibiotic resistance genes in the KO mice, particularly for tetracycline, cephalosporin, and sulfonamides, suggesting a potential risk for clinical antibiotic treatment efficacy. Moreover, KEGG pathway enrichment analysis revealed significant enrichment for fructose and mannose metabolism, streptomycin biosynthesis in the KO group. Furthermore, an increase in protective microbes alongside a decrease in potential pathogens in the KO microbiota hinted at altered immune responses due to USP25 deletion.<br><br>CONCLUSION: Our findings elucidate the essential role of USP25 in modulating gut microbiota composition and function, providing insights for future therapeutic strategies targeting gut microbiota in disease contexts.<br><br>CLINICAL TRAIL NUMBER: Not applicable.}, }
@article {pmid40404683, year = {2025}, author = {Terbtothakun, P and Visedthorn, S and Klomkliew, P and Chanchaem, P and Sawaswong, V and Sivapornnukul, P and Sunantawanit, S and Khamwut, A and Rotcheewaphan, S and Kaewsapsak, P and Payungporn, S}, title = {Clinical metagenomics analysis of bacterial and fungal microbiota from sputum of patients suspected with tuberculosis infection based on nanopore sequencing.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17772}, pmid = {40404683}, issn = {2045-2322}, support = {HEA_FF_68_100_3000_016//Thailand Science research and Innovation Fund, Chulalongkorn University/ ; B05-F640122//The National Science, Research and Innovation Fund (NSRF) via the Program Management Unit for Human Resources and Institutional Development, Research and Innovation/ ; GA68/047//The Ratchadapisek Sompotch Fund, Faculty of Medicine, Chulalongkorn University/ ; }, mesh = {Humans ; *Sputum/microbiology ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Tuberculosis/microbiology/diagnosis ; *Fungi/genetics/isolation &amp; purification/classification ; *Bacteria/genetics/classification/isolation &amp; purification ; Male ; Female ; Mycobacterium tuberculosis/genetics/isolation &amp; purification ; Middle Aged ; Adult ; }, abstract = {Tuberculosis (TB) remains a significant global health challenge, demanding rapid and comprehensive diagnostics for effective treatment. Secondary infections further complicate TB infection, worsening outcomes. Conventional diagnostics are hindered by prolonged turnaround times, high costs, and inability to detect co-infections. This study utilizes full-length 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing based on Oxford Nanopore Technologies (ONT) to analyze clinical metagenomics of sputum microbiota from patients suspected with TB Infection. Our findings highlight the potential of ONT for profiling microbial communities associated with TB infection. The MTB group exhibited a significant abundance of Mycobacterium tuberculosis (M. tuberculosis) and Stenotrophomonas maltophilia. In contrast, Prevotella melaninogenica, Veillonella parvula, Corynebacterium striatum and Pseudomonas aeruginosa were more abundant in the negative samples. Fungal analysis revealed Candida orthopsilosis was enriched in MTB samples, while Aureobasidium leucospermi and Wallemia muriae predominated in negative samples. Correlation network analysis revealed M. tuberculosis exhibits positive and negative correlations with other microbial species, suggesting cooperative and competitive interactions that may influence microbial community dynamics and disease progression in TB patients. This study demonstrates the promise of ONT-based clinical metagenomics for rapid, comprehensive detection of bacterial and fungal co-infections, addressing limitations of conventional diagnostics and improving outcomes.}, }
@article {pmid40404632, year = {2025}, author = {Dillard, LR and Glass, EM and Kolling, GL and Thomas-White, K and Wever, F and Markowitz, R and Lyttle, D and Papin, JA}, title = {Genome-scale metabolic network reconstruction analysis identifies bacterial vaginosis-associated metabolic interactions.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4768}, pmid = {40404632}, issn = {2041-1723}, support = {R01-AI154242//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01-AT010253//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; NRT-ROL 2021791//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 1 T 32 GM 145443-1//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 5T32GM136615-03//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1842490//National Science Foundation (NSF)/ ; }, mesh = {*Vaginosis, Bacterial/microbiology/metabolism ; Humans ; Female ; *Metabolic Networks and Pathways/genetics ; Vagina/microbiology ; Microbiota/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metabolomics ; Metagenomics ; Genome, Bacterial ; Computer Simulation ; }, abstract = {Bacterial vaginosis (BV) is the most prevalent vaginal condition among reproductive-age women presenting with vaginal complaints. Despite its significant impact on women's health, limited knowledge exists regarding the microbial community composition and metabolic interactions associated with BV. In this study, we analyze metagenomic data obtained from human vaginal swabs to generate in silico predictions of BV-associated bacterial metabolic interactions via genome-scale metabolic network reconstructions (GENREs). While most efforts to characterize symptomatic BV (and thus guide therapeutic intervention by identifying responders and non-responders to treatment) are based on genomic profiling, our in silico simulations reveal functional metabolic relatedness between species as quite distinct from genetic relatedness. We grow several of the most common co-occurring bacteria (Prevotella amnii, Prevotella buccalis, Hoylesella timonensis, Lactobacillus iners, Fannyhessea vaginae, and Aerrococcus christenssii) on the spent media of Gardnerella species and perform metabolomics to identify potential mechanisms of metabolic interaction. Through these analyses, we identify BV-associated bacteria that produce caffeate, a compound implicated in estrogen receptor binding, when grown in the spent media of other BV-associated bacteria. These findings underscore the complex and diverse nature of BV-associated bacterial community structures and several of these mechanisms are of potential significance in understanding host-microbiome relationships.}, }
@article {pmid40404216, year = {2025}, author = {Thng, KX and Tiew, PY and Mac Aogáin, M and Narayana, JK and Jaggi, TK and Ivan, FX and Shuttleworth, M and Long, MB and Richardson, H and Lind, H and Alferes de Lima Headley, D and Robertson, K and Pollock, J and Goeminne, PC and Shteinberg, M and De Soyza, A and Aliberti, S and Altenburg, J and Haworth, CS and Sibila, O and Polverino, E and Loebinger, MR and Ringshausen, FC and Lorent, N and Dimakou, K and Shoemark, A and Chalmers, JD and Chotirmall, SH}, title = {Sputum metagenomics in bronchiectasis reveals pan-European variation: an EMBARC-BRIDGE study.}, journal = {The European respiratory journal}, volume = {}, number = {}, pages = {}, doi = {10.1183/13993003.00054-2025}, pmid = {40404216}, issn = {1399-3003}, abstract = {BACKGROUND: The EMBARC registry shows considerable variation in culturable microbes in sputum between different European countries. The additive role of next generation metagenomic sequencing remains unexplored and association with antimicrobial resistomes unknown.<br><br>METHODS: We prospectively assessed sputum from N=349 individuals recruited into the EMBARC-BRIDGE study with next-generation shotgun metagenomic sequencing including three European regions: Northern and Western Europe, Southern Europe and the United Kingdom, including samples from ten European countries. Microbiome and resistome profiles were assessed in relation to clinical outcomes.<br><br>RESULTS: Next generation metagenomic sequencing reproduced differences between countries in microbial profiles previously shown by culture in the EMBARC study. Metagenomics provided enhanced detection for some bronchiectasis pathogens including P. aeruginosa, H. influenzae and S. pneumoniae. Three metagenomic microbial clusters dominated by the genera Pseudomonas, Streptococcus and Haemophilus demonstrated pan-European but variable distribution. Diverse resistomes, linked to underlying microbiomes, were identified across Europe, with significantly higher diversity of resistance gene determinants in Southern Europe. Resistome composition significantly differed between regions characterised by regionally contrasting multi-drug-resistant profiles. The EMBARC-BRIDGE cohort validated established bronchiectasis resistotypes: RT1 and RT2, which occur at varying frequency across regions. Despite geographic variation in microbiome and resistome profiles in bronchiectasis across Europe, analogous antimicrobial resistance gene profiles associate with the key bronchiectasis genera Pseudomonas, Streptococcus and Haemophilus, independent of country or region.<br><br>CONCLUSION: Sputum metagenomics confirms and extends prior observations of regional variation in bronchiectasis microbiology. Important variation in the distribution of pathogens and antimicrobial resistance genes has implications for antimicrobial practices across Europe.}, }
@article {pmid40403370, year = {2025}, author = {Liang, X and Li, B and Dong, X and Zhao, X and Li, H and Ye, Y and Ma, H and Ran, S and Li, J}, title = {Impact of microplastics exposure on the reconfiguration of viral community structure and disruption of ecological functions in the digestive gland of Mytilus coruscus.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138692}, doi = {10.1016/j.jhazmat.2025.138692}, pmid = {40403370}, issn = {1873-3336}, abstract = {Microplastics (MPs) pose ecological risks by serving as viral vectors and disrupting host microbiomes. This study investigated the impact of MPs on the digestive gland virome of Mytilus coruscus through an in situ exposure experiment on Xixuan Island, Zhoushan, China, using polyethylene MPs and metagenomic sequencing. MPs biofilms were dominated by lytic viruses (> 99 %) with low diversity (Shannon index = 4.10 ± 0.39), whereas digestive glands harbored a more diverse virome (Shannon index = 7.26 ± 1.26). MPs ingestion significantly reduced virome diversity and altered viral community composition. Functional analysis showed that MPs biofilms were enriched in genes related to genetic processing, carbohydrate metabolism and membrane biogenesis, while transcription- and replication-related genes declined (P < 0.05) in digestive glands post-ingestion. MPs biofilms carried abundant antibiotic resistance genes (ARGs) and virulence factors, selectively enriching multidrug resistance genes (efrA, patB) while reducing functional viral gene abundance. Metal (Zn, Hg, As) and biocide resistance genes were prevalent in MPs biofilms but declined post-ingestion. Additionally, MPs ingestion weakened microbial network stability, potentially impairing immune regulation and metabolic homeostasis. These findings underscore MPs' role in shaping viral communities and spreading resistance genes, heightening ecological risks in marine environments.}, }
@article {pmid40402820, year = {2025}, author = {Alberdi, A and Limborg, MT and Groussin, M and Aizpurua, O and Gilbert, MTP}, title = {Metagenomic spaces: a framework to study the effect of microbiome variation on animal ecology and evolution.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jeb/voaf063}, pmid = {40402820}, issn = {1420-9101}, abstract = {Microorganisms are essential for the normal functioning of most vertebrates. Hence, identifying and measuring the factors that shape host-associated microbial communities is necessary to understand ecological and evolutionary implications of host-microbiota associations. We propose a framework, built on the so-called 'metagenomic space' concept, which incorporates multiple definitions and quantifiable features relating to the variation of microbial communities that are associated with vertebrate hosts. By drawing on diverse theories and concepts developed in different fields of biology, our framework sets a conceptual landscape that transcends the mere characterisation of microbial communities. This provides the basis to study more complex attributes, such as 'potential' and 'fundamental metagenomic spaces', 'metagenomic plasticity' and 'metagenomic evolvability', which we argue are essential for understanding the microbial contribution to vertebrate host ecology and evolution-and hold considerable promise for advancing applied research and innovation. In doing so, we hope to contribute to an improved understanding of the impact of spatio-temporal variation of vertebrate host-microbiota associations, and inspire new approaches to address testable hypotheses related to ecological, evolutionary and applied processes.}, }
@article {pmid40402242, year = {2025}, author = {Shahzad, S and Sharma, A and Mehdi, SEH and Gurung, A and Hussain, F and Kang, W and Jang, M and Oh, SE}, title = {Assessment of Metals Toxicity Using a Nitrifying Bacteria Bioassay Kit Based on Oxygen Consumption.}, journal = {Archives of environmental contamination and toxicology}, volume = {}, number = {}, pages = {}, pmid = {40402242}, issn = {1432-0703}, support = {2023R1A2C1004608//National Research Foundation of Korea/ ; }, abstract = {The escalating concentrations of emerging contaminants in water systems and the possible environmental threats they emphasize the necessity for more sophisticated methods in the evaluation of water quality. Traditional bioassays raise ethical concerns, require intricate procedures, entail significant expenses, and only allow for endpoint measurements. The using of nitrifying bacteria in bioassays has resulted in increased sensitivity to a wide range of toxic substances, making them valuable for the identification of water pollution. This study introduces a novel nitrifying bacteria bioassay kit for detecting heavy metal contaminants in water. This bioassay is specifically designed for expedited analysis of oxygen consumption. This technique enables the identification of a range of toxic metals. Optimization studies indicated that 100 mg ammonia NH4[+]-N/L, and 1 mL acclimated culture were the ideal conditions facilitating the necessary volume of gas consumption for sensitive data generation. Determined EC50 values of the selected toxic metals were: chromium (Cr[6+]), 0.51 mg/L; silver (Ag[+]), 2.90 mg/L; copper (Cu[2+]), 2.90 mg/L; nickel (Ni[2+]), 3.60 mg/L; arsenic (As[3+]), 4.10 mg/L; cadmium (Cd[2+]), 5.56 mg/L; mercury (Hg[2+]), 8.06 mg/L; and lead (Pb[2+]), 19.3 mg/L. Metagenomics analysis found key species in the research included Nitrosomonas eutropha, Nitrosomonas oligotropha, Nitrosomonas europaea, Nitrobacter vulgaris, Nitrobacter winogradskyi, Nitrospira moscoviensis and Nitrospira lenta. In addition, this bioassay is ideal for field screening and real-time monitoring due to its simplicity and reliability. This bioassay provides a precise, economical, and effective substitute for more intricate and ethically problematic techniques, enhancing the effectiveness of water quality monitoring programs.}, }
@article {pmid40402042, year = {2025}, author = {Moosavi, D and Curtis, KR and Randolph, TW and Kahsai, OJ and Ammar, H and Lim, U and Cheng, I and Wilkens, LR and Le Marchand, L and Lampe, JW and Hullar, MAJ}, title = {Stability and Variability of the Human Fecal Microbiome Over Two Years in the Multiethnic Cohort Study: A Metagenomic Analysis.}, journal = {Cancer epidemiology, biomarkers &amp; prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {}, number = {}, pages = {}, doi = {10.1158/1055-9965.EPI-24-1770}, pmid = {40402042}, issn = {1538-7755}, abstract = {BACKGROUND: Understanding the longitudinal variability of the gut microbiome is essential for advancing microbiome-based measurements and designing robust sampling protocols in observational and intervention studies of cancer and other health outcomes. The aim of this study was to explore the temporal variability and stability of the fecal microbiome over a 2-year period, using intraclass correlation (ICC) analysis of metagenomic sequencing data.<br><br>METHODS: We studied 25 older adults from the Multiethnic Cohort Adiposity Phenotype Study (MEC-APS, 2013-2016). Stool samples were collected every six months over a two-year period (5 samples) and analyzed using metagenomic sequencing. The temporal stability was evaluated using ICCs across taxonomic levels, diversity, and functional genes and pathways.<br><br>RESULTS: The microbial community showed stability in alpha diversity and overall structure, with no significant changes across time points (Shannon diversity, p = 0.95). Taxonomic composition showed strong reliability over time, with median ICCs of 0.7 at the genus level and 0.75 at species level. Functional genes also demonstrated good stability (median ICC = 0.68). However, microbial pathways were more variable, with a fair median ICC of 0.49.<br><br>CONCLUSION: While the fecal microbiome was generally stable, some taxa and functions were more dynamic and responsive to external influences.<br><br>IMPACT: Findings highlight the need for reliable microbiome measurements and sampling strategies to reduce bias in studies of the microbiome and cancer.}, }
@article {pmid40401991, year = {2025}, author = {Sheam, MM and Luo, E}, title = {Vertical transport and spatiotemporal dynamics of giant viruses in the North Pacific Subtropical Gyre.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf094}, pmid = {40401991}, issn = {1751-7370}, abstract = {Nucleocytoplasmic large DNA viruses, or "giant viruses," are prevalent in marine environments, infecting diverse eukaryotic lineages and influencing the marine carbon cycle. Their genomes harbor wide range of auxiliary metabolic genes that influence biogeochemical processes. This study integrates planktonic (5-4000 m) and particle-associated (4000 m) metagenomic samples in the North Pacific Subtropical Gyre, along with particulate export flux data at 4000 m, to investigate the vertical transport of giant viruses and their correlation with carbon export through space and time. By analyzing metagenomic samples over a period of 6 years across 15 depths, we curated a database of 37 giant virus population genomes and 1496 contigs and investigated their spatiotemporal variability and functional capacity in the open ocean. We reported multiple lines of evidence supporting the viral shuttle hypothesis, including the vertical transport of giant viruses from the upper ocean to abyssal depths and their positive correlation with particulate carbon export flux at 4000 m, particularly a giant species closely related to Phaeocystis globosavirus known to infect a bloom-forming alga. We identified giant viruses encoding diverse AMGs, including genes associated with photosynthesis, nutrient transport, and energy metabolism. These auxiliary metabolic genes displayed depth-specific distributions, which we postulate reflect depth-specific adaptations to light-energy and nutrient-limited conditions along the water column. Together, this study provides critical insights into the biogeochemical impacts of giant viruses by identifying key giant viruses that can impact export processes and depth-specific distributions of auxiliary metabolic genes impacting biogeochemical processes along the open ocean water column.}, }
@article {pmid40401938, year = {2025}, author = {Punchihewage-Don, AJ and Hasan, NA and Parveen, S}, title = {Shotgun metagenomic sequencing for detection of foodborne pathogens in retail chicken.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0003325}, doi = {10.1128/mra.00033-25}, pmid = {40401938}, issn = {2576-098X}, abstract = {We applied shotgun metagenomic sequencing to microbiomes from retail chicken processed using whole carcass enrichment and rinse methodologies to evaluate their effectiveness in detecting foodborne pathogens. The dataset has been made publicly available to facilitate future analysis of microbial diversity and pathogen presence across different sample processing methods.}, }
@article {pmid40401929, year = {2025}, author = {Toaquiza-Vilca, B and Quito-Avila, D and Maldonado-Alvarado, P and Ruiz-Barzola, O and Debut, A and Montiel, M}, title = {Physicochemical, genomic, and phenotypic characterization of Escherichia phage BME3.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0130124}, doi = {10.1128/spectrum.01301-24}, pmid = {40401929}, issn = {2165-0497}, abstract = {Infections caused by pathogenic Escherichia coli strains are increasing, and with the rising of antimicrobial resistance among bacterial pathogens, alternative therapeutic options are being actively explored, including phage therapy. In this research, a new bacteriophage, provisionally named BME3, with lytic activity against Escherichia coli was identified and characterized at the physicochemical, morphological, and genetic levels. BME3 was isolated from the tropical estuarine waters of Estero Salado, Guayaquil, Ecuador. Subsequently, it was purified and amplified, followed by a series of tests that included host range, stability studies, morphological characterization by transmission electron microscopy (TEM), and whole genome sequencing. The genomic analysis revealed that BME3 is closely related to members of the genus Justusliebigvirus, with a double-stranded DNA genome of 147,371 bp in length, a GC content of 37.5%, and 16 tRNA genes. In addition, BME3 lacks genes associated with lysogenesis, antibiotic resistance, or virulence. BME3 infected approximately 48% (13/27) of environmental E. coli strains. Among these, the infection rate was higher for antibiotic-resistant strains (67%) compared to intermediate and sensitive strains (33%). The phage infected E. coli and Salmonella sp. strains but did not affect Bacillus sp., Pseudomonas sp., or Vibrio sp. Moreover, BME3 was found to be stable at temperatures below 60°C, in pH ranges between 5 and 9, and was not sensitive to chloroform. TEM analysis supported the genetic sequence that assigned BME3 to the class Caudoviricetes. Phenotypic, genomic, and physicochemical characterization suggests that BME3 represents a promising option for phage therapy, with the potential to control antibiotic-resistant bacteria.IMPORTANCEAlthough metagenomics offers a wealth of information, not all microorganisms can be isolated and cultivated in the laboratory. In this study, we successfully isolated and characterized a phage belonging to the Justusliebigvirus genus. This group has been poorly studied regarding its physicochemical properties and lysis profile against antibiotic-resistant environmental bacteria. These bacteriophages have received less attention compared to well-studied models such as phage T4. The isolation and characterization of the indigenous polyvalent bacteriophage BME3, obtained from tropical estuarine waters in Ecuador, provide valuable insights into its potential applications for environmental control of Escherichia coli and for mitigating the spread of bacterial resistance.}, }
@article {pmid40401909, year = {2025}, author = {Morel-Letelier, I and Yuen, B and Orellana, LH and Kück, AC and Camacho-García, YE and Lara, M and Leray, M and Wilkins, LGE}, title = {Seasonal transcriptomic shifts reveal metabolic flexibility of chemosynthetic symbionts in an upwelling region.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0168624}, doi = {10.1128/msystems.01686-24}, pmid = {40401909}, issn = {2379-5077}, abstract = {Upwelling in the Tropical Eastern Pacific profoundly affects marine coastal ecosystems by driving drastic seasonal changes in water temperature, oxygen levels, and nutrient availability. These conditions serve as a natural experiment that provides a unique opportunity to study how marine animals and their associated microorganisms respond in the face of environmental change. Lucinid bivalves host chemosynthetic Candidatus Thiodiazotropha symbionts equipped with diverse metabolic pathways for sulfur, carbon, and nitrogen use. However, how these symbionts employ their metabolic toolkit in a changing environment remains poorly understood. To address this question, we conducted metagenomic and metatranscriptomic analyses of Ctena cf. galapagana symbionts before and during a Papagayo upwelling event in Santa Elena Bay, Costa Rica. The C. cf. galapagana were co-colonized mainly by two Ca. Thiodiazotropha symbiont clades regardless of the sampling season. We observed a concerted shift in the transcriptomic profiles of both symbiont clades before and during upwelling, suggesting changes in energy source use. Dissimilatory methanol oxidation genes were upregulated before upwelling, while sulfide oxidation genes were upregulated during upwelling. These physiological changes were potentially driven by upwelling-induced changes in sediment biogeochemistry and resource availability. Our findings highlight the adaptability of the lucinid symbiosis and the crucial role of symbiont metabolic flexibility in their resilience to environmental challenges.IMPORTANCEThe oceans are undergoing rapid change, and marine animals together with their associated microorganisms must adjust to these changes. While microbes are known to play a critical role in animal health, we are only beginning to understand how symbiotic relationships help animals cope with environmental variability. Annual upwelling events cause drastic and abrupt increases in nutrient availability and productivity, while temperature and oxygen decrease. In this study, we investigated how bacterial symbionts of the lucinid bivalve Ctena cf. galapagana respond to upwelling in the Tropical Eastern Pacific. The symbionts, from the genus Candidatus Thiodiazotropha, are chemosynthetic (i.e., they use inorganic chemicals for energy and fix carbon) and provide nutrition to their host. Our results show that these symbionts adjust their use of different energy sources in response to environmental changes that affect resource availability. This metabolic flexibility underscores the resilience of animal-microbe relationships in coping with environmental change.}, }
@article {pmid40401771, year = {2025}, author = {Callens, M and Le Berre, G and Van den Bulcke, L and Lolivier, M and Derycke, S}, title = {An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14126}, doi = {10.1111/1755-0998.14126}, pmid = {40401771}, issn = {1755-0998}, support = {RT/24/DNASense_ILVO//Belgian Federal Science Policy Office/ ; //Biodiversa+/ ; //Belgian Federal Public Service Economy/ ; BAR0159//Directorate-General for Regional Policy of the European Union/ ; }, abstract = {DNA-based techniques are a popular approach for assessing biodiversity in ecological research, especially for organisms which are difficult to detect or identify morphologically. Metabarcoding, the most established method for determining species composition and relative abundance in bulk samples, can be more sensitive and time- and cost-effective than traditional morphological approaches. However, one drawback of this method is PCR bias caused by between-species variation in the amplification efficiency of a marker gene. Metagenomics, bypassing PCR amplification, has been proposed as an alternative to overcome this bias. Several studies have already shown the promising potential of metagenomics, but they all indicate the unavailability of reference genomes for most species in any ecosystem as one of the primary bottlenecks preventing its wider implementation. In this study, we present a strategy that combines unassembled reads of low-coverage whole genome sequencing and publicly available reference genomes to construct a genomic reference database, thus circumventing high sequencing costs and intensive bioinformatic processing. We show that this approach is superior to metabarcoding for approximating relative biomass of macrobenthos species from bulk samples. Furthermore, these results can be obtained with a sequencing effort comparable to metabarcoding. The strategy presented here can thus accelerate the implementation of metagenomics in biodiversity assessments, as it should be relatively easy to adopt by laboratories familiar with metabarcoding and can be used as an accessible alternative.}, }
@article {pmid40400688, year = {2025}, author = {Zhou, M and Chen, W and Zhang, D and Ma, S and Liu, M and Ren, L and Guo, J and Gao, Y and Lu, M and Su, H and Zhao, Y and Xu, Y and Yang, Q}, title = {Identification and characterization of a novel human adenovirus type HAdV-D116.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1566316}, pmid = {40400688}, issn = {1664-302X}, abstract = {INTRODUCTION: Human adenovirus infections are typically associated with acute respiratory infection, keratoconjunctivitis, acute cystitis, hepatitis, and gastroenteritis, while central nervous system (CNS) related infections are rarely reported.<br><br>METHODS: In this study, a novel human adenovirus was identified in the cerebrospinal fluid from an encephalitis patient with X-linked agammaglobulinemia via metagenomic next-generation sequencing (mNGS). Probe capture enrichment sequencing and PCR validation further confirmed the presence of this adenovirus in the patient's cerebrospinal fluid.<br><br>RESULTS: Whole-genome analysis classified the virus within the Human mastadenovirus D species, revealing an approximately 2000&#x202f;bp deletion in the E3 gene that resulted in the loss of CR1-gamma and RID-alpha regions and the formation of a novel open reading frame (ORF). The penton base, hexon, and fiber genes were identified as P33H28F71, designating this virus as a novel type, subsequently named HAdV-D116 by the Human Adenovirus Working Group. Recombination analysis suggested that HAdV-D116 is a recombinant strain derived from HAdV-D33, HAdV-D28, and HAdV-D71. Structural analysis of the fiber-knob domain indicated that HAdV-D116 likely uses sialic acid as a receptor.<br><br>DISCUSSION: The unique genomic features of HAdV-D116, combined with the patient's immunodeficiency, are proposed to contribute to its possible CNS infectivity. The discovery of HAdV-D116 expands our understanding of human adenovirus tropism and underscores the need for vigilance regarding the emergence of novel adenovirus-related CNS infections.}, }
@article {pmid40400039, year = {2025}, author = {Chen, Y and Wang, Y and Shaoyong, W and He, Y and Liu, Y and Wei, S and Gan, Y and Sun, L and Wang, Y and Zong, X and Xiang, Y and Wang, Y and Jin, M}, title = {High-fertility sows reshape gut microbiota: the rise of serotonin-related bacteria and its impact on sustaining reproductive performance.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {73}, pmid = {40400039}, issn = {1674-9782}, support = {32372889//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Compelling evidence has established a strong link between the gut microbiota and host reproductive health. However, the specific regulatory roles of individual bacterial species on reproductive performance are not well-understood. In the present study, Jinhua sows with varying reproductive performances under the same diet and management conditions were selected to explore potential mechanisms on the intricate relationship between the gut microbiome and host reproductive performance using 16S rRNA sequencing, metagenomics and serum metabolomics.<br><br>RESULTS: Our findings revealed that the KEGG pathways for base excision repair and DNA replication were enriched, along with gene-level enhancements in spore formation, in sows with higher reproductive performance, indicating that the gut microbiome experiences stress. Further analysis showed a positive correlation between these changes and litter size, indicating that the host acts as a stressor, reshaping the microbiome. This adaptation allows the intestinal microbes in sows with high reproductive performance to enrich specific serotonin-related bacteria, such as Oxalobacter formigenes, Ruminococcus sp. CAG 382, Clostridium leptum, and Clostridium botulinum. Subsequently, the enriched microbiota may promote host serotonin production, which is positively correlated with reproductive performance in our study, known to regulate follicle survival and oocyte maturation.<br><br>CONCLUSION: Our study provides a theoretical basis for understanding the interactions between gut microbes and the host. It highlights new insights into reassembling gut microbiota in sows with higher litter sizes and the role of serotonin-related microbiota and serotonin in fertility.}, }
@article {pmid40399550, year = {2025}, author = {Dahal, A and Chang, WC and Johansson, E and Grashel, B and Morgan, D and Williams, L and Hammonds, M and Sachdeva, S and Spagna, D and Satish, L and Biagini, JM and Martin, LJ and Haslam, DB and Ollberding, NJ and Khurana Hershey, GK}, title = {Skin Staphylococcus aureus detection and relationship to atopic dermatitis outcomes using culture and metagenomic sequencing.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17606}, pmid = {40399550}, issn = {2045-2322}, support = {F30AI181481-01//National Institute of Allergy and Infectious Diseases/ ; U19AI070235//National Institues of Health/ ; R01 AI127392/NH/NIH HHS/United States ; }, mesh = {*Dermatitis, Atopic/microbiology ; Humans ; *Staphylococcus aureus/genetics/isolation &amp; purification ; Female ; Male ; *Metagenomics/methods ; Child ; *Skin/microbiology ; Child, Preschool ; Immunoglobulin E/blood ; *Staphylococcal Infections/microbiology/diagnosis ; Infant ; Asthma/microbiology ; }, abstract = {Staphylococcus aureus (SA) skin colonization in pediatric atopic dermatitis (AD) increases risk for severe AD and development of other allergic diseases. Despite this, there is no consensus regarding the optimal method to detect SA. Studies comparing metagenomic shotgun sequencing (MSS) and culture-based methods in SA detection and relationships to AD outcomes are lacking. In the Mechanisms of Progression of Atopic Dermatitis to Asthma in Children (MPAACH) cohort, we defined SA colonization categories by contact agar plate sampling/culture and skin tape sampling/MSS: double negative, sequencing only positive, contact plate only positive, and double positive (n = 759). We assessed AD severity, sensitization, total IgE, and atopic outcomes across categories. Culture missed 69% of samples detected by MSS and MSS missed 54% of samples detected by culture. The double positive group exhibited higher AD severity, sensitization load, and total serum IgE, and was more likely to develop allergic rhinitis (AR) compared to other groups. Detection of SA by MSS or culture missed over half of the SA detected by the other method. Importantly, detection via both methods correlated with increased AD severity, sensitization, total IgE, and AR. Thus, these methods are complementary and both may be necessary for comprehensive evaluation of SA and its clinical and biologic impact.}, }
@article {pmid40399402, year = {2025}, author = {Jarmukhanov, Z and Vinogradova, E and Mukhanbetzhanov, N and Kozhakhmetov, S and Khassenbekova, D and Kushugulova, A}, title = {Parity influences postpartum adaptations in the maternal gut microbiota.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17636}, pmid = {40399402}, issn = {2045-2322}, support = {AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; AP23489538, AP19575153, BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, mesh = {Female ; Humans ; *Gastrointestinal Microbiome ; *Postpartum Period/physiology ; Pregnancy ; Adult ; *Parity ; *Adaptation, Physiological ; Bacteria/genetics/classification ; Milk, Human ; }, abstract = {The gut microbiome undergoes substantial modifications during pregnancy, yet its postpartum adaptations remain poorly understood, particularly with respect to the influence of parity. Here, we investigated the impact of childbirth history on maternal gut microbiome composition and function one month postpartum. By conducting metagenomic sequencing analysis on 60 participants (34 postpartum mothers and 26 controls), we demonstrated significant differences in microbial diversity and community structure between postpartum mothers and control, as well as subtle differences between first-time mothers and multiple-birth mothers. We identified parity-specific signatures, with first-time mothers showing enrichment in Dysosmobacter welbionis, Candidatus Saccharibacteria, and Anaerotruncus species. Functional analysis revealed distinct metabolic reprogramming patterns, including increased amino acid biosynthesis and modified fermentation pathways supporting postpartum recovery. We observed significant correlations between specific bacterial taxa and metabolic pathways, particularly in energy metabolism and immune modulation. Notably, the enhanced capacity for short-chain fatty acid production in primiparous mothers, mediated by Anaerotruncus and Dysosmobacter welbionis, suggests a potential role in shaping breast milk composition, which may influence neonatal development. These findings establish the concept of parity-dependent microbiome programming and provide insights into the biological mechanisms underlying maternal adaptation to pregnancy and childbirth.}, }
@article {pmid40399144, year = {2025}, author = {Wang, Y and Zhang, K and Liu, L and Qu, R}, title = {Disseminated Cunninghamella bertholletiae Infection From Latent Lower Limb Mass After Kidney Transplant: A Case Report.}, journal = {Transplantation proceedings}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.transproceed.2025.03.032}, pmid = {40399144}, issn = {1873-2623}, abstract = {BACKGROUND: Cunninghamella bertholletiae (C. bertholletiae), a rare yet highly virulent species within the Mucorales order, predominantly affects individuals with compromised immune systems. Disseminated infections caused by this pathogen frequently lead to severe complications, underscoring the necessity for prompt diagnosis and aggressive therapeutic interventions. Invasive fungal diseases (IFDs) continue to be a major cause of morbidity and mortality among kidney transplant recipients, characterized by elevated incidence and mortality rates. The early and precise identification of fungal pathogens is crucial for optimizing patient outcomes.<br><br>CASE PRESENTATION: This report presents a case study of a 37-year-old male kidney transplant recipient who developed a disseminated C. bertholletiae infection from a latent lower limb lesion. Initially, he showed symptoms of high fever and dyspnea, leading to diagnoses of sepsis, severe pneumonia, acute respiratory distress syndrome, and allograft dysfunction. After surgery, he had recurrent pleural effusion and worsening pulmonary nodules. Metagenomic next-generation sequencing (mNGS) confirmed C. bertholletiae infection, and histopathology revealed mucormycosis with vascular invasion, thrombosis, and tissue necrosis. The patient underwent a 13-month antifungal treatment with amphotericin B lipid complex, posaconazole, and isavuconazole.<br><br>CONCLUSION: This case highlights the essential role of histopathology and mNGS in early detection of rare IFDs and stresses the need for a multidisciplinary approach combining surgery with antifungal therapy. The effective management of disseminated C. bertholletiae infection using a triple antifungal regimen offers important insights for future cases, underscoring the importance of early diagnosis and personalized treatment in immunocompromised patients.}, }
@article {pmid40398313, year = {2025}, author = {Shen, H and Zhang, X and Xu, J and Ma, W and Chen, W and Wang, Y and Zhang, C and Fan, P and Zhu, X and He, L and Yan, H and Shen, M and Lu, G and Yan, G}, title = {Real-world pathogen diagnosis in critically ill infected children: A retrospective study using metagenomic next-generation sequencing with different enrichment strategies.}, journal = {Journal of infection and public health}, volume = {18}, number = {8}, pages = {102823}, doi = {10.1016/j.jiph.2025.102823}, pmid = {40398313}, issn = {1876-035X}, abstract = {BACKGROUND: Study on the clinical pathogen diagnosis in large cohort of critically ill children using metagenomic next-generation sequencing (mNGS) with different enrichment strategies has been limited.<br><br>METHODS: 763 samples were enrolled and we summarized the clinical pathogen diagnosis and compared the performance between mNGS and clinical microbial tests (CMTs) in different sample types, as well as between shotgun-based (S-mNGS) and hybrid capture-based mNGS (C-mNGS).<br><br>RESULTS: A total of 93 clinical diagnosed pathogens were identified from763 samples with suspected infections, with a positive rate of 60.16&#x202f;%. Respiratory specimens had the highest positive rate (90.73&#x202f;%, 235/259), while the lowest was cerebrospinal fluid (26.94&#x202f;%, 59/219). mNGS showed higher sensitivity (90.85&#x202f;% vs. 83.66&#x202f;%, P&#x202f;=&#x202f;0.001), specificity (77.30&#x202f;% vs. 67.43&#x202f;%, P&#x202f;=&#x202f;0.007), positive predictive value (PPV, 85.80&#x202f;% vs. 79.50&#x202f;%, P&#x202f;=&#x202f;0.01), negative predictive value (NPV, 84.84&#x202f;% vs. 73.21&#x202f;%, P&#x202f;<&#x202f;0.001), and accuracy (85.45&#x202f;% vs. 77.20&#x202f;%, P&#x202f;<&#x202f;0.001) than CMTs. The corrected true positive rate of mNGS was higher than CMTs (83.88&#x202f;% vs. 75.60&#x202f;%, P&#x202f;=&#x202f;0.002), and its advantage in virus detection was more obvious (OR=1.39, 95&#x202f;%CI: 1.08-1.78, P&#x202f;=&#x202f;0.010). S-mNGS and C-mNGS shown significantly higher sensitivity and accuracy than CMTs. However, the total true positive rate between S-mNGS and C-mNGS were close (83.15&#x202f;% vs. 85.00&#x202f;%, P&#x202f;=&#x202f;0.600). According to the mNGS results, the adjusted pathogen diagnosis rate was 45.48&#x202f;% (417/763), and the adjusted anti-infection strategy ratio was 42.86&#x202f;% (327/763).<br><br>CONCLUSIONS: mNGS provided an efficient pathogen diagnosis method for critically ill children with suspected infection. Different enrichment strategies of mNGS can play their respective advantages in clinical practice.}, }
@article {pmid40398297, year = {2025}, author = {Shen, Y and Li, Y and Xiao, J and Li, J and Wu, Y and Wu, Y and Tang, H and Fang, X and Wang, L and Gong, Y and Chen, H and Yan, X}, title = {Comparative microbiomic analysis of fecal microbiota associated with abdominal fat in ducks.}, journal = {Poultry science}, volume = {104}, number = {8}, pages = {105282}, doi = {10.1016/j.psj.2025.105282}, pmid = {40398297}, issn = {1525-3171}, abstract = {The gut microbiota, which features complex community structures, colonizes the duck intestine and plays a crucial role in metabolism, immune regulation, and meat quality. Gut-microbiota-regulated abdominal fat deposition is a key factor that affects the meat quality of livestock and poultry. We used 16S rDNA and metagenomic sequencing to investigate the microbial community characteristics of 187 fecal samples from 10 Chinese indigenous duck breeds (five breeds for each of the high/low abdominal fat categories). We explored the relationship between fecal microbiota and abdominal fat deposition. The α diversity of the fecal microbiome in high abdominal fat ducks (HAF) was higher than that in low abdominal fat ducks (LAF). The fecal microbiota and function were also significantly different. At the phylum level, Actinobacteria was significantly enriched in HAF, whereas Proteobacteria, Candidatus, Saccharibacteria, and Fusobacteria were abundant in LAF. At the genus level, Lactobacillus, Alistipes, Corynebacterium, and Lachnoclostridium were more abundant in HAF than in LAF. The Streptococcus, Campylobacter, Helicobacter, Enterobacter, Gallibacterium, and Escherichia genera were significantly enriched in LAF. Microbial functional analysis indicated that the HAF fecal microbiota was mainly involved in carbohydrate, nucleotide, lipid, amino acid, terpenoids, polyketides, and xenobiotic metabolism. In addition, bacteria related to signal transduction, cofactor and vitamin metabolism, and infectious disease were enriched in LAF. This study revealed the relationship between gut microbiota and abdominal fat deposition in ducks. Our findings lay a foundation for the abdominal fat deposition mechanism in ducks and provide a reference for Chinese indigenous duck husbandry.}, }
@article {pmid40398057, year = {2025}, author = {Ding, J and Liu, F and Huang, J and Li, P and Zhang, J and Wu, B and Shu, L and He, Z and Wang, C}, title = {In situ addition of layered double hydroxides promotes sulfate-dependent anaerobic methane oxidation and microbial community shifts in freshwater-influenced mangroves sediments.}, journal = {Water research}, volume = {283}, number = {}, pages = {123851}, doi = {10.1016/j.watres.2025.123851}, pmid = {40398057}, issn = {1879-2448}, abstract = {Freshwater-influenced mangrove wetlands are significant sources of methane emissions, potentially offsetting up to 27 % of their carbon storage. The targeted reduction of these emissions offers a critical avenue for enhancing climate resilience. While laboratory studies have shown that elevated sulfate concentrations can suppress methane emissions, the in situ-based effects on methane cycling and associated microbial communities remain poorly understood. To explore this, we introduced magnesium-aluminum layered double hydroxides (Mg-Al-SO4-LDH), a slow-release sulfate mineral, into freshwater-influenced mangrove sediments in Guangzhou, China, over a 74-day period, resulting in sulfate levels that were 8.9 times higher than those of the control. Isotope tracing, full-length 16S rDNA sequencing, and metagenomic analysis revealed that this sulfate augmentation significantly altered the methane cycling and functional microbial communities. Notably, we observed substantial stimulation of sulfate reduction coupled with anaerobic oxidation of methane (SR-AOM) within Mg-Al-SO4-LDH-attached microbial communities, characterized by a 6.9-fold increase of anaerobic methane-oxidizing archaea (ANME-1b subtype). Contrary to laboratory observations, the elevated sulfate conditions selectively promoted hydrogenotrophic methanogenesis in situ. These findings establish Mg-Al-SO4-LDH as a promising approach for enhancing SR-AOM activity while modulating methanogenic pathways, offering novel perspectives for methane management strategies and climate change mitigation within mangrove ecosystems.}, }
@article {pmid40398020, year = {2025}, author = {Sazykin, I and Khmelevtsova, L and Azhogina, T and Lanovaya, O and Karchava, S and Klimova, M and Khammami, M and Polinichenko, A and Sazykina, M}, title = {Ecotoxicological characteristics, antibiotic resistance genes and hydrocarbon-degrading potential of the coastal zone surface sediments of the Taganrog Bay (Azov Sea).}, journal = {Marine pollution bulletin}, volume = {218}, number = {}, pages = {118174}, doi = {10.1016/j.marpolbul.2025.118174}, pmid = {40398020}, issn = {1879-3363}, abstract = {A comprehensive study of surface sediments (SS) of the surf zone of the coast of the eastern part of the Taganrog Bay of the Sea of Azov was conducted. Using a battery of whole-cell bacterial lux-biosensors, ecotoxicological parameters were determined, including genotoxicity, the presence of substances causing oxidative stress, damaging proteins and membranes. The content of 14 drug resistance genes, 4 metal resistance genes and integrase genes of types 1, 2 and 3 were estimated using real-time PCR of metagenomic DNA. Oxidation of 7 hydrocarbon substrates was determined by a colorimetric method with 2,6-dichlorophenolindophenol (2,6-DCPIP). The relationships were established between individual antibiotic resistance (ARG) and metal resistance (MRG) genes with integrons of types 1 and 3, facilitating their spread in the microbiome. Correlations between the content of various ARGs and between ARGs and metal resistance genes were also established, indicating their probable colocalization on the same mobile elements of the bacterial genome. The distribution and high content of MRGs are probably a consequence of large-scale pollution of SS with metals. The highest hydrocarbon-degrading potential of microbial communities was found in sampling points closest to the Don River delta, known as the largest source of hydrocarbon pollution in the Taganrog Bay.}, }
@article {pmid40397921, year = {2025}, author = {Abdillah, A and Ravaux, I and Mokhtari, S and Ranque, S}, title = {Do Malassezia yeasts colonize the guts of people living with HIV?.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0322982}, pmid = {40397921}, issn = {1932-6203}, mesh = {Humans ; *Malassezia/isolation &amp; purification/genetics ; *HIV Infections/microbiology/complications/immunology ; Female ; Male ; Adult ; Feces/microbiology ; Middle Aged ; Immunocompromised Host ; Metagenomics ; *Gastrointestinal Microbiome ; Prospective Studies ; }, abstract = {Malassezia yeasts are commensals of human skin. In contrast to culture-based studies, metagenomic studies have detected abundant Malassezia reads in the gut, especially in patients living with HIV. Whether Malassezia colonizes and persists in the gut remains an open question. This study aimed to describe the influence of HIV-associated immunodeficiency on gut colonization by Malassezia and to assess whether Malassezia are alive. Stool samples were prospectively collected over one-five visits from ten controls and 23 patients living with HIV (10 had CD4 < 200/mm3 and 13 had CD4 > 500/mm3). Each sample was cultured and subjected to Malassezia viability PCR and both fungal and bacterial metabarcoding. Abundant M. furfur colonies were cultured from an HIV-immunocompromised patient. M. furfur and M. globosa were isolated in very low quantities from healthy volunteers. Viability Malassezia-specific qPCR was positive in three HIV-immunocompromised patients. Metagenomic analyses showed that Malassezia reads were significantly more abundant in immunocompromised patients living with HIV and erratic over time in all participants. Our findings emphasise that Malassezia are rarely cultured from human stool samples, despite the use of specific culture media. Although HIV-related immunosuppression appears to be associated with the presence of Malassezia, these yeasts do not persist and colonise the gut, even in immunocompromised patients.}, }
@article {pmid40397799, year = {2025}, author = {Huang, CY and Nuwagira, E and Tisza, M and Kim, M and Tayebwa, M and Vieira, J and Lam, N and Wallach, E and Wiens, M and Tsai, AC and Valeri, L and Vallarino, J and Allen, JG and Lai, PS}, title = {Effect of household air pollution on the gut microbiome and virome of adult women living in Uganda.}, journal = {Environmental health perspectives}, volume = {}, number = {}, pages = {}, doi = {10.1289/EHP16002}, pmid = {40397799}, issn = {1552-9924}, abstract = {BACKGROUND: Emerging observational studies suggest air pollution can influence the gut microbiome. However, this association is often highly confounded by factors such as diet and poverty. The gut virome may influence respiratory health independent of the gut microbiome. We recently demonstrated in a randomized waitlist-controlled trial (ClinicalTrials.gov NCT03351504) that a clean lighting intervention reduced personal exposure to air pollution among adult women in rural Uganda.<br><br>OBJECTIVES: To determine the effect of a solar lighting intervention on changes to the gut microbiome and virome and secondarily to determine association between these changes on lung health.<br><br>METHODS: Between 2018 and 2019, we collected stool samples and assessed respiratory symptoms and spirometry from 80 adult women living in rural Uganda at baseline, 12 and 18 months post-randomization. The intervention group received a solar lighting system after randomization, while the waitlist-controlled group received one at 12 months. Deep metagenomics sequencing of stool was performed and profiled for non-viral and viral taxonomic composition. The primary analysis focused on pre- vs. post-intervention changes due power considerations, adjusting for potential confounding by age, diet, antibiotic use, and season. A sensitivity analysis was conducted using intention-to-treat principles. When comparing pre- vs. post-intervention periods, we used sparse partial least squares models to identify non-viral and viral signatures of reduced air pollution exposure. Mixed effects models were used to evaluate changes in health outcomes as well as associations between microbial signatures of reduced air pollution exposure and health.<br><br>RESULTS: The average age was 39.2 years. The solar lighting intervention led to larger changes in viral compared to non-viral microbial community structure and differential abundance of bacteria, eukaryotes, and viruses. Provision of solar lighting systems was associated with a reduction in the presence of respiratory symptoms from 57.1% to 36.1% (p = 0.002) while there was no impact on lung function. Microbiome and virome signatures had AUCs of 0.74 and 0.76 respectively, in predicting pre- vs. post-intervention stool samples. Microbiome signatures were associated with a lower risk of respiratory symptoms (OR 0.68 (0.49-0.94), p = 0.020).<br><br>CONCLUSION: Among adult women living in rural Uganda, both non-viral and viral components of the gut microbial community changed after a clean lighting intervention. Microbiome signatures reflective of lower air pollution exposures were associated with improved respiratory symptoms. These observations suggest that air pollution may influence lung health through the gut-lung axis, warranting further exploration in future intervention studies. https://doi.org/10.1289/EHP16002.}, }
@article {pmid40397796, year = {2025}, author = {Khalil, S and Sohail, MR}, title = {From Suspected to Rejected: Role of Serial Plasma mcfDNA Sequencing as a Diagnostic Adjunct in CIED Infections.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf264}, pmid = {40397796}, issn = {1537-6591}, }
@article {pmid40397663, year = {2025}, author = {Gast, K and Baker, S and Borges, AL and Ward, S and Banfield, JF and Barrangou, R}, title = {Metagenome-Derived CRISPR-Cas12a Mining and Characterization.}, journal = {The CRISPR journal}, volume = {}, number = {}, pages = {}, doi = {10.1089/crispr.2024.0099}, pmid = {40397663}, issn = {2573-1602}, abstract = {The advent of clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies has revolutionized genome editing, with continued interest in expanding the CRISPR-associated proteins (Cas) toolbox with diverse, efficient, and specific effectors. CRISPR-Cas12a is a potent, programmable RNA-guided dual nickase, broadly used for genome editing. Here, we mined dairy cow microbial metagenomes for CRISPR-Cas systems, unraveling novel Cas12a enzymes. Using in silico pipelines, we characterized and predicted key drivers of CRISPR-Cas12a activity, encompassing guides and protospacer adjacent motifs for five systems. We next assessed their functional potential in cell-free transcription-translation assays with GFP-based fluorescence readouts. Lastly, we determined their genome editing potential in vivo in Escherichia coli by generating 1 kb knockouts. Unexpectedly, we observed natural sequence variation in the bridge-helix domain of the best-performing candidate and used mutagenesis to alter the activity of Cas12a orthologs, resulting in increased gene editing capabilities of a relatively inefficient candidate. This study illustrates the potential of underexplored metagenomic sequence diversity for the development and refinement of genome editing effectors.}, }
@article {pmid40397438, year = {2025}, author = {Howland, KE and Nygaard, HJ and Steen, AD and Halanych, KM and Mahon, AR and Learman, DR}, title = {Potential for microbial denitrification coupled with methanol oxidation found in abundant MAGs in Antarctic Peninsula sediments.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf050}, pmid = {40397438}, issn = {1574-6968}, abstract = {Denitrification accounts for a substantial nitrogen loss from environmental systems, shifting microbial composition and impacting other biogeochemical cycles. In Antarctica, rising temperatures cause increased organic matter deposition in marine sediments, which can significantly alter microbially mediated denitrification. To examine the genetic potential of microorganisms driving N-cycling in these sediments, benthic sediment cores were collected at two sites in the Weddell Sea, Antarctica. DNA was extracted from multiple depths at each site, resulting in the reconstruction of seventy-five high-quality metagenome-assembled genomes (MAGs). Forty-seven of these MAGs contained reductases involved in denitrification. MAGs belonging to the genus Methyloceanibacter were the most abundant MAGs at both sites and all depths, except depth 3-6 cmbsf at one site, where they were not identified. The abundance of these Methyloceanibacter MAGs suggests the potential for nitrate-driven methanol oxidation at both sites. MAGs belonging to Beggiatoaceae and Sedimenticolaceae were found to have the genetic potential to produce intermediates in denitrification and the complete pathway for dissimilatory nitrate reduction to ammonia (DNRA). MAGs within Acidimicrobiia and Dadabacteria had the potential to complete the final denitrification step. Based on MAGs, Antarctic peninsula sediment communities have the potential for complete denitrification and dissimilatory nitrate reduction to ammonia (DNRA) via a consortium.}, }
@article {pmid40397179, year = {2025}, author = {Matsumoto, Y and Fukushima, K and Zhang, S and Fauzyah, Y and Motooka, D and Saito, H and Yamauchi, J and Nitta, T and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Kida, H and Nakamura, S}, title = {mlstverse-web: advancing real-time identification of mycobacteria from sputum using targeted sequencing NALC-Seq.}, journal = {Functional &amp; integrative genomics}, volume = {25}, number = {1}, pages = {105}, pmid = {40397179}, issn = {1438-7948}, support = {JP19K16643//Japan Society for the Promotion of Science/ ; JP21K08194//Japan Society for the Promotion of Science/ ; JP21K08194//Japan Society for the Promotion of Science/ ; JP20KK0179//Japan Society for the Promotion of Science/ ; JP22ym0126809j0001//Japan Agency for Medical Research and Development/ ; }, mesh = {*Sputum/microbiology ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *Multilocus Sequence Typing/methods ; Male ; }, abstract = {The identification of mycobacteria, including Mycobacterium tuberculosis (MTB) and non-tuberculous mycobacteria (NTM), remains a critical challenge in clinical and public health settings due to their pathogenicity and increasing drug resistance. Traditional diagnostic methods, such as PCR and mass spectrometry, are limited by species detectability and prolonged culture requirements. To address these limitations, this study introduces a novel approach, named NALC-Seq, which integrates next-generation sequencing (NGS) and target capture sequencing for the direct and comprehensive identification of mycobacteria from sputum samples. A total of 54 patients were prospectively or retrospectively enrolled between April 6, 2021, and November 8, 2022, and sputum samples were subjected to next generation sequencing. The NALC-Seq methodology utilizes custom-designed RNA probes for targeted enrichment of mycobacterial DNA, coupled with species identification via the mlstverse-web system. This system integrates web, upload, head, and cloud nodes to streamline data management and analysis. Our evaluation demonstrated that NALC-Seq achieved high sensitivity (98.1%) and accuracy (83.3%) in detecting diverse mycobacterial species, including rare and drug-resistant subspecies. There were discrepancies with MGIT-Seq in nine samples. These samples exhibited low smear positivity rates, and the detection of environmental mycobacteria suggested potential contamination. Furthermore, real-time identification using the MinION device significantly reduced the turnaround time from 686 to 19 h.These findings highlight the potential of NALC-Seq and mlstverse-web as an integrated diagnostic solution for overcoming the limitations of current methods. The proposed approach offers a rapid, accurate, and comprehensive strategy for mycobacterial identification, with significant implications for clinical diagnostics and public health surveillance.}, }
@article {pmid40396743, year = {2025}, author = {Zhang, T and Han, Y and Peng, Y and Deng, Z and Shi, W and Xu, X and Wu, Y and Dong, X}, title = {The risk of pathogenicity and antibiotic resistance in deep-sea cold seep microorganisms.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0157124}, doi = {10.1128/msystems.01571-24}, pmid = {40396743}, issn = {2379-5077}, abstract = {UNLABELLED: Deep-sea cold seeps host high microbial biomass and biodiversity that thrive on hydrocarbon and inorganic compound seepage, exhibiting diverse ecological functions and unique genetic resources. However, potential health risks from pathogenic or antibiotic-resistant microorganisms in these environments remain largely overlooked, especially during resource exploitation and laboratory research. Here, we analyzed 165 metagenomes and 33 metatranscriptomes from 16 global cold seep sites to investigate the diversity and distribution of virulence factors (VFs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A total of 2,353 VFs are retrieved in 689 metagenome-assembled genomes (MAGs), primarily associated with indirect pathogenesis like adherence. In addition, cold seeps harbor nearly 100,000 ARGs, as important reservoirs, with high-risk ARGs (11.22%) presenting at low abundance. Compared to other environments, microorganisms in cold seeps exhibit substantial differences in VF and ARG counts, with potential horizontal gene transfer facilitating their spread. These virulome and resistome profiles provide valuable insights into the evolutionary and ecological implications of pathogenicity and antibiotic resistance in extreme deep-sea ecosystems. Collectively, these results indicate that cold seep sediments pose minimal public health risks, shedding light on environmental safety in deep-sea resource exploitation and research.<br><br>IMPORTANCE: In the "One Health" era, understanding pathogenicity and antibiotic resistance in vast and largely unexplored regions like deep-sea cold seeps is critical for assessing public health risks. These environments serve as critical reservoirs where resistant and virulent bacteria can persist, adapt, and undergo genetic evolution. The increasing scope of human activities, such as deep-sea mining, is disrupting these previously isolated ecosystems, heightening the potential for microbial exchange between deep-sea communities and human or animal populations. This interaction poses a significant risk for the dissemination of resistance and virulence genes, with potential consequences for global public health and ecosystem stability. This study offers the first comprehensive analysis of virulome, resistome, and mobilome profiles in cold seep microbial communities. While cold seeps act as reservoirs for diverse ARGs, high-risk ARGs are rare, and most VFs were low risk that contribute to ecological functions. These results provide a reference for monitoring the spread of pathogenicity and resistance in extreme ecosystems, informing environmental safety assessments during deep-sea resource exploitation.}, }
@article {pmid40396735, year = {2025}, author = {Zhang, J and Chen, B-Y and Zhi, M-F and Lin, W-Z and Li, Y-L and Ye, H-L and Xu, S and Zhu, H and Zhou, L-J and Du, L-J and Meng, X-Q and Liu, Y and Feng, Q and Duan, S-Z}, title = {Linking oral microbiota to periodontitis and hypertension unveils that Filifactor alocis aggravates hypertension via infiltration of interferon-γ[+] T cells.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0008425}, doi = {10.1128/msystems.00084-25}, pmid = {40396735}, issn = {2379-5077}, abstract = {UNLABELLED: Periodontal disease (PD), an inflammatory disease initiated by oral microbiota, may aggravate hypertension (HTN). Few studies were employed to characterize the oral microbiota in hypertensive patients with periodontitis. To investigate the interplay between oral microbiota and hypertension in individuals with periodontitis, we initiated a metagenomic sequencing study on subgingival plaque and saliva samples sourced from HTN patients and those with hypertension and periodontitis (PDHTN). Our primary objective was to characterize species serving as pivotal links (bridge species) in exacerbating hypertension induced by periodontal disease. Within subgingival plaque and saliva specimens, we pinpointed 31 and 28 bridge species, respectively. Furthermore, we noted a decrease in the abundance of nitrate-reducing bacteria, such as Actinomyces spp., Rothia spp., and Veillonella spp., in PDHTN samples. Employing network analysis, we distinguished distinct polymicrobial clusters within the two patient groups. These bridge species coalesced into polymicrobial clusters, revealing intricate symbiotic and competitive relationships. To substantiate our findings, we leveraged an angiotensin II-infused animal model of ligature-induced periodontitis (LIP), confirming the contributory role of Filifactor alocis-a selectively analyzed subgingival bridge species-in exacerbating hypertension and upregulating the frequency of renal CD4[+]IFNγ[+] and CD8[+]IFNγ[+] T cells. Our study screened a list of species linking PD and HTN. PD may aggravate HTN by decreasing the abundance of nitrate-reducing bacteria and increasing the abundance of pathogens. Using an animal model, we demonstrated that F. alocis aggravates HTN via the accumulation of IFNγ[+] T cells in the kidneys.<br><br>IMPORTANCE: Both periodontal disease and hypertension are widely prevalent all over the world. PD may aggravate the development of HTN via oral microbiota. However, few studies were employed to characterize the oral microbiota in hypertensive patients with periodontitis. Here, the present study profiled the oral microbiota in hypertensive participants with periodontitis. We found that the depleted abundance of nitrate-reducing bacteria and the enriched abundance of pathogens. Finally, we validated the role of Filifactor alocis in exacerbating HTN via infiltration of IFN&#x3b3;[+] T cells in mice kidneys. Our study improved the understanding of oral microbiota linking PD and HTN.}, }
@article {pmid40396732, year = {2025}, author = {Xin, T and Ye, Q and Hu, D}, title = {A relationship between body size and the gut microbiome suggests a conservation strategy.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0029425}, doi = {10.1128/spectrum.00294-25}, pmid = {40396732}, issn = {2165-0497}, abstract = {A key goal of conservation is to protect the biodiversity of wild species to support their continued evolution and survival. Conservation practice has long been guided by genetic, ecological, and demographic indicators of risk. Cope's rule suggests that species tend to evolve larger body sizes over time. Here, we provide strong evidence to support the inclusion of body size when formulating wildlife conservation strategies. The gut microbiome can mirror the physiological and environmental adaptation status of the host. This study established a connection between body size and the gut microbiome in the Felidae family using 70 fecal samples collected from 18 individuals through metagenomic data analysis and mining metagenome-assembled genomes (MAGs). Two enterotypes were identified in the Felidae gut: Bacteroides and Clostridium. Medium-sized felids predominantly harbored Clostridium, associated with pathogenicity, whereas large and small felids harbored both beneficial Bacteroides and pathogenic Clostridium. Species that evolved larger body sizes over time exhibited distinct changes in gut microbial communities, such as enhanced nutrient extraction and metabolic capabilities. Larger felids exhibited a more diverse, stable gut microbiome engaged in metabolic processes and extensive host interactions, indicating an evolved functional role in various biological processes. Conversely, that of smaller felids is less diverse, with more viruses and pathogenic elements primarily involved in chemical synthesis. These findings provide essential insights for developing conservation strategies that consider the nutritional needs of different-sized feline species, control the transmission of pathogens, and allocate resources based on their unique gut microbiome characteristics.IMPORTANCEBody size is a fundamental trait that varies greatly among taxa and has important implications for life history and ecology. Cope's rule suggests that species tend to evolve larger body sizes over time. However, its correlation to body size evolution remains unclear. This study aimed to establish a connection between body size and the gut microbiome in the Felidae family through metagenomic data analysis. Our results support Cope's rule, illustrating that increased body size correlates with shifts in the gut microbiome, enhancing survival and adaptability.}, }
@article {pmid40396729, year = {2025}, author = {Cunningham, AL and Zhbannikov, IY and Myers, R and Tran, TH and Gao, W and Lemon, KP and Aquino, JN and Hurst, JH and Yoon, JW and Seed, PC and Kelly, MS}, title = {Genome mining identifies a diversity of natural product biosynthetic capacity in human respiratory Corynebacterium strains.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0025825}, doi = {10.1128/msphere.00258-25}, pmid = {40396729}, issn = {2379-5042}, abstract = {Corynebacterium species, integral to the healthy human upper respiratory tract (URT) microbiota, remain underexplored in microbial genomics for their potential to promote respiratory health and exclude pathobionts. This genomic study investigated the diversity and capacity for natural product synthesis within these species, as indicated by their biosynthetic gene clusters (BGCs). We aimed to map and quantify the BGC diversity in a contemporary collection of Corynebacterium strains, representative of their prevalence in the respiratory microbiota, and to elucidate intra- and interspecies variation in BGC content. The outcomes of this research could reveal key factors in maintaining the ecological balance of the upper respiratory tract and identify novel antimicrobial agents targeting respiratory pathobionts. Employing an in silico approach, we analyzed the biosynthetic potential of respiratory strains of non-diphtheriae Corynebacterium species and their reference genomes through genome sequencing and antiSMASH6 analysis. Among 161 genomes, we identified 672 BGCs, 495 of which were unique, including polyketide synthase, non-ribosomal peptide synthetase, ribosomally synthesized and post-translationally modified peptide, and siderophore families. To understand how this biosynthetic capacity compared to other respiratory bacteria, we then downloaded genomes from eight species that are associated with the URT and conducted BGC searches. We found that despite their compact genomes, Corynebacterium species possess a multitude of predicted BGCs, exceeding the diversity of natural product BGCs identified in multiple other respiratory bacteria. This research lays the foundation for future functional genomics studies on the role of Corynebacterium species in the respiratory microbiome and the discovery of novel therapeutics derived from this bacterial genus.IMPORTANCEBacterial secondary metabolites, produced by enzymes encoded by biosynthetic gene clusters, are ecologically important for bacterial communication and competition in nutrient-scarce environments and are a historically rich source of antibiotics and other medications. Human-associated Corynebacterium species, abundant in the healthy upper respiratory tract, are understudied despite evidence of their roles in promoting human health and preventing pathobiont colonization. Through genome mining of a large collection of Corynebacterium strains isolated from the human respiratory tract and publicly available genomes of other respiratory bacteria, our study suggests that Corynebacterium species have a high biosynthetic capacity and are predicted to harbor a wide range of biosynthetic gene cluster families. These findings substantially expand current knowledge regarding the production of secondary metabolites by human-associated Corynebacterium species. Our study also lays the foundations for understanding how Corynebacterium species interact in the healthy human upper respiratory tract and the potential for discovering novel biotherapeutics.}, }
@article {pmid40396715, year = {2025}, author = {Yang, J and Wang, Y and Yang, L and Wu, J}, title = {Laboratory validation of targeted next-generation sequencing assay for pathogen detection in lower respiratory infection.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0175124}, doi = {10.1128/spectrum.01751-24}, pmid = {40396715}, issn = {2165-0497}, abstract = {UNLABELLED: Lower respiratory tract infection (LRTI) is a serious global public health issue and poses significant challenges for detection and diagnosis. We validated the detection performance of targeted next-generation sequencing (tNGS) based on multiplex PCR using simulated microbial sample panels and clinical samples, providing a theoretical basis for promoting and applying tNGS in clinical diagnosis. We used a series of simulated microbial sample panels to validate the analytical validity of tNGS comprehensively. We also use tNGS to test respiratory specimens from 108 diagnosed or suspected LRTI patients to validate its clinical validity in diagnosing LRTI. Finally, we summarize the drug-resistance genes obtained from tNGS, the detection cost, and the turnaround time. tNGS has good analytical specificity, sensitivity, and precision. It has good stability when stored under low-temperature conditions. Using the composite diagnostic criteria as the gold standard, our internal tNGS platform has a sensitivity of 84.38%, specificity of 91.67%, positive predictive value of 98.78%, and negative predictive value of 42.31%. In terms of turnaround time, tNGS (about 16 h) and metagenomic next-generation sequencing (about 24 h) are similar, both significantly superior to traditional microbial detection methods (3-5 days). The cost of tNGS is approximately one-fourth of metagenomic next-generation sequencing. As a novel method with acceptable performance and cost, tNGS can compensate for the shortcomings of commonly used pathogen detection schemes in clinical practice, and its application prospects are worth looking forward to.<br><br>IMPORTANCE: Lower respiratory tract infection (LRTI) is a serious global public health problem, and detecting its pathogenic microorganisms is difficult. Targeted next-generation sequencing (tNGS) is a rising star in microbial detection, with enormous potential. To understand the detection performance of tNGS and provide a theoretical basis for promoting its application in clinical diagnosis, this study prepared simulated microbial sample panels using reference materials to evaluate the analytical and clinical validity of tNGS. Our research suggests that tNGS has good analytical specificity and sensitivity, precision, and stability. Additionally, it can reliably detect common LRTI pathogens. It has advantages in identifying co-infections and atypical pathogens. Moreover, tNGS significantly reduces turnaround time, allowing faster treatment. In summary, tNGS is expected to be used in clinical practice to diagnose and manage LRTI.}, }
@article {pmid40396204, year = {2025}, author = {Zöggeler, T and Kavallar, AM and Pollio, AR and Aldrian, D and Decristoforo, C and Scholl-Bürgi, S and Müller, T and Vogel, GF}, title = {Meta-analysis of shotgun sequencing of gut microbiota in obese children with MASLD or MASH.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2508951}, doi = {10.1080/19490976.2025.2508951}, pmid = {40396204}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Child ; *Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; *Pediatric Obesity/microbiology/complications ; *Fatty Liver/microbiology ; Male ; Metagenomics ; Female ; *Obesity/microbiology ; Adolescent ; Shotgun Sequencing ; }, abstract = {Alterations in the gut microbiome affect the development and severity of metabolic dysfunction-associated steatotic liver disease (MASLD) or metabolic dysfunction-associated steatohepatitis (MASH). We analyzed microbiomes of obese children with and without MASLD, MASH, and healthy controls. Electronic databases were searched for studies on the gut microbiome in children with obesity with/without MASLD or MASH, providing shotgun-metagenomic-sequencing data. Nine studies and an additionally recruited cohort were included. Fecal microbiomes of children with MASLD (n = 153) and MASH (n = 70) were significantly different in alpha- and beta-diversity (p < 0.001) compared to obese (n = 58) and healthy (n = 132). Species Faecalibacterium_prausnitzii and Prevotella_copri are differentially abundant between obese, MASLD and MASH groups. XGBoost and random forest-models accurately predict MASLD over obesity with an AUROC of 87% and MASH over MASLD with 89%. Pathway-abundance-based models accurately predict MASLD over obesity with an AUROC of 81% and MASH over MASLD with 88%. The composition of the gut microbiome is altered with increasing hepatic fibrosis and concomitant species-abundance increase of Prevotella_copri (p = 0.0082). Machine-learning models discriminate pediatric from adult MASH with an AUROC of 97%. The gut microbial composition is increasingly altered in children with the progression of MASLD toward MASH. This can be utilized as a fecal biomarker and highlights the impact of diet on the gut microbiome for disease intervention.}, }
@article {pmid40395807, year = {2025}, author = {Zhang, R and Hu, W and Zhong, S and Chen, W and Xie, S and Chen, M and Yu, Q}, title = {The alleviating effects and mechanisms of Enterococcus faecium Kimate-X and Lactobacillus plantarum Kimate-F combination on canine inflammatory bowel disease.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1534665}, pmid = {40395807}, issn = {2297-1769}, abstract = {INTRODUCTION: Canine inflammatory bowel disease (IBD) is characterized by chronic intestinal inflammation and dysbiosis. Conventional treatments often result in adverse effects and contribute to antibiotic resistance, highlighting the need for safe, effective alternatives. Probiotics have gained attention for their potential in modulating gut microbiota and immune responses. This study investigates the therapeutic mechanisms of Enterococcus faecium Kimate-X and Lactobacillus plantarum Kimate-F, individually and in combination, in alleviating canine IBD.<br><br>METHODS: In vitro antibacterial and anti-inflammatory activities were assessed using agar well diffusion assays and LPS-induced RAW 264.7 macrophages, respectively. In vivo efficacy was evaluated in dextran sulfate sodium (DSS)-induced colitis models in mice and dogs. Metagenomic sequencing was performed on canine fecal samples to analyze microbiota composition and functional pathways. Short-chain fatty acid (SCFA) levels were quantified, and key host signaling pathways were examined.<br><br>RESULTS: Kimate-F showed strong antibacterial effects against Escherichia coli, Salmonella enteritidis, and Yersinia enterocolitica. Kimate-X significantly suppressed nitric oxide (NO) and TNF-&#x3b1; production in the in vitro inflammation model. In both mouse and canine DSS-induced colitis models, the probiotic combination significantly reduced weight loss, colonic damage, and serum inflammatory cytokines, while increasing IL-10 levels. Metagenomic analysis revealed enhanced microbial diversity, with enrichment of Bifidobacterium species and upregulation of metabolic pathways involved in nutrient absorption and immune regulation. The probiotic combination also modulated the PPAR and AMPK signaling pathways and promoted SCFA production in canine feces.<br><br>DISCUSSION: These findings suggest that E. faecium Kimate-X and L. plantarum Kimate-F act synergistically to restore gut homeostasis, reduce intestinal inflammation, and enhance host immunity. Their ability to modulate gut microbiota composition, host signaling, and metabolic output underscores their potential as safe and effective probiotic candidates for managing canine IBD.}, }
@article {pmid40395765, year = {2025}, author = {Jia, G and Yang, C and Feng, Y}, title = {Diabetes-associated central nervous system mucormycosis with delayed diagnosis: a case report.}, journal = {Frontiers in neurology}, volume = {16}, number = {}, pages = {1596136}, pmid = {40395765}, issn = {1664-2295}, abstract = {BACKGROUND: Central nervous system (CNS) mucormycosis is a rare, life-threatening fungal infection predominantly affecting diabetic and immunocompromised patients. Early diagnosis remains challenging, resulting in poor outcomes. We report a case highlighting the diagnostic challenges and rapid progression in a patient with uncontrolled diabetes and COVID-19 infection.<br><br>CASE PRESENTATION: A 31-year-old male with untreated type 2 diabetes mellitus presented with severe pneumonia due to COVID-19 infection. His condition rapidly deteriorated, developing CNS symptoms and characteristic nasal lesions. Cerebrospinal fluid (CSF) analysis revealed lymphocytic pleocytosis, high protein, and low glucose. Metagenomic next-generation sequencing (mNGS) of CSF confirmed Rhizopus oryzae infection. Despite initiating amphotericin B therapy, his condition worsened.<br><br>RESULTS: The patient succumbed to progressive multi-organ failure secondary to disseminated mucormycosis. This case emphasizes the significance of uncontrolled diabetes and COVID-19 as critical risk factors and highlights the diagnostic utility of CSF mNGS.<br><br>CONCLUSION: Prompt recognition of risk factors, early utilization of advanced diagnostic methods, and aggressive treatment are essential to improve outcomes in CNS mucormycosis.}, }
@article {pmid40394176, year = {2025}, author = {Kawasaki, J and Suzuki, T and Hamada, M}, title = {Hidden challenges in evaluating spillover risk of zoonotic viruses using machine learning models.}, journal = {Communications medicine}, volume = {5}, number = {1}, pages = {187}, pmid = {40394176}, issn = {2730-664X}, support = {JPMJPR23R4//MEXT | JST | Precursory Research for Embryonic Science and Technology (PRESTO)/ ; JP22KJ2901//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {BACKGROUND: Machine learning models have been deployed to assess the zoonotic spillover risk of viruses by identifying their potential for human infectivity. However, the lack of comprehensive datasets for viral infectivity poses a major challenge, limiting the predictable range of viruses.<br><br>METHODS: In this study, we address this limitation through two key strategies: constructing expansive datasets across 26 viral families and developing the BERT-infect model, which leverages large language models pre-trained on extensive nucleotide sequences.<br><br>RESULTS: Here we show that our approach substantially boosts model performance. This enhancement is particularly notable in segmented RNA viruses, which are involved with severe zoonoses but have been overlooked due to limited data availability. Our model also exhibits high predictive performance even with partial viral sequences, such as high-throughput sequencing reads or contig sequences from de novo sequence assemblies, indicating the model's applicability for mining zoonotic viruses from virus metagenomic data. Furthermore, models trained on data up to 2018 demonstrate robust predictive capability for most viruses identified post-2018. Nonetheless, high-resolution evaluation based on phylogenetic analysis reveals general limitations in current machine learning models: the difficulty in alerting the human infectious risk in specific zoonotic viral lineages, including SARS-CoV-2.<br><br>CONCLUSIONS: Our study provides a comprehensive benchmark for viral infectivity prediction models and highlights unresolved issues in fully exploiting machine learning to prepare for future zoonotic threats.}, }
@article {pmid40393758, year = {2025}, author = {Jiang, JY and Fan, ZX and Yang, F and Liu, HM and Mao, M and Feng, L and Xiong, F and Li, P}, title = {[Composition of gut microbiota and characteristics of virulence factors genes in overweight or obese children and their relationship with liver metabolic inflammation].}, journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics}, volume = {63}, number = {6}, pages = {642-648}, doi = {10.3760/cma.j.cn112140-20241128-00873}, pmid = {40393758}, issn = {0578-1310}, support = {2023YFS0034//Key R&amp;D Project of Science and Technology Department of Sichuan Province/ ; }, abstract = {Objective: To explore the composition of gut microbiome, the characteristics of virulence factor genes and their relationship with liver metabolic inflammation in overweight or obese children. Methods: A case-control design was conducted. From the children who visited the West China Second University Hospital of Sichuan University for medical or physical examinations between August 2021 and April 2022, a total of 23 obese children (obesity group), 8 overweight children (overweight group), and 22 healthy children (control group) were recruited. The body mass index of children was calculated after anthropometric measurements; metabolic inflammation indexes such as the levels of fasting blood glucose and hepatic function and renal function etc. were detected. The composition and abundance of gut microbiota in the feces of the children were detected by metagenomic sequencing technology and the Shannon index and Simpson index were calculated to assess the α diversity of virulence factor genes. The Wilcoxon rank-sum test was used for pairwise comparison between groups. The Spearman's rank correlation test was used for correlation analysis, and the Benjamini-Hochberg method was used to correct the P-value of multiple tests. Results: The obese group included 23 children aged 8.5 (6.3, 11.8) years, of whom 9 (39%) were male. The overweight group consisted of 8 children aged 9.2 (5.5, 12.3) years, of whom 4 were male. The control group comprised 22 children aged 5.3 (5.1, 5.4) years, of whom 10 (45%) were male. The obese group exhibited higher levels of alanine aminotransferase (ALT), gamma-glutamyl transferase (γ-GT), globulin, and uric acid compared to those of the control group (all P<0.05), with ALT also higher than that of the overweight group (P<0.05). The levels of fasting blood glucose, γ-GT, globulin, and uric acid in the overweight group were all higher than those in the control group (all P<0.05). The abundance of Coprococcus A (0.76 (0.00, 3.11) vs. 0.00 (0.00, 0.00), false discovery rate (FDR)<0.05) and Parasutterella (0.89 (0.08, 1.79) vs. 0.00 (0.00, 0.08), FDR<0.05) in the gut of children in the obese group were both higher than those of the control group. The number of virulence factor genes in the obese group was higher than those of the control group (941 (886, 977) vs. 890 (807, 920), P<0.05). The Simpson index and Shannon index of gut microbial virulence factor genes in the obese group were both higher than those of the control group (0.993 (0.992, 0.993) vs. 0.991(0.990, 0.991), (5.50 (5.46, 5.56) vs. 5.37 (5.30, 5.43), both P<0.01). The abundance of gut microbiota virulence factors genes all showed positive correlations with fasting blood glucose, ALT, γ-GT, and uric acid levels in children (all r>0.3, all FDR<0.05). The abundance of 17 gut microbial virulence factor genes were all positively associated with γ-GT levels (all r>0.3, all FDR<0.05). The virulence factor genes (LpxH, LpxB, LpxK) of lipopolysaccharide were all positively correlated with plasma γ-GT and globulin levels (all r>0.3, all FDR<0.05). Conclusions: Overweight or obese children exhibited elevated liver metabolic-inflammatory markers compared to their normal-weight counterparts. Notably, obese children demonstrated gut microbiota dysbiosis accompanied by enrichment of virulence factor genes, which may promote liver metabolic inflammation through pathways such as lipopolysaccharide biosynthesis.}, }
@article {pmid40393581, year = {2025}, author = {Huang, S and Wang, M and Yuan, J and Chen, Y and Tang, L}, title = {Enhancing medium-chain-length polyhydroxyalkanoate (mcl-PHA) synthesis in mixed microbial cultures via targeted substrate composition: A meta-omics guided approach.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132700}, doi = {10.1016/j.biortech.2025.132700}, pmid = {40393581}, issn = {1873-2976}, abstract = {This study investigates how varying medium-chain fatty acid (MCFA) ratios in substrates (caproate-rich [C6], heptanoate-rich [C7], octanoate-rich [C8], and Control) affect medium-chain-length PHA (mcl-PHA) synthesis in mixed microbial cultures, assessing their impacts on PHAs yield and PHA monomer composition. Results demonstrate that increasing MCFA concentrations enhanced total PHAs accumulation. Maximum PHAs production was achieved with a caproate-rich substrate (5:1 ratio), yielding 63 wt% of PHA (26% mcl-PHA), while heptanoate-rich substrate (5:1 ratio) produced 58 wt% of PHA (29% mcl-PHA). In contrast, octanoate-rich substrates resulted in significantly lower mcl-PHA fractions (20%), attributed to β-oxidation-driven precursor depletion. Metagenomic analysis revealed substrate-dependent microbial community shifts, alongside differential expression of β-oxidation genes (FadD, FadE, FadA) and PHA synthases genes (PhaC). These findings highlight the critical role of MCFA composition in optimizing mcl-PHA biosynthesis, demonstrating that tailoring MCFA ratios in feedstocks enhances production efficiency and enables scalable and sustainable biopolymer synthesis from renewable waste resources.}, }
@article {pmid40392941, year = {2025}, author = {Feng, C and Liang, Z and Liao, X and Lin, K and Zhai, Y and Liu, G and Malpei, F and Hu, A}, title = {Microbial Dynamics on Different Microplastics in Coastal Urban Aquatic Ecosystems: The Critical Roles of Extracellular Polymeric Substances.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c03796}, pmid = {40392941}, issn = {1520-5851}, abstract = {Microplastics (MPs) serve as carriers for microbial community colonization, forming unique ecosystems known as plastispheres in urban aquatic ecosystems. However, interactions among microbes, extracellular polymeric substances (EPS), and MPs remain poorly understood. This study investigates microbial consortia and their EPS secretion behaviors across various plastispheres at two representative coastal urban water sites. Permutational multivariate analysis of variance revealed that MP type significantly influenced microbial community structures in reservoir environments (R[2] = 0.60, p < 0.001), highlighting the pronounced impact of MP types in high-quality urban waters. Specific microbial phyla and genera were identified as key contributors to EPS compositional variations across different plastispheres. Hierarchical partitioning results identified Acidobacteria, Nitrospirae, and Planctomycetes as influential phyla positively affecting EPS composition. Spearman correlation analysis pinpointed Robiginitialea (positive correlation) and Fimbriiglobus (negative correlation) as critical genera influencing EPS dynamics. Moreover, EPS-related gene abundance corresponded closely with observed EPS compositional differences. Dominant genes associated with protein biosynthesis included xapD in reservoirs and glnA in bays, while glmS and eno were predominant for polysaccharide biosynthesis in bays. This research advances our understanding of microbial-EPS-MP interactions in urban water systems, offering critical insights into ecological remediation and risk assessment of MP pollution.}, }
@article {pmid40392689, year = {2025}, author = {Wang, W and Yan, CL and Xue, QS}, title = {Clinical Characteristics of Five Cases of Chlamydia psittaci Pneumonia Diagnosed Using Metagenomics Next-Generation Sequencing.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {}, number = {}, pages = {}, doi = {10.1089/vbz.2025.0009}, pmid = {40392689}, issn = {1557-7759}, abstract = {Objective: This study aimed to analyze the clinical characteristics of five cases of Chlamydia psittaci pneumonia diagnosed using metagenomics next-generation sequencing (mNGS) and to provide help for its diagnosis and treatment. Methods: Five patients who were admitted to the department of Respiratory and Critical Care Medicine of Beijing Aerospace General Hospital between June 2020 and December 2021 and diagnosed with C. psittaci pneumonia using mNGS were selected, including one case with severe pneumonia. We analyzed the clinical characteristics, epidemiology, laboratory results, treatment, and prognosis of the five participating patients. Results: The main clinical manifestations were high fever, dry cough, chest tightness, shortness of breath, and myalgia. All five patients had a history of contact with poultry. The white blood cell count was normal or slightly increased, the lymphocyte count was significantly decreased, and the percentage of neutrophil granulocyte, C-reactive protein (CRP), erythrocyte sedimentation rate, and procalcitonin were significantly increased. Chest computed tomography showed inflammatory infiltration and consolidation of one or more lung lobes, possibly accompanied by pleural effusion and liver function impairment. Bronchoscopy mainly showed congestion and edema of airway mucosa with less sputum in the airway. In all patients, we detected the nucleic acid sequences of C. psittaci in alveolar lavage fluid or sputum using mNGS and confirmed the diagnosis of C. psittaci pneumonia based on clinical manifestations and exposure history. After adjusting antibiotics to a moxifloxacin-based treatment regimen, the disease improved. The application of the mNGS assay enables us to make faster diagnoses of diseases so that timely medication can be administered, thus shortening the duration of a patient's illness. Conclusion: C. psittaci pneumonia has an acute onset, and fever and cough are common symptoms. A history of contact between the patient and birds is an important diagnostic clue; however, clinical symptoms and laboratory and imaging examinations lack specificity. The detection using mNGS of bronchoalveolar lavage fluid can quickly confirm the diagnosis and reduce missed diagnoses and misdiagnoses. Moxifloxacin-based therapy is effective, and patients require combination therapy if they have other bacterial infections.}, }
@article {pmid40392601, year = {2025}, author = {Ferreira, NE and Berg, MG and da Costa, AC and Rodgers, MA and Kallas, EG and Terrasani Silveira, CG and Thomazella, MV and de Oliveira, ACS and Honorato, L and Paião, HG and Barros Domingues, R and Senne, C and Côrtes, MF and Tozetto-Mendoza, TR and Gomes, HR and Mariano Matos, ML and de Oliveria Ribeiro, G and Witkin, SS and Cloherty, GA and Mendes-Correa, MC}, title = {Metagenomic detection of central nervous system infections missed by conventional testing.}, journal = {JCI insight}, volume = {}, number = {}, pages = {}, doi = {10.1172/jci.insight.189295}, pmid = {40392601}, issn = {2379-3708}, abstract = {Community-acquired infectious meningoencephalitis is associated with high rates of mortality and morbidity, compounded by limited access to diagnostic resources. The current study assessed acute central nervous system (CNS) infections in patients with meningoencephalitis enrolled in a hospital-based diagnostic surveillance study in São Paulo, Brazil. Cerebrospinal fluid (CSF) was collected from 600 subjects between March 2018 and November 2019 and initially screened for a broad range of pathogens according to a local diagnostic algorithm. Standard microbiological and molecular diagnostic methods were applied. Metagenomic sequencing was used as a complementary approach to investigating etiology in cases where no pathogen was initially identified. Standard testing identified infectious etiologies in 292 cases (48.6%), with 227 (77.7%) confirmed as viral infections, predominantly caused by enteroviruses (n=144) and herpesviruses (n=40). Non-viral agents were identified in 65 cases (22.3%). Metagenomic sequencing (mNGS) of 279 out of 308 undiagnosed cases revealed several additional potential etiologies, including Parvovirus B19, Toxoplasma gondii, Picobirnavirus, other enterovirus species and Vesivirus, the latter being associated with CNS infection for the first time. These findings underscore the complexity of CNS infections and highlight the potential of metagenomics to improve diagnostic accuracy, inform treatment strategies, and support efforts to address future pandemics.}, }
@article {pmid40392071, year = {2025}, author = {You, Q and Wang, K and Zhao, Z and Zhou, H and Lan, Z and Liang, H and Deng, R and Li, W and Shen, S and Wang, R and Zhang, K and Zheng, D and Sun, J}, title = {Reduction of Bacteroides fragilis in Gut Microbiome of Chronic Hepatitis B Patients Promotes Liver Injury.}, journal = {Journal of medical virology}, volume = {97}, number = {5}, pages = {e70395}, doi = {10.1002/jmv.70395}, pmid = {40392071}, issn = {1096-9071}, support = {//This study was supported by the Guangzhou Science and Technology Plan Project (Grant 2024B03J0326), the Guangdong Basic and Applied Basic Research Foundation of Guangzhou Joint Fund (Grant 2022B1515120039), the National Natural Science Foundation of China (Grant U22A20274), and the Guangdong Basic and Applied Basic Research Foundation (Grant 2023A1515010437)./ ; }, mesh = {Humans ; *Bacteroides fragilis/isolation &amp; purification/genetics ; *Gastrointestinal Microbiome ; *Hepatitis B, Chronic/microbiology/complications/pathology ; Male ; Female ; Adult ; Case-Control Studies ; Animals ; Middle Aged ; Mice ; Liver/pathology ; Alanine Transaminase/blood ; Metagenomics ; Disease Models, Animal ; }, abstract = {In chronic hepatitis B (CHB) patients under antiviral treatment, liver injury, as evidenced by elevated alanine transaminase (ALT), is associated with unfavorable outcomes and needs effective treatment. The interaction between gut microbiota and liver injury in CHB patients remains unclear. Using a case-control design, 28 cases with elevated ALT and 28 matched controls with normal ALT were randomly selected from CHB patients with viral control. Clinical characteristics were comparable between groups. Metagenomic sequencing revealed that Bacteroides fragilis was decreased in cases and exhibited the greatest disparity between cases and controls. Mice colonized by gut microbiota from cases exhibited more severe liver damage in both LPS-induced and MCD diet-induced liver injury models, and had a lower abundance of B. fragilis compared to mice colonized by gut microbiota from controls. Oral gavage of B. fragilis improved both LPS-induced and MCD diet-induced liver injury. Metabolomics analysis revealed that the levels of 7-Ketolithocholic acid (7-Keto-LCA) were positively correlated with B. fragilis and significantly increased in the cultural supernatant of B. fragilis. Consistently, 7-Keto-LCA exerted protective effects against both LPS-induced and MCD diet-induced liver damage. Targeting gut microbiota might be a promising therapeutic treatment for alleviation residual liver inflammation in CHB patients with viral control.}, }
@article {pmid40391935, year = {2025}, author = {Gao, R and Ding, H and Gu, M and Chen, C and Sun, Y and Xin, Y and Liang, S and Huang, X}, title = {Mild Tuning of the Microbial Habitat via Titanium-Based Pre-coagulation Mitigates Reverse Osmosis Membrane Fouling.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c03970}, pmid = {40391935}, issn = {1520-5851}, abstract = {Membrane fouling remains a persistent challenge in reverse osmosis (RO) systems. Devising effective strategies to mitigate membrane fouling has become crucial for sustainable water treatment. Here, we propose a titanium-based pre-coagulation strategy for RO fouling mitigation through regulation of the microbial habitat in RO feed. The pre-coagulation performance of Ti(SO4)2 for desulfurization wastewater and the subsequent RO fouling mechanism were systematically investigated. Our findings revealed that the Ti pre-coagulation induced an acidized environment, maintained a balance between organic and inorganic depositions, and fostered a beneficial microbial community that resisted rapid fouling. The 20 day RO operations in different pre-coagulation scenarios (Ti, Al, and Ctrl) showed that the Ti group membranes maintained the highest normalized flux at 57.15%, outperforming the Ctrl and Al groups by 7.92% and 15.16%, respectively. Microbial community analyses, including taxonomic profiling and metagenomic analysis, demonstrated that Ti-based pre-coagulation reduced the dominance of extracellular polymeric substance (EPS)-secreting genera, such as Sphingopyxis, while promoting Terrimonas and Paenarthrobacter, with acid-tolerance traits and reduced EPS production. This shift mitigated biofouling by enhancing microbial balance and limiting biofilm formation. These results underscored the potential of the Ti pre-coagulation-based microbial habitat tuning strategy in enhancing RO system sustainability, offering a practical solution for improving industrial wastewater treatment.}, }
@article {pmid40391897, year = {2025}, author = {Hill, MS and Minnis, VR and Simpson, AC and Salas Garcia, MC and Bone, D and Chung, RK and Rushton, E and Hameed, A and Rekha, PD and Gilbert, JA and Venkateswaran, K}, title = {Genomic description of Microbacterium mcarthurae sp. nov., a bacterium collected from the International Space Station that exhibits unique antimicrobial-resistant and virulent phenotype.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0053725}, doi = {10.1128/msystems.00537-25}, pmid = {40391897}, issn = {2379-5077}, abstract = {UNLABELLED: A novel bacterial strain, designated as 1F8SW-P5[T], was isolated from the wall of the crew quarters on the International Space Station. Cells were Gram-staining-positive, strictly aerobic, non-spore-forming, chemoheterotrophic, and mesophilic rods exhibiting catalase-positive and oxidase-negative reactivity. Strain 1F8SW-P5[T] shared the highest 16S rRNA gene similarity with Microbacterium proteolyticum CECT 8356[T] (99.34%) and the highest gyrB gene similarity with Microbacterium algihabitans KSW2-21[T] (91.34%). Its strongest matches via average nucleotide identity and DNA-DNA hybridization were to Microbacterium hydrothermale CGMCC_1.12512[T] (84.36% and 25.80%, respectively). 1F8SW-P5[T] formed a distinct lineage during phylogenetic and phylogenomic analysis. The biochemical, phenotypic, chemotaxonomic, and phylogenomic features substantiated the affiliation to 1F8SW-P5[T] as a new species of Microbacterium, for which we propose the name Microbacterium mcarthurae, with the type strain 1F8SW-P5[T] (=DSM 115934[T] =NRRL B-65667[T]). Based on metagenomic data collected during the Microbial Tracking mission series, M. mcarthurae was identified from all surfaces (n = 8) over an 8-year period, with an increase in relative abundance over time. This is of potential concern, as we observed resistance to all tested fluoroquinolone antibiotics (n = 6), two β-lactam antibiotics, and one macrolide antibiotic, which was not predicted based on isolate or plasmid genotype alone. Furthermore, we found an increase in virulence, compared to Escherichia coli, when tested within a Caenorhabditis elegans model. This pathogenic profile highlights the importance of continued characterization of spacecraft-associated microbes, the characterization of previously unidentified antimicrobial resistance and virulence genes, and the implementation of targeted mitigation strategies during spaceflight.<br><br>IMPORTANCE: Crew members are at an increased risk for exposure to and infection by pathogenic microbes during spaceflight. Therefore, it is imperative to characterize the species that are able to colonize and persist on spacecraft, how those organisms change in abundance and distribution over time, and their genotypic potential for and phenotypic expression of pathogenic traits (i.e., whether they encode for or exhibit traits associated with antibiotic resistance and/or virulence). Here, we describe a novel species of Microbacterium collected from the crew quarters on the International Space Station (ISS), 1F8SW-P5[T], for which we propose the name Microbacterium mcarthurae. M. mcarthurae was found to be distributed throughout the ISS with an increase in relative abundance over time. Additionally, this bacterium exhibits a unique antibiotic resistance phenotype that was not predicted from whole-genome sequencing, as well as increased virulence, suggesting the need for the identification of previously undescribed antimicrobial resistance genes and monitoring/mitigation during spaceflight.}, }
@article {pmid40391895, year = {2025}, author = {Hillege, LE and Trepka, KR and Guthrie, BGH and Fu, X and Aarnoutse, R and Paymar, MR and Olson, C and Zhang, C and Ortega, E and Ramirez, L and de Vos-Geelen, J and Valkenburg-van Iersel, L and van Hellemond, IEG and Baars, A and Vestjens, JHMJ and Penders, J and Deutschbauer, A and Atreya, CE and Kidder, WA and Smidt, ML and Ziemons, J and Turnbaugh, PJ}, title = {Microbial vitamin biosynthesis links gut microbiota dynamics to chemotherapy toxicity.}, journal = {mBio}, volume = {}, number = {}, pages = {e0093025}, doi = {10.1128/mbio.00930-25}, pmid = {40391895}, issn = {2150-7511}, abstract = {Dose-limiting toxicities pose a major barrier to cancer treatment. While preclinical studies show that the gut microbiota influences and is influenced by anticancer drugs, data from patients paired with careful side effect monitoring remains limited. Here, we investigate capecitabine (CAP)-microbiome interactions through longitudinal metagenomic sequencing of stool from 56 advanced colorectal cancer patients. CAP significantly altered the gut microbiome, enriching for menaquinol (vitamin K2) biosynthesis genes. Transposon library screens, targeted gene deletions, and media supplementation revealed that menaquinol biosynthesis protects Escherichia coli from drug toxicity. Stool menaquinol gene and metabolite levels were associated with decreased peripheral sensory neuropathy. Machine learning models trained in this cohort predicted toxicities in an independent cohort. Taken together, these results suggest treatment-associated increases in microbial vitamin biosynthesis serve a chemoprotective role for bacterial and host cells. Further, our findings provide a foundation for in-depth mechanistic dissection, human intervention studies, and extension to other cancer treatments.IMPORTANCESide effects are common during the treatment of cancer. The trillions of microbes found within the human gut are sensitive to anticancer drugs, but the effects of treatment-induced shifts in gut microbes for side effects remain poorly understood. We profiled gut microbes in colorectal cancer patients treated with capecitabine and carefully monitored side effects. We observed a marked expansion in genes for producing vitamin K2 (menaquinone). Vitamin K2 rescued gut bacterial growth and was associated with decreased side effects in patients. We then used information about gut microbes to develop a predictive model of drug toxicity that was validated in an independent cohort. These results suggest that treatment-associated increases in bacterial vitamin production protect both bacteria and host cells from drug toxicity, providing new opportunities for intervention and motivating the need to better understand how dietary intake and bacterial production of micronutrients like vitamin K2 influence cancer treatment outcomes.}, }
@article {pmid40391805, year = {2025}, author = {Aminov, R}, title = {Novel Antibiotic Discovery and the Antibiotic resistome.}, journal = {Expert opinion on drug discovery}, volume = {}, number = {}, pages = {}, doi = {10.1080/17460441.2025.2490838}, pmid = {40391805}, issn = {1746-045X}, abstract = {INTRODUCTION: The success of antibiotics in therapy of infectious diseases is overshadowed by almost inevitable emergence and dissemination of resistances toward these agents, which results in higher morbidity and mortality rates and increased costs. New strategies are now needed to both limit the risk of resistance and to discover new drugs that are efficacious.<br><br>AREAS COVERED: This review investigates the resistance problems through evolutionary lenses to better understand and potentially design improved therapeutics for infectious diseases. Furthermore, it gives an overview of the evolutionary history of antibiotic resistance genes and antibiotic biosynthesis genes/clusters, the structures of natural resistomes, and the regulatory roles of antibiotics. The author utilized ScienceDirect, PubMed, Web of Science and Google Scholar using the article's keywords and their combinations to retrieve the most relevant and up-to-date information.<br><br>EXPERT OPINION: Antibiotics and their corresponding resistances are ancient phenomena with their evolutionary timescales measured over a vast amount of time. Humans have also benefited from access to, and the use of, a diverse range of antibiotics for many years also but have disrupted the balance by producing and using enormous amounts of antibiotics that have not existed before in natural ecosystems. This selective pressure has resulted in a tremendous expansion of resistomes. Future antibiotic discovery and development may need to pivot from exploiting extant antibiotic scaffolds and bacterial targets to reduce the risk of the rapid emergence of resistance from existing resistomes.}, }
@article {pmid40391192, year = {2025}, author = {Meng, Z and Li, D and Yang, W and Tang, J}, title = {Metagenomic next-generation sequencing of alveolar lavage fluid improves the detection of pulmonary infection.}, journal = {Open life sciences}, volume = {20}, number = {1}, pages = {20251074}, pmid = {40391192}, issn = {2391-5412}, abstract = {This study evaluated the effectiveness of metagenomic next-generation sequencing (mNGS) in detecting pathogens in patients with pulmonary infections, comparing a low-data-volume, human-depleted quantitative (Q) method and a high-data-volume, non-human-depleted pathogen capture engine (PACE) method. A total of 133 patients were enrolled, comprising 59 in a control group (traditional culture) and 74 in an mNGS group (51 Q and 23 PACE). Bronchoalveolar lavage fluid samples were collected for pathogen detection. Mycobacterium tuberculosis was predominantly detected via general mNGS, whereas Candida albicans and Epstein-Barr virus were more frequently identified by PACE and Q, respectively. Among participants, 22.97% had bacterial mono-infections, and 2.70% had viral mono-infections; the most common co-infection involved bacteria and viruses (25.68%). Patients with fever, abnormal white blood cell, neutrophil percentage, and D-dimer levels exhibited higher detection rates. PACE showed consistently high sensitivity (decreasing from 100 to 92% as thresholds became more stringent) and specificity and accuracy that peaked at 100 and 96%, respectively. The Q method maintained 100% sensitivity at the lowest threshold but showed variable specificity (0.52-0.67) and accuracy (71-75%). These findings highlight the need for caution in clinical applications when using low-data-volume, human-depleted approaches, especially for complex pulmonary infection cases.}, }
@article {pmid40391128, year = {2025}, author = {Yatera, K and Wang, Z and Shibata, Y and Ishikawa, N and Homma, T and Fukushima, K and Hataji, O and Inoue, Y and Kawabata, H and Miki, K and Sato, K and Tobino, K and Yoshida, M and Ishii, T and Ito, R and Kobayashi, T and Kawamatsu, S and Compton, CH and Jones, PW}, title = {Sputum Microbiome, Potentially Pathogenic Organisms, and Clinical Outcomes in Japanese Patients with COPD and Moderate Airflow Limitation: The Prospective AERIS-J Study.}, journal = {International journal of chronic obstructive pulmonary disease}, volume = {20}, number = {}, pages = {1477-1492}, pmid = {40391128}, issn = {1178-2005}, mesh = {Humans ; *Sputum/microbiology ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis ; Male ; Aged ; Female ; Prospective Studies ; Middle Aged ; Japan/epidemiology ; *Microbiota ; Aged, 80 and over ; Adult ; *Lung/microbiology/physiopathology ; Severity of Illness Index ; *Bacteria/pathogenicity/genetics/isolation &amp; purification ; Forced Expiratory Volume ; Disease Progression ; East Asian People ; }, abstract = {BACKGROUND: In Western studies, lung microbiome changes are reported in patients with chronic obstructive pulmonary disease (COPD) and are associated with poorer outcomes, but similar studies in Asian patients or those with less severe COPD are limited.<br><br>METHODS: The Acute Exacerbation and Respiratory InfectionS in COPD Japan (AERIS-J; jRCT1080224632/NCT03957577) was a prospective, non-interventional study to evaluate sputum microbiome diversity at baseline and after 12 months (V2; exploratory analysis), in patients aged 40-80 years with stable COPD (June 2019-June 2022). Baseline sputum potentially pathogenic organisms (PPOs) were identified. Blood cell counts and COPD Assessment Test (CAT) scores were collected at baseline and COPD symptoms measured over 12 months using the Evaluating Respiratory Symptoms in COPD and EXAcerbations of Chronic pulmonary disease Tool, collected by eDiary.<br><br>RESULTS: Patients (N=63) had a mean age of 72.8 years, and percent predicted post-bronchodilator forced expiratory volume in 1 second was 58.3%; 92% were male. Across 62 baseline sputum samples, microbiome composition was similar between 16S rRNA/metagenomic datasets. Patients graded Global Initiative for Chronic Obstructive Lung Disease (GOLD) III versus GOLD I/II had minimal differences in their microbial taxonomic profile and no differences in microbial diversity (Wilcoxon P=0.71). Alpha diversity (Shannon index) positively correlated with blood basophils (rho=0.41; P=0.0019) and negatively correlated with CAT score (rho=0.36; P=0.0069). Alpha diversity and sputum (rho: -0.0637; P=0.7836) or blood (rho: 0.1739; P=0.2043) eosinophils were not correlated. No difference in alpha (P=0.5) or beta (P=0.3) diversity or Operational Taxonomic Unit (Anosim R=-0.024; P=0.892) was observed between PPO-positive or -negative sputum.<br><br>CONCLUSION: A less diverse microbiome correlated with poorer health status and lower blood basophils in patients with COPD and moderate airflow limitation. There was no relationship between PPO presence and microbiome diversity.}, }
@article {pmid40391085, year = {2025}, author = {Fletcher, SJ and Lawrence, J and Sawyer, A and Manzie, N and Gardiner, DM and Mitter, N and Brosnan, CA}, title = {dsRNAmax: a multi-target chimeric dsRNA designer for safe and effective crop protection.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {2}, pages = {lqaf064}, pmid = {40391085}, issn = {2631-9268}, mesh = {*RNA, Double-Stranded/genetics ; RNA Interference ; Animals ; *Software ; *Crop Protection/methods ; *Crops, Agricultural/genetics/parasitology ; }, abstract = {Crop protection is undergoing significant evolution, transitioning towards sustainable approaches that minimize impacts on the environment and human health. Exogenous application of double-stranded RNA (dsRNA) that silences pest or pathogen genes via RNA interference (RNAi) has promise as a safe and effective next-generation crop protection platform without the need for genetic modification. However, exogenous dsRNA application at scale presents challenges. Specifically, a single dsRNA sequence needs to balance targeting the standing variation in a target pest or pathogen group against the potential for adverse impacts in a vast array of non-target and beneficial organisms at the application site and broader environment. To address these competing demands, we present dsRNAmax (https://github.com/sfletc/dsRNAmax), a software package that employs k-mer-based assembly of chimeric dsRNA sequences to target multiple related RNA sequences, to broaden the target spectrum. The package ensures that designed dsRNAs have no defined contiguous sequence homology with any off-target sequences, which can range from single transcriptomes through to metagenome sequence data and beyond. The efficacy of this package is demonstrated by a dsRNAmax-designed dsRNA that inhibits multiple root-knot nematode species but not a non-target nematode species, despite its susceptibility to environmental RNAi and high homology of the target gene.}, }
@article {pmid40390443, year = {2025}, author = {Xu, M and Gao, P and Chen, HQ and Gao, Y and Xiong, SJ and Wang, XH}, title = {[Effects of Typical Microplastics on Methanogenesis and Antibiotic Resistance Genes in Anaerobic Digestion of Sludge].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {5}, pages = {3189-3199}, doi = {10.13227/j.hjkx.202405273}, pmid = {40390443}, issn = {0250-3301}, mesh = {*Sewage/microbiology/chemistry ; *Methane/metabolism/biosynthesis ; *Drug Resistance, Microbial/genetics ; Anaerobiosis ; *Microplastics ; *Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; Bacteria/genetics ; }, abstract = {Waste sludge is an important carrier of antibiotic resistance genes （ARGs） and an important place for the enrichment of microplastics （MPs）. To explore the impacts of typical MPs on sludge recycling and harmless disposal, the effects of polyamide （PA）, polyethylene （PE）, and polypropylene （PP） MPs on the methanogenesis efficiency of anaerobic digestion were investigated. Meanwhile, based on metagenomic sequencing, the effects of MPs on ARGs, mobile genetic elements （MGEs）, microbial community structure, and host bacteria during anaerobic digestion were analyzed. The results showed that PA-MPs, PE-MPs, and PP-MPs increased the distribution of methane production by 2.2%, 22.3%, and 28.8%, respectively. MPs promoted methanation by improving the dissolution and hydrolysis efficiency of organic matter, and the enrichment of hydrogenotrophic methanogens by PP-MPs further improved the methanogenic efficiency. PA-MPs contributed to the removal of ARGs, while PE-MPs and PP-MPs had adverse effects on the reduction of ARGs. Horizontal gene transfer mediated by integron and insertion sequences was an important factor in the spread of ARGs. Proteobacteria was the key host leading to the diffusion of ARGs. The removal of pathogens from Bacteroidetes by anaerobic digestion contributed to the reduction of ARGs. The selective enrichment or inhibition of Arenimonas, Acinetobacter, Actinobacillus, Nitrospira, and other important host bacteria by MPs was the major cause for the difference in the removal effect of ARGs.}, }
@article {pmid40390350, year = {2025}, author = {Liu, Y and Wang, J and Pu, Y and Tang, S}, title = {Rapid diagnosis of disseminated Mycobacterium avium complex infection mimicking metastatic malignancy using metagenomic next-generation sequencing.}, journal = {The National medical journal of India}, volume = {38}, number = {1}, pages = {16-17}, doi = {10.25259/NMJI_872_2022}, pmid = {40390350}, issn = {2583-150X}, mesh = {Humans ; Diagnosis, Differential ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Mycobacterium avium Complex/genetics/isolation &amp; purification ; *Mycobacterium avium-intracellulare Infection/diagnosis ; Neoplasm Metastasis/diagnosis ; }, abstract = {Disseminated non-tuberculous mycobacteria (NTM) disease, which is mainly found in immunocompromised individuals, is a rare and severe infection whose diagnosis poses a challenge to clinicians. We present a patient with disseminated NTM infection mistaken for metastatic malignancy in an otherwise healthy patient and the tortuous diagnostic process. Metagenomic next-generation sequencing (mNGS) played a critical role in the diagnosis. Further screening for anti-interferon-γ antibodies revealed that the patient had a potential immunodeficiency.}, }
@article {pmid40390177, year = {2025}, author = {Ren, Z and Wang, M and Yu, J and Zhang, L and Lin, Z and Li, X and Zhang, Y}, title = {Unearthing Vertical Stratified Archaeal Community and Associated Methane Metabolism in Thermokarst Sediments.}, journal = {Environmental microbiology}, volume = {27}, number = {5}, pages = {e70110}, doi = {10.1111/1462-2920.70110}, pmid = {40390177}, issn = {1462-2920}, support = {42301132//National Natural Science Foundation of China/ ; NKL2023-QN02//Key Laboratory of Lake and Watershed Science for Water Security/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Archaea/metabolism/classification/genetics/isolation &amp; purification ; *Lakes/microbiology ; Phylogeny ; Biodiversity ; Tibet ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Thermokarst lakes are hotspots for greenhouse gas emissions across the Arctic and Qinghai-Tibet Plateau. Investigating the vertical stratification of archaeal communities in thermokarst lake sediments is essential for understanding their ecological roles and contributions to methane production. Here, we analysed archaeal communities along a depth gradient in thermokarst lake sediments. Alpha diversity (richness and Shannon index) generally decreased with depth. Euryarchaeota was the most abundant phylum, though its relative abundance declined with depth, while Thaumarchaeota increased. At the order level, Methanosarcinales and Nitrosopumilales showed increased relative abundance with depth, indicating adaptation to deeper anoxic layers, whereas Methanomicrobiales and Methanotrichales decreased. Beta diversity increased with depth, shifting from stochastic to deterministic processes. Network topology revealed reduced species connectivity but heightened modularity at depth, signalling niche specialisation. Functionally, genes associated with the initial steps of methane metabolism (Fwd, Mtd, Mer) increased with depth, while those involved in later steps (Mtr, Mcr) decreased, suggesting reduced energy conservation efficiency and lower overall methanogenesis rates in deeper sediments. These findings highlight the significant impact of vertical stratification on archaeal community structure, interaction networks, and functional capabilities.}, }
@article {pmid40390150, year = {2025}, author = {Cunningham-Oakes, E and Perez-Sepulveda, BM and Li, Y and Hinton, JCD and Nelson, CA and McIntyre, KM and Wardeh, M and Haldenby, S and Gregory, R and Iturriza-Gómara, M and Hertz-Fowler, C and O'Brien, SJ and Cunliffe, NA and Darby, AC and , }, title = {Enhancing infectious intestinal disease diagnosis through metagenomic and metatranscriptomic sequencing of 1000 human diarrhoeal samples.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {55}, pmid = {40390150}, issn = {1756-994X}, support = {WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; WT096200, HICF-T5-354//Health Innovation Challenge Fund/ ; NIHR203756//NIHR Senior Investigator Award/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Diarrhea/diagnosis/microbiology/virology ; Feces/microbiology/virology ; *Transcriptome ; Metagenome ; Gene Expression Profiling ; Female ; Male ; }, abstract = {BACKGROUND: Current surveillance of diarrhoeal disease is hindered by limitations of traditional diagnostic approaches, which often fail to identify the causative organism, particularly for novel or hard-to-culture bacterial pathogens. Sequencing nucleic acids directly from stool can overcome such constraints, but such approaches need to reliably detect pathogens identifiable by conventional methods.<br><br>METHODS: As part of the INTEGRATE study, we analysed stool microbiomes from 1067 patients with gastroenteritis symptoms using direct sequencing, and compared findings with standard diagnostic techniques (culture, immunoassay, microscopy, and single-target PCR) and molecular assays (Luminex xTAG GPP) for detection of bacterial and viral pathogens in the UK.<br><br>RESULTS: We found strong positive correlations between metatranscriptomic reads and traditional diagnostics for six out of 15 pathogens. The metatranscriptomic data were highly correlated with the Luminex assay for eight out of 14 pathogens. In contrast, metagenomic sequencing only showed a strong positive correlation with traditional diagnostics for three of 15 pathogens, and with Luminex for four of 14 pathogens. Compared with metagenomics, metatranscriptomics had increased sensitivity of detection for four pathogens, while metagenomics was more effective for detecting five pathogens. Metatranscriptomics gave near-complete transcriptome coverage for Human mastadenovirus F and detected Cryptosporidium via identification of Cryptosporidium parvum virus (CSpV1). A comprehensive transcriptomic profile of Salmonella enterica serovar Enteritidis was recovered from the stool of a patient with a laboratory-confirmed Salmonella infection. Furthermore, comparison of RNA/DNA ratios between pathogen-positive and pathogen-negative samples demonstrated that metatranscriptomics can distinguish pathogen-positive/negative samples and provide insights into pathogen biology. Higher RNA/DNA ratios were observed in samples that tested positive via gold-standard diagnostics.<br><br>CONCLUSIONS: This study highlights the power of directly sequencing nucleic acids from human samples to augment gastrointestinal pathogen surveillance and clinical diagnostics. Metatranscriptomics was most effective for identifying a wide range of pathogens and showed superior sensitivity. We propose that metatranscriptomics should be considered for future diagnosis and surveillance of gastrointestinal pathogens. We assembled a rich data resource of paired metagenomic and metatranscriptomic datasets, direct from patient stool samples, and have made these data publicly available to enhance the understanding of pathogens associated with infectious intestinal diseases.}, }
@article {pmid40390128, year = {2025}, author = {Liao, H and Wen, C and Huang, D and Liu, C and Gao, T and Du, Q and Yang, QE and Jin, L and Ju, F and Yuan, MM and Tang, X and Yu, P and Zhou, S and Alvarez, PJ and Friman, VP}, title = {Harnessing phage consortia to mitigate the soil antibiotic resistome by targeting keystone taxa Streptomyces.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {127}, pmid = {40390128}, issn = {2049-2618}, support = {42277357//National Natural Science Foundation of China/ ; }, mesh = {*Streptomyces/virology/genetics/drug effects ; *Soil Microbiology ; *Bacteriophages/physiology/genetics ; Metagenomics/methods ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Soil/chemistry ; China ; *Drug Resistance, Bacterial/genetics ; Sewage/virology ; }, abstract = {BACKGROUND: Antimicrobial resistance poses a substantial and growing threat to global health. While antibiotic resistance genes (ARGs) are tracked most closely in clinical settings, their spread remains poorly understood in non-clinical environments. Mitigating the spread of ARGs in non-clinical contexts such as soil could limit their enrichment in food webs.<br><br>RESULTS: Multi-omics (involving metagenomics, metatranscriptomics, viromics, and metabolomics) and direct experimentation show that targeting keystone bacterial taxa by phages can limit ARG maintenance and dissemination in natural soil environments. Based on the metagenomic analysis, we first show that phages from activated sludge can regulate soil microbiome composition and function in terms of reducing ARG abundances and changing the bacterial community composition. This effect was mainly driven by a reduction in the abundance and activity of Streptomyces genus, which is well known for encoding both antibiotic resistance and synthesis genes. To validate the significance of this keystone species for the loss of ARGs, we enriched phage consortia specific to Streptomyces and tested their effect on ARG abundances on 48 soil samples collected across China. We observed a consistent reduction in ARG abundances across all soils, confirming that Streptomyces-enriched phages could predictably change the soil microbiome resistome and mitigate the prevalence of ARGs. This study highlights that phages can be used as ecosystem engineers to control the spread of antibiotic resistance in the environment.<br><br>CONCLUSION: Our study demonstrates that some bacterial keystone taxa are critical for ARG maintenance and dissemination in soil microbiomes, and opens new ecological avenues for microbiome modification and resistome control. This study advances our understanding of how metagenomics-informed phage consortia can be used to predictably regulate soil microbiome composition and functioning by targeting keystone bacterial taxa. Video Abstract.}, }
@article {pmid40390074, year = {2025}, author = {Kazmi, FA and Mander, &#xdc; and Khanongnuch, R and Öpik, M and Ranniku, R and Soosaar, K and Masta, M and Tenhovirta, SAM and Kasak, K and Ah-Peng, C and Espenberg, M}, title = {Distinct microbial communities drive methane cycling in below- and above-ground compartments of tropical cloud forests growing on peat.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {54}, pmid = {40390074}, issn = {2524-6372}, support = {101096403/ERC_/European Research Council/International ; 101079192//HORIZON EUROPE European Research Council/ ; PRG2032//Eesti Teadusagentuur/ ; PRG1789//Eesti Teadusagentuur/ ; PSG714//Eesti Teadusagentuur/ ; TK232//Estonian Ministry of Education and Research/ ; }, abstract = {Cloud forests are unique yet understudied ecosystems regarding CH4 exchange despite their significance in carbon storage. We investigated CH4 fluxes in peat soil and tree stems of two tropical cloud forests on Réunion Island, one featuring Erica reunionensis and the second a mix of E. reunionensis and Alsophila glaucifolia. The study examined microbiomes across below-ground (soil) and above-ground (canopy soil, leaves, and stems) forest compartments. Metagenomics and qPCR analyses targeted key genes in methanogenesis and methanotrophy in soil and above-ground samples, alongside soil physicochemical measurements. CH4 fluxes from peat soil and tree stems were measured using gas chromatography and portable trace gas analyzers. Peat soil in both forests acted as a CH4 sink (- 23.8 ± 4.84 µg C m[- 2] h[- 1]) and CO2 source (55.5 ± 5.51 µg C m[- 2] h[- 1]), with higher CH4 uptake in sites dominated by endemic tree species E. reunionensis. In forest soils, a high abundance of n-DAMO 16 S rRNA gene (3.42 × 10[7] ± 7 × 10[6] copies/g dw) was associated with nitrate levels and higher rates of CH4 uptake and CO2 emissions. NC-10 bacteria (0.1-0.3%) were detected in only the Erica forest soil, verrucomicrobial methanotrophs (0.1-3.1%) only in the mixed forest soil, whereas alphaproteobacterial methanotrophs (0.1-3.3%) were present in all soils. Tree stems in both forests were weak sinks of CH4 (-0.94 ± 0.4 µg C m[- 2] h[- 1]). The canopy soil hosted verrucomicrobial methanotrophs (0.1-0.3%). The leaves in both forests exhibited metabolic potential for CH4 production, e.g., exhibiting high mcrA copy numbers (3.5 × 10[5] ± 2.3 × 10[5] copies/g dw). However, no CH4-cycling functional genes were detected in the stem core samples. Tropical cloud forest peat soils showed high anaerobic methanotrophy via the n-DAMO process, while aerobic methanotrophs were abundant in canopy soils. Leaves hosted methanotrophs but predominantly methanogens. These results highlight the significant differences between canopy and soil microbiomes in the CH4 cycle, emphasizing the importance of above-ground microbiomes in forest CH4 gas budgets.}, }
@article {pmid40390033, year = {2025}, author = {Teng, T and Huang, F and Xu, M and Li, X and Zhang, L and Yin, B and Cai, Y and Chen, F and Zhang, L and Zhang, J and Geng, A and Chen, C and Yu, X and Sui, J and Zhu, ZJ and Guo, K and Zhang, C and Zhou, X}, title = {Microbiota alterations leading to amino acid deficiency contribute to depression in children and adolescents.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {128}, pmid = {40390033}, issn = {2049-2618}, support = {82301714//the National Natural Science Foundation of China/ ; 22425404//the National Natural Science Foundation of China/ ; 82271565//the National Natural Science Foundation of China/ ; 2023TQ0398//the China Postdoctoral Science Foundation/ ; CSTB2023NSCQ-BHX0106//Natural Science Foundation of Chongqing, China/ ; 2208013341918508//Postdoctoral Innovation Talents Support Program of Chongqing, China/ ; 2022YFC3400702//National Key R&amp;D Program of China/ ; 2024YFC2707800//National Key R&amp;D Program of China/ ; 2022ZD0212900//STI2030-Major Projects/ ; }, mesh = {Humans ; Adolescent ; Child ; *Gastrointestinal Microbiome/physiology ; Male ; *Depressive Disorder, Major/microbiology/metabolism ; Female ; *Amino Acids/deficiency/blood/metabolism ; Magnetic Resonance Imaging ; Animals ; Rats ; Brain/diagnostic imaging/metabolism ; Feces/microbiology ; Metagenomics/methods ; Metabolomics/methods ; *Depression/microbiology ; }, abstract = {BACKGROUND: Major depressive disorder (MDD) in children and adolescents is a growing global public health concern. Metabolic alterations in the microbiota-gut-brain (MGB) axis have been implicated in MDD pathophysiology, but their specific role in pediatric populations remains unclear.<br><br>RESULTS: We conducted a multi-omics study on 256 MDD patients and 307 healthy controls in children and adolescents, integrating plasma metabolomics, fecal metagenomics, and resting-state functional magnetic resonance imaging (rs-fMRI) of the brain. KEGG enrichment analysis of 360 differential expressed metabolites (DEMs) indicated significant plasma amino acid (AA) metabolism deficiencies (p-value&#x2009;<&#x2009;0.0001). We identified 58 MDD-enriched and 46 MDD-depleted strains, as well as 6 altered modules in amino acid metabolism in fecal metagenomics. Procrustes analysis revealed the association between the altered gut microbiome and circulating AA metabolism (p-value&#x2009;=&#x2009;0.001, M[2]&#x2009;=&#x2009;0.932). Causal analyses suggested that plasma AAs might mediate the impact of altered gut microbiota on depressive and anxious symptoms. Additionally, rs-fMRI revealed that connectivity deficits in the frontal lobe are associated with depression and 22 DEMs in AA metabolism. Furthermore, transplantation of fecal microbiota from MDD patients to adolescent rats induced depressive-like behaviors and 14 amino acids deficiency in the prefrontal cortex (PFC). Moreover, the dietary lysine restriction increased depression susceptibility in adolescent rats by reducing the expression of excitatory amino acid transporters in the PFC.<br><br>CONCLUSIONS: Our findings highlight that gut microbiota alterations contribute to AAs deficiency, particularly lysine, which plays a crucial role in MDD pathogenesis in children and adolescents. Targeting AA metabolism may offer novel therapeutic strategies for pediatric depression. Video Abstract.}, }
@article {pmid40389724, year = {2025}, author = {Yang, M and Qi, Y and Gao, P and Li, L and Guo, J and Zhao, Y and Liu, J and Chen, Z and Yu, L}, title = {Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {766}, pmid = {40389724}, issn = {2399-3642}, support = {202449CE340009, 202201AU070043, 202101BA070001-174//Yunnan Provincial Science and Technology Department (Yunnan Department of Science and Technology)/ ; 202501AU070008//Yunnan Provincial Science and Technology Department (Yunnan Department of Science and Technology)/ ; 2025J0753//Yunnan Provincial Department of Education (Department of Education, Yunnan Province)/ ; 2023J0827//Yunnan Provincial Department of Education (Department of Education, Yunnan Province)/ ; }, mesh = {*Endophytes/physiology ; *Plant Diseases/microbiology ; *Amorphophallus/microbiology ; *Microbiota ; *Disease Resistance ; *Adaptation, Physiological ; Stress, Physiological ; *Bacteria ; }, abstract = {Pcc is one of the key pathogenic factors responsible for destructive soft rot in konjac. To date, the assembly and functional adaptation of the plant endophytic microbiome under Pcc stress remain poorly understood. Here, we found that Pcc stress leads to rapid reorganization of the endogenous microbiome in multiple organs of both susceptible and resistant konjac plants. Under Pcc stress, the negative interactions within the bacterial-fungal interdomain network intensified, suggesting an increase in ecological competition between bacterial and fungal taxa. We further discovered that the relative abundance dynamics of the classes Dothideomycetes and Sordariomycetes, as core fungal taxa, changed in response to Pcc stress. By isolating culturable microorganisms, we demonstrated that 46 fungal strains strongly inhibited the growth of Pcc. This implies that endophytic fungal taxa in konjac may protect the host plant through ecological competition or by inhibiting the growth of pathogenic bacteria. Metagenomic analysis demonstrated that microbial communities associated with resistant Amorphophallus muelleri exhibited unique advantages over susceptible Amorphophallus konjac in enhancing environmental adaptability, regulating plant immune signaling, strengthening cell walls, and inducing defense responses. Our work provides important evidence that endophytic fungal taxa play a key role in the host plant's defense against necrotizing bacterial pathogens.}, }
@article {pmid40389632, year = {2025}, author = {Doyle, B and Reynolds, GZM and Dvorak, M and Maghini, DG and Natarajan, A and Bhatt, AS}, title = {Absolute quantification of prokaryotes in the microbiome by 16S rRNA qPCR or ddPCR.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {40389632}, issn = {1750-2799}, support = {R01 AI148623/AI/NIAID NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; T32GM007276//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; D43TW010540//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {Measurements of prokaryotic absolute abundance can provide important insights into human gut microbiome biology and correct misinterpretations of relative abundance data. Despite the existence of several relatively well-established methods for making these measurements, most microbiome studies do not report absolute abundance. To enable researchers equipped with standard molecular biology capabilities to incorporate absolute quantification into their microbiome studies, we present a detailed, step-by-step protocol for rigorous and reproducible quantification of prokaryotic concentration in stool samples. We include methods for measuring stool sample moisture content, quantifying the concentration of the 16S rRNA prokaryotic marker gene by qPCR or digital droplet PCR (ddPCR) and analyzing the resulting data. We also highlight and provide strategies to overcome common pitfalls of the quantification method, such as 16S rRNA gene contamination. The final output of this approach is 16S rRNA copies per wet or dry gram of stool. In cases where samples have matched metagenomic sequencing information, data can be converted into absolute concentration of prokaryotes and taxon-specific absolute concentrations. To enable researchers to choose the appropriate method for their specific applications, we also compare and contrast our qPCR and ddPCR methods. In 4 days, ~80 samples can be taken from frozen stool to absolute concentration by using qPCR or ddPCR without the need for resequencing. Overall, this protocol provides a sensitive and straightforward way to measure the absolute concentration of prokaryotes in human gut microbiome samples stored with or without preservative.}, }
@article {pmid40389466, year = {2025}, author = {Salehi, M and Laitinen, V and Bhanushali, S and Bengtsson-Palme, J and Collignon, P and Beggs, JJ and Pärnänen, K and Lahti, L}, title = {Gender differences in global antimicrobial resistance.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {79}, pmid = {40389466}, issn = {2055-5008}, support = {952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 952914//European Union's Horizon 2020 research and innovation programme/ ; 330887//Research Council of Finland,Finland/ ; 330887//Research Council of Finland,Finland/ ; 348439//Research Council of Finland,Finland/ ; 330887//Research Council of Finland,Finland/ ; 20220114//Alhopuro Foundation/ ; 20220114//Alhopuro Foundation/ ; 2019-00299//Swedish Research Council/ ; FFL21-0174//Swedish Foundation for Strategic Research/ ; KAW 2020.0239//Data-Driven Life Science/ ; }, mesh = {Humans ; Female ; Male ; Sex Factors ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Gastrointestinal Microbiome/genetics ; Adult ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Global Health ; Middle Aged ; }, abstract = {Antimicrobial resistance is one of the leading causes of mortality globally. However, little is known about the distribution of antibiotic resistance genes (ARGs) in human gut metagenomes, collectively referred to as the resistome, across socio-demographic gradients. In particular, limited evidence exists on gender-based differences. We investigated how the resistomes differ between women and men in a global dataset of 14,641 publicly available human gut metagenomes encompassing countries with widely variable economic statuses. We observed a 9% higher total ARG load in women than in men in high-income countries. However, in low- and middle-income countries, the difference between genders was reversed in univariate models, but not significant after adjusting for covariates. Interestingly, the differences in ARG load between genders emerged in adulthood, suggesting resistomes differentiate between genders after childhood. Collectively, our data-driven analyses shed light on global, gendered antibiotic resistance patterns, which may help guide further research and targeted interventions.}, }
@article {pmid40389207, year = {2025}, author = {Echeveste Medrano, MJ and Lee, S and de Graaf, R and Holohan, BC and Sánchez-Andrea, I and Jetten, MSM and Welte, CU}, title = {Physiological Stress Response to Sulfide Exposure of Freshwater Anaerobic Methanotrophic Archaea.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12489}, pmid = {40389207}, issn = {1520-5851}, abstract = {Freshwater wetlands and coastal sediments are becoming hotspots for the emission of the greenhouse gas methane. Eutrophication-induced deposition of organic matter leads to elevated methanogenesis and sulfate reduction, thereby increasing the concentrations of methane and toxic sulfide, respectively. However, the effects of sulfide stress on the anaerobic methanotrophic biofilter have not been well explored. Here, we show how an enrichment culture dominated by the freshwater anaerobic methane-oxidizing archaeon "Candidatus (Ca.) Methanoperedens" responds to short-term and long-term exposure to sulfide in a bioreactor. The methane-oxidizing activity decreased to 45% and 20% but partially recovered to 70% and 30% within 5 days after short- and long-term sulfide exposure, respectively. Metagenomics indicated that "Ca. Methanoperedens" remained dominant in the enrichment throughout the entire experiment. The first short-term sulfide pulse led to increased expression of genes encoding for sulfide detoxification by low abundant community members, whereas long-term exposure resulted in upregulation of "Ca. Methanoperedens" genes encoding sulfite reductases of group III (Dsr-LP). "Ca. Methanoperedens" consumed polyhydroxyalkanoates during long-term sulfide exposure, possibly to aid in stress adaptation. Together, these results provide a valuable baseline for understanding fundamental ecophysiological adaptations to methane cycling in sulfate- and nitrate-rich aquatic ecosystems.}, }
@article {pmid40389018, year = {2025}, author = {Leekitcharoenphon, P and Bortolaia, V and Tornblom, VKW and Siriphap, A and Suthienkul, O and Borthong, J and Chonsin, K and Møller, FD and Avot, B and Otani, S and Aarestrup, FM}, title = {Effect of large-scale population-based dietary change to vegetarianism on antimicrobial resistance and bacterial composition of sewage in Thailand.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105765}, doi = {10.1016/j.meegid.2025.105765}, pmid = {40389018}, issn = {1567-7257}, abstract = {Antimicrobial resistance (AMR) is on one of the global priority challenges. This study explored the impact of diet alteration on AMR bacteria through metagenomic analysis during the annual vegetarian festival in Thailand in October 2019. The study investigated the effects of a 10-day shift from a regular to a vegetarian diet by collecting urban sewage from Nakhon Sawan, Surat Thani, and Bangkok before, during, and after the festival. Additionally, faecal samples from individuals in the northern city were analyzed. Using shotgun metagenomic sequencing, the samples were mapped against bacterial, AMR genes, and carbohydrate-active enzymes databases. The results revealed significant changes in AMR gene abundance and increased carbohydrate metabolism genes in sewage samples from all three cities during the festival. There was also a notable shift in the composition and diversity of bacterial species, particularly in the northern city. The total abundance of AMR genes increased during the vegetarian festival across all locations. This study highlights the correlation between a population's vegetarian diet and increased AMR in Thailand. It also demonstrates that metagenomic analysis of sewage can effectively assess the impact of dietary changes on bacterial communities and AMR at a population level, providing valuable insights for public health strategies.}, }
@article {pmid40388929, year = {2025}, author = {Dong, X and Xie, C and Zhang, Z and Ye, H and Liu, R and Chen, W and Kong, YZ and Yang, X}, title = {Diagnostic challenges in peritoneal dialysis-associated peritonitis with atypical and rare pathogens: A new era of metagenomic next-generation sequencing precision diagnosis.}, journal = {Peritoneal dialysis international : journal of the International Society for Peritoneal Dialysis}, volume = {}, number = {}, pages = {8968608251333879}, doi = {10.1177/08968608251333879}, pmid = {40388929}, issn = {1718-4304}, abstract = {Peritonitis caused by atypical and rare pathogens is challenging to diagnose. Although the International Society for Peritoneal Dialysis (ISPD) guidelines significantly improve the diagnostic rate by placing peritoneal dialysis fluid into blood culture bottles, peritonitis caused by atypical pathogens, such as tuberculosis and fungi, is difficult to diagnose due to challenges in culturing these organisms using traditional methods, leading to high mortality. Metagenomic next-generation sequencing (mNGS) technology has been widely used as an accurate diagnostic technique for infectious diseases. First used in identifying and quantifying environmental micro-organisms, mNGS technology can identify rare, novel, difficult-to-detect and mixed pathogens directly from clinical samples, and has potential in predicting antibiotic resistance. This paper summarizes the application of mNGS in atypical and rare pathogens peritonitis clinical cases in recent years, and provides reference for the diagnosis of peritonitis in combination with new ISPD guidelines and diagnostic techniques. The development and principles of mNGS technology, diagnostic efficiency in peritonitis, challenges in diagnosis of atypical and rare pathogen-associated peritonitis, and application of mNGS technology are discussed in detail. The development of mNGS technology provides clinicians with powerful tools to more accurately identify and treat peritonitis. Future research needs to focus on reducing costs, improving test accessibility, and developing new bioinformatics tools to better integrate mNGS results into clinical practice.}, }
@article {pmid40388761, year = {2025}, author = {Liu, Q and Li, Q and Liu, B and Fu, T}, title = {Pulmonary nocardiosis with hilar mass misdiagnosed as lung cancer: A case report.}, journal = {Medicine}, volume = {104}, number = {20}, pages = {e42524}, doi = {10.1097/MD.0000000000042524}, pmid = {40388761}, issn = {1536-5964}, mesh = {Humans ; Female ; *Nocardia Infections/diagnosis/drug therapy/diagnostic imaging ; Middle Aged ; *Diagnostic Errors ; *Lung Neoplasms/diagnosis ; Tomography, X-Ray Computed/methods ; Diagnosis, Differential ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Nocardia/isolation &amp; purification ; Lung/diagnostic imaging/pathology ; *Lung Diseases/diagnosis ; }, abstract = {RATIONALE: Pulmonary nocardiosis (PN) is an opportunistic infectious disease caused by Nocardia of the lungs, which lacks specificity in clinical symptoms and imaging, is rare in individuals with normal immune function, and is highly prone to clinical misdiagnosis and missed diagnosis.<br><br>PATIENT CONCERNS: A 55-year-old woman with normal immune function was admitted to the hospital due to a cough and expectoration for more than 20 days.<br><br>DIAGNOSES: Chest computed tomography revealed a mass in the left hilum and obstructive atelectasis in the lingular segment of the left upper lobe. Initially suspected to be a malignant tumor, bronchoscopy with pathological examination suggested inflammation. Finally, metagenomic next-generation sequencing of pathological tissue confirmed PN.<br><br>INTERVENTIONS: After discharge, the patient regularly took trimethoprim-sulfamethoxazole for anti-infective treatment.<br><br>OUTCOMES: Regular follow-ups with the patient revealed that subsequent chest computed tomography scans showed a gradual reduction in the extent of the lesions, and the patient demonstrated a good clinical response and radiological improvement.<br><br>LESSONS: This case highlights the diagnostic complexity of PN. The radiological manifestations are diverse, commonly including pulmonary consolidation, nodules, and cavities, making it difficult to differentiate from other diseases. Clinicians need to be vigilant and find appropriate testing methods to improve the diagnostic rate of PN.}, }
@article {pmid40388614, year = {2025}, author = {Peek, J and Bhattacharjee, A and Burian, J and Hsieh, DC and Hernandez, Y and Ternei, M and Panfil, C and Brady, SF}, title = {Environmental resistome-guided development of resistance-tolerant antibiotics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {21}, pages = {e2504781122}, doi = {10.1073/pnas.2504781122}, pmid = {40388614}, issn = {1091-6490}, support = {5R35GM122559//HHS | NIH (NIH)/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology/chemistry ; *Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; Metagenome ; Bacteria/drug effects/genetics ; }, abstract = {Failure to anticipate new forms of antibiotic resistance has led to resistance developing rapidly to virtually all antibiotics that have entered clinical use. Many of the most problematic types of resistance originated in the environment, where ancient arms races between antibiotic-producing microbes and their competitors have created vast arsenals of antibiotics and resistance. Seizing on the knowledge that resistance in nature is frequently a harbinger of future clinical resistance, we propose introducing an additional step into the antibiotic development process that exploits the susceptibility of development candidates to environmental resistance as a metric for prioritizing lead compounds and as a roadmap for their structural optimization. Using the antibiotic albicidin as a model, we show how the environmental resistome can guide the development of more resistance-tolerant leads. We used metagenomic surveys to identify resistance vulnerabilities for albicidin and guide the synthesis of analogs that evade the resistance threats. We found that natural albicidin analogs (congeners) were especially enriched in structural features that escape resistance, which inspired our syntheses and provided compelling evidence for the evolution of families of antibiotics in response to resistance in nature. The coupling of metagenomics-based resistance surveillance with structural optimizations of new antibiotics is a broadly applicable approach that is easily integrated into antibiotic development programs to generate compounds that are more resilient in the face of resistance.}, }
@article {pmid40388589, year = {2025}, author = {Lei, Z and Wang, H and Zhang, H and Liu, W and He, Z and Wang, Z and Zhang, H and Wang, Y and Tang, Y and Hu, C and Zhao, X}, title = {Sultr1;2-Mediated Recruitment of Selenium-Oxidizing Bacteria Promotes Plant Selenium Uptake.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c01540}, pmid = {40388589}, issn = {1520-5118}, abstract = {Plants can shape their root microbiome to promote growth and selenium uptake. Here, we used metagenomics, 16S high-throughput sequencing, and liquid chromatography-mass spectrometry (LC-MS) metabolomics assays to investigate the role of Sultr1;2, which is the major selenium transporter gene, in recruiting microbial communities to regulate soil selenium bioavailability and plant selenium uptake. Results shows that the overexpression of Sultr1;2 in tomato significantly enriched Methylobacterium genus. The isolated strains of Methylobacterium possess multiple plant-growth-promoting functions and selenium oxidation capability and inoculation with these strains increases soil selenium availability. The upregulated metabolites of Sultr1;2-overexpressing tomato were significantly enriched in the arginine and proline metabolism pathway. The key upregulated metabolites significantly improved the growth rate and selenium-oxidizing ability of Methylobacterium strains, and the combined addition of key upregulated metabolites and synthetic microbial community significantly increased soil selenium bioavailability and plant selenium uptake. This study provides insights into leveraging plant genetic engineering to identify key functional microbial communities for sustainable selenium-rich agricultural development.}, }
@article {pmid40388544, year = {2025}, author = {Kohnert, E and Kreutz, C}, title = {Benchmarking Differential Abundance Tests for 16S microbiome sequencing data using simulated data based on experimental templates.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0321452}, doi = {10.1371/journal.pone.0321452}, pmid = {40388544}, issn = {1932-6203}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Benchmarking ; Computer Simulation ; Humans ; *Metagenomics/methods ; Computational Biology/methods ; }, abstract = {Differential abundance (DA) analysis of metagenomic microbiome data is essential for understanding microbial community dynamics across various environments and hosts. Identifying microorganisms that differ significantly in abundance between conditions (e.g., health vs. disease) is crucial for insights into environmental adaptations, disease development, and host health. However, the statistical interpretation of microbiome data is challenged by inherent sparsity and compositional nature, necessitating tailored DA methods. This benchmarking study aims to simulate synthetic 16S microbiome data using metaSPARSim (Patuzzi I, Baruzzo G, Losasso C, Ricci A, Di Camillo B. MetaSPARSim: a 16S rRNA gene sequencing count data simulator. BMC Bioinformatics. 2019;20:416. https://doi.org/10.1186/s12859-019-2882-6 PMID: 31757204) MIDASim (He M, Zhao N, Satten GA. MIDASim: a fast and simple simulator for realistic microbiome data. Available from: https://doi.org/10.1101/2023.03.23.533996), and sparseDOSSA2 (Ma S, Ren B, Mallick H, Moon YS, Schwager E, Maharjan S, et al. A statistical model for describing and simulating microbial community profiles. PLOS Comput Biol. 2021;17(9):e1008913. https://doi.org/10.1371/journal.pcbi.1008913 PMID: 34516542) , leveraging 38 real-world experimental templates (S3 Table) previously utilized in a benchmark study comparing DA tools. These datasets, drawn from diverse environments such as human gut, soil, and marine habitats, serve as the foundation for our simulation efforts. We employ the same 14 DA tests that were previously used with the same experimental data in benchmark studies alongside 8 DA tests that were developed subsequently. Initially, we will generate synthetic data closely mirroring the experimental datasets, incorporating a known truth to cover a broad range of real-world data characteristics. This approach allows us to assess the ability of DA methods to recover known true differential abundances. We will further simulate datasets by altering sparsity, effect size, and sample size, thus creating a comprehensive collection for applying the 22 DA tests. The outcomes, focusing on sensitivities and specificities, will provide insights into the performance of DA tests and their dependencies on sparsity, effect size, and sample size. Additionally, we will calculate data characteristics (S1 and S2 Table) for each simulated dataset and use a multiple regression to identify informative data characteristics influencing test performance. Our prior study, where we used simulated data without incorporating a known truth, demonstrated the feasibility of using synthetic data to validate experimental findings. This current study aims to enhance our understanding by systematically evaluating the impact of known truth incorporation on DA test performance, thereby providing further information for the selection and application of DA methods in microbiome research.}, }
@article {pmid40388308, year = {2025}, author = {Wang, S and Kong, F and Dai, D and Li, C and Hao, Y and Wang, E and Cao, Z and Wang, Y and Wang, W and Li, S}, title = {Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf042}, pmid = {40388308}, issn = {2047-217X}, support = {2022YFD1301400//National Key Research and Development Program/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Female ; *Peripartum Period/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Pregnancy ; }, abstract = {BACKGROUND: Metabolic disorders in peripartum ruminants affect health and productivity, with gut microbiota playing a key role in host metabolism. Therefore, our study aimed to characterize the gut microbiota of peripartum dairy cows to better understand the relationship between metabolic phenotypes and the rumen and fecal microbiomes during the peripartum period.<br><br>RESULTS: In a longitudinal study of 91 peripartum cows, we analyzed rumen and fecal microbiomes via 16S rRNA and metagenomic sequencing across six time points. By using enterotype classification, ecological model, and random forest analysis, we identified distinct deterministic succession patterns in the rumen and fecal microbiomes (rumen: rapid transition-transition-stable; hindgut: stable-transition-stable). Key microbes, such as Succiniclasticum and Bifidobacterium, were found to drive microbial succession by balancing stochastic and deterministic processes. Notably, we observed that changes in gut microbiota succession patterns significantly influenced metabolic phenotypes (e.g., serum non-esterified fatty acid, glucose, and insulin levels). Mediation analysis suggested that specific gut microbes (e.g., Prevotella sp900315525 in the rumen and Alistipes sp015059845 in the hindgut) and metabolic pathways (e.g., glucose-related pathway) were associated with host metabolic phenotypes.<br><br>CONCLUSIONS: Overall, utilizing a large gut microbiome dataset and enterotype- and ecological model-based microbiome analyses, we comprehensively elucidated the succession and assembly of the gut microbiota in peripartum dairy cows. We further confirmed that changes in gut microbiota succession patterns were significantly related to the metabolic phenotypes of peripartum dairy cows. These findings provide valuable insights for developing health management strategies for peripartum ruminants.}, }
@article {pmid40387602, year = {2025}, author = {Bonacolta, AM and Krause-Massaguer, J and Unuma, T and Del Campo, J}, title = {The Sea Cucumber-Infecting Parasite Apostichocystis gudetama gen. nov. sp. nov. Expands Marine-Host-Specific Clade of Apicomplexans.}, journal = {The Journal of eukaryotic microbiology}, volume = {72}, number = {3}, pages = {e70013}, doi = {10.1111/jeu.70013}, pmid = {40387602}, issn = {1550-7408}, support = {//University of Miami/ ; PID2020-118836GA-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 2021 SGR 00420//Departament de Recerca i Universitats de la Generalitat de Catalunya/ ; }, mesh = {Animals ; Phylogeny ; *Sea Cucumbers/parasitology ; *Apicomplexa/genetics/classification/isolation &amp; purification ; Host Specificity ; Female ; Host-Parasite Interactions ; Genome, Mitochondrial ; }, abstract = {Unknown ellipsoid bodies, later classified as apicomplexan cysts, are prevalent in the ovaries of Japanese sea cucumbers (Apostichopus japonicus), where they can lead to lower fecundity in infected individuals and adverse effects on wild populations as well as aquaculture efforts for this endangered species. Apicomplexans are widespread and essential to marine environments, where they can affect the health and fitness of host populations. We performed genomic sequencing of recovered cysts to gain more ecological and evolutionary information on this parasite. We recovered this apicomplexan's complete nuclear ribosomal RNA (rrn) operon, the entire mitochondrial genome, and a partial apicoplast (relic chloroplast) genome. The rrn operon phylogeny revealed this parasite as being closely related to coccidian-like parasites of marine fish (ichthyocolids) and cnidarians (corallicolids), while organelle phylogenomics hint at a closer relation to the protococcidian Eleutheroschizon. Using this new phylogenetic context and previous morphological descriptions, we describe this parasite as Apostichocystis gudetama gen. nov. sp. nov. Mining available microbiomes reveal the presence of Apostichocystis spp. beyond its host range, alluding to other potential hosts or cryptic, closely related lineages. Its phylogenetic placement has important implications concerning the evolution of parasitism within Apicomplexa and the divergence of a marine-host-specific clade of coccidian-like parasites.}, }
@article {pmid40387408, year = {2025}, author = {Rahimlou, S and Amend, AS and James, TY}, title = {Malassezia in environmental studies is derived from human inputs.}, journal = {mBio}, volume = {}, number = {}, pages = {e0114225}, doi = {10.1128/mbio.01142-25}, pmid = {40387408}, issn = {2150-7511}, abstract = {UNLABELLED: The fungus Malassezia is the most prevalent member of the human skin mycobiota, known for its lipid dependence and inability to synthesize long-chain fatty acids. Malassezia exhibits remarkable niche breadth, inhabiting soils, dust, as well as various marine environments from polar regions to deep-sea vents. The consistent presence of Malassezia in marine habitats, including those associated with marine animals, suggests that the fungus is able to grow and play a fundamental role in marine ecosystems. In this study, we explored metagenomic sequences from the Sequence Read Archive database to investigate the presence, distribution, and origins of Malassezia species within marine ecosystems, with the goal of assembling Malassezia genomes. Using various search methods, we found that up to 10% of the shotgun and amplicon data sets analyzed contained Malassezia sequences. However, the relative abundance of Malassezia in each data set was low, and there was a strong correlation between human and Malassezia sequences in marine environments, consistent with contamination. From the most Malassezia-rich data sets, we attempted to generate metagenome-assembled genomes. However, Malassezia contigs together showed low genome completeness levels, with a maximum of 2.2% in a sample. Phylogenetic analysis identified the contigs as closely related to human-associated Malassezia globosa and Malassezia restricta, along with Malassezia sympodialis and Malassezia pachydermatis, which were the most prevalent species across all studied environments. Our data suggest that many observations of Malassezia in the environment are derived from human sources and that widespread contamination confounds the exploration of Malassezia diversity and ecological role in the marine environment.<br><br>IMPORTANCE: Malassezia is the singular fungus most associated with humans. It colonizes mammalian skin and requires host-derived fatty acids to grow. Widespread sequencing of environmental DNA surprisingly showed that Malassezia is also ubiquitous outside of mammalian hosts. Malassezia is frequently found in marine habitats where it is associated with corals, deep sea vents, diatoms, and more. Given its widespread presence, we reasoned that public metagenomic data could be used to assemble a genome sequence of an uncultured marine Malassezia. However, we found that Malassezia was ubiquitous but never abundant in marine samples and that the few metagenomes we could assemble were consistent with recent human introduction. We also found that the presence of human DNA in sequencing data sets is strongly correlated with the presence of Malassezia DNA, and while not ruling out the growth and survival of Malassezia in marine habitats, they suggest widespread contamination of public data with Malassezia.}, }
@article {pmid40387372, year = {2025}, author = {Lei, Z and Zhang, H and Liu, W and Sheng, J and Zhang, H and Wang, Y and Tang, Y and Wang, H and Ding, C and Qiao, W and Zhu, Y and Yang, G and Zhang, Y and Liu, Z and Zhou, N and Hu, C and Zhao, X}, title = {Dynamic and Stable Core Microbiota Assist Plants in Enriching Selenium and Reducing Cadmium Absorption.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e00862}, doi = {10.1002/advs.202500862}, pmid = {40387372}, issn = {2198-3844}, support = {2023YFD1900904//National Key Research and Development Program of China/ ; SKLEG2024225//State Key Laboratory of Environmental Geochemical/ ; 23567601H//State Key Laboratory of North China Crop Improvement and Regulation, S&amp;T Program of Hebei/ ; 24XJTRZW13//Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; WY22B04//Wuhan Municipal Health Commission/ ; Grants KJ2025-5//2025 Science and Technology Project of Hubei Geological Bureau/ ; Grants 2023AFD215//Hubei Provincial Natural Science Foundation and Hubei Geological Bureau of China/ ; D20234501//Science and Technology Research Project of Hubei Province/ ; 23xjz05R//Hubei Polytechnic University/ ; }, abstract = {Rhizosphere microbiome is crucial for regulating rhizosphere complex nutrient dynamics. However, mechanisms by which plants regulate rhizosphere microbes to manage nutrient availability under coexisting beneficial and harmful elements remain unclear. This study focuses on the rhizosphere microbiome of Brassica napus in different naturally selenium (Se)-cadmium (Cd)-rich soils, the functionality of this rhizosphere, and the changes in the availability of rhizosphere nutrients. Microbiome analysis, metagenomics, genomic analysis, strain isolation, and functional validation are performed to investigate these relationships. Results show that a significant negative correlation is observed between the rhizosphere available Se and Cd content across the plant whole growth cycle and identified a group of core microbiota that are highly positively correlated with available Se and negatively correlated with available Cd. Genomics and metagenomics analyses reveal that the core microbiota has a higher substrate preference for amino acids related to the glutathione metabolic pathway. Key glutathione-related-amino acids and synthetic microbial community significantly improve the expression of glutathione anabolism and related amino acid transport genes and enhance Se uptake and reduce Cd absorption in plants grown in various Se-Cd-rich soils. This study provides insights into the mechanisms of root-associated microbes responding to complex soil nutrients during plant growth.}, }
@article {pmid40387216, year = {2025}, author = {Steriade, C and Thomas, SC and Xu, F and Ahituv, A and Hanin, A and Pleshkevich, M and Hwang, S and Ramirez, A and Foreman, B and Yoo, J and Eka, O and Kellogg, M and Oliger, A and Wainwright, MS and Morales, M and Gaspard, N and Hirsch, LJ and Devinsky, O and Saxena, D}, title = {Patients with status epilepticus and new-onset refractory status epilepticus display drastically altered fecal microbiomes compared to chronic epilepsy patients.}, journal = {Epilepsia}, volume = {}, number = {}, pages = {}, doi = {10.1111/epi.18450}, pmid = {40387216}, issn = {1528-1167}, support = {//NORSE Institute, the Daniel Raymond Wong Memorial Research Fund and CCEMRC/ ; //Parekh Center for Interdiscplinary Neurology/ ; //National Organization for Rare Disorders and American Epilepsy Society/ ; }, abstract = {OBJECTIVE: New-onset refractory status epilepticus (NORSE) occurs in people without pre-existing epilepsy or a rapidly identified structural, toxic, metabolic, or other cause. NORSE is a rare disorder with high morbidity and mortality rates and limited evidence for effective therapies. We aimed to assess whether the gut microbiome of NORSE and status epilepticus (SE) differs from that of chronic epilepsy, whether NORSE differs from SE at different disease time points, and to examine the correlations between specific gut microbiota and cytokines in NORSE and SE.<br><br>METHODS: This longitudinal cohort study observed patients with NORSE (n&#x2009;=&#x2009;15), SE (n&#x2009;=&#x2009;17), and chronic epilepsy who were not in SE (n&#x2009;=&#x2009;12). NORSE patients were recruited through the NORSE Consortium. Patients with NORSE and SE underwent longitudinal serial biospecimen collection. Fecal samples were subjected to whole-community shotgun metagenomics to characterize microbiome features. Cohorts were evaluated for prokaryotic, eukaryotic, and functional diversity. Correlations between blood inflammatory cytokine levels and microbiome features and covariate analysis with critical illness and clinical treatments were examined for NORSE and SE patients during and after SE resolution.<br><br>RESULTS: During SE, NORSE and SE patients had significantly different prokaryotic, eukaryotic, and functional microbiome levels compared to chronic epilepsy patients without SE. Limited microbiome differences were observed within and between NORSE and SE, although these groups displayed differing correlation patterns between microbial species and cytokines. Patients who later died or were tube-fed harbored significantly different microbiomes than those who survived or were orally fed.<br><br>SIGNIFICANCE: NORSE and SE patients present with a more variable and dramatically different fecal microbiome than chronic epilepsy patients, which may indicate gut dysbiosis that may be reciprocally linked to inflammatory responses. Although NORSE and SE patients had similar microbiome structures, fungal and bacterial correlates with inflammatory cytokines differed between NORSE and SE, with confounding factors influencing microbiome structure. Our data suggest a microbiome-specific response to NORSE and SE, with implications for future treatment strategies.}, }
@article {pmid40386988, year = {2025}, author = {Lin, Y and Shi, X and Mu, J and Ren, H and Jiang, X and Zhu, L and Cai, X and Lian, C and Pei, Z and Zhang, Y and Wang, C and Hou, G and Lin, L and Nie, C and Song, C and Gao, S and Zhao, L and Wang, J and Jiang, X and Wang, J and Guo, Y}, title = {Uncovering stage-specific neural and molecular progression in Alzheimer's disease: Implications for early screening.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {21}, number = {5}, pages = {e70182}, doi = {10.1002/alz.70182}, pmid = {40386988}, issn = {1552-5279}, support = {2022ZD0211600//the Ministry of Science and Technology of China/ ; 2023YFC3603300//National Key R&amp;D Program of China/ ; 82371471//Natural Science Foundation of China/ ; 2024YB59//Research Program of Central Health Commission/ ; JCYJ20240813103817024//Special Foundation for Shenzhen Basic Research Program/ ; }, mesh = {Humans ; *Alzheimer Disease/diagnosis/physiopathology/metabolism/diagnostic imaging ; Disease Progression ; Male ; Female ; *Cognitive Dysfunction/diagnosis/physiopathology ; Aged ; Early Diagnosis ; Magnetic Resonance Imaging ; Electroencephalography ; Metabolomics ; Brain/diagnostic imaging/physiopathology ; Machine Learning ; Biomarkers ; Aged, 80 and over ; }, abstract = {INTRODUCTION: Understanding molecular, neuroanatomical, and neurophysiological changes in cognitive decline is crucial for comprehending Alzheimer's disease (AD) progression and facilitating objective staging and early screening.<br><br>METHODS: We enrolled 277 participants and employed a multimodal approach, integrating genomics, metagenomics, metabolomics, magnetic resonance imaging (MRI), and electroencephalogram (EEG) to investigate the AD continuum, from subjective cognitive decline (SCD) through mild cognitive impairment (MCI) to advanced AD.<br><br>RESULTS: Key markers and mechanisms were identified for each stage: initial neurophysiological deficits in SCD with compensatory metabolomic responses, gut-brain axis dysregulation in MCI, and extensive metabolic disruption and multisystem breakdown in AD. Using random forest models, we identified specific feature combinations that achieved predictive areas under the curve (AUCs) of 0.78 for SCD, 0.84 for MCI, and 0.98 for AD, highlighting EEG as a particularly effective early screening tool.<br><br>DISCUSSION: This study elucidates AD's pathophysiological progression and highlights the potential of machine learning-assisted multimodal strategies for early detection and staging.<br><br>HIGHLIGHTS: Early electroencephalogram (EEG) changes and compensatory metabolomic responses define subjective cognitive decline (SCD) stage. In mild cognitive impairment (MCI), gut-brain axis dysfunction alters microbial diversity and functional pathways. In Alzheimer's disease (AD), systemic breakdown disruption enables near-perfect machine learning (ML) detection. Random forest models yield predictive areas under the curve (AUCs) of 0.78 (SCD), 0.84 (MCI), 0.98 (AD). EEG is a convenient, cost-efficient marker for early screening.}, }
@article {pmid40385501, year = {2025}, author = {George, UE and De Coninck, L and George, OA and Adeyanju, T and Oragwa, A and Kamani, J and Igbokwe, J and Adamu, A and Faleye, T and Adeleke, R and Adesoji, T and Soh, TK and Sowemimo, O and Eromon, P and Adewumi, OM and Adeniji, JA and Folarin, O and Weaver, SC and Happi, A and Bosse, JB and Cross, RW and Komolafe, I and Matthijnssens, J and Happi, C}, title = {Identification and Genomic Characterization of Known and Novel Highly Divergent Sapoviruses in Frugivorous and Insectivorous Bats in Nigeria.}, journal = {EMI. Animal &amp; environment}, volume = {}, number = {}, pages = {1-37}, pmid = {40385501}, issn = {2998-6990}, abstract = {Sapovirus (SaV) infections have been linked with moderate-to-severe acute gastroenteritis (AGE) in animals and humans and represent a significant risk to public health. SaVs from animals including pigs, chimpanzees, and rodents have been reported to be closely related with human SaVs, indicating the possibility of cross-species transmission. Divergent SaVs have been reported in various bat species across various continents including Asia, Europe, Oceania and Africa. However, little is known about the evolutionary history of SaVs across various bat species and their zoonotic potential. In this report, we describe the findings of a surveillance study across various bat species in Nigeria. Samples were pooled and subjected to metagenomics sequencing and analyses. Nine of 57 sample pools (containing 223 rectal swabs from five bat species) had SaV reads from which we assembled a total of four complete and three near-complete (having complete coding sequences) genomes. The bat SaV (BtSaV) strains from this study formed five distinct lineages of which four represented novel genogroups. BtSaV lineages clustered mainly according to bat families, which might suggest a likely virus-host-specific evolution. The BtSaV VP1 capsid protein structure prediction confirmed three main domains (S, P1, and P2) as reported for Human SaV (HuSaV). We found that the P2 subdomain of the VP1 protein contains a degree of homology to known immunoreactive epitopes suggesting these conserved regions may be valuable for diagnostics or medical countermeasure development. This study expands our understanding of reservoir hosts, provides information on the genetic diversity and continuous evolution of SaVs in bats.}, }
@article {pmid40385308, year = {2025}, author = {Geonczy, SE and Ter Horst, AM and Emerson, JB}, title = {Soil viral communities shifted significantly after wildfire in chaparral and woodland habitats.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf073}, pmid = {40385308}, issn = {2730-6151}, abstract = {Increased wildfire activity warrants more research into fire-driven biotic changes in soil, including soil viral communities, given the roles of soil microbes in organic matter decomposition, nutrient cycling, and post-fire recovery. Leveraging viral size-fraction metagenomes (viromes), here we studied viral community responses to wildfire in woodland and chaparral soils at five timepoints over 1 year following the California LNU Complex wildfire. We also compared post-fire samples to unburned controls at the final three timepoints and leveraged published viromes from the same sites nine months before the fire as pre-burn controls. Viral community composition differed significantly in burned samples compared to controls from both habitats, as did soil chemistry and prokaryotic communities (16S rRNA gene amplicons). Viromic DNA yields (a proxy for viral particle abundances) indicated initial viral biomass reductions due to the fire, but a return to baseline abundances (indistinguishable from controls) within five months. Fire-associated habitat filtering was further indicated by a comparison to the PIGEON viral "species" (viral operational taxonomic unit (vOTU)) reference database, with vOTUs from a burned conifer forest representing 19%-31% of PIGEON vOTUs detected in the burned habitats but only 0.6%-6% in controls. Together, these results indicate significant changes in soil viral communities due to wildfire, attributable at least in part to concomitant changes in their prokaryotic host communities and soil physicochemistry.}, }
@article {pmid40384975, year = {2025}, author = {Que, T and Li, W and Zhang, Z and He, Y and He, K and Qiu, H and Huang, J and Lu, Z and Jiang, C and Huang, Y and Huang, H and Wu, Q and Chen, P and Hu, Y and Liu, W}, title = {HPD-Kit: a comprehensive toolkit for pathogen detection and analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1580165}, pmid = {40384975}, issn = {2235-2988}, mesh = {Humans ; *Computational Biology/methods ; *Metagenomics/methods ; *Software ; Animals ; *Communicable Diseases/diagnosis/microbiology ; }, abstract = {INTRODUCTION: Unbiased metagenomic sequencing (mNGS) is crucial for infectious disease diagnosis and epidemiological surveillance. However, its analysis requires specialized bioinformatics skills, creating barriers for clinicians. We developed HPD-Kit (Henbio Pathogen Detection Toolkit) with an integrated pathogen database to simplify pathogen detection and analysis for both human and animal pathogens.<br><br>METHODS: HPD-Kit includes a specifically curated pathogen database and optimized bioinformatics pipeline. We evaluated its performance using simulated datasets at varying pathogen abundances and clinical samples. The toolkit provides both open-source software and a web interface for streamlined one-click analysis.<br><br>RESULTS: Validation with simulated data showed HPD-Kit maintains high detection accuracy even at low pathogen abundance. Clinical dataset analysis demonstrated superior pathogen identification compared to conventional methods. The web interface retained this performance while significantly improving usability.<br><br>DISCUSSION: HPD-Kit effectively addresses the bioinformatics barrier in mNGS analysis while maintaining high accuracy. Its dual open-source and web-based implementation facilitates clinical and public health applications, promoting wider adoption of mNGS technology in diagnostic settings.}, }
@article {pmid40384881, year = {2025}, author = {Oehler, JB and Burns, K and Warner, J and Schmitz, U}, title = {Long-Read Sequencing for the Rapid Response to Infectious Diseases Outbreaks.}, journal = {Current clinical microbiology reports}, volume = {12}, number = {1}, pages = {10}, pmid = {40384881}, issn = {2196-5471}, abstract = {PURPOSE OF REVIEW: Long-read sequencing (LRS) has revolutionized pathogen surveillance by enabling real-time, high-fidelity genomic analysis critical for outbreak response. This review synthesizes recent breakthroughs in LRS, evaluating its impact on genomic epidemiology, metagenomics, and public health decision-making while addressing limitations and prospects for integrating LRS into global outbreak surveillance.<br><br>RECENT FINDINGS: Unlike short-read sequencing, LRS-pioneered by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio)-resolves complex genomic structures, antimicrobial resistance determinants, and transmission dynamics with unprecedented accuracy. The portability of some LRS devices has facilitated rapid pathogen identification in field settings, notably during the Ebola and COVID-19 pandemics. Despite advancements in basecalling algorithms and target enrichment, challenges including sequencing errors, computational bottlenecks, and cost barriers remain.<br><br>SUMMARY: By critically evaluating recent findings and discussing future directions, this review highlights the importance of leveraging LRS for outbreak preparedness and response, equipping researchers and public health professionals with the knowledge necessary to navigate the complexities of modern infectious disease challenges.}, }
@article {pmid40384801, year = {2025}, author = {Deng, C and Hong, L and Sun, D and Miao, H and Tang, F and Li, Z and Liu, X}, title = {Diagnosis of Mycoplasma Hominis Peritonitis in a CAPD Patient with Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {2469-2473}, pmid = {40384801}, issn = {1178-6973}, abstract = {BACKGROUND: Mycoplasma hominis (Mh) is a conditional pathogenic microorganism in humans, typically colonizing the genitourinary tract of adults and causing infections in this system. However, Mh is rarely reported as a causative agent of peritoneal dialysis (PD)-associated peritonitis.<br><br>CASE PRESENTATION: A 46-year-old woman undergoing maintenance PD presented with abdominal pain and cloudy PD effluent. Her PD modality is continuous ambulatory peritoneal dialysis (CAPD). Cultures of the PD effluent and blood were negative, and empirical antibiotic therapy was ineffective, leading to a diagnosis of refractory peritonitis. Metagenomic next-generation sequencing (mNGS) detected Mh in the PD effluent. Treatment was adjusted to intraperitoneal (IP) clindamycin combined with intravenous drip(ivdrip) moxifloxacin, resulting in complete recovery.<br><br>CONCLUSION: Patients with culture-negative PD-associated peritonitis or refractory peritonitis should be evaluated for potential Mh infection. mNGS enables rapid detection of pathogens that traditional methods may fail to identify. A combination of moxifloxacin and clindamycin is effective for treating PD-associated peritonitis caused by Mh.}, }
@article {pmid40384785, year = {2025}, author = {Rivera, I and Harlow, K and Cole, RN and O'Meally, R and Garrett, W and Xiong, W and Oliver, W and Wells, JE and Summers, KL and Chhetri, N and Postnikova, O and Rempel, L and Crouse, M and Neville, B and Davies, CP}, title = {A metaproteomic analysis of the piglet fecal microbiome across the weaning transition.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1504433}, pmid = {40384785}, issn = {1664-302X}, abstract = {Microbiome analysis has relied largely on metagenomics to characterize microbial populations and predict their functions. Here, we used a metaproteomic analysis of the fecal microbiome in piglets before and after weaning to compare protein abundances as they pertain to microbial populations specific to either a milk- or plant-based diet. Fecal samples were collected from six piglets on the day of weaning and 4 weeks after transitioning to a standard nursery diet. Using the 12,554 protein groups identified in samples, we confirmed the shift in protein composition that takes place in response to the microbial succession following weaning and demonstrated the redundancy in metabolic processes between taxa. We identified taxa with roles as primary degraders based on corresponding proteins synthesized, thereby providing evidence for cross-feeding. Proteins associated with the breakdown of milk-specific carbohydrates were common among pre-weaned pigs, whereas the proteome of post-weaned piglets contained a greater abundance of proteins involved in the breaking down plant-specific carbohydrates. Furthermore, output revealed that production of propionate takes place via the propionaldehyde pathway in pre-weaned piglets, but changes to production via the succinate pathway in post-weaned piglets. Finally, a disproportionate quantity of carbohydrate-active enzymes (CAZymes) (~8%) were produced by fungi, which typically only represent ~0.1% of the microbiome taxa. Information gathered through this characterization of the metaproteome before and after weaning revealed important differences regarding the role of members in the microbial community, thereby providing information for the optimization of diets and products for both piglet and microbiome health.}, }
@article {pmid40383397, year = {2025}, author = {Merrick, B and Prossomariti, D and Allen, E and Bisnauthsing, K and Kertanegara, M and Sergaki, C and Le Guennec, AD and Delord, M and Bell, JT and Conte, MR and Moyes, DL and Shankar-Hari, M and Douiri, A and Goodman, AL and Shawcross, DL and Goldenberg, SD}, title = {Faecal microbiota transplant to ERadicate gastrointestinal carriage of Antibiotic-Resistant Organisms (FERARO): a feasibility randomised controlled trial.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106504}, doi = {10.1016/j.jinf.2025.106504}, pmid = {40383397}, issn = {1532-2742}, abstract = {OBJECTIVES: The gastrointestinal tract (GIT) is a reservoir of multidrug-resistant organisms (MDRO). Colonisation with MDRO precedes invasive infections which can be challenging to treat with excess morbidity and mortality compared to antimicrobial susceptible infections. Currently, there are no effective GIT decolonisation strategies. Whilst Faecal Microbiota Transplant (FMT) has emerged as a potential therapeutic, there remains uncertainty about its feasibility, safety and efficacy.<br><br>METHODS: Population: Patients with invasive infection with Extended-spectrum Beta-Lactamase (ESBL-) or Carbapenem-resistant Enterobacterales (CRE) and persistent GIT carriage.<br><br>INTERVENTION: Three doses of encapsulated lyophilised FMT.<br><br>COMPARATOR: Matched placebo capsules.<br><br>OUTCOMES: Primary outcome was participant consent rate as a proportion of those approached to be screened for GIT carriage of ESBL-E/CRE. Secondary outcomes were additional feasibility, safety and tolerability, and efficacy metrics. Exploratory outcomes included stool metagenomic analysis.<br><br>RESULTS: Of 460 approached individuals, 124 (27%) consented. 53/124 participants (43%) fulfilled all eligibility criteria. 44/53 (83%) of those eligible were randomised and 41/44 (93%) received investigational medicinal product (IMP): 20 FMT and 21 placebo. 39/41 (95%) completed IMP dosing. Abdominal bloating and skin and subcutaneous tissue disorders were more common following FMT but there were no unanticipated harms. MDRO carriage decreased over time across arms but was lower at all time points in the FMT arm. FMT increased microbiome diversity and microbiome-based health measures. FMT recipients' samples clustered into two groups with those with more dissimilar community composition to donors more likely to decolonise post-FMT (3/5 vs. 0/12, p=0.01). Patients that decolonised exhibited a trend towards increased proportional representation of donor-derived strains in their post-FMT samples (p=0.05) and change in strain dominance within MDRO at species-level.<br><br>CONCLUSIONS: Progression to a substantive trial is feasible with modifications to the existing FERARO protocol. FMT was safe, well tolerated, and acceptable to patients colonised with MDRO. Microbiome analysis infers that greater donor-recipient microbiome dissimilarity at baseline and higher rates of donor-derived strain engraftment favour MDRO decolonisation, which in turn maybe facilitated by conspecific strain replacement.}, }
@article {pmid40383308, year = {2025}, author = {Zhang, G and Hu, M and Wang, X and Liu, C and Ya, T and Wang, X}, title = {Self-regulatory mechanisms of anammox system in response to CuO nanoparticles revealed by microbial ecological networks and metagenomics.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132682}, doi = {10.1016/j.biortech.2025.132682}, pmid = {40383308}, issn = {1873-2976}, abstract = {Anaerobic ammonia oxidation (Anammox) has attracted widespread attention as an advanced biological nitrogen removal technology. CuO nanoparticles (CuO NPs) is one of the most common nanomaterials widely used in industrial production. In this study, microbial network construction, metagenomics and binning analysis were integrated to elucidate the impact of CuO NPs on anammox system. Nitrogen removal efficiency initially fluctuated but eventually stabilized after the addition of 1 mg/L CuO NPs. Network analysis revealed a significant increase in cooperative associations between anammox bacteria (AnAOB: Candidatus_Kuenenia, Candidatus_Jettenia, and Candidatus_Brocadia) and Chloroflexi from 0 % to 75 %. Metagenomic and binning analysis elucidated the intricate metabolic interactions between AnAOB and Chloroflexi, particularly in the biosynthesis of polysaccharide, protein, and cofactors.The collaboration between AnAOB and Chloroflexi was crucial for maintaining the ecological balance of the community structure under CuO NPs stress in anammox system.}, }
@article {pmid40382874, year = {2025}, author = {Miao, S and Zhang, Y and Wu, L and Wang, Y and Zuo, J}, title = {Resistance induction potency assessment of antibiotic production wastewater and associated resistome shaping mechanisms.}, journal = {Water research}, volume = {283}, number = {}, pages = {123811}, doi = {10.1016/j.watres.2025.123811}, pmid = {40382874}, issn = {1879-2448}, abstract = {Antibiotic production wastewater (APW) contains multiple substances known to select for and facilitate horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs); however, whether these substances can induce the evolution of antibiotic resistance in real wastewater environments and the fate of such resistance induction potency during the treatment process are poorly understood, nor are its relationship with wastewater quality parameters and function in shaping the antibiotic resistome. In this study, the impacts of filter-sterilized APW and municipal wastewater on the resistance selection of Escherichia coli and the transfer dynamics of conjugative RP4 plasmid-borne ARGs across indigenous sludge communities were evaluated. The resistance development and transfer processes were accelerated in APW owing to enhanced growth inhibition, oxidative stress, and membrane permeability, with antibiotic concentrations much lower than their minimum inhibition concentrations. The effects were reduced simultaneously with the removal of COD and NH3N, but APW effluents still exhibited significant resistance induction potency with wastewater quality parameters meeting discharge standards. In contrast, municipal wastewater did not result in any detectable changes. Based on the metagenomic assembly and binning, stronger resistance induction potency in the antibiotic production wastewater treatment plant endowed indigenous sludge and effluent with greater accumulation, genetic mobility, and pathogenic accessibility of ARGs than in the municipal wastewater treatment plant. Antibiotic resistome assembly was determined primarily by deterministic processes, driven jointly by resistance induction potency, mobilome variance, and microbiome shifts. These results provide novel insights into the application of bioassays to comprehensively evaluate the antibiotic resistance induction effects of APW and their relationships with the resistome to manage risks during the treatment process.}, }
@article {pmid40382544, year = {2025}, author = {Zhang, S and Fu, Y and Fang, L and Xu, Q and Gu, S and Zhou, H and Zhou, J}, title = {Psittacosis pneumonia with the reversed halo sign: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {717}, pmid = {40382544}, issn = {1471-2334}, support = {2021YFC2301805//National Key Research and Development Program of China/ ; WKJ-ZJ-2109//Medical and Health Technology Program of Zhejiang Province/ ; }, mesh = {Humans ; Male ; Adult ; *Psittacosis/diagnostic imaging/drug therapy/diagnosis/microbiology ; *Chlamydophila psittaci/isolation &amp; purification/genetics ; Tomography, X-Ray Computed ; Animals ; Lung/diagnostic imaging/microbiology ; Columbidae/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Lung Diseases/diagnosis ; }, abstract = {BACKGROUND: Chlamydia psittaci is a rare pathogen that causes community-acquired pneumonia. The reversed halo sign (RHS) is a computed tomography (CT) finding that is commonly observed in diseases such as cryptogenic organizing pneumonia, invasive fungal infections, tuberculosis, sarcoidosis, and pulmonary thromboembolism, but has seldom been described in association with psittacosis pneumonia.<br><br>CASE PRESENTATION: We report a case in which a 26-year-old man with a history of close contact with pigeons and chicken manure presented with fever and cough for 6 days. A CT examination revealed the RHS in the right lower lobe of the lung. Psittacosis pneumonia was diagnosed by metagenomic next-generation sequencing of the patient's bronchoalveolar lavage fluid. Treatment with omadacycline abolished his symptoms. We also discuss six other cases of psittacosis pneumonia with the RHS identified by literature search.<br><br>CONCLUSIONS: When clinicians encounter patients with atypical pneumonia with the RHS and a history of contact with poultry, psittacosis should be considered.}, }
@article {pmid40382475, year = {2025}, author = {Yang, Q and Downey, R and Stark, JS and Johnstone, GJ and Mitchell, JG}, title = {The Microbial Ecology of Antarctic Sponges.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {44}, pmid = {40382475}, issn = {1432-184X}, mesh = {*Porifera/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Archaea/classification/genetics/isolation &amp; purification ; Ecosystem ; Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.}, }
@article {pmid40382365, year = {2025}, author = {Schilling, M and Jagdev, M and Thomas, H and Johnson, N}, title = {Metagenomic analysis of mosquitoes from Kangerlussuaq, Greenland reveals a unique virome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17141}, pmid = {40382365}, issn = {2045-2322}, mesh = {Animals ; Greenland ; *Virome/genetics ; *Metagenomics/methods ; *Aedes/virology/genetics ; *Mosquito Vectors/virology ; Metagenome ; Phylogeny ; *Culicidae/virology ; Climate Change ; }, abstract = {Climate change is dramatically affecting vector ecology in extreme environments such as the Arctic. However, little is known about the current status of viruses of arthropod vectors located in such northerly locations. As part of a field survey on the role of wildlife in international movement of zoonotic pathogens, we sampled mammalophilic mosquitoes near the settlement of Kangerlussuaq, Greenland in July 2022 and July 2023 to investigate their virome. The majority of mosquitoes were identified as either Aedes impiger or Aedes nigripes. Metagenomic analysis of RNA extracted from species pools detected a number of novel RNA viruses belonging to a range of different virus families, including Flaviviridae, Orthomyxoviridae, Bunyavirales, Totiviridae and Rhabdoviridae. However, the sequence identities when compared to previously published, were as low as 34% at the amino acid level. Furthermore, a comparison of virome diversity between Aedes species emphasises the uniqueness of both Aedes impiger and Aedes nigripes from this secluded ecosystem. It also highlights the need to better understand the viromes of potential pathogen vectors as the impacts of climate change are experienced in such northerly ecosystems.}, }
@article {pmid40382068, year = {2025}, author = {Zhang, Z and Ran, X and Guo, Z and Hou, Q and Qu, D and Wang, C and Xu, Y and Wang, Y}, title = {Microbial diversity, functional properties, and flavor characteristics of high-temperature Daqu with different colors.}, journal = {Food research international (Ottawa, Ont.)}, volume = {212}, number = {}, pages = {116406}, doi = {10.1016/j.foodres.2025.116406}, pmid = {40382068}, issn = {1873-7145}, mesh = {Color ; *Taste ; *Food Microbiology ; *Hot Temperature ; Odorants/analysis ; Humans ; *Bacteria/classification/genetics ; *Microbiota ; China ; }, abstract = {High-temperature Daqu (HTD) plays a crucial role in the quality of sauce-flavor baijiu. Daqu of different colors serves distinct functions in the baijiu brewing process. However, indicators for distinguishing among different-colored Daqu remain insufficient. This study investigated the microbial community structures, physicochemical properties, and E-sensory characteristics of different-colored HTD from Shandong Province. The results revealed significant differences in microbial communities among the three HTD types (P < 0.05). Kroppenstedtia eburnea, three Bacillus species, and Weizmannia coagulans were significantly enriched in white Daqu; an unclassified Staphylococcus species dominated in black Daqu; and Aspergillus oryzae, Aspergillus fumigatus, and Proteus mirabilis were highly abundant in yellow Daqu. Compared to HTD from Guizhou and Hubei, Shandong HTD was characterized by microbial species such as Proteus mirabilis and Bacillus velezensis. Using metagenomic analysis, we, for the first time, identified Thermomyces lanuginosus, Lentibacillus daqui, and an unclassified Thermoascus species as potential major contributors to pyrazine synthesis in HTD. The primary differences among the three colored Shandong Daqu types lay in their aroma profiles rather than taste. Electronic nose and electronic tongue analyses demonstrated that the W6S and W3S sensors effectively distinguished black and white Daqu, respectively, marking a novel application of these technologies in Daqu analysis. Acidity was identified as a key factor influencing microbial community structure, flavor characteristics, and enzyme activities, with a nonlinear relationship observed between acidity and enzyme activities. This study highlights the microbial and sensory distinctions among different-colored HTD and provides effective indicators for distinguishing these three types of Daqu.}, }
@article {pmid40381442, year = {2025}, author = {Zhang, X and Li, M and Xiao, Y and Yang, X and Zhou, H and Qu, Y and Zhan, J}, title = {Metagenomics reveals combined effects of microplastics and antibiotics on microbial community structure and function in coastal sediments.}, journal = {Marine pollution bulletin}, volume = {218}, number = {}, pages = {118153}, doi = {10.1016/j.marpolbul.2025.118153}, pmid = {40381442}, issn = {1879-3363}, abstract = {Microplastics and antibiotics are emerging pollutants in marine environments, yet their combined effects on coastal sediments remain poorly understood. This study examined the impacts of microplastics and antibiotics on sediment properties and microbial communities through a 60-day laboratory simulation. Results showed that microplastics significantly reduced carbon, nitrogen, and phosphorus levels in sediments, while both antibiotics and combined pollution decreased phosphorus content. Combined pollution also increased NH4[+]-N concentration. Enzyme activity analysis revealed that microplastics elevated alkaline phosphatase activity, antibiotics increased fluorescein diacetate (FDA) hydrolase activity but decreased urease activity, and their combination further enhanced FDA hydrolase activity. Metagenomics analysis demonstrated that the presence of microplastics and antibiotics altered microbial community structure and metabolic functions. The dominant phylum Pseudomonadota (42.62 %-56.24 %) showed reduced abundance under combined pollution. Antibiotics significantly increased resistance gene abundance, while combined pollution led to selective enrichment of these genes. Both pollutants inhibited ammonia assimilation, and antibiotics also suppressed dissimilatory nitrate reduction. Conversely, combined pollution promoted nitrification and nitrogen fixation. While microplastics and antibiotics inhibited methane synthesis, combined pollution increased methane production via elevated mttB and hdrA genes. Antibiotics also reduced methane-oxidizing bacteria and genes, suppressing methane oxidation. These findings provide crucial insights into the ecological impacts of microplastics and antibiotics on coastal sediments, offering a theoretical basis for future marine pollution management strategies.}, }
@article {pmid40381353, year = {2025}, author = {Xin, Y and Zhang, J and Tang, Q and Wei, M and Zhu, L and Zhao, Y and Cui, Y and Sun, T and Wei, Y and Richnow, HH}, title = {Virus-host interactions driving the transfer of antibiotic resistance genes in a river-reservoir system under heavy rainfall.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138605}, doi = {10.1016/j.jhazmat.2025.138605}, pmid = {40381353}, issn = {1873-3336}, abstract = {Global river systems are grappling with severe pollution from antibiotic resistance genes (ARGs), with river-reservoir (R-R) systems being a common feature in urban waterways. The intensified extreme rainfall events triggered by global climate change exacerbate the spread of ARGs posed by non-point source pollution and combined sewage overflows. This study employs a metagenomics approach to decipher the profile of ARGs and virus-host interactions driving their transfer under heavy rainfall in North Canal, Beijing, with extensive R-R systems. Results indicated that R-R systems contributed to ARGs reduction despite continuous discharge of treated wastewater into the North Canal. The ARGs assembly is predominantly governed by stochastic process, and heavy rainfall enhances the dispersal capability. Nonetheless, the deterministic process determined the assembly of both microbial and viral community. Heavy rainfall not only significantly increased the abundance and diversity of ARGs within the rivers with minimal change in the reservoir, but also promotes the horizontal gene transfer of ARGs with higher conjugative mobility. Although the species accumulation curves approached saturation, no viruses carrying ARGs were detected among the 23,835 non-redundant viral operational taxonomic units (vOTUs), and lytic phage-ARB interactions drove the ARGs reduction with higher VHRs, highlighting its contribution to the reduction of ARGs in R-R system after heavy rainfall.}, }
@article {pmid40381349, year = {2025}, author = {Feng, W and Ye, Y and Xiang, Y and Peng, S and He, S and Peng, H and Zhang, Z and Yang, Z and Xiong, W}, title = {Unraveling the dual role in enhancing methane production and mitigating antibiotic resistance gene spread in anaerobic co-digestion of microalgae and waste activated sludge.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138606}, doi = {10.1016/j.jhazmat.2025.138606}, pmid = {40381349}, issn = {1873-3336}, abstract = {Waste activated sludge (WAS) is a double-edged sword - a recognized repository for antibiotic resistance genes (ARGs) but also a renewable substrate for methane production. Developing effective WAS treatment strategies is therefore of both ecological and practical importance. In this study, we proposed an anaerobic co-digestion approach of WAS and microalgae Chlorella sp. at a 1:2 ratio (MAcoD-1:2). Results showed that MAcoD-1:2 notably increased cumulative methane production by 52.7 %. Co-digestion also demonstrated a significant increase in the abundance of hydrolyzing acidifying bacteria Candidatus_Promineofilum (12.25 %) and methanogenic archaea Methanothrix (61.2 %). This microbial shift suggested that cosubstrates availability fostered a stable bacterial community structure and synergistic metabolic interactions, thus enhancing methane production. Metagenomic analysis revealed a significant reduction in both ARGs and mobile genetic elements in MAcoD-1:2. Notably, substrate level regulation was found to drive restructuring of microbial communities and metabolic patterns. Investigation showed that the Embden-Meyerhof-Parnas pathways were significantly inhibited while the pentose phosphate pathway was promoted, which constrained the cellular energy budget available for ARG horizontal transfer. Partial least squares path modelling (PLS-PM) further substantiated these findings, revealing methane metabolism negatively affected ARGs (-4.52), whereas confirming its positive correlation with methane production (0.22). Our findings provided distinctive perspectives on WAS resource utilization and novel technologies to inhibit the spread of ARGs.}, }
@article {pmid40380820, year = {2025}, author = {Lakamp, AD and Neujahr, AC and Fernando, SC and Snelling, WM and Spangler, ML}, title = {Short Communication: Imputation accuracy of host genomic data from metagenomic sequence information.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skaf175}, pmid = {40380820}, issn = {1525-3163}, abstract = {Metagenomic sequencing is the process of extracting all the genomic information from a given sample. Most metagenomic studies remove any host reads as a matter of course. However, host reads can be used as the basis for genotype imputation to obtain whole genomic sequences. The accuracy of these imputed genotypic calls from a bovine ocular sample was determined by comparing results to those from a commercial array. Overall, imputed genotype calls proved to have a high concordance with array genotype calls (average concordance of 83% and correlation of 0.81 with no filtering). Accuracy increased as filters for host read depth and imputed call confidence were implemented. With filters in place the average percent concordance was 98% (88 - 99%) while the mean correlation was 0.98 (0.89-0.99). Further, identity verification of the metagenomic samples can be carried out if the host is genotyped on another platform.}, }
@article {pmid40380332, year = {2025}, author = {Kapandji, N and Salmona, M and Lemoine, A and Ulmann, G and Calderaro, J and Roche, B and Kapel, N and Biard, L and Lengline, E and Goff, JL and Rodriguez, C and Thomas, M and Zafrani, L}, title = {Unravelling neutropenic enterocolitis: insights from gut microbiota, and intestinal barrier analyses.}, journal = {Experimental hematology &amp; oncology}, volume = {14}, number = {1}, pages = {74}, pmid = {40380332}, issn = {2162-3619}, abstract = {BACKGROUND: Neutropenic enterocolitis (NE) is a severe digestive complication of chemotherapy, primarily affecting patients with acute myeloid leukemia (AML). We hypothesized that NE is linked to intestinal barrier dysfunction and gut dysbiosis.<br><br>METHODS: Sixty-five AML patients undergoing induction chemotherapy were included in this prospective monocentric cohort. Among them, 26 patients (40%) were diagnosed with NE. Stool samples were subjected to bacterial load quantification (all bacteria quantitative PCR), 16s rRNA metagenomic analysis, and short-chain-fatty-acids quantification. Additionally, fecal calprotectin and human &#x1d6c3;-defensin 2 along with plasmatic inflammatory cytokines, and citrulline levels were measured. Human transcriptomic analysis was conducted on samples obtained from anatomical specimens of colectomies of NE patients.<br><br>RESULTS: Gut microbiota underwent significant alterations after chemotherapy, transitioning from a diverse and balanced enterotype to enterotypes exhibiting a reduced &#x3b1;-diversity, an increased abundance of Enterococcus faecalis, and a decreased abundance of butyrate-producing genera, which correlated with a decreased fecal concentration of butyrate. Simultaneously, post-chemotherapy, plasma citrulline concentrations decreased indicating enterocyte damages. Finally, human transcriptomic analysis found a significant upregulation of the JAK-STAT signaling KEGG pathway in the colons of NE patients encompassing cytokines (IL-6, OSM-OSMR) that play a pivotal role in sustaining local inflammation within the digestive tract.<br><br>CONCLUSIONS: This work reaffirms the significant influence of chemotherapy on the gut microbiota and the integrity of the enterocyte barrier. Severe NE is marked by the development of a local inflammatory response that may be induced by the reduction in butyrate levels.<br><br>TRIAL REGISTRATION: The study was registered on Clinicaltrials.gov (identifier: NCT04438278).}, }
@article {pmid40380289, year = {2025}, author = {Amutuhaire, H and Faigenboim-Doron, A and Kraut-Cohen, J and Friedman, J and Cytryn, E}, title = {Identifying rhizosphere bacteria and potential mechanisms linked to compost suppressiveness towards Fusarium oxysporum.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {52}, pmid = {40380289}, issn = {2524-6372}, abstract = {BACKGROUND: Soilborne fungal phytopathogens pose a significant threat to global food security. While chemical control remains an effective method for managing these pathogens, increasing regulations due to health and environmental concerns, along with rising fungicide resistance, have restricted their use, underscoring the urgent need for sustainable alternatives. The use of compost to enhance soil fertility and suppress plant diseases is well documented. Several studies have underlined the role of microorganisms in disease suppression, but the mechanisms facilitating this disease suppression remain unclear. We evaluated the impact of compost amendment on the composition and functional capacity of the rhizosphere microbiome in cucumber plants (Cucumis sativus) inoculated with Fusarium oxysporum f. sp. radicis-cucumerinum (FORC) under controlled greenhouse conditions using amplicon sequencing, shotgun metagenomic and culture-based techniques.<br><br>RESULTS: Compost amendment significantly reduced FORC-induced disease in cucumber relative to non-amended treatments. While FORC inoculation resulted in significant shifts in microbial (bacterial and fungal) community composition in the rhizosphere of non-amended plants, this phenomenon was substantially less pronounced in the rhizosphere of compost-amended plants. Specifically, compost amendment sustained the presence of Actinomycetota (Streptomyces, Actinomadura, Saccharomonospora, Pseudonocardia, Glycomyces, Thermobifida) and Bacillota (Planifilum, Novibacillus) in FORC inoculated plants, that diminished significantly in inoculated plants without compost. These taxa contained a myriad of non-ribosomal peptides and polyketides synthetases biosynthetic gene clusters (BGCs) with putative antimicrobial and iron-chelating functions. We successfully isolated two Streptomyces strains from FORC-suppressing compost amended rhizospheres that were almost identical to the Streptomyces bin2 (99% ortho ANI) metagenome assembled genome identified in the shotgun metagenome analysis. These strains produced extracellular metabolites that inhibited growth of FORC in-vitro and contained BGCs that encode for compounds with potential antimicrobial capacity.<br><br>CONCLUSIONS: Based on results presented in this study, we demonstrate that compost alleviates FORC-induced dysbiosis of the rhizosphere microbiome, maintaining abundance of specific bacterial taxa. These bacterial groups may contribute to disease suppression through a myriad of mechanisms including iron chelation and production of fungal antagonizing secondary metabolites.}, }
@article {pmid40380272, year = {2025}, author = {Zhang, S and Zheng, N and Zhao, S and Wang, J}, title = {Allicin enhances urea-N conversion to microbial-N by inhibiting urease activity and modulating the rumen microbiome in cattle.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {124}, pmid = {40380272}, issn = {2049-2618}, support = {2023M743835//Project Funded by China Postdoctoral Science Foundation/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; 2022YFD1301000//National Key Research and Development Program of China/ ; 2004DA125184G2406//State Key Laboratory of Animal Nutrition and Feeding/ ; }, mesh = {Animals ; *Sulfinic Acids/pharmacology/chemistry ; *Urease/antagonists &amp; inhibitors/metabolism/chemistry ; *Rumen/microbiology ; *Urea/metabolism ; Disulfides/pharmacology ; *Nitrogen/metabolism ; Cattle ; Molecular Docking Simulation ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/metabolism/drug effects/classification/genetics ; Enzyme Inhibitors/pharmacology ; }, abstract = {BACKGROUND: Urea serves as a vital nonprotein nitrogen source in ruminant nutrition, but its efficient utilization is often hampered due to rapid urease activity in the rumen. This study explores the potential of allicin, a garlic-derived compound, as a urease inhibitor to improve urea nitrogen utilization. Enzyme inhibition kinetics and molecular docking were used to identify allicin's interaction sites on urease. Additionally, metagenomic and [15]N-urea metabolic flux analyses were conducted to evaluate allicin's impact on microbial populations and urea-N metabolism.<br><br>RESULTS: Allicin was identified as an inhibitor of ruminal urease, with an IC50 of 126.77&#x2009;&#xb1;&#x2009;1.21&#xa0;&#x3bc;M. Molecular docking studies have shown that allicin forms hydrogen bonds with key urease residues, leading to the preemption of the urease active site and thus impeding urea binding. In a simulated rumen environment, allicin significantly reduced urea hydrolysis and ammonia production. Furthermore, allicin modified the rumen microbial community by inhibiting Prevotella species while promoting the growth of Ruminobacter species and Denitrobacterium detoxificans. A [15]N-urea metabolic flux analysis revealed that allicin facilitated the incorporation of urea-derived nitrogen into microbial amino acids and nucleotides.<br><br>CONCLUSION: Allicin effectively inhibits urease activity in the rumen, enhancing the conversion of urea-N into microbial biomass. These findings suggest that allicin has significant potential to optimize urea metabolism in the rumen, offering a novel strategy for improving ruminant nitrogen nutrition. Video Abstract.}, }
@article {pmid40379383, year = {2025}, author = {Haas, G and Lee, B}, title = {De novo rescue of new henipaviruses under BSL-4 conditions - From sequence to pathogen.}, journal = {Advances in virus research}, volume = {121}, number = {}, pages = {61-99}, doi = {10.1016/bs.aivir.2025.03.004}, pmid = {40379383}, issn = {1557-8399}, mesh = {Animals ; Humans ; *Reverse Genetics/methods ; *Henipavirus/genetics/pathogenicity/isolation &amp; purification ; Genome, Viral ; *Henipavirus Infections/virology/transmission ; *Containment of Biohazards/methods ; Zoonoses/virology ; }, abstract = {Zoonotic paramyxoviruses, including the highly pathogenic henipaviruses (HNVs), pose significant risks to global health due to their high mortality rates, potential for human-to-human transmission, and lack of approved countermeasures. Recent metagenomic surveys have uncovered an extensive diversity of HNVs and related paramyxoviruses circulating in wildlife, the majority of which remain uncharacterized due to the dearth of viral isolates. In lieu of viral isolates, reverse genetics systems offer an approach to derive infectious clones de novo in the laboratory, facilitating research into the biology, zoonotic potential, and pathogenicity of novel HNVs. This chapter explores the methodologies and applications of reverse genetics systems for novel HNVs, including considerations for virus sequence validation, full-length virus recovery, and the development of platforms such as minigenomes, replicons, and virus replicon particles. Such biologically-contained life cycle modeling systems enable research to be conducted at lower biocontainment, and provide accessible tools through which to investigate HNV biology. This work demonstrates the versatility of reverse genetics systems in advancing our understanding of high-consequence pathogens, enabling the proactive development of vaccines, antivirals, and diagnostic tools. By integrating these methodologies within a framework of biosafety and biosecurity, researchers can better prepare for and respond to future zoonotic threats.}, }
@article {pmid40379020, year = {2025}, author = {Goto, M and Yamamoto, K and Horiba, K and Hashino, M and Kubono, Y and Ohmagari, N}, title = {Detection of Prevotella species in anaerobic culture-negative multiple abscesses using next-generation sequencing.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {}, number = {}, pages = {102733}, doi = {10.1016/j.jiac.2025.102733}, pmid = {40379020}, issn = {1437-7780}, abstract = {Next-generation metagenomic sequencing (mNGS) provides a comprehensive analysis of DNA and RNA in samples. In this case report, pus specimens were collected from an 86-year-old male with multiple muscle, periarticular, and bone abscesses, and osteomyelitis, without prior antimicrobial therapy. Results of bacterial culture tests, including anaerobic and intensified cultures, were negative. Despite this, mNGS using shotgun sequencing revealed a significant number of DNA and RNA nucleic acid reads from Prevotella spp. Although the subspecies could not be identified, mNGS allowed the selection of an appropriate antimicrobial agent and suggested significant oral contamination as the portal of entry. In summary, mNGS helped identify the causative organism in a case without prior antimicrobial therapy wherein culture test results were negative.}, }
@article {pmid40378832, year = {2025}, author = {Sarhan, MS and Antonello, G and Weissensteiner, H and Mengoni, C and Mascalzoni, D and Waldron, L and Segata, N and Fuchsberger, C}, title = {Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?.}, journal = {Cell}, volume = {188}, number = {10}, pages = {2561-2566}, doi = {10.1016/j.cell.2025.03.023}, pmid = {40378832}, issn = {1097-4172}, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Metagenome ; *Metagenomics/ethics ; Privacy ; Microbiota ; *Genetic Privacy/ethics ; }, abstract = {Human DNA is unavoidably present in metagenomic analyses of human microbiomes. While current protocols remove human DNA before submission to public repositories, mitochondrial DNA (mtDNA) has been overlooked and frequently persists. We discuss the privacy risks and research opportunities associated with mtDNA, urging consideration by the scientific, ethics, and legal communities.}, }
@article {pmid40378756, year = {2025}, author = {Zhan, Y and Chen, N and Feng, C and Dai, T and Gao, H and Yuan, Y and Hu, W and Dong, H}, title = {Electron flow dynamics in sulfur-based autotrophic bioreduction of Cr(VI) mediated by inorganic carbon species: Insights for environmental remediation.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138585}, doi = {10.1016/j.jhazmat.2025.138585}, pmid = {40378756}, issn = {1873-3336}, abstract = {The deployment of sulfur-based autotrophic bioremediation for in situ groundwater remediation faces hurdles due to electron competition among electron acceptors, impacting contaminant removal efficiency and causing pH instability. Notably, the sulfur-based bioreduction of Cr(VI) [Cr(VI)-SAR] exemplifies gaps in our comprehension of electron competition dynamics with inorganic carbon (IC), and its subsequent influence on pH. Herein, we established a Cr(VI)-SAR system interfaced with diverse IC species, providing definitive insights into electron transfer mechanisms through rigorous multi-biocycle analysis and thermodynamically consistent half-reaction calculations. Through quantification of electron transfer pathways, we derived reaction equations for Cr(VI) reduction in conjunction with various IC species. Furthermore, metagenomics were used to quantify functional enzymes and identify diverse electron transport patterns alongside IC fixation pathways. Notably, the enrichment of genes associated with electron shuttles and conductive pili expands the paradigm of extracellular electron transfer, while the Wood-Ljungdahl pathway streamlines microbial metabolic proliferation with reduced energy expenditure. Quantitative analysis of these functional genes offers a plausible mechanism underlying the observed shifts in electron competition between IC and Cr(VI). This research marks an advancement in the Cr(VI)-SAR foundational theory, with a particular focus on the dynamics of electron competition, contributing to a deeper understanding of this environmentally significant process.}, }
@article {pmid40378749, year = {2025}, author = {Yu, YL and Lin, WH and Surampalli, RY and Chen, SC and Kao, CM}, title = {Adaptive fluoride removal across concentration scales: Potential roles of microbial and acicular gypsum interactions in nitrogen and phosphate cycling.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138628}, doi = {10.1016/j.jhazmat.2025.138628}, pmid = {40378749}, issn = {1873-3336}, abstract = {Fluoride contamination in groundwater is a critical environmental and public health concern. Traditional remediation methods, including chemical precipitation and adsorption, are hindered by low nucleation efficiency at low fluoride concentrations and severe microbial inhibition under high fluoride stress. This study introduces an adaptive two-stage remediation system that synergistically integrates abiotic and biotic mechanisms to achieve effective fluoride removal across concentration scales. In Stage I, under elevated fluoride stress (100 mg/L), acicular gypsum (AG) facilitated abiotic calcium precipitation, effectively reducing fluoride toxicity and creating favorable conditions for microbial activity. Residual calcium released from AG further supported microbial-induced calcium precipitation (MICP) in Stage II under lower fluoride stress (10 mg/L). The system achieved a fluoride removal efficiency of 98.85 % under high fluoride conditions and demonstrated consistent performance across a broad concentration range. This integrated approach, combining abiotic and biotic mechanisms, offers a promising strategy for addressing diverse fluoride contamination scenarios. Here, phosphate (P)-mediated mineralization and microbial denitrification drive pH modulation, stabilizing fluoride as fluorapatite [Ca5(PO4)3F]. Microbial community and network analysis revealed key taxa, including Cupriavidus and Ralstonia, which facilitated P cycling and fluorapatite formation. Additionally, Bradyrhizobium enhanced nitrogen (N) cycling and supported early microbial adaptation, emphasizing the interplay of microbial interactions in driving system functionality. Functional predictions using PICRUSt2 identified genes associated with N and P cycling, highlighting the capacity of the system for nutrient adaptation under complex environmental conditions.}, }
@article {pmid40378468, year = {2025}, author = {Siddiquee, M and Cornelius, S and Seo, Y and Bullerjahn, GS and Bridgeman, TB and Sudman, M and Kang, DW}, title = {Uncovering microbial interactions in a persistent Planktothrix bloom: Towards early biomarker identification in hypereutrophic lakes.}, journal = {Water research}, volume = {283}, number = {}, pages = {123683}, doi = {10.1016/j.watres.2025.123683}, pmid = {40378468}, issn = {1879-2448}, abstract = {Cyanobacterial harmful algal blooms pose significant threats to global water supplies, ecosystems, and economies. Among the harmful cyanobacteria, Planktothrix, a resilient and toxin-producing filamentous cyanobacterium, has garnered increasing attention. However, an understanding of the entire microbiome, particularly the phycosphere surrounding Planktothrix blooms, remains largely unexplored. To the best of our knowledge, this is the first comprehensive study combining 16S rDNA and fungal internal transcribed spacer amplicon sequencing and shotgun metagenomics to elucidate Planktothrix bloom microbiomes and identify potential microbial or functional biomarkers for CyanoHABs. Our observations revealed that a summer bloom in Grand Lake St. Marys was initiated with Dolichospermum and then shifted to Planktothrix dominance. This transition was associated with nitrogen metabolism genes, suggesting that nitrogen plays a key role in bloom persistence through interactions among nitrogen-fixing bacteria, ammonia-oxidizing archaea, anammox bacteria, and denitrifiers. Additionally, metagenomic data revealed a strong positive correlation of toxin concentration with carbohydrate-nitrogen-sulfur-fatty acid associated metabolic pathways and a strong negative correlation with pollutant degradation pathways. Intriguingly, diazotrophic methane-related microbes were detected, which opens discussion on potential symbiosis that couples nitrogen and carbon metabolism. Toxin-degrading bacteria, such as Polynucleobacter and Acidovorax, were positively correlated with fungi like Vishniacozyma, proposing their cooperative roles during bloom events. Notably, Rhodobacter, a photosynthetic purple non-sulfur bacterium, showed strong negative correlations with both Planktothrix and the toxin-producing gene mcyE, positioning it as a promising biomarker for early bloom detection. Overall, this study advances the understanding of Planktothrix-dominated bloom ecology and highlights microbial signatures for proactive CyanoHAB management in freshwater systems.}, }
@article {pmid40378175, year = {2025}, author = {Wan, J and Liu, T and Li, F and Xu, S}, title = {Diagnosis, clinical features, and mortality risk factors in a Chinese cohort with pulmonary mucormycosis.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0323624}, pmid = {40378175}, issn = {1932-6203}, mesh = {Humans ; *Mucormycosis/mortality/diagnosis ; Male ; Middle Aged ; Female ; Risk Factors ; Retrospective Studies ; Adult ; *Lung Diseases, Fungal/mortality/diagnosis ; Aged ; China/epidemiology ; Tomography, X-Ray Computed ; East Asian People ; }, abstract = {BACKGROUND: Pulmonary mucormycosis is a rare and often fatal fungal infection. Identifying high-risk factors for pulmonary mucormycosis holds the potential to improve patient outcomes. This study aimed to identify the clinical characteristics and risk factors associated with pulmonary mucormycosis outcomes in a Chinese cohort.<br><br>MATERIALS AND METHODS: A retrospective analysis was conducted on 37 patients diagnosed with pulmonary mucormycosis, focusing on clinical records, laboratory findings, and computed tomography (CT) imaging. Diagnosis was primarily based on histopathology or next-generation sequencing.<br><br>RESULTS: The median age of the patients was 55 years, and the most common underlying conditions were hematological malignancies, diabetes, and organ transplantation. Imaging frequently revealed bilateral lung involvement with ground-glass opacities and nodular lesions. The overall mortality rate was 29.7%, with significant risk factors for 90-day mortality including hypertension (Hazard Ratio [HR] = 3.36, 95% Confidence Interval [CI] = 1.01-11.12, P&#x2009;=&#x2009;0.048), organ transplantation (HR&#x2009;=&#x2009;4.93, 95% CI&#x2009;=&#x2009;1.48-16.4, P&#x2009;=&#x2009;0.009), and immunosuppression (HR&#x2009;=&#x2009;8.83, 95% CI&#x2009;=&#x2009;1.13-69.14, P&#x2009;=&#x2009;0.038).<br><br>CONCLUSIONS: Early suspicion and timely diagnostic measures, such as biopsy or metagenomic sequencing, are crucial for improving patient outcomes. These findings underscore the importance of recognizing and managing pulmonary mucormycosis in high-risk populations.}, }
@article {pmid40377870, year = {2025}, author = {Amen, RA and Hassan, YM and Essmat, RA and Ahmed, RH and Azab, MM and Shehata, NR and Elgazzar, MM and El-Sayed, WM}, title = {Harnessing the Microbiome: CRISPR-Based Gene Editing and Antimicrobial Peptides in Combating Antibiotic Resistance and Cancer.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40377870}, issn = {1867-1314}, abstract = {The growing crisis of antibiotic resistance and the increasing incidence of cancer have prompted the exploration of innovative approaches, such as gene editing and antimicrobial peptides (AMPs). The human microbiome is integral to various aspects of health, disease, and therapeutic development, influencing metabolic pathways, immune function, and pathogen resistance. Recent advances in gene editing technologies, particularly CRISPR (clustered regularly interspaced short palindromic repeats), have opened new avenues for leveraging the microbiome to address complex medical challenges, including combating multidrug-resistant pathogens and cancer. The microbiome plays a crucial role in combating antibiotic resistance by modulating microbial communities, influencing pathogen survival and susceptibility to treatments. This review explores the microbiome's dynamic role in metabolic regulation, its contribution to cancer management, and how AMPs help maintain homeostasis and exhibit emerging anticancer properties, supported by both preclinical findings and clinical evidence. Additionally, CRISPR-based microbiome engineering offers potential to enhance host-microbiome interactions, optimizing therapeutic outcomes. The integration of microbiome metagenomics and proteomics has led to the discovery of novel AMPs with targeted anticancer effects. Innovative strategies, such as engineered probiotics and CRISPR-based microbiome engineering, present exciting prospects for next-generation therapies. Despite these advances, the translation of microbiome-based therapies into clinical settings remains challenging due to ethical, regulatory, and ecological hurdles. This review underscores the transformative potential of microbiome-based interventions, emphasizing the role of personalized medicine in maximizing therapeutic efficacy. Furthermore, we also address critical research gaps, limitations, and future directions, including optimizing AMP stability, delivery, and bioavailability, as well as overcoming the regulatory and ethical challenges in clinical translation.}, }
@article {pmid40377844, year = {2025}, author = {Paul, B and Pan, P and Bhattacharyya, N}, title = {Investigating the impact of fly ash contamination on soil microbial diversity: a metagenomic study near Kolaghat Thermal Power Plant, India.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {40377844}, issn = {1614-7499}, abstract = {Soil metagenomics using whole genome shotgun sequencing (WGS) uncovers microbial diversity and functionality in soils. This study aimed to explore microbial diversity and functional adaptation in soils exposed to fly ash near the Kolaghat Thermal Power Plant, West Bengal, India, using whole genome shotgun sequencing. Understanding how microbial communities respond to such contamination is essential for developing effective bioremediation strategies. Soil samples were collected from the area, designated as BP1 sample selected for detailed metagenomics analysis. The study extracted DNA with a concentration of 46.2 ng/µl, followed by quality checks and profiling to identify microbial communities. Analysis showed that bacterial communities were dominated by Actinobacteria (48.28%) and Proteobacteria (40.80%), while fungi were primarily represented by Ascomycota (89.50%). Among viruses, Negarnaviricota were most prevalent, with the class Insthoviricetes accounting for 94.60%. Diversity analysis indicated that bacterial populations remained stable, fungal diversity fluctuated, and viral diversity increased, reflecting complex ecological interactions. The presence of key genes involved in lipid and carbohydrate metabolism suggests that microbes adapted to contamination by heavy metals and organic pollutants. The dominance of stress-tolerant Proteobacteria and Actinobacteria highlights their potential role in bioremediation. Future research should explore the potential of these microbes, particularly the role of ABC transporters, in improving pollutant degradation.}, }
@article {pmid40377330, year = {2025}, author = {Thajudeen, J and Venkatachalam, S and Vipindas, PV}, title = {Antibiotic resistome in the glacier forelands of polar regions.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0076225}, doi = {10.1128/aem.00762-25}, pmid = {40377330}, issn = {1098-5336}, abstract = {UNLABELLED: Antibiotic resistance genes (ARGs) pose a significant threat, exacerbated by climate change impacts on polar regions, particularly melting glaciers and permafrost. While ancient antibiotic resistance exists in the environments, the release and dissemination of ARGs remain poorly understood. This study investigated ARG composition and distribution in 43 metagenomes from Arctic and Antarctic glacier forelands. We identified 154 ARGs, predominantly bacitracin resistance, followed by rifamycin, fosfomycin, vancomycin, tetracycline, and beta-lactam resistance genes. Significant correlations were observed between ARGs and mobile genetic elements (MGEs), with 20 ARGs associated with tnpA MGEs. Actinomycetota and Pseudomonadota were the primary ARG-carrying phyla. Metagenome-assembled genomes revealed Mycobacterium sp., Pseudomonas sp., and Tatlockia sp. as major ARG-harboring pathogens in the glacier forelands. Evolutionarily adapted, distinct ancient ARGs were abundant in the polar environments, varying between different geographic regions. The environmental parameters such as pH and total organic carbon significantly influenced the ARG distribution in the Arctic and Antarctic glacier forelands. This study provides crucial baseline data on antimicrobial resistance, highlighting potential risks associated with rapid environmental change in the regions.<br><br>IMPORTANCE: Antibiotic resistance poses a significant global health threat, exacerbated by the release of antibiotic resistance genes from melting glaciers and permafrost due to climate change. This study provides crucial baseline data on the composition and distribution of antibiotic resistance genes in these vulnerable polar environments, which is essential for understanding and mitigating the risks associated with their release. The findings have far-reaching implications for global health security and emphasize the need for further research to address this emerging threat.}, }
@article {pmid40377187, year = {2025}, author = {Veseli, I and Chen, YT and Schechter, MS and Vanni, C and Fogarty, EC and Watson, AR and Jabri, B and Blekhman, R and Willis, AD and Yu, MK and Fernàndez-Guerra, A and Füssel, J and Eren, AM}, title = {Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {40377187}, issn = {2050-084X}, support = {1746045//National Science Foundation Graduate Research Fellowship Program/ ; R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM128716/NH/NIH HHS/United States ; RC2 DK122394/NH/NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Stress, Physiological ; Metagenome ; *Bacteria/metabolism/genetics/classification ; }, abstract = {A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health vs IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.}, }
@article {pmid40376801, year = {2025}, author = {Prisco, SZ and Blake, M and Kazmirczak, F and Moon, R and Kremer, BP and Hartweck, LM and Kim, M and Vogel, N and Mendelson, JB and Moutsoglou, D and Thenappan, T and Prins, KW}, title = {Lactobacillus Restructures the Micro/Mycobiome to Combat Inflammation-Mediated Right Ventricular Dysfunction in Pulmonary Arterial Hypertension.}, journal = {Circulation. Heart failure}, volume = {}, number = {}, pages = {e012524}, doi = {10.1161/CIRCHEARTFAILURE.124.012524}, pmid = {40376801}, issn = {1941-3297}, abstract = {BACKGROUND: Inflammation suppresses right ventricular (RV) function in pulmonary arterial hypertension (PAH). In particular, we showed GP130 (glycoprotein-130) signaling promotes pathological microtubule remodeling and RV dysfunction in rodent PAH. Emerging data demonstrate the intestinal microbiome regulates systemic inflammation, but the impact of modulating the gut microbiome on the GP130-microtubule axis in RV failure is unknown.<br><br>METHODS: Two weeks following monocrotaline injection, rats were administered daily Lactobacillus rhamnosus (4&#xd7;10[7] colony-forming units) via oral gavage for 10 days. Next-generation metagenomics and internal transcribed spacer 2 sequencing delineated fecal bacterial and fungal compositions. SomaScan proteomics measured levels of 7596 serum proteins. RV immunoblots quantified protein abundances. Light or super resolution confocal microscopy assessed RV, lung, and jejunal morphology. Echocardiography and invasive closed-chest pressure-volume loops evaluated PAH severity and RV function. The relationship between Lactobacillus abundance and RV function was assessed in 65 patients with PAH.<br><br>RESULTS: Lactobacillus administration restructured both the intestinal micro- and mycobiome. The alteration in the gut ecosystem improved intestinal health as demonstrated by increased jejunal villus length and glycocalyx thickness and diminished intestinal permeability biomarkers. Serum proteomics revealed Lactobacillus modulated systemic inflammation and decreased circulating GP130 ligands. Lactobacillus-mediated suppression of GP130 signaling blunted pathological microtubule remodeling in RV cardiomyocytes. Microtubule-associated phenotypes, including RV cardiomyocyte and nuclear hypertrophy, transverse tubule integrity, and connexin-43 localization, were all corrected with Lactobacillus. These cellular changes manifested as improved RV function despite no significant alteration in PAH severity. Finally, patients with PAH and detectable fecal Lactobacillus had superior RV function despite similar mean pulmonary arterial pressure and pulmonary vascular resistance as compared with those without detectable Lactobacillus.<br><br>CONCLUSIONS: Lactobacillus supplementation restructures the gut micro/mycobiome, restores intestinal health, dampens systemic inflammation, and reduces GP130 ligands and associated RV cardiomyocyte microtubule remodeling. These data identify a novel microbiome-inflammation-microtubule axis that has therapeutic relevance for RV dysfunction.}, }
@article {pmid40376464, year = {2025}, author = {Shao, X and Yang, C and Chen, Y and Liu, C and Liu, C and Shi, X and Zhou, Y}, title = {Sorghum-peanut intercropping under salt stress mediates rhizosphere microbial community shaping in sorghum by affecting soil sugar metabolism pathways.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1589415}, pmid = {40376464}, issn = {1664-302X}, abstract = {Soil salinization is a substantial impediment to agricultural production, and investigating sustainable mitigation measures is essential for addressing food security. We conducted a two-year pot experiment to investigate the shaping mechanism of sorghum rhizosphere microbial community in sorghum-peanut intercropping system under salt stress. The experiment comprised four treatments: sole-cropped sorghum under normal soil conditions (NSS), intercropped sorghum under normal soil conditions (NIS), sole-cropped sorghum under salt-stress conditions (SSS), and intercropped sorghum under salt-stress conditions (SIS). The sorghum rhizosphere soil metabolites were examined using GC-MS, and the rhizosphere microbial community was characterized through metabolome sequencing. We identified 123 metabolites across treatments, with significant differences between normal and salt-stress soil conditions. The major metabolite classes included carbohydrates, alcohols, and acids. Key carbohydrates, including fructose and sucrose, were significantly reduced in the SIS than in SSS, NSS, and NIS treatments. Metabolic pathway analyses revealed that these differences were primarily associated with "Fructose and mannose metabolism," "Starch and sucrose metabolism" and "ABC transporter." Metabolome analyses revealed significant differences in microbial community structure across diverse soil conditions and cropping patterns. At phylum level, Proteobacteria, Gemmatimonadetes, and Verrucomicrobia predominated, with their relative abundance experiencing substantial changes under salt stress. SIS facilitated the enrichment of specific genera (Rhodanobacter), which were associated with soil health and stress tolerance. Additionally, the responses of rare microbial taxa to salt stress and intercropping varied, with specific rare microbial taxa (Rhizopus) exhibiting relative abundance under salt stress. Correlation analysis of metabolites and microbial taxa revealed that certain carbohydrates were significantly positively correlated with specific microbial phyla (Cyanobacteria and Nitrospirae) while demonstrating a significant negative correlation with Planctomycetota and Bacteroidota. These correlations indicate that sorghum intercropped with peanuts can promote the enrichment of microbial taxa under salt stress, thereby enhancing soil metabolic functions and stress tolerance by optimizing the rhizosphere microbial community. This study reveals the mechanism through which sorghum-peanut intercropping under salt stress influences the composition of sorghum's rhizosphere microbial community by modulating soil sugar metabolism pathways. This finding provides a new perspective on sustainable agricultural practices in saline soils and emphasizes the pivotal role of plant-metabolite-microbe interactions in abiotic stress mitigation.}, }
@article {pmid40376462, year = {2025}, author = {Han, Y and Cao, B and Tang, J and Wang, J}, title = {A comprehensive multi-omics analysis uncovers the associations between gut microbiota and pancreatic cancer.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1592549}, pmid = {40376462}, issn = {1664-302X}, abstract = {Pancreatic cancer is one of the most lethal malignant neoplasms. Pancreatic cancer is related to gut microbiota, but the associations between its treatment and microbial abundance as well as genetic variations remain unclear. In this study, we collected fecal samples from 58 pancreatic cancer patients including 43 pancreatic ductal adenocarcinoma (PDAC) and 15 non-PDAC, and 40 healthy controls, and shotgun metagenomic sequencing and untargeted metabolome analysis were conducted. PDAC patients were divided into five groups according to treatment and tumor location, including treatment-naive (UT), chemotherapy (CT), surgery combined with chemotherapy (SCT), Head, and body/tail (Tail) groups. Multivariate association analysis revealed that both CT and SCT were associated with increased abundance of Lactobacillus gasseri and Streptococcus equinus. The microbial single nucleotide polymorphisms (SNPs) densities of Streptococcus salivarius, Streptococcus vestibularis and Streptococcus thermophilus were positively associated with CT, while Lachnospiraceae bacterium 2_1_58FAA was positively associated with Head group. Compared with Tail group, the Head group showed positive associations with opportunistic pathogens, such as Escherichia coli, Shigella sonnei and Shigella flexneri. We assembled 424 medium-quality non-redundant metagenome-assembled genomes (nrMAGs) and 276 high-quality nrMAGs. In CT group, indole-3-acetic acid, capsaicin, sinigrin, chenodeoxycholic acid, and glycerol-3-phosphate were increased, and the accuracy of the model based on fecal metabolites reached 0.77 in distinguishing healthy controls and patients. This study identifies the associations between pancreatic cancer treatment and gut microbiota as well as its metabolites, reveals bacterial SNPs are related to tumor location, and extends our knowledge of gut microbiota and pancreatic cancer.}, }
@article {pmid40376454, year = {2025}, author = {Yu, T and Cheng, L and Zhang, Q and Yang, J and Zang, H and Zeng, Z and Yang, Y}, title = {Characterization of antibiotic resistance genes and virulence factors in organic managed tea plantation soils in southwestern China by metagenomics.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1580450}, pmid = {40376454}, issn = {1664-302X}, abstract = {Sustainable organic management practices have gained significant attentions for its potential health and environmental benefits. However, the spread of antibiotic resistance genes (ARGs) and virulence factors (VFs) in soils, plants, and agricultural products has severely limited the development of organic managements on agriculture. At present, the distribution and assembly of ARGs and VFs in organic managed tea plantation systems remains largely unknown. Here, we used metagenomic analysis to explore soil microbial taxa, ARGs and VFs in 20 years of conventional managed (CM) and organic managed (OM) tea plantation soils. Results showed that total abundance of ARGs in OM was 16.9% (p < 0.001) higher than that in CM, and the increased ARGs were rpoB2, evgS, MuxB, TaeA, and efrA. As for VFs, OM significantly increased the abundance of adherence, stress protein and actin-based motility compared to CM. Moreover, OM increased the relative abundance of soil microbial taxa harboring ARGs and VFs, which were Streptomyces, Pseudomonas, and Terrabacter, compared to CM. Network analysis suggested that OM increased the positive interactions of microbial taxa-ARGs, microbial taxa-VFs and ARGs-VFs compared to CM. Impact of stochastic process on the assembly of soil microbial taxa, ARGs and VFs in OM was stronger than that in CM. Overall, these findings provide a basis for integrating ARGs, VFs and pathogen hosts to assess the ecological and health risks in long-term organic managed soils, and increased efforts need to be done in reducing ARGs, VFs and bacterial pathogens in fertilizers for organic managements on agriculture.}, }
@article {pmid40375904, year = {2025}, author = {Santarelli, G and Bianco, DM and Capriati, M and Sanguinetti, M and Rendeli, C and De Maio, F}, title = {Bladder Microbiota Snapshots Help to Monitor Urinary Tract Infections in Vulnerable Patients.}, journal = {Mediterranean journal of hematology and infectious diseases}, volume = {17}, number = {1}, pages = {e2025028}, pmid = {40375904}, issn = {2035-3006}, }
@article {pmid40375895, year = {2025}, author = {Chen, S and Ouyang, T and Wang, K and Hou, X and Zhang, R and Li, M and Zhang, H and He, Q and Li, X and Liu, Z and Wang, X and Huang, B}, title = {Application of metagenomic next-generation sequencing in pathogen detection of lung infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1513603}, pmid = {40375895}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Middle Aged ; Aged ; *Bacteria/genetics/isolation &amp; purification/classification ; Adult ; Viruses/genetics/isolation &amp; purification/classification ; Fungi/genetics/isolation &amp; purification/classification ; Sensitivity and Specificity ; *Respiratory Tract Infections/microbiology/diagnosis ; Aged, 80 and over ; *Lung Diseases/microbiology/diagnosis ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been widely reported to provide crucial information for the diagnosis and treatment of infectious diseases. In this study, we aimed to evaluate mNGS in pathogens diagnosis of lung infections.<br><br>METHODS: A total of 188 patients who were suspected of pulmonary infection and received medical treatment at the Second Affiliated Hospital of Nanchang University from August 2022 to December 2023 were enrolled in this study. Conventional microbiological tests (CMTs) and mNGS were employed for pathogens diagnosis.<br><br>RESULTS: Statistical results indicated that mNGS were significantly better than CMTs in sensitivity, negative predictive value, and negative likelihood ratio. Remarkably, the positive detection rate of mNGS was significantly higher than that of CMTs (86.17% vs 67.55%, P < 0.01). Through mNGS, we identified 96 pathogens, comprising 59 bacteria, 18 fungi, 15 viruses, and 4 special pathogens. In contrast, CMTs detected 28 species, including 25 bacteria and 3 fungi. The effectiveness rate of antibiotic treatment decisions based on mNGS results was 40.60%. Out of 54 cases with positive treatment impacts, mNGS results contributed to the treatment and improved prognosis of 16 infections caused by atypical pathogens.<br><br>CONCLUSION: Our results proved the essential role of mNGS in lung infection diagnosis, enabling early detection and the prompt development of targeted anti-infection therapies. We recommended that the clinical application of mNGS can enhance treatment effectiveness and improve patient prognosis.}, }
@article {pmid40375193, year = {2025}, author = {Chen, P and Wei, X and Que, T and Yan, T and Li, S and Zhong, Y and Li, Y and He, M and Liu, W and Hu, Y}, title = {Molecular detection of novel Jingmen tick virus in hard ticks from diverse hosts in Guangxi, southwestern China.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {143}, pmid = {40375193}, issn = {1743-422X}, support = {2023GXNSFAA026517//Natural Science Foundation of Guangxi Province/ ; 2023GXNSFAA026517//Natural Science Foundation of Guangxi Province/ ; 2023GXNSFAA026517//Natural Science Foundation of Guangxi Province/ ; No. Guike AB22035027//Guangxi Key Research and Development Program/ ; 2023YFC2605400//National Natural Science Foundation of China/ ; }, mesh = {Animals ; China ; Phylogeny ; *Ixodidae/virology/classification ; Genome, Viral ; Genetic Variation ; Metagenomics ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Ticks are the second most important vectors of arboviruses after mosquitoes, and they also serve as reservoir hosts for some zoonotic diseases. It is essential to understand the prevalence of tick-borne viruses in ticks from different sampling sites and vectors, as this information can facilitate the surveillance and prevention of arboviral infectious diseases.<br><br>METHODS: We systematically collected ticks from a variety of animals, including wildlife and domestic livestock, across 18 distinct regions in Guangxi Zhuang Autonomous Region(Guangxi). We then identified the ticks using traditional morphological classification and molecular biology methods to investigate the diversity of ticks in the regionWe also systematically examined the diversity of viruses carried by ticks using comprehensive virological methods based on viral metagenomics. We performed phylogenetic and recombination analyses for the assembled viral sequences.<br><br>RESULTS: We collected 1286 Ixodidae from 18 sampling sites in 17 districts of Guangxi. We identified 4 genera and 6 species of Ixodidae. We annotated 2 unclassified viruses and 13 known viral families. We assembled 208 nucleotide sequences and obtained six near full-length sequences of Jingmen tick virus (JMTV). Among these sequences, GXTV-PC4.2 and GXTV-43 were new mutant strains of JMTV. We detected genetic recombination of JMTV in segments 2, 3, and 4 of JMTV.<br><br>CONCLUSIONS: Our study uncovers a diverse tick fauna in Guangxi, including 4 genera and 6 species, and a broad virome with 13 viral families and 2 novel viruses. The JMTV, in particular, shows significant genetic diversity and potential for cross-species transmission, marked by new strains and recombination events. These findings underscore the need for vigilant tick-borne disease surveillance in Guangxi.}, }
@article {pmid40375084, year = {2025}, author = {Rahman Hera, M and Koslicki, D}, title = {Estimating similarity and distance using FracMinHash.}, journal = {Algorithms for molecular biology : AMB}, volume = {20}, number = {1}, pages = {8}, pmid = {40375084}, issn = {1748-7188}, support = {R01GM146462//National Institutes of Health, United States/ ; R01GM146462//National Institutes of Health, United States/ ; }, abstract = {MOTIVATION: The increasing number and volume of genomic and metagenomic data necessitates scalable and robust computational models for precise analysis. Sketching techniques utilizing k -mers from a biological sample have proven to be useful for large-scale analyses. In recent years, FracMinHash has emerged as a popular sketching technique and has been used in several useful applications. Recent studies on FracMinHash proved unbiased estimators for the containment and Jaccard indices. However, theoretical investigations for other metrics are still lacking.<br><br>THEORETICAL CONTRIBUTIONS: In this paper, we present a theoretical framework for estimating similarity/distance metrics by using FracMinHash sketches, when the metric is expressible in a certain form. We establish conditions under which such an estimation is sound and recommend a minimum scale factor s for accurate results. Experimental evidence supports our theoretical findings.<br><br>PRACTICAL CONTRIBUTIONS: We also present frac-kmc, a fast and efficient FracMinHash sketch generator program. frac-kmc is the fastest known FracMinHash sketch generator, delivering accurate and precise results for cosine similarity estimation on real data. frac-kmc is also the first parallel tool for this task, allowing for speeding up sketch generation using multiple CPU cores - an option lacking in existing serialized tools. We show that by computing FracMinHash sketches using frac-kmc, we can estimate pairwise similarity speedily and accurately on real data. frac-kmc is freely available here: https://github.com/KoslickiLab/frac-kmc/.}, }
@article {pmid40374064, year = {2025}, author = {Wang, J and Zhou, Y and Zhang, T and Zhang, Y and Lian, Q}, title = {Pre-treatment of excess sludge with sulfide-containing wastewater for composite electron donor formation to enhance denitrification.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132673}, doi = {10.1016/j.biortech.2025.132673}, pmid = {40374064}, issn = {1873-2976}, abstract = {Utilizing the fermentation liquor of excess sludge (ES) for the denitrification process represents an effective strategy for the valorization of ES and achieving environmentally friendly denitrification. However, ES fermentation technologies require significant energy or chemical product inputs. The present study proposes a novel method utilizing sulfide-containing wastewater to pretreat ES for generating dissolved organic matter (DOM), with sulfides and DOM collectively forming a composite electron donor (S-ES-DOM). The introduction of S-ES-DOM enables the establishment of integrated autotrophic and heterotrophic denitrification (IAHD) process, achieving 100 % denitrification efficiency. Molecular analysis identified an increase in biodegradable components within S-ES-DOM, which were effectively utilized during the IAHD process. The functional genes associated with nitrate-sulfide-organic carbon metabolism and electron transfer exhibited upregulation. The mixotrophic microbial community enables flexible adoption of multiple metabolic pathways. This strategy simultaneously achieves low-cost ES valorization and low-carbon nitrate/sulfide removal through integrated nitrogen-sulfur-carbon metabolism.}, }
@article {pmid40373994, year = {2025}, author = {Pereira, S and Rubina, M and Roga, A and Selga, T and Skinderskis, E and Gudrā, D and Kalniņa, I and Vonda, K and Fridmanis, D and Muter, O}, title = {Evaluation of functional capacity and plastic-degrading potential of Bacillus spp. and other bacteria derived from the Getliņi landfill (Latvia).}, journal = {Environmental research}, volume = {}, number = {}, pages = {121849}, doi = {10.1016/j.envres.2025.121849}, pmid = {40373994}, issn = {1096-0953}, abstract = {The mechanisms of plastic biodegradation by microorganisms remain poorly understood because of high variability in environmental conditions. This study aimed to isolate, identify, and characterise bacteria with plastic-degrading potential derived from the Getliņi EKO landfill (Riga, Latvia). Among the bacteria selected, Bacillus was the predominant genus identified, whereas Pseudomonas dominated the metagenome. Comparative testing revealed the highest non-specific esterase activity in cultures of B. licheniformis and B. altitudinis. Following a 6-week batch experiment, a newly developed bacterial consortium biologically reduced the weight of untreated low-density polyethylene (LDPE), polyethylene terephthalate (PET), and high-density polyethylene (HDPE) by 19.44%, 5.99%, and 2.58%, respectively. Thermally pre-treated PET and acid pre-treated HDPE resulted in greater weight losses than their respective untreated forms. Scanning electron microscopy primarily showed single cells and microcolonies attached to the granule surfaces. Microbial respiration and fluorescein diacetate hydrolysis tests suggested that the granules had a stimulating effect on the metabolic activity of planktonic cells. Cultures with untreated LDPE and PET exhibited the highest ecotoxicity for Thamnocephalus platyurus, reducing ingestion activity by 60.39% and 71.25% of the control, respectively. In conclusion, the Getliņi EKO landfill appears to be a promising sampling source for bacteria capable of biodegrading fossil-based polymers. Further refinement of methods for the isolation and evaluation of plastic degraders will provide new insights into the potential of microbial resources for plastic degradation.}, }
@article {pmid40373900, year = {2025}, author = {Yin, CY and Sadiq, H and Liao, WH and Wang, HN and Fu, Z and Yu, WG and Han, F}, title = {Identification and functional characterization of two novel hyaluronate lyases BxHly33 and BiHly33, from the human gut microbiome.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {144153}, doi = {10.1016/j.ijbiomac.2025.144153}, pmid = {40373900}, issn = {1879-0003}, abstract = {Hyaluronic acid (HA) is a key glycosaminoglycan in the extracellular matrix, essential for cellular signaling, hydration, and tissue homeostasis. This study identified two novel polysaccharide lyase family 33 (PL33) hyaluronate lyases, BxHly33 and BiHly33, from the human gut microbiome using metagenomic screening. These enzymes demonstrated high specificity and stability in degrading HA, with optimal activity at pH 6.6-7.6 and temperatures of 35-40 °C. Furthermore, structural and biochemical analyses revealed their catalytic mechanisms, highlighting key residues responsible for their function. Notably, specific alanine substitutions significantly enhanced their enzymatic activity. BxHly33 and BiHly33 present promising alternatives to conventional hyaluronidases, which are often costly and immunogenic, for drug delivery and tissue engineering applications. This study will provide novel insights into exploring their therapeutic potential in HA degradation therapies.}, }
@article {pmid40373514, year = {2025}, author = {Tong, X and Zhang, X and Fu, J and He, R}, title = {Mechanisms on nitrogen amendment stimulating methane oxidation in landfill cover soils.}, journal = {Waste management (New York, N.Y.)}, volume = {203}, number = {}, pages = {114893}, doi = {10.1016/j.wasman.2025.114893}, pmid = {40373514}, issn = {1879-2456}, abstract = {Landfill cover soil plays a pivotal role in mitigating CH4 input to the atmosphere. However, the community and activity of methane-oxidizing bacteria (MOB), and their responses to nutrient amendment remain insufficiently understood in landfill cover soils. In this study, the influencing mechanisms of nitrogen amendment on MOB activity, and their functional microorganisms and genes were investigated in landfill cover soils. An exogenous ammonium and nitrate addition could enhance CH4 oxidation activity of 13.9-34.1 times in the landfill cover soil. The NH4[+]-N addition of 800 mg kg[-1] could cause a maximum nitrite accumulation of 41.2 mg kg[-1] in the landfill cover soils and inhibit CH4 oxidation. Nitrogen was mainly deposited in the landfill cover soil in the form of organic nitrogen, with a slight loss of 1.47-3.21 % in the treatments amended with ammonium and nitrate at each stage. A high CH4 oxidation could increase the secretion of CH4-derived carbon and improve the organic matter of soil. Compared with ammonium, the nitrate addition had a greater stimulating effect on microbial and MOB growth. Type I MOB predominated in the soils amended with ammonium and nitrate, whereas type II MOB dominated in the nitrogen-deficient soils. Metagenomic analysis showed that the genes related to nitrogen fixation (nifDKH) were more abundant in the nitrogen-deficient soil than the others. These findings suggest that an appropriate ammonium and nitrate addition could induce carbon and nitrogen accumulation, and stimulate microbial metabolism such as CH4 oxidation and element cycles in the landfill cover soils to mitigate CH4 emission.}, }
@article {pmid40373448, year = {2025}, author = {Liu, H and Fan, Y and Su, E and Liu, S and Ming, Y and Huang, Z and Yu, H and Liu, F and Wang, C and Yu, X and Niu, M and Wu, K and Yang, Y and He, Z and Zhang, T and Yan, Q}, title = {Mariculture increases microbially-driven carbon metabolism and sequestration in coastal ecosystems.}, journal = {Journal of environmental management}, volume = {386}, number = {}, pages = {125756}, doi = {10.1016/j.jenvman.2025.125756}, pmid = {40373448}, issn = {1095-8630}, abstract = {Mariculture has expanded significantly in recent decades due to rising seafood demand and its contribution to ocean carbon sequestration. While the mechanisms of carbon sequestration in mariculture are well-established, the roles of microorganisms in sedimentary carbon sequestration have rarely been explored. How microorganisms mediate organic carbon metabolism and their effects on coastal carbon pools remain unclear. Here we tested the carbon fraction and contents, as well as extracellular hydrolase activities in macroalgae culture area, fish or abalone culture area, and control area without mariculture. We profiled microbial community composition and carbon metabolism characteristics in sediments through 16S rRNA gene amplicon sequencing and metagenomics. Our findings revealed that macroalgae culture areas exhibited a significantly greater potential for carbon sequestration than the control area, the concentration of TOC in seawater and the contents of SOC, DOC, and ROC in sediments were significantly (p < 0.05) increased by 18.93 %, 6.98 %, 33.98 %, and 18.30 % respectively. These results can be attributed to decreased activities of extracellular hydrolase and a lower abundance of carbon-degrading genes. Moreover, metabolic profiling identified taxa from families such as Alteromonadaceae, Pseudomonadaceae, Rhodobacteraceae, Enterobacteriaceae, and Flavobacteriaceae, which are highly metabolically flexible in utilizing a wide range of organic and inorganic energy sources, playing crucial roles in carbon formation. Their respiratory metabolism, such as sulfate reduction, thiosulfate oxidation, and denitrification as well as secondary metabolism products could also affect the formation and persistence of sedimentary carbon pools. Specifically, increased total nitrogen (TN) and nitrate-nitrogen (NO3[-]) could potentially enhance microbial degradation of organic carbon, decreasing carbon stock within coastal sediments. This study enhanced our understanding of microbial regulation of the organic carbon pool in the mariculture ecosystem.}, }
@article {pmid40373419, year = {2025}, author = {Orsi, AS and Lemos Junior, WJF and Alegbeleye, OO and Muniz, DC and Horita, CN and Sant'Ana, AS}, title = {Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.}, journal = {Meat science}, volume = {226}, number = {}, pages = {109848}, doi = {10.1016/j.meatsci.2025.109848}, pmid = {40373419}, issn = {1873-4138}, abstract = {This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.}, }
@article {pmid40373403, year = {2025}, author = {Zhao, F and Wu, S and Shen, X and Huang, Y and Zhang, B and Luo, Z and Wu, D and Shen, L and Cao, S and Wang, Y and Zhang, J and Yu, S}, title = {Metagenomic analysis reveals the diversity, transmission and potential ecological risks of yak nasal bacteria-carried antibiotic resistance genes in the Sichuan region of Qinghai-Tibet plateau.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138476}, doi = {10.1016/j.jhazmat.2025.138476}, pmid = {40373403}, issn = {1873-3336}, abstract = {The Qinghai-Tibet Plateau (QTP) and yaks play respectively vital roles in global and plateau ecosystems. Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants. However, few studies have investigated the abundance and diversity of ARGs and mobile genetic elements (MGEs) in the yak upper respiratory tract and their surrounding pastures. Moreover, the possible pathways for ARG transmission within these ecosystems have not yet been elucidated. Therefore, we investigated the ARG profiles, MGE profiles, and ARG-carrying host bacteria in yaks and their pasture collected from Ganzi and Aba region in Sichuan Province. Metagenomic analyses showed that 22 ARG types and 5 MGEs types were identified in 18 samples. Multidrug resistance gene (mexT) and bacitracin resistance gene (bacA) was identiffed as hotspots, which may compromise medical treatment options. Co-occurrence network analysis revealed that 12 bacterial genera may be potential hosts at the genus level. The enrich of ARGs and MGEs diversity were observed in QTP (Sichuan province) pasture ecosystems which demands evidence-based interventions to mitigate ARGs transmission risks.}, }
@article {pmid40373385, year = {2025}, author = {Xu, Z and Pei, Y and Wang, H and Li, X}, title = {Comparative analysis of gut microbiota-mediated bile acid profiles in Bufo gargarizans and Rana chensinensis tadpoles.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {55}, number = {}, pages = {101530}, doi = {10.1016/j.cbd.2025.101530}, pmid = {40373385}, issn = {1878-0407}, abstract = {Bile acids (BAs) are cholesterol derivatives synthesized by the liver, exhibit variation between different species. Researchers have long appreciated that microbiota play the roles in the biotransformation of BAs. However, relatively few studies have been reported on microbial-mediated production and transformation of BAs in amphibians. Our focus here is principally on difference of intestinal microbial diversity and BAs profiles between two common amphibians, Bufo gargarizans (B. gargarizans) and Rana chensinensis (R. chensinensis) tadpoles, through intestinal targeted BAs metabolomics and fecal metagenomic sequencing. The results demonstrated that B. gargarizans possessed higher levels of total BAs and higher ratio of unconjugated / conjugated BAs. In addition, the relative abundance of microbiota with bile salt hydrolase (BSH) activity in B. gargarizans was significantly higher than that of R. chensinensis, which may facilitate the conversion of conjugated to unconjugated BAs. Meanwhile the higher prevalence of bile-acid-induced (BAI) gene encoding microbiota in R. chensinensis may promote the synthesis of deoxycholic acid (DCA). Furthermore, discrepancies in virulence factors (VFs) and energy metabolism were observed between the two species, which may be linked to differences in the microbiota. This study revealed substantial differences in intestinal microbes and BAs across amphibian species, emphasizing the significant impact of intestinal microbes on BAs metabolism.}, }
@article {pmid40373374, year = {2025}, author = {Li, Y and Bhatt, P and Xagoraraki, I}, title = {In-depth comparison of untargeted and targeted sequencing for detecting virus diversity in wastewater.}, journal = {Water research}, volume = {283}, number = {}, pages = {123803}, doi = {10.1016/j.watres.2025.123803}, pmid = {40373374}, issn = {1879-2448}, abstract = {Sequencing approaches may enable monitoring of a broad range of viruses in wastewater, including potential emerging and non-reportable human viruses. Considering the fact that metagenomic sequencing may be non-specific for low-abundance human viruses, integration of viral amplification and enrichment strategies are proposed to enhance the accurate detection of a broad range of human viruses in municipal wastewater. In this study, we focused on the in-depth comparison analysis of three untargeted amplification methods (Multiple Displace Amplification [MDA], Reverse Transcription - MDA [RT-MDA], and a PCR-based random amplification [PCR-based]) and one targeted method (Twist Comprehensive Viral Research Panel [TWIST]) for detecting virus diversity in wastewater. In addition, we included the comparisons of two extraction kits (Qiagen QIAamp VIRAL RNA Mini Kit and ZymoBIOMICSTM DNA/RNA Minipre Kit) and four virus identification tools (Diamond blast, Kraken2, VirSorter2 and geNomad) for a systematic study. Performances of Qiagen and Zymo extraction kits in recovering viruses and human viruses in wastewater were comparable. By the three untargeted methods we detected 12,808 contigs with lengths longer than 10,000 bp. No contig longer than 10,000 bp was detected by the targeted method. Presence of human viruses were analyzed further by comparing the viral contigs against a custom Swiss-Prot human virus database. There were 45 viruses that are potentially associated with human health found in wastewater, 8 of them were unique to the targeted method and 7 of them were unique to the three untargeted methods. Four enteric viruses Mamastrovirus, Norovirus, Rotavirus and Sapovirus were detected with high abundance in samples prepared with the targeted method. Dimensional scaling analysis demonstrated the divergent virus and human virus communities from the untargeted and targeted methods. Patterns of virus and human virus populations identified by Kraken2 and geNomad were similar. Presence of selected viruses (SARS-CoV-2 [N1&amp;N2], SC2, RSV, Norovirus GI and GII) were confirmed with ddPCR. This work indicates integration of untargeted and targeted sequencing methods, and complementary ddPCR can ensure the accurate detection of known and novel viruses using wastewater surveillance.}, }
@article {pmid40372916, year = {2025}, author = {Ramar, M and Wiscovitch-Russo, R and Yano, N and Singh, H and Lamere, E and Short, M and Gonzalez-Juarbe, N and Fedulov, AV}, title = {Live bacteria in gut microbiome dictate asthma onset triggered by environmental particles via modulation of DNA methylation in dendritic cells.}, journal = {Cell reports}, volume = {44}, number = {5}, pages = {115684}, doi = {10.1016/j.celrep.2025.115684}, pmid = {40372916}, issn = {2211-1247}, abstract = {Despite broad knowledge of the pathogenesis, our understanding of the origin of allergy and asthma remains poor, preventing etiotropic treatments. The gut microbiome is seen to be altered in asthmatics; however, proof of causality of the microbiome alterations is lacking. We report on gut microbiome transplantation (GMT) from mice predisposed to asthma by maternal exposure to pro-allergy environmental particles into naive recipients. This GMT confers asthma predisposition, and the effect is abrogated by gamma sterilization of the transplant material or by co-administration of antibacterials, indicating that viable bacteria are mediating the effect. Metagenomics identifies key changes in the "pro-asthma" microbiome, and metabolomics links the identified species to altered production of butyrate known to act on immune cells and epigenetic mechanisms. We further show that transplant recipients develop DNA methylation alterations in dendritic cells. Finally, dendritic cells with an altered methylome present allergen to T cells, and this effect is abrogated by an epigenetically acting drug in vitro.}, }
@article {pmid40372723, year = {2025}, author = {Al-Najim, A and Hauns, S and Tran, VD and Backofen, R and Alkhnbashi, OS}, title = {HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, pmid = {40372723}, issn = {2047-217X}, support = {2168/23//Deutsche Forschungsgemeinschaft/ ; 2168/25-1//Deutsche Forschungsgemeinschaft/ ; //University of Freiburg/ ; }, mesh = {*Deep Learning ; *Metagenomics/methods ; *Bacteriophages/genetics ; Genome, Viral ; *DNA, Viral/genetics ; Metagenome ; *Computational Biology/methods ; *Sequence Analysis, DNA/methods ; Humans ; *Software ; }, abstract = {BACKGROUND: Bacteriophages are among the most abundant organisms on Earth, significantly impacting ecosystems and human society. The identification of viral sequences, especially novel ones, from mixed metagenomes is a critical first step in analyzing the viral components of host samples. This plays a key role in many downstream tasks. However, this is a challenging task due to their rapid evolution rate. The identification process typically involves two steps: distinguishing viral sequences from the host and identifying if they come from novel viral genomes. Traditional metagenomic techniques that rely on sequence similarity with known entities often fall short, especially when dealing with short or novel genomes. Meanwhile, deep learning has demonstrated its efficacy across various domains, including the bioinformatics field.<br><br>RESULTS: We have developed HVSeeker-a host/virus seeker method-based on deep learning to distinguish between bacterial and phage sequences. HVSeeker consists of two separate models: one analyzing DNA sequences and the other focusing on proteins. In addition to the robust architecture of HVSeeker, three distinct preprocessing methods were introduced to enhance the learning process: padding, contigs assembly, and sliding window. This method has shown promising results on sequences with various lengths, ranging from 200 to 1,500 base pairs. Tested on both NCBI and IMGVR databases, HVSeeker outperformed several methods from the literature such as Seeker, Rnn-VirSeeker, DeepVirFinder, and PPR-Meta. Moreover, when compared with other methods on benchmark datasets, HVSeeker has shown better performance, establishing its effectiveness in identifying unknown phage genomes.<br><br>CONCLUSIONS: These results demonstrate the exceptional structure of HVSeeker, which encompasses both the preprocessing methods and the model design. The advancements provided by HVSeeker are significant for identifying viral genomes and developing new therapeutic approaches, such as phage therapy. Therefore, HVSeeker serves as an essential tool in prokaryotic and phage taxonomy, offering a crucial first step toward analyzing the host-viral component of samples by identifying the host and viral sequences in mixed metagenomes.}, }
@article {pmid40372371, year = {2025}, author = {Li, X and He, N and Wang, H and Wu, Z and Wang, M and Liang, H and Xiao, L and Yang, Z and Li, C and Xu, P and Dai, T and Li, S and Zou, Y}, title = {Therapeutic effect of Faecalibacterium longum CM04-06 on DSS-induced ulcerative colitis in mice.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf119}, pmid = {40372371}, issn = {1365-2672}, abstract = {AIMS: This study explores the impact of Faecalibacterium longum CM04-06 on inflammatory bowel disease (IBD) by regulating gut microbiota in mice.<br><br>METHODS AND RESULTS: We reanalyzed the distribution of the CM04-06 genome in the metagenome of the IBD cohort and observed a significantly higher abundance of CM04-06 in healthy individuals compared to patients with UC or CD. The prophylactic administration of CM04-06 was evaluated for its effects on intestinal microbial diversity and community composition after a two-week trial in mice. The intestinal microbiota was characterized using metagenomic sequencing of fecal samples on the DNBSEQ platform. CM04-06 treatment resulted in a significant reduction in the Disease Activity Index (DAI) and histological scores, as well as a decrease in the levels of pro-inflammatory cytokines, including IL-1&#x3b2;, IL-6, and TNF-&#x3b1;, in both the colon and serum of DSS-induced mice. Furthermore, supplementation with CM04-06 significantly reduced the levels of pro-inflammatory cytokines in both the colon and serum. Additionally, CM04-06 enhanced the integrity of the intestinal epithelial barrier by increasing the expression of tight junction proteins and mucin. Moreover, we observed greater abundances of Faecalibaculum rodentium, Alistipes onderdonkii, Alistipes shahii, and Bifidobacterium animalis after CM04-06 treatment.<br><br>CONCLUSIONS: CM04-06 prevents and alleviates intestinal inflammation by modulating the composition of the microbiota community, increasing the abundance of beneficial probiotics, and suppressing pro-inflammatory cytokine levels.}, }
@article {pmid40372056, year = {2025}, author = {Kok, CR and Thissen, JB and Cerroni, M and Tribble, DR and Cancio, A and Tran, S and Schofield, C and Colombo, RE and Troth, T and Joya, C and Lalani, T and Be, NA}, title = {Field expedient stool collection methods for gut microbiome analysis in deployed military environments.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0081824}, doi = {10.1128/msphere.00818-24}, pmid = {40372056}, issn = {2379-5042}, abstract = {Field expedient devices and protocols for the collection, storage, and shipment of stool samples in deployed settings are needed for the advancement of microbiome research in military health. Relevant assessments include the evaluation of microbiome signatures associated with susceptibility to travelers' diarrhea and recovery of gut function following infection. However, inherent biases in microbial measurements due to preservatives and sampling methods are unclear and should be assessed for an accurate evaluation of the microbiome. We performed shotgun metagenomic sequencing and compared the microbiome composition in paired fecal samples collected using Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes, prior to and during international travel, from 49 adult participants, 39 of whom remained asymptomatic and 10 experienced travelers' diarrhea. Higher concentrations of nucleic acid and sequencing libraries were observed in OG samples. A majority of genera (82.9%) were detected with both methods, and detections of genera limited to one collection method were not highly prevalent across samples and were present in extremely low relative abundances (<0.01%). Differences in beta diversity were largely explained by inter-individuality of microbiome composition, followed by the effect of collection method and timepoint-disease states. Differential abundance analysis indicated that Corynebacterium and Blautia were consistently higher in abundance across all groups with FTA and OG collection, respectively. The observed differences in microbiome composition between methods suggest the need for consistent and standardized protocols within a study. Overall, the data presented here could help guide the future design of fecal microbiome study protocols in field and military deployment settings.IMPORTANCEThe assessment of field-deployable methods for fecal sample collection and storage is required to reliably capture samples collected in remote and austere locations. This study describes a comparative metagenomics analysis between samples collected by two different commercially available methods in a military-deployed setting. The results presented here are foundational for the future design of fecal microbiome study protocols in an operational context.}, }
@article {pmid40371968, year = {2025}, author = {Jansen, D and Deleu, S and Caenepeel, C and Marcelis, T and Simsek, C and Falony, G and Machiels, K and Sabino, J and Raes, J and Vermeire, S and Matthijnssens, J}, title = {Virome drift in ulcerative colitis patients: faecal microbiota transplantation results in minimal phage engraftment dominated by microviruses.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2499575}, doi = {10.1080/19490976.2025.2499575}, pmid = {40371968}, issn = {1949-0984}, mesh = {Humans ; *Fecal Microbiota Transplantation ; *Colitis, Ulcerative/therapy/virology/microbiology ; *Virome ; Male ; Female ; Feces/virology ; Adult ; Gastrointestinal Microbiome ; Middle Aged ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Young Adult ; }, abstract = {Ulcerative colitis (UC) is an inflammatory bowel disease characterized by recurrent colonic inflammation. Standard treatments focus on controlling inflammation but remain ineffective for one-third of patients. This underscores the need for alternative approaches, such as fecal microbiota transplantation (FMT), which transfers healthy donor microbiota to patients. The role of viruses in this process, however, remains underexplored. To address this, we analyzed the gut virome using metagenomic sequencing of enriched viral particles from 320 longitudinal fecal samples of 44 patients enrolled in the RESTORE-UC FMT trial. Patients were treated with FMTs from healthy donors (allogenic, treatment) or themselves (autologous, control). We found that colonic inflammation, both its presence and location, had a greater impact on the gut virome than FMT itself. In autologous FMT patients, the virome was unstable and showed rapid divergence over time, a phenomenon we termed virome drift. In allogenic FMT patients, the virome temporarily shifted toward the healthy donor, lasting up to 5 weeks and primarily driven by microviruses. Notably, two distinct virome configurations were identified and linked to either healthy donors or patients. In conclusion, inflammation strongly affects the gut virome in UC patients, which may lead to instability and obstruct the engraftment of allogeneic FMT.}, }
@article {pmid40371337, year = {2025}, author = {Lehner, MD and Ulsemer, P and Christochowitz, S}, title = {Menthacarin, a proprietary combination of peppermint and caraway oil, alters cultured human fecal microbiota composition, resulting in increased SCFA production.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1569052}, pmid = {40371337}, issn = {1663-9812}, abstract = {BACKGROUND: Disruptions in the gut microbiota metabolism may contribute to the pathophysiology of gut-brain interaction disorders, and correction of intestinal dysbiosis is considered a promising therapeutic approach. Menthacarin, a proprietary fixed combination of Mentha x piperita L. and Carum carvi L. essential oils, is used clinically for the treatment of functional dyspepsia and irritable bowel syndrome. Rodent model data indicate that treatment effects of Menthacarin on visceral hypersensitivity could be mediated via the normalization of gut dysbiosis. However, the impact of Menthacarin on human bacterial gut microbiota has not yet been studied.<br><br>AIM: The aim of the present study was to assess whether Menthacarin affects the composition and metabolic activity of human fecal microbiota.<br><br>METHODS: Fecal slurry samples from 10 healthy volunteers were cultivated for 36&#xa0;h under anoxic conditions with and without Menthacarin. Relative bacterial abundance at the phylum and genus levels was evaluated using 16S rRNA metagenomic analysis. Short-chain fatty acids (SCFAs) in the supernatants were measured using the LC-MS technology.<br><br>RESULTS: Menthacarin induced robust changes in microbial composition at both the phylum and genus levels among the 10 donor microbiomes. The relative abundance of Firmicutes (+13.6 &#xb1; 8.6%) and Actinobacteria (+54.9 &#xb1; 47.6%) significantly increased, whereas that of Bacteroidetes (-27.7% &#xb1; 21.9%) and Proteobacteria (-25.7% &#xb1; 12.3%) significantly decreased in the presence of Menthacarin. At the genus level, the most notable changes were significant increases in Bifidobacterium (+105.1 &#xb1; 78.4%) and several SCFA-producing genera accompanied by a significant decrease in genera containing members involved in pro-inflammatory processes. In addition, Menthacarin significantly increased the levels of several SCFAs, namely, propionate, butyrate, isobutyrate, valerate, and isovalerate.<br><br>CONCLUSION: Menthacarin alters the microbiota composition and enhances SCFA production in human microbiota samples under in vitro conditions. These effects may contribute to the clinical benefits observed with Menthacarin treatment.}, }
@article {pmid40371178, year = {2025}, author = {Lanclos, VC and Feng, X and Cheng, C and Yang, M and Hider, CJ and Coelho, JT and Kojima, CY and Barnes, SJ and Cleveland, CS and Xie, M and Zhao, Y and Luo, H and Thrash, JC}, title = {New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf068}, pmid = {40371178}, issn = {2730-6151}, abstract = {The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all Roseobacters in surface oceans and has predicted roles in biogeochemical cycling via heterotrophy, aerobic anoxygenic photosynthesis (AAnP), CO oxidation, DMSP degradation, and other metabolisms. Though cultures of CHAB-I-5 have been reported, none have been explored and the best-known representative, strain SB2, was lost from culture after obtaining the genome sequence. We have isolated two new CHAB-I-5 representatives, strains US3C007 and FZCC0083, and assembled complete, circularized genomes with 98.7% and 92.5% average nucleotide identities with the SB2 genome. Comparison of these three with 49 other unique CHAB-I-5 metagenome-assembled and single-cell genomes indicated that the cluster represents a genus with two species, and we identified subtle differences in genomic content between the two species subclusters. Metagenomic recruitment from over fourteen hundred samples expanded their known global distribution and highlighted both isolated strains as representative members of the clade. FZCC0083 grew over twice as fast as US3C007 and over a wider range of temperatures. The axenic culture of US3C007 occurs as pleomorphic cells with most exhibiting a coccobacillus/vibrioid shape. We propose the name Candidatus Thalassovivens spotae, gen nov., sp. nov. for the type strain US3C007[T] (= ATCC TSD-433[T] = NCMA B160[T]).}, }
@article {pmid40370734, year = {2025}, author = {Yu, F and Guo, Y and Li, Y and Gai, W and Zhang, Q and Li, P and Xu, R and Zhang, L and Zheng, Y and Zhang, X}, title = {Liver abscess and septic shock due to Clostridium perfringens infection: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1575454}, pmid = {40370734}, issn = {2296-858X}, abstract = {Clostridium perfringens causes liver abscesses with a low incidence, rapid progression, and high mortality. Within a few days or even within 24 h, patients may progress from a liver abscess to sepsis, multi-organ failure, and potentially death. Diagnosing Clostridium perfringens infection by routine microbiological testing (CMT) is often challenging. Here, we present a patient with negative blood cultures who was ultimately diagnosed with a liver abscess due to Clostridium perfringens infection, confirmed by metagenomic next-generation sequencing (mNGS). The patient initially presented with fever only, and his blood cultures were negative. Subsequently, the patient's condition progressed rapidly, and he developed signs of septic shock. Immediately after admission to the ICU, he received combined anti-infective therapy with meropenem and tigecycline, as well as urgent ultrasound-guided puncture and drainage. Blood mNGS identified Clostridium perfringens and a variety of anaerobic bacteria, confirming that the pathogen had been covered by empirical antibiotics. Continued anti-infective therapy and drainage improved the patient's symptoms, and he was eventually discharged from the hospital. Clinicians should be highly suspicious of liver abscesses with negative blood cultures. The use of mNGS to identify the pathogen, appropriate antibiotics, and abscess aspiration and drainage are key to patient survival.}, }
@article {pmid40370716, year = {2025}, author = {Yang, Z and Zhou, S and Yang, Z and Liu, P and Chen, S and Zhu, W}, title = {Metagenomic next-generation sequencing enabled diagnosis of Aspergillus spondylitis in an immunocompetent patient: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1575363}, pmid = {40370716}, issn = {2296-858X}, abstract = {BACKGROUND: Aspergillus fumigatus spondylitis is a rare fungal spondylitis that often occurs in immunocompromised patients. This article reports a case of Aspergillus spondylitis with specific image signs, which is rarely reported in an immunocompetent patient.<br><br>CASE PRESENTATION: This is a case of L3-4 segmental Aspergillus spondylitis diagnosed. The diagnosis was confirmed by intraoperative metagenomic next-generation sequencing (mNGS) testing of the diseased tissue. The patient was treated with voriconazole and underwent surgical debridement and internal fixation with pedicle screws.<br><br>CONCLUSION: The diagnosis of Aspergillus spondylitis is often delayed or missed. Doctors should consider Aspergillus spondylitis in the differential diagnosis of unexplained low back pain so that appropriate treatment can be administered to prevent spinal cord injury and disability. Aspergillus spondylitis usually results in endplate inflammatory response line on fluid or enhancement sequences and a diffuse low signal in the diseased vertebral body on T2-weighted imaging (T2WI). It also results in large paraspinal abscesses, which requires further research to better differentiate between Aspergillus spondylitis and tuberculous spondylitis. Prompt diagnosis and treatment can improve the patient's prognosis.}, }
@article {pmid40370098, year = {2025}, author = {Wang, N and Wu, M and Gu, W and Dai, C and Shao, Z and Subbalakshmi, KP}, title = {MSFT-transformer: a multistage fusion tabular transformer for disease prediction using metagenomic data.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {3}, pages = {}, pmid = {40370098}, issn = {1477-4054}, support = {JUSRP123035//Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Computational Biology/methods ; Algorithms ; }, abstract = {More and more recent studies highlight the crucial role of the human microbiome in maintaining health, while modern advancements in metagenomic sequencing technologies have been accumulating data that are associated with human diseases. Although metagenomic data offer rich, multifaceted information, including taxonomic and functional abundance profiles, their full potential remains underutilized, as most approaches rely only on one type of information to discover and understand their related correlations with respect to disease occurrences. To address this limitation, we propose a multistage fusion tabular transformer architecture (MSFT-Transformer), aiming to effectively integrate various types of high-dimensional tabular information extracted from metagenomic data. Its multistage fusion strategy consists of three modules: a fusion-aware feature extraction module in the early stage to improve the extracted information from inputs, an alignment-enhanced fusion module in the mid stage to enforce the retainment of desired information in cross-modal learning, and an integrated feature decision layer in the late stage to incorporate desired cross-modal information. We conduct extensive experiments to evaluate the performance of MSFT-Transformer over state-of-the-art models on five standard datasets. Our results indicate that MSFT-Transformer provides stable performance gains with reduced computational costs. An ablation study illustrates the contributions of all three models compared with a reference multistage fusion transformer without these novel strategies. The result analysis implies the significant potential of the proposed model in future disease prediction with metagenomic data.}, }
@article {pmid40369676, year = {2025}, author = {Zhang, Y and Liu, H and Jing, H}, title = {Community differences and potential function along the particle size spectrum of microbes in the twilight zone.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {121}, pmid = {40369676}, issn = {2049-2618}, support = {424QN341//the Hainan Provincial Natural Science Foundation of China/ ; JRC2023C37//the Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; 2023YFC2812804//the National Key R&amp;D Program of China/ ; 183446KYSB20210002//the International Partnership Program of Chinese Academy of Sciences for Big Science/ ; }, mesh = {Particle Size ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Seawater/microbiology/chemistry ; *Microbiota/genetics ; Metagenomics/methods ; Carbon/metabolism ; Metagenome ; }, abstract = {BACKGROUND: The twilight zone, which extends from the base of the euphotic zone to a depth of 1000 m, is the major area of particulate organic carbon (POC) remineralization in the ocean. However, little is known about the microbial community and metabolic activity that are directly associated with POC remineralization in this consistently underexplored realm. Here, we utilized a large-volume in situ water transfer system to collect the microbes on different-sized particles from the twilight zone in three regions and analyzed their composition and metabolic function by metagenomic analysis.<br><br>RESULTS: Distinct prokaryotic communities with significantly lower diversity and less endemic species were detected on particles in the South East Asian Time-series Study (SEATS) compared with the other two regions, perhaps due to the in situ physicochemical conditions and low labile nutrient availability in this region. Observable transitions in community composition and function at the upper and lower boundaries of the twilight zone suggest that microbes respond differently to (and potentially drive the transformation of) POC through this zone. Substantial variations among different particle sizes were observed, with smaller particles typically exhibiting lower diversity but harboring a greater abundance of carbon degradation-associated genes than the larger particles. Such a pattern might arise due to the relatively larger surface area of the smaller particles relative to their volume, which likely provides more sites for microbial colonization, increasing their chance of being remineralized. This makes them less likely to be transferred to the deep ocean, and thus, they contribute more to carbon recycling than to long-term sequestration. Both contig-based and metagenome-assembled genome-(MAG-) based analyses revealed a high diversity of the Carbohydrate-Active enZymes (CAZy) family. This indicates the versatile carbohydrate metabolisms of the microbial communities associated with sinking particles that modulate the remineralization and export of POC in the twilight zone.<br><br>CONCLUSION: Our study reveals significant shifts in microbial community composition and function in the twilight zone, with clear differences among the three particle sizes. Microbes with diverse metabolic potential exhibited different responses to the POC entering the twilight zone and also collectively drove the transformation of POC through this zone. These findings provided insights into the diversity of prokaryotes in sinking particles and their roles in POC remineralization and export in marine ecosystems. Video Abstract.}, }
@article {pmid40369669, year = {2025}, author = {Purse, C and Parker, A and James, SA and Baker, DJ and Moss, CJ and Evans, R and Durham, J and Funnell, SGP and Carding, SR}, title = {Intestinal microbiota profiles of captive-bred cynomolgus macaques reveal influence of biogeography and age.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {47}, pmid = {40369669}, issn = {2524-4671}, support = {BB/T008717/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1//BBSRC/ ; }, abstract = {BACKGROUND: Age-associated changes to the intestinal microbiome may be linked to inflammageing and the development of age-related chronic diseases. Cynomolgus macaques, a common animal model in biomedical research, have strong genetic physiological similarities to humans and may serve as beneficial models for the effect of age on the human microbiome. However, age-associated changes to their intestinal microbiome have previously only been investigated in faecal samples. Here, we have characterised and investigated the effects of age in the cynomolgus macaque intestinal tract in luminal samples from both the small and large intestine.<br><br>RESULTS: Whole metagenomic shotgun sequencing was used to analyse the microbial communities in intestinal content obtained from six different intestinal regions, covering the duodenum to distal colon, of 24 healthy, captive-bred cynomolgus macaques, ranging in age from 4 to 20&#xa0;years. Both reference-based and assembly-based computational profiling approaches were used to analyse changes to intestinal microbiota composition and metabolic potential associated with intestinal biogeography and age. Reference-based computational profiling revealed a significant and progressive increase in both species richness and evenness along the intestinal tract. The microbial community composition also significantly differed between the small intestine, caecum, and colon. Notably, no significant changes in the taxonomic abundance of individual taxa with age were found except when sex was included as a covariate. Additionally, using an assembly-based computational profiling approach, 156 putative novel bacterial and archaeal species were identified.<br><br>CONCLUSIONS: We observed limited effects of age on the composition of the luminal microbiota in the profiled regions of the intestinal tract except when sex was included as a covariate. The enteric microbial communities of the small and the large intestine were, however, distinct, highlighting the limitations of frequently used faecal microbial profiling as a proxy for the intestinal microbiota. The identification of a number of putative novel microbial taxa contributes to knowledge of the full diversity of the cynomolgus macaque intestinal microbiome.}, }
@article {pmid40368959, year = {2025}, author = {Song, XL and Wang, ZJ and Yin, XW and Sun, YL and Jang, DJ and Hong, SK}, title = {The impact of nitrogen deposition on nitrogen metabolism in ryegrass lawn with different soil nutrient levels.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {16755}, pmid = {40368959}, issn = {2045-2322}, mesh = {*Nitrogen/metabolism ; *Lolium/metabolism ; *Soil/chemistry ; Soil Microbiology ; Nitrogen Fixation ; Nitrification ; *Nutrients/metabolism ; Denitrification ; Nitrogen Cycle ; Microbiota ; Nitrates/metabolism ; }, abstract = {Nitrogen deposition is a crucial factor in global change, which is widespread across various regions globally. It has drawn extensive attention due to its direct modification of soil nitrogen retention and nitrogen species distribution, thereby influencing nitrogen metabolism across entire ecosystems. Previous studies on its influence on nitrogen metabolism have not reached a consensus. In an urban ryegrass lawn mesocosm experiment, we set two levels of nitrogen deposition and soil nutrients respectively, aiming to study the impacts of these factors on the N-cycling process through metagenomic analysis. The results demonstrated nitrogen deposition increased nitrification, nitrogen fixation, denitrification, and dissimilatory nitrate reduction, but decreased assimilatory nitrate reduction in the nitrogen metabolism process by changing soil nitrogen availability and the abundance of N-cycling functional genes in the soil microbial community. The soil nutrient levels exhibited effects opposite to those of nitrogen deposition, negatively impacting nitrification, denitrification, and nitrogen fixation in the nitrogen metabolism process. This work further elucidates the impacts of nitrogen deposition on the ecological functions of the ryegrass lawn with different soil nutrient levels, and predicts the potential impacts of intensified nitrogen deposition on these ecological functions. It provides valuable theoretical support for understanding and evaluating complex ecological interactions.}, }
@article {pmid40368955, year = {2025}, author = {Krishnavajhala, A and Gingras, MC and Urquieta, E and Chao, H and Bandaranaike, D and Chen, Y and Bhamidipati, S and Korchina, V and Griffin, SM and Masternak, MM and Moreno, H and Mohammed, J and Murugan, M and Posey, JE and Wu, JH and Muzny, D and Gibbs, RA and Doddapaneni, H}, title = {The GENESTAR manual for biospecimen collection biobanking and omics data generation from commercial space missions.}, journal = {NPJ microgravity}, volume = {11}, number = {1}, pages = {16}, pmid = {40368955}, issn = {2373-8065}, abstract = {The surge in commercial and civilian spaceflight enables the systematic and longitudinal, large-scale biospecimen collection to understand the prospective effects of space travel on human health. The Genomics and Space Medicine (Space Omics) project at BCM-HGSC involves a comprehensive biospecimen collection plan from commercial/private space flight participants. The manuscript addresses the critical gaps in the biospecimen collection process including details of the informed consent process, a provision for subjects to obtain custom CLIA-WGS reports, a data dictionary and a LIMS enabled biobank. The manuscript also discusses the biospecimens collection, processing methodologies and nucleic acid suitability for Omics data generation. Results from Axiom-2 mission where, 339 biospecimens were collected using 'Genomic Evaluation of Space Travel and Research (GENESTAR)' manual, at two different sites, showed that 98% of the blood samples and 91.6% of the non-blood samples passed the QC requirements for Omics assays, underscoring the reliability and effectiveness of the GENESTAR manual.}, }
@article {pmid40368948, year = {2025}, author = {Serivichyaswat, PT and Scholte, T and Wilms, T and Stranddorf, L and van der Valk, T}, title = {Metagenomic biodiversity assessment within an offshore wind farm.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {16786}, pmid = {40368948}, issn = {2045-2322}, mesh = {*Biodiversity ; *Metagenomics/methods ; North Sea ; Animals ; *Wind ; Seawater ; *DNA, Environmental/genetics/analysis ; Ecosystem ; *Metagenome ; Denmark ; }, abstract = {Environmental DNA (eDNA) analysis can be a powerful tool for monitoring biodiversity and assessing human impacts on ecosystems. In this study, we employed a genome-wide metagenomic eDNA approach to assess the marine biodiversity within and around the Horns Rev 1 offshore wind farm in the Danish North Sea. Seawater samples were collected from both within the windfarm and surrounding control sites, sequenced, and analyzed using a combination of DNA k-mer matching and alignment-based classification methods. We identified a wide range of species across the tree of life-highlighting the species richness of this marine ecosystem. Our results revealed a high degree of species diversity congruence between the wind farm and control sites. While this could suggest minimal ecological disruption of the wind farm, we cannot rule out that the influence of ocean currents and water mixing the DNA from different regions dominate the species detection. We detected bioindicator species, such as Thalassiosira, Phaeocystis and Skeletonema, which can provide insights into water quality. Our metagenomic approach also enabled us to obtain population genomics insights for species, such as the European anchovy (Engraulis encrasicolus) and the diatom Rhizosolenia setigera, and genetically confirmed the origin of the invasive Sea walnut (Mnemiopsis leidyi) in the North Sea. This study highlights the potential of genome-wide eDNA metagenomics as a framework for assessing marine biodiversity and detecting population-level genetic signals, contributing to informed and scalable ecosystem monitoring strategies.}, }
@article {pmid40368316, year = {2025}, author = {Wang, P and He, D and Zhao, J and Xiao, Z and Tan, J and Ma, J and Zheng, M}, title = {Transition from Anammox to Feammox metabolic modes: Regulation strategies for nitrite in Anammox enrichment cultures.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132674}, doi = {10.1016/j.biortech.2025.132674}, pmid = {40368316}, issn = {1873-2976}, abstract = {This studyachievedthe metabolic transition from anaerobic ammonium oxidation (Anammox) to Fe(III)-mediated ammonium oxidation (Feammox)usingiron-carbon micro-electrolytic spheres as a slow-release iron sourcethrougha stepwise reductionin influent NO2[-]-N concentration. The results demonstrated that sustained Feammox activitywas governed bynitrate-dependent ferrous oxidation (NDFO) metabolismcombined withoxygen-regulated Fe(III) regeneration,resulting ina peak total nitrogen removal efficiency of 91.6 %at40 mg/L NO2[-]-N.Whileexclusive NH4[+]-N feeding inhibited Feammox activity,this suppression was reversible upon NO2[-]-N supplementation. Intriguingly, Anammox activityremained robustdespite decreasing NO2[-]-N levelsand showedsignificant positive correlation with Feammox activity,suggesting shared metabolic modules. Metagenomic profilingfurther identifiedCa. Brocadia as the core functional genus driving NH4[+]-N oxidation,highlighting its niche adaptationin iron-mediated systems.These mechanistic insights establish a framework fordesigning energy-efficient nitrogen removal processesleveraging iron-redox cycling.}, }
@article {pmid40368259, year = {2025}, author = {Wu, S and Zhang, N and Wan, Q}, title = {Disulfide bonds enhance thermal stability and thumb region drives activity of the glycoside hydrolase 11 xylanase rMxyl[cd].}, journal = {Journal of structural biology}, volume = {}, number = {}, pages = {108209}, doi = {10.1016/j.jsb.2025.108209}, pmid = {40368259}, issn = {1095-8657}, abstract = {Thermostable enzymes have significant advantages in industries, yet uncovering novel candidates with superior properties remains a scientific pursuit. This study identified rMxyl[cd], a glycoside hydrolase 11 family thermophilic xylanase from compost-soil metagenome, which exhibited a high specific activity of 5954 U·mg[-1] at pH 5.5 and 80°C. rMxyl[cd] was crystallized and diffracted to 1.5 Å resolution. Compared to the mesophilic xylanase Xyn II, rMxyl[cd] exhibits a more compact architecture. Notably, B-factor analysis reveals a uniquely flexible thumb region, hinting at its critical role in the enzyme's catalytic mechanism. rMxyl[cd] contains two disulfide bonds in the thumb and the N-terminal regions. Breaking these disulfide bonds by mutagenesis has dramatically decreased activities and thermostability. Conversely, introducing an extra disulfide bond at the N-terminal region of its α-helix extended its half-life for more than five folds at 80°C. Our studies firmly establish that the disulfide bonds are essential for its high thermal stability and the flexibility of the thumb region is crucial for its activity. Comparing the rMxyl[cd] crystal structure with the AlphaFold2-predicted model shows overall similarity, but the crystal structure offers higher local accuracy, especially in key functional regions. These findings not only deepen our understanding of the structure-function relationship of thermophilic xylanases but also inform a rational design of industrial enzymes.}, }
@article {pmid40368038, year = {2025}, author = {Silvester, R and Perry, WB and Webster, G and Rushton, L and Baldwin, A and Pass, DA and Byrnes, NA and Farkas, K and Heginbothom, M and Craine, N and Cross, G and Kille, P and Kasprzyk-Hordern, B and Weightman, AJ and Jones, DL}, title = {Metagenomic profiling of hospital wastewater: A comprehensive national scale analysis of antimicrobial resistance genes and opportunistic pathogens.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106503}, doi = {10.1016/j.jinf.2025.106503}, pmid = {40368038}, issn = {1532-2742}, abstract = {BACKGROUND: Healthcare settings are recognised as potential hotspots for the emergence and spread of antimicrobial resistance (AMR).<br><br>METHOD: Metagenomic sequencing was conducted on a national scale using wastewater from hospitals across Wales to screen for antimicrobial resistance genes (ARGs) and opportunistic pathogens.<br><br>RESULTS: The total abundance and diversity of ARGs varied significantly across the hospitals. Genes conferring resistance to aminoglycosides, beta-lactams, and Macrolide-Lincosamide-Streptogramin-class antibiotics were predominant, with distinct resistome patterns emerging spatially. OXA-type beta-lactamases were the dominant ARG types. Spatial variability was observed in the distribution of the "big five" carbapenemases (KPC, IMP, VIM, NDM, OXA-48-like) and mcr genes, as well as WHO-listed fungal priority pathogens and Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli (ESKAPEE) pathogens. Furthermore, antibiotic concentrations in the effluents often exceeded risk quotients, posing a substantial risk for AMR emergence.<br><br>CONCLUSIONS: Overall, the study highlights the effectiveness of combining wastewater-based epidemiology with metagenomics to gain critical insights into the distinct resistome and microbiome profiles in hospital settings. Tailored strategies are essential to mitigate the spread of antibiotics, clinically relevant ARGs and pathogens in these settings. This study underscores the necessity of implementing pre-treatment processes for hospital effluents before release into community sewers and environmental waters to curb the spread of these micro-pollutants.<br><br>AVAILABILITY OF DATA: The data will be made available upon request.}, }
@article {pmid40367945, year = {2025}, author = {Antonaru, LA and Rad-Menéndez, C and Mbedi, S and Sparmann, S and Pope, M and Oliver, T and Wu, S and Green, DH and Gugger, M and Nürnberg, DJ}, title = {Evolution of far-red light photoacclimation in cyanobacteria.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.04.038}, pmid = {40367945}, issn = {1879-0445}, abstract = {Cyanobacteria oxygenated the atmosphere of early Earth and continue to be key players in global carbon and nitrogen cycles. A phylogenetically diverse subset of extant cyanobacteria can perform photosynthesis with far-red light through a process called far-red light photoacclimation, or FaRLiP. This phenotype is enabled by a cluster of ∼20 genes and involves the synthesis of red-shifted chlorophylls d and f, together with paralogs of the ubiquitous photosynthetic machinery used in visible light. The FaRLiP gene cluster is present in diverse, environmentally important cyanobacterial groups, but its origin, evolutionary history, and connection to early biotic environments have remained unclear. This study takes advantage of the recent increase in (meta)genomic data to help clarify this issue: sequence data mining, metagenomic assembly, and phylogenetic tree networks were used to recover more than 600 new FaRLiP gene sequences, corresponding to 51 new gene clusters. These data enable high-resolution phylogenetics and-by relying on multiple gene trees, together with gene arrangement conservation-support FaRLiP appearing early in cyanobacterial evolution. Sampling information shows that considerable FaRLiP diversity can be observed in microbialites to the present day, and we hypothesize that the process was associated with the formation of microbial mats and stromatolites in the early Paleoproterozoic. The ancestral FaRLiP cluster was reconstructed, revealing features that have been maintained for billions of years. Overall, far-red-light-driven oxygenic photosynthesis may have played a significant role in Earth's early history.}, }
@article {pmid40367908, year = {2025}, author = {Yuan, L and Chen, Y and Xie, M and Wang, J and Zheng, J and Zhou, J and Li, B and Zhang, D and Han, D}, title = {Utility of clinical metagenomics in complex infections: Cryptococcal meningitis complicated by Nocardia brain abscess.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {1}, pages = {116895}, doi = {10.1016/j.diagmicrobio.2025.116895}, pmid = {40367908}, issn = {1879-0070}, abstract = {Nocardia farcinica brain abscess (BA) is a rare yet life-threatening infection of the central nervous system (CNS) that predominantly affects immunocompromised patients. Its nonspecific symptoms often lead to delayed diagnosis and poor outcomes. Early diagnosis and precise treatment are essential to improve the prognosis of patients. We report the rare case of a 75-year-old man with IgG4-related disease undergoing long-term methylprednisolone therapy who presented with a N. farcinica brain abscess. The patient initially presented with cryptococcal meningitis but exhibited persistent symptoms despite standard antifungal treatment. Follow-up neuroimaging revealed new intracranial abscess formations. Metagenomic next-generation sequencing (mNGS) of brain tissue and cerebrospinal fluid (CSF) identified abundant N. farcinica-specific sequences, confirming a concurrent Nocardia brain abscess complicating the cryptococcal infection. The patient's condition gradually improved with timely antibiotic treatment and is currently in recovery. This case underscores the heightened risk of sequential opportunistic infections in immunocompromised individuals and exemplifies the clinical value of mNGS in detecting rare infectious diseases. We further conducted a systematic review of patients with Nocardia central nervous system infections confirmed by mNGS, analyzing their clinical presentations, laboratory parameters, therapeutic regimens, and prognostic outcomes. In summary, our study demonstrates that mNGS offers significant diagnostic advantages compared to conventional microbiological methods for uncommon infections. These findings provide clinically actionable, evidence-based guidance for the diagnosis and management of Nocardia brain abscesses.}, }
@article {pmid40367885, year = {2025}, author = {Mo, S and Wu, X and Kashif, M and Zeng, S and Sang, Y and Meng, C and He, S and Jiang, C}, title = {Effects of Spartina alterniflora invasion on carbon fixation and sulfate reduction in a subtropical marine mangrove ecosystem.}, journal = {Marine pollution bulletin}, volume = {217}, number = {}, pages = {118128}, doi = {10.1016/j.marpolbul.2025.118128}, pmid = {40367885}, issn = {1879-3363}, abstract = {Mangrove sediments host diverse microbial communities that are crucial for carbon fixation, but their functions and pathways in subtropical ecosystems-particularly under Spartina alterniflora invasion and across varying sediment depths-remain unclear. This study employed metagenomic and qPCR analyses to explore microbial carbon fixation in Rhizophora stylosa, S. alterniflora, and bare beach habitats. Environmental factors like Cd, sulfide, pH, and salinity significantly influenced carbon fixation and sulfate reduction. Specifically, the invasion increased the abundance of key carbon fixation genes, including aclA/B, cbbL, and korA, which are involved in the Calvin-Benson-Bassham (CBB) and Arnon-Buchanan (rTCA) cycles, respectively. This shift in gene abundance was accompanied by elevated Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) activity (0.47-21.82 nmol CO2 g[-1] soil min[-1]), suggesting a potential increase in microbial CO2 fixation rates in S. alterniflora-invaded sediments. Sediment depth also affected the distribution of carbon fixation genes and carbon-metabolizing microbes. Desulfobacterota were identified as major contributors to carbon fixation via both the rTCA and CBB cycles. Moreover, a strong correlation was observed between carbon fixation and sulfate reduction. These findings reveal how S. alterniflora invasion impacts carbon fixation and enhance our understanding of the mangrove ecosystems' role in climate change regulation.}, }
@article {pmid40367854, year = {2025}, author = {Ahmad, W and Coffman, L and Ray, R and Woldesenbet, S and Singh, G and Khan, AL}, title = {Flooding episodes and seed treatment influence the microbiome diversity and function in the soybean root and rhizosphere.}, journal = {The Science of the total environment}, volume = {982}, number = {}, pages = {179554}, doi = {10.1016/j.scitotenv.2025.179554}, pmid = {40367854}, issn = {1879-1026}, abstract = {Climate change-related events such as flooding have threatened crop productivity, agricultural sustainability, and global food security by causing hypoxic conditions. Such conditions impaire root development and nutrient acquisition, and alter root rhizospheric microbial communities that are vital for plant health and productivity. Seed treatment with pathogen protection have been key to maintaining early seed germination and plant productivity in field conditions. Still, their role in flooding stress and microbiome diversity and functionality in soybeans is poorly understood. Here, we performed field-based investigations to understand the impact of flooding episodes (0, 3, and 7 days after floodings; DAF) and seed treatment (Cruiser MAXX) on soybean plant growth and rhizosphere microbiome diversity and functionality. Flooding episodes significantly reduced seed yield (746 kg ha[-1]) compared to untreated control. However, the seed treatment increased plant height and pods per plant (3-DAF) and reduced flood injury by 33 % (7-DAF). The shotgun metagenomic analysis showed that seed treatment significantly enhanced the microbial community in rhizospheric soil. Flooding episodes impacted the microbial communities with higher abundance at 3-DAF than at 7-DAF. Flooding stress reduced the microbial diversity, although Proteobacteria increased as root endophytes. Seed treatment and flooding combinations decreased microbiome functionality and reduced gene counts for phytohormone biosynthesis, fermentation, nitrogen, symbiosis, and degradation pathways. Similarly, flooding stress shifted the carbohydrate synthesis to a more specialized substrate. These findings enhance understanding of soybean root and rhizosphere microbiome diversity and functionality dynamics during flooding stress and provide a platform to develop sustainable agricultural practices for enhancing soybean stress tolerance to flooding.}, }
@article {pmid40367785, year = {2025}, author = {Wang, Y and Huang, S and He, J and Feng, Z and Wu, W and Guo, C and He, J}, title = {Unveiling the dynamic viral landscape across developmental stages of cold seep ecosystems: Implications for global marine biogeochemistry.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138594}, doi = {10.1016/j.jhazmat.2025.138594}, pmid = {40367785}, issn = {1873-3336}, abstract = {Cold seeps are methane-rich ecosystems playing pivotal roles in global biogeochemical cycling, yet their viral communities remain underexplored. We present the first comprehensive viral metagenomic analysis across developmental stages of the Haima Cold Seep. Characterizing viral assemblages from chemoautotrophic, mature, and extinct seep sediments revealed 4272 viral operational taxonomic units, with 77 % representing novel lineages, highlighting cold seeps' unique viral diversity. Viral community structure and diversity varied significantly by seep stage, with highest diversity in the chemoautotrophic stage. While Siphoviridae and Microviridae dominated, their relative abundances shifted with maturity. Gammaproteobacteria emerged as predominant viral hosts, exhibiting distinct interaction patterns across stages. Notably, the chemoautotrophic stage harbored the highest abundance and diversity of virus-encoded auxiliary metabolic genes (AMGs; ∼450 AMGs), with significantly enriched carbohydrate metabolism and central carbon pathway genes (2.2-fold and 1.8-fold higher respectively, p < 0.005), amino acid metabolism (1.9-fold, p = 0.003), and sulfur relay system genes (2.0-fold, p = 0.002). In contrast, the mature stage exhibited distinct enrichment in energy metabolism genes (up to 3.9-fold difference between sites, p < 0.001) and xenobiotics degradation pathways, suggesting stage-specific viral impacts on biogeochemical cycling. Lytic lifestyles prevailed across stages, indicating dynamic virus-host interactions during seep development. These findings unveil complex viral ecology in cold seeps, with potential influences on microbial community structure and biogeochemical processes. Providing a foundation for understanding viral roles in cold seep ecosystem functioning and biogeochemical cycles, this study has implications for marine microbial ecology and environmental biotechnology.}, }
@article {pmid40367670, year = {2025}, author = {Yu, S and Cao, T and Xu, Z and Zhou, H and Li, Q}, title = {Metagenomic next-generation sequencing (mNGS) identified Clostridium perfringens infection presenting as acute hemolysis after surgery.}, journal = {Journal of infection and public health}, volume = {18}, number = {8}, pages = {102798}, doi = {10.1016/j.jiph.2025.102798}, pmid = {40367670}, issn = {1876-035X}, abstract = {Clostridium perfringens (C. perfringens) septicaemia is a rare, but rapidly fatal infection, characterized by massive hemolysis. In numerous documented instances, the patient was not diagnosed in time due to the absence of typical clinical features. In order to enhance diagnostic accuracy, metagenomic next-generation sequencing (mNGS) has been adopted as a novel approach to pathogen identification. CASE PRESENTATION: A 67-year-old male who had undergone transcatheter arterial chemoembolization (TACE) surgery four days earlier presented with severe anemia, and laboratory investigations disclosed intravascular hemolysis. Swift and accurate identification was imperative, resulting in the confirmation of mNGS analysis, his medical history, clinical symptoms, physical signs, additional tests, and C. perfringens as the causative pathogen of hemolysis. After successful treatment with effective antibiotics, the patient recovered and was discharged from the hospital after 19 days. CONCLUSIONS: mNGS achieves expedited diagnostic turnaround time through rapid pathogen identification, significantly surpassing conventional culture methods. This may enable the diagnosis of atypical cases of C. perfringens infection, which can cause rapid systemic shock, renal failure, intravascular hemolysis, and even death.}, }
@article {pmid40367615, year = {2025}, author = {Guo, Y and Cheng, S and Fang, H and Geng, J and Shi, F and Wang, H and Chen, L and Pu, H and Liu, B and Zhou, Y}, title = {Water regime alters microbial mechanisms of N2O emission in metal-contaminated paddy soils.}, journal = {Ecotoxicology and environmental safety}, volume = {298}, number = {}, pages = {118304}, doi = {10.1016/j.ecoenv.2025.118304}, pmid = {40367615}, issn = {1090-2414}, abstract = {Microorganisms are essential for soil nitrous oxide (N2O) emissions through participating in key nitrogen (N)-related processes. However, the effect of water regimes on the interactions between N2O emissions and microbial processes in metal-contaminated soils is unclear. Here, we conducted a soil microcosm experiment with two water management strategies (non-flooding and flooding) and six metal addition treatments including low (2 and 200 mg kg[-1]) and high (10 and 1000 mg kg[-1]) levels of individual and combined Cd and Cu. The effects of high levels of individual Cd and Cu contamination on soil N2O emissions varied depending on water regimes, showing antagonistic effects under non-flooding conditions and synergistic effects under flooding conditions. High levels of co-contamination significantly inhibited nitrification under both water regimes, primarily due to reduced abundance of Nitrosospira. In contrast, this co-contamination decreased the abundance of Ramlibacter, thereby inhibiting denitrification and dissimilatory nitrate reduction to ammonium (DNRA) under flooding conditions. The inhibition of these key microorganisms and their mediated N-cycle processes reduced soil N2O emissions under both water regimes. This reduction was greater under flooding conditions because more N-related processes were inhibited. Metagenomic binning further indicated that Nitrosospira carried nitrifying genes, while Ramlibacter contained genes involved in denitrification, assimilatory nitrate reduction to ammonium (ANRA), and DNRA. These findings implied that both microorganisms had potential to produce N2O. Overall, water management strategies and metal contamination altered the microbial processes of N2O emissions, highlighting the importance of appropriate water management in mitigating greenhouse gas emissions from metal-contaminated paddy soils in southern China.}, }
@article {pmid40367351, year = {2025}, author = {Heo, H and Nguyen-Dinh, T and Jung, MY and Greening, C and Yoon, S}, title = {Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth of Campylobacterota isolates.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf092}, pmid = {40367351}, issn = {1751-7370}, abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) is a key process used by diverse microorganisms in the global nitrogen cycle. For long, DNRA has been considered primarily as an organotrophic reaction, despite evidence that oxidation of inorganic electron donors also supports DNRA. Evidence of DNRA coupling with molecular hydrogen (H2) oxidation has been reported for several microbial isolates; however, the underlying physiology of the microbial process remains understudied. In this study, we report the isolation of two Campylobacterotastrains, Aliarcobacter butzlerihDNRA1 and Sulfurospirillumsp. hDNRA2, which grow using H2as the sole electron donor for DNRA, and physiological insights gained from a close examination of hydrogenotrophic DNRA in these isolates. In both batch and continuous cultures, DNRA sensu stricto(i.e. NO3-reduction that includes stoichiometric NO2--to-NH4+reduction) was strictly dependent on the presence of H2and exhibited stoichiometric coupling with H2oxidation, indicating that electrons required for NO2-reduction were unequivocally derived from H2. Successful chemostat incubation further demonstrated that hydrogenotrophic DNRA is viable under NO3-limiting, H2-excess conditions. Genomic and transcriptomic analyses identified group 1b [NiFe]-hydrogenase and cytochrome c552nitrite reductase as the key enzymes catalyzing hydrogenotrophic DNRA. Additionally, metagenomic surveys revealed that bacteria capable of hydrogenotrophic DNRA are taxonomically diverse and abundant in various ecosystems, particularly in the vicinity of deep-sea hydrothermal vents. These findings, integrating physiological, genomic, and transcriptomic analyses, clarify that H2can solely serve as a growth-supporting electron donor for DNRA and suggest potential significance of this microbial process in nitrogen- and hydrogen-related environmental biogeochemical cycles.}, }
@article {pmid40366862, year = {2025}, author = {Wang, L and Chen, X and Pollock, NR and Villafuerte Gálvez, JA and Alonso, CD and Wang, D and Daugherty, K and Xu, H and Yao, J and Chen, Y and Kelly, CP and Cao, Y}, title = {Metagenomic analysis reveals distinct patterns of gut microbiota features with diversified functions in C. difficile infection (CDI), asymptomatic carriage and non-CDI diarrhea.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2505269}, doi = {10.1080/19490976.2025.2505269}, pmid = {40366862}, issn = {1949-0984}, abstract = {Clostridioides difficile infection (CDI) has been recognized as a leading cause of healthcare-associated infections and a considerable threat to public health globally. Increasing evidence suggests that the gut microbiota plays a key role in the pathogenesis of CDI. The taxonomic composition and functional capacity of the gut microbiota associated with CDI have not been studied systematically. Here, we performed a comprehensive shotgun metagenomic sequencing in a well-characterized human cohort to reveal distinct patterns of gut microbiota and potential functional features associated with CDI. Fecal samples were collected from 104 inpatients, including : (1) patients with clinically significant diarrhea and positive nucleic acid amplification testing (NAAT) and received CDI treatment (CDI, n = 47); (2) patients with positive stool NAAT but without diarrhea (Carrier, n = 17); (3) patients with negative stool NAAT but with diarrhea (Diarrhea, n = 14); and (4) patients with negative stool NAAT and without diarrhea (Control, n = 26). Downstream statistical analyses (including alpha and beta diversity analysis, differential abundance analysis, correlation network analysis, and potential functional analysis) were then performed. The gut microbiota in the Control group showed higher Chao1 index (p < 0.05), while Shannon index at KEGG module level was higher in CDI than in Carrier and Control (p < 0.05). Beta diversity for species composition differed significantly between CDI vs Carrier/Control cohorts (p < 0.05). Microbial Linear discriminant analysis Effect Size and ANCOM analysis both identified 8 species (unclassified_f_Enterobacteriaceae, Veillonella_parvula, unclassified_g_Klebsiella and etc.) were enriched in CDI, Enterobacter_aerogenes was enriched in Diarrhea, Collinsella_aerofaciens, Collinsella_sp_4_8_47FAA, Collinsella_tanakaei and Collinsella_sp_CAG_166 were enriched in Control (LDA >3.0, adjusted p < 0.05). Correlation network complexity was higher in CDI with more negative correlations than in other three cohorts. Modules involved in iron complex transport system (M00240) was enriched in CDI, ABC-2 type transport system (M00254), aminoacyl-tRNA biosynthesis (M00359), histidine biosynthesis (M00026) and inosine monophosphate biosynthesis (M00048) were enriched in Carrier, ribosome (M00178 and M00179) was enriched in Diarrhea, fluoroquinolone resistance (M00729) and aminoacyl-tRNA biosynthesis (M00360) were enriched in Control (LDA > 2.5, adjusted p < 0.05). Resistance functions of acriflavine and glycylcycline were enriched in CDI, while resistance function of bacitracin was enriched in Carrier (LDA > 3.0, adjusted p < 0.05), and the contributions of phylum and species to resistance functions differed among the four groups. Our results reveal alterations of gut microbiota composition and potential functions among four groups of differential colonization/infection status of Clostridioides difficile. These findings support the potential roles of gut microbiota and their potential functions in the pathogenesis of CDI.}, }
@article {pmid40366770, year = {2025}, author = {Baba, Y and Tsuge, D and Aoki, R}, title = {Enhancement of carbohydrate metabolism by probiotic and prebiotic intake promotes short-chain fatty acid production in the gut microbiome: A randomized, double-blind, placebo-controlled crossover trial.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/bbb/zbaf071}, pmid = {40366770}, issn = {1347-6947}, abstract = {Short-chain fatty acids (SCFAs) are thought to be a key factor in the health benefits of prebiotics and probiotics. This study investigated the effect of Bifidobacterium animalis subsp. lactis GCL2505 and inulin (BL+IN) on fecal SCFAs and gut microbial composition and function. A placebo-controlled, randomized, double-blind, crossover study was conducted with 120 participants. Two weeks of BL+IN intake significantly increased acetate, propionate, and butyrate concentrations and Bifidobacterium abundance compared to placebo. Functional analysis of the gut metagenome showed enrichment of genes associated with carbohydrate and amino acid metabolism, suggesting an enhanced capacity for SCFA production. A responder was defined as a participant with increased fecal SCFAs after BL+IN consumption. Responder metagenomes exhibited greater enrichment of genes involved in SCFA production and carbohydrate metabolism. In conclusion, short-term BL+IN ingestion may benefit healthy adults by increasing fecal SCFAs through influencing the composition and functional activation of SCFA-associated pathways in the gut microbiome.}, }
@article {pmid40366182, year = {2025}, author = {Martin Říhová, J and Vodička, R and Hypša, V}, title = {An obligate symbiont of Haematomyzus elephantis with a strongly reduced genome resembles symbiotic bacteria in sucking lice.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0022025}, doi = {10.1128/aem.00220-25}, pmid = {40366182}, issn = {1098-5336}, abstract = {The parvorder Rhynchophthirina with a single genus Haematomyzus is a small group of ectoparasites of unclear phylogenetic position, related to sucking and chewing lice. Previous screening based on the 16S rRNA gene indicated that Haematomyzus harbors a symbiotic bacterium whose DNA exhibits a strong shift in nucleotide composition typical of obligate mutualistic symbionts in insects. Within Phthiraptera, the smallest known genomes are found in the symbionts associated with sucking lice, which feed exclusively on mammal blood, compared to the generally larger genomes of the symbionts inhabiting chewing lice, which feed on skin derivatives. In this study, we investigate the genome characteristics of the symbiont associated with Haematomyzus elephantis. We sequenced and assembled the H. elephantis metagenome, extracted a genome draft of its symbiotic bacterium, and showed that the symbiont has a significantly reduced genome, which is with 0.39 Mbp the smallest genome among the symbionts known from Phthiraptera. Multigenic phylogenetic analysis places the symbiont into one of three clusters composed of long-branched symbionts from other insects. More specifically, it clusters together with symbionts from several other sucking lice and also with Wigglesworthia glossinidia, an obligate symbiont of tsetse flies. Consistent with the dramatic reduction of its genome, the H. elephantis symbiont lost many metabolic capacities. However, it retained functional pathways for four B vitamins, a trait typical for symbionts in blood-feeding insects. Considering genomic, metabolic, and phylogenetic characteristics, the new symbiont closely resembles those known from several sucking lice rather than chewing lice.IMPORTANCERhynchophthirina is a unique small group of permanent ectoparasites that is closely related to both sucking and chewing lice. These two groups of lice differ in their morphology, ecology, and feeding strategies. As a consequence of their different dietary sources, i.e., mammals' blood vs vertebrate skin derivatives, they also exhibit distinct patterns of symbiosis with obligate bacterial symbionts. While Rhynchophthirina shares certain traits with sucking and chewing lice, the nature of its obligate symbiotic bacterium and its metabolic role is not known. In this study, we assemble the genome of symbiotic bacterium from Haematomyzus elephantis (Rhynchophthirina), demonstrating its close similarity and phylogenetic proximity to several symbionts of sucking lice. The genome is highly reduced (representing the smallest genome among louse-associated symbionts) and exhibits a significant loss of metabolic pathways. However, similar to other sucking louse symbionts, it retains essential pathways for the synthesis of several B vitamins.}, }
@article {pmid40366158, year = {2025}, author = {Geonczy, SE and Hillary, LS and Santos-Medellín, C and Sorensen, JW and Emerson, JB}, title = {Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0174924}, doi = {10.1128/msystems.01749-24}, pmid = {40366158}, issn = {2379-5077}, abstract = {UNLABELLED: Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire.<br><br>IMPORTANCE: The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.}, }
@article {pmid40366141, year = {2025}, author = {Li, J and Zheng, K and Ding, W and Lu, L and Liang, Y and Xiong, Y and Wei, Z and Gao, C and Su, Y and Wang, Z and Chen, X and Bao, Z and Hu, X and McMinn, A and Wang, M}, title = {Healthy and moribund Zhikong scallops (Chlamys farreri) developed different viral communities during a mass mortality event.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0034225}, doi = {10.1128/msystems.00342-25}, pmid = {40366141}, issn = {2379-5077}, abstract = {UNLABELLED: Viral assemblages of scallops are still relatively unknown. Here, metagenomic analysis was used to study virus communities in the gut of scallops to establish the first scallop virome data set (SVD); this contains 7,447 viral operational taxonomic units. Protein-sharing networks and phylogenetic analyses demonstrated the high diversity and novelty of the SVD, which is very different from viromes from other habitats. Potentially pathogenic viruses are prevalent in the gut of scallops. In particular, the novel smacoviruses were identified, indicating that scallops may be a potential hotspot for this viral group. Inference of virus-host associations found extensive interactions between viruses and major prokaryotic lineages. Intriguingly, moribund scallops showed a higher diversity of auxiliary metabolic genes (AMGs) related to amino acid metabolism and cofactor and vitamin genes, while healthy scallops had fewer AMGs, with those present focusing on secondary metabolite biosynthesis and carbohydrate metabolism. These findings provide the first landscape of scallop gut viruses based on metagenomes and highlight the potential roles of diverse and unique gut viruses for the health of filter-feeding bivalves.<br><br>IMPORTANCE: This study uses metagenome sequencing to establish the first scallop virome database. The study reveals previously unknown diversity of scallop-associated viruses and provides insights into links between disease status and viral diversity and genome content. The study will interest many aquatic virologists and could have important implications in managing marine resources.}, }
@article {pmid40366139, year = {2025}, author = {Crouch, AL and Severance, BM and Creary, S and Hood, D and Bailey, M and Mejias, A and Ramilo, O and Gillespie, M and Ebelt, S and Sheehan, V and Kopp, BT and Anderson, MZ}, title = {Altered nasal and oral microbiomes define pediatric sickle cell disease.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0013725}, doi = {10.1128/msphere.00137-25}, pmid = {40366139}, issn = {2379-5042}, abstract = {UNLABELLED: Sickle cell disease (SCD) is a chronic blood disorder that disrupts multiple organ systems and can lead to severe morbidity. Persistent and acute symptoms caused by immune system dysregulation in individuals with SCD could contribute to disease either directly or indirectly via dysbiosis of commensal microbes and increased susceptibility to infection. Here, we explored the nasal and oral microbiomes of children with SCD (cwSCD) to uncover potential dysbiotic associations with the blood disorder. Microbiota collected from nasal and oral swabs of 40 cwSCD were compared to eight healthy siblings using shotgun metagenomic sequencing. Commensal taxa were present at similar levels in the nasal and oral microbiome of both groups. However, the nasal microbiomes of cwSCD contained a higher prevalence of Pseudomonadota species, including pathobionts such as Yersinia enterocolitica and Klebsiella pneumoniae. Furthermore, the oral microbiome of cwSCD displayed lower α-diversity and fewer commensal and pathobiont species compared to the healthy siblings. Thus, subtle but notable shifts seem to exist in the nasal and oral microbiomes of cwSCD, suggesting an interaction between SCD and the microbiome that may influence health outcomes.<br><br>IMPORTANCE: The oral and nasal cavities are susceptible to environmental exposures including pathogenic microbes. In individuals with systemic disorders, antibiotic exposure, changes to the immune system, or changes to organ function could influence the composition of the microbes at these sites and the overall health of individuals. Children with sickle cell disease (SCD) commonly experience respiratory infections, such as pneumonia or sinusitis, and may have increased susceptibility to infection because of disrupted microbiota at these body sites. We found that children with SCD (cwSCD) had more pathobiont bacteria in the nasal cavity and reduced bacterial diversity in the oral cavity compared to their healthy siblings. Defining when, why, and how these changes occur in cwSCD could help identify specific microbial signatures associated with susceptibility to infection or adverse outcomes, providing insights into personalized treatment strategies and preventive measures.}, }
@article {pmid40366134, year = {2025}, author = {Gilbert, NE and Kimbrel, JA and Samo, TJ and Siccardi, AJ and Stuart, RK and Mayali, X}, title = {A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0037525}, doi = {10.1128/msystems.00375-25}, pmid = {40366134}, issn = {2379-5077}, abstract = {Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.}, }
@article {pmid40366096, year = {2025}, author = {Ragupathy, V and Kelley, K and Hewlett, I}, title = {Near-complete torque teno virus (TTV) genome identified in a blood donor infected with hepatitis B virus (HBV).}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0117824}, doi = {10.1128/mra.01178-24}, pmid = {40366096}, issn = {2576-098X}, abstract = {We have identified a near full-length torque teno virus (TTV) genome sequence in plasma from a blood donor infected with hepatitis B virus. The consensus sequence of TTV was extracted from Nanopore metagenomic sequencing. The identified TTV open reading frame 1 is 3,062 nucleotides (nt) long and shares 90%-100% identity with other human TTVs.}, }
@article {pmid40365535, year = {2025}, author = {Li, M and Chen, J and Zhang, L and Chen, X and Zhou, J and Liu, F and Zhou, X and Xiao, J and Yang, K and Qi, L and Han, X and Liu, T and Zhao, H and Zhou, Z and Chen, X and Sun, L}, title = {Clinicopathological characteristics and diagnostic performance of metagenomic pathogen detection technology in mycobacterial infections among HIV patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1584189}, pmid = {40365535}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; *HIV Infections/complications ; Adult ; Middle Aged ; Mycobacterium tuberculosis/isolation &amp; purification/genetics ; *Metagenomics/methods ; Sputum/microbiology ; *Mycobacterium Infections/diagnosis/microbiology/pathology ; Sensitivity and Specificity ; *Molecular Diagnostic Techniques/methods ; Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Biopsy ; }, abstract = {BACKGROUND: Mycobacterial infections represent a major cause of morbidity and mortality in HIV-infected individuals. This study evaluated diagnostic techniques for mycobacterial identification and compared clinicopathological features between HIV-positive and HIV-negative patients.<br><br>METHODS: We analyzed 88 tissue samples (with 41 matched blood and 28 sputum samples) using histopathology (HE and acid-fast staining), bacterial culture, MTB-PCR (sputum/biopsy), PCR-reverse dot blot hybridization (RDBH), and metagenomic pathogen detection technology (MetaPath&#x2122;). Logistic regression analyses were performed to identify factors affecting detection rates.<br><br>RESULTS: Mycobacterial infection was detected in 95.5% (84/88) of patients. Among HIV-positive patients (n=63), 46% (29/63) had Mycobacterium tuberculosis (MTB) infections, and 44% (28/63) had non-tuberculous mycobacteria (NTM) infections, significantly higher than the 20% (5/25) NTM rate in HIV-negative patients. Univariate analysis identified HIV-positive status (p=0.009), lymph node involvement (p=0.020), and positive MetaPath&#x2122; results (p=0.002) as significant predictors of detection, while multivariate analysis confirmed these as independent factors (p=0.036; p=0.042; p=0.006). Lymph nodes were the most common infection site in HIV-positive patients (42.9%, 27/63), while lung tissue predominated in HIV-negative patients (48%, 12/25). MetaPath&#x2122; demonstrated superior sensitivity and specificity for detecting both MTB and NTM. Biopsy samples provided higher diagnostic accuracy than sputum or blood for lung and lymph node infections, but not for brain. In HIV-positive patients, NTM infections showed significantly more granuloma formation (p=0.032) and foam cells (p=0.005), but less necrosis (p=0.0005) compared to MTB infections. No significant differences were observed in HIV-negative patients.<br><br>CONCLUSIONS: MetaPath&#x2122; is a highly effective diagnostic tool for mycobacterial infections, particularly in tissue biopsies. HIV-positive status, lymph node involvement, and MetaPath&#x2122; positivity independently predict mycobacterial detection. HIV-positive patients exhibit distinct clinicopathological features, emphasizing the need for tailored diagnostic and therapeutic approaches based on immune status.}, }
@article {pmid40365473, year = {2025}, author = {Pu, T and Tan, Y and Zhao, Y and Zhao, Z and Zhang, N and Li, C and Song, Y}, title = {Effect of Seasonal Variations on Soil Microbial, Extracellular Enzymes, and Ecological Stoichiometry in Tea Plantations.}, journal = {Ecology and evolution}, volume = {15}, number = {5}, pages = {e71362}, pmid = {40365473}, issn = {2045-7758}, abstract = {Tea plantations are important agricultural ecosystems in karst areas, yet the seasonal dynamics of soil microbial communities, functional genes, and extracellular enzyme activities (EEA) under different management practices remain poorly understood. This study investigated organic (HY), pollution-free (TS), and conventional (XY) tea plantations in Weng'an County, Southwest China, during the spring (April) and autumn (August) tea seasons via metagenomics and stoichiometric analyses. Seasonal variations significantly altered the soil physicochemical properties (e.g., SOC, TN, and TP) and EEA (p < 0.05), with higher C-acquiring enzyme activity in autumn and elevated soil C:N:P ratios in spring. The soil extracellular enzyme stoichiometry (EES C:N:P) deviated from the theoretical 1:1:1 ratio, indicating that microbial metabolism was constrained by soil resource availability rather than homeostasis. Phosphorus limitation (vector angle > 45°) persisted across seasons, contradicting initial hypotheses, with acid phosphatase (ACP) activity and EES C:P identified as critical drivers. Random forest (RF) and structural equation modeling (SEM) revealed that the spring season had stronger impacts on microbial communities and functional genes, with the soil TN, C:N, NAG, ACP, and EES C:P ratios as key predictors. Compared with conventional practices, organic management enhances microbial diversity and functional redundancy, buffering seasonal fluctuations. These findings highlight the interplay between seasonal climatic shifts and agricultural practices regulating soil nutrient cycling and microbial adaptation. Strategic interventions-such as spring carbon supplementation, autumn organic phosphorus fertilization, and intercropping-are proposed to optimize microbial resilience and ecosystem stability in fragile karst tea plantations. This study provides novel insights into soil ecological stoichiometry and microbial metabolic strategies, offering a reference for the sustainable management of agroecosystems in karst areas.}, }
@article {pmid40365061, year = {2025}, author = {Liu, L and Wang, Z and Luo, C and Deng, Y and Wu, W and Jin, Y and Wang, Y and Huang, H and Wei, Z and Zhu, Y and He, X and Guo, L}, title = {Beneficial soil microbiome profiles assembled using tetramycin to alleviate root rot disease in Panax notoginseng.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1571684}, pmid = {40365061}, issn = {1664-302X}, abstract = {BACKGROUND: Root rot disease is a major threat to the sustainable production of Panax notoginseng. Tetramycin has a broad-spectrum fungicidal efficacy, low toxicity, and high efficiency, However, the prevention and control of root rot disease of P. notoginseng and the specific mechanism of action are still unclear.<br><br>METHODS: In this paper, a combination of indoor and pot experiments was used to assess the effectiveness of tetramycin at alleviating root rot disease challenges encountered by P. notoginseng. Amplicon sequencing, metagenomic analysis with microbial verification were used to investigate the microecological mechanisms underlying tetramycin's ability to reduce soil biological barriers.<br><br>RESULTS: We found that tetramycin significantly inhibited mycelial growth and spore germination of pathogenic fungi. Tetramycin, T2 (1000&#xd7;) and T3 (500&#xd7;), applied to continuous cropping soil, increased the seedling survival rates of P. notoginseng. Additionally, tetramycin reduced fungal &#x3b1;-diversity and shifted the fungal community assembly from deterministic to stochastic process. The microbial functions influenced by tetramycin were primarily associated with antibiotic synthesis and siderophore synthesis. Antibiotic efflux and inactivation have also been identified as the main resistance mechanisms. Microbial verification results showed that the artificially assembled tetramycin-regulated microbial community could indeed alleviate the occurrence of diseases. Furthermore, the cross-kingdom synthetic community assembled by the three key strains (Pseudomonas aeruginosa, Variovorax boronicumulans, and Cladosporium cycadicola) significantly improved the control of root rot disease and promoted plant growth.<br><br>DISCUSSION: This study provides novel insights into developing efficient biological control strategies and elucidates the role and mechanism of tetramycin in modulating soil microflora assembly to strengthen host disease resistance.}, }
@article {pmid40364394, year = {2025}, author = {Cao, K and Shi, P and Xu, X and Wang, J}, title = {Self-Inhibition Effects of Litter-Mediated Plant-Phyllosphere Feedback on Seedling Growth in Invasive and Native Congeneric Species.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {9}, pages = {}, doi = {10.3390/plants14091355}, pmid = {40364394}, issn = {2223-7747}, abstract = {Plant-phyllosphere feedback (PPF) is an ecological process in which phyllosphere microbiota, originating from plant litter, are transmitted via aerosols and subsequently influence the growth of conspecific or heterospecific plants. However, the cross-species generality of this mechanism and its role in invasive plant success remain to be fully elucidated. This study systematically examined PPF effects using three invasive/native congeneric plant pairs from distinct families (Phytolaccaceae, Asteraceae, and Amaranthaceae) in Jiangxi Province, China. Key findings include the following: (1) Wide conspecific negative feedback across families, with four of six species exhibiting 6.2-12.7% biomass reduction under their own litter treatments (p < 0.05). (2) Comparable feedback intensity between invasive and native species, as indicated by average pairwise indices (invasive I = -0.05 vs. native I = -0.04; p = 0.15). Notably, the invasive species Phytolacca americana uniquely showed a positive biomass response (+7.1%), though underlying mechanisms (phytochemical or microbial) were not investigated. (3) Lack of correlation between PPF strength and plant functional traits or phylogenetic distance, as indicated by Mantel tests (p > 0.8), in contrast to the trait/phylogeny associations commonly observed in soil feedback systems. This study provided the first evidence of PPF universality across multiple plant families-previously documented only within Asteraceae-and highlights the potential microbial-mediated advantages in plant invasions. Future research should integrate spatiotemporal metagenomic and metabolomic approaches to decipher the dynamic pathogen/microbe networks and their phytochemical interactions.}, }
@article {pmid40363788, year = {2025}, author = {Zhou, L and Li, J and Ding, C and Zhou, Y and Xiao, Z}, title = {Mechanistic Advances in Hypoglycemic Effects of Natural Polysaccharides: Multi-Target Regulation of Glycometabolism and Gut Microbiota Crosstalk.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {9}, pages = {}, doi = {10.3390/molecules30091980}, pmid = {40363788}, issn = {1420-3049}, support = {2024JJ8163//Hunan Natural Science Foundation/ ; C2023005//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 201923//Key Project of Hunan Provincial Administration of Traditional Chinese Medicine/ ; 2022ZYYGN06//2022 Annual Natural Drug Resources and Function Development Fund Project/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Polysaccharides/pharmacology/chemistry/therapeutic use ; Animals ; *Hypoglycemic Agents/pharmacology/chemistry/therapeutic use ; Signal Transduction/drug effects ; Insulin Resistance ; Glucose/metabolism ; }, abstract = {Natural polysaccharides (NPs), as a class of bioactive macromolecules with multitarget synergistic regulatory potential, exhibit significant advantages in diabetes intervention. This review systematically summarizes the core hypoglycemic mechanisms of NPs, covering structure-activity relationships, integration of the gut microbiota-metabolism-immunity axis, and regulation of key signaling pathways. Studies demonstrate that the molecular weight, branch complexity, and chemical modifications of NPs mediate their hypoglycemic activity by influencing bioavailability and target specificity. NPs improve glucose metabolism through multiple pathways: activating insulin signaling, improving insulin resistance (IR), enhancing glycogen synthesis, inhibiting gluconeogenesis, and regulating gut microbiota homeostasis. Additionally, NPs protect pancreatic β-cell function via the nuclear factor E2-related factor 2 (Nrf2)/Antioxidant Response Element (ARE) antioxidant pathway and Toll-like receptor 4 (TLR4)/nuclear factor-κB (NF-κB) anti-inflammatory pathway. Clinical application of NPs still requires overcoming challenges such as resolving complex structure-activity relationships and dynamically integrating cross-organ signaling. Future research should focus on integrating multi-omics technologies (e.g., metagenomics, metabolomics) and organoid models to decipher the cross-organ synergistic action networks of NPs, and promote their translation from basic research to clinical applications.}, }
@article {pmid40362493, year = {2025}, author = {Žukienė, G and Narutytė, R and Rudaitis, V}, title = {Association Between Vaginal Microbiota and Cervical Dysplasia Due to Persistent Human Papillomavirus Infection: A Systematic Review of Evidence from Shotgun Metagenomic Sequencing Studies.}, journal = {International journal of molecular sciences}, volume = {26}, number = {9}, pages = {}, doi = {10.3390/ijms26094258}, pmid = {40362493}, issn = {1422-0067}, mesh = {Humans ; Female ; *Papillomavirus Infections/complications/microbiology/virology ; *Vagina/microbiology/virology ; *Microbiota/genetics ; Metagenomics/methods ; *Uterine Cervical Dysplasia/microbiology/virology/etiology ; Papillomaviridae ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The role of vaginal dysbiosis in the progression of human papilloma virus (HPV) associated cervical lesions has gained attention in recent years. While many studies use 16S rRNA gene sequencing for microbiota analysis, shotgun metagenomic sequencing offers higher taxonomic resolution and insights into microbial gene functions and pathways. This systematic review evaluates the relationship between compositional and functional changes in the vaginal microbiome during HPV infection and cervical lesion progression. A literature search was performed according to PRISMA guidelines in PubMed, Web of Science, Scopus, and ScienceDirect databases. Seven studies utilizing metagenomic sequencing in patients with HPV infection or HPV-associated cervical lesions were included. Progression from HPV infection to cervical lesions and cancer was associated with a reduction in Lactobacillus species (particularly Lactobacillus crispatus) and an enrichment of anaerobic and pathogenic species, especially Gardnerella vaginalis. Heterogeneous enriched metabolic pathways were also identified, indicating functional shifts during lesion progression. As most studies were conducted in Asia, further research in diverse regions is needed to improve the generalizability of findings. Future studies employing metagenomic sequencing may help identify biomarkers for early pre-cancerous lesions and clarify the role of vaginal microbiota in persistent HPV infection and cervical dysplasia.}, }
@article {pmid40362462, year = {2025}, author = {Chakraborty, N and Holmes-Hampton, G and Rusling, M and Kumar, VP and Hoke, A and Lawrence, AB and Gautam, A and Ghosh, SP and Hammamieh, R}, title = {Delayed Impact of Ionizing Radiation Depends on Sex: Integrative Metagenomics and Metabolomics Analysis of Rodent Colon Content.}, journal = {International journal of molecular sciences}, volume = {26}, number = {9}, pages = {}, doi = {10.3390/ijms26094227}, pmid = {40362462}, issn = {1422-0067}, support = {xxxxx//AFRRI/ ; }, mesh = {Animals ; Male ; Female ; Mice ; *Metabolomics/methods ; *Metagenomics/methods ; *Radiation, Ionizing ; *Colon/radiation effects/metabolism/microbiology ; *Gastrointestinal Microbiome/radiation effects ; Sex Factors ; Whole-Body Irradiation/adverse effects ; Mice, Inbred C57BL ; }, abstract = {There is an escalating need to comprehend the long-term impacts of nuclear radiation exposure since the permeation of ionizing radiation has been frequent in our current societal framework. A system evaluation of the microbes that reside inside a host's colon could meet this knowledge gap since the microbes play major roles in a host's response to stress. Indeed, our past study suggested that these microbes might break their symbiotic association with moribund hosts to form a pro-survival condition exclusive to themselves. In this study, we undertook metagenomics and metabolomics assays regarding the descending colon content (DCC) of adult mice. DCCs were collected 1 month and 6 months after 7 Gy or 7.5 Gy total body irradiation (TBI). The assessment of the metagenomic diversity profile in DCC found a significant sex bias caused by TBI. Six months after 7.5 Gy TBI, decreased Bacteroidetes were replaced by increased Firmicutes in males, and these alterations were reflected in the functional analysis. For instance, a larger number of networks linked to small chain fatty acid (SCFA) synthesis and metabolism were inhibited in males than in females. Additionally, bioenergy networks showed regression dynamics in females at 6 months post-TBI. Increased accumulation of glucose and pyruvate, which are typical precursors of beneficial SCFAs coupled with the activated networks linked to the production of reactive oxygen species, suggest a cross-sex energy-deprived state. Overall, there was a major chronic adverse implication in male mice that supported the previous literature in suggesting females are more radioresistant than males. The sex-biased chronic effects of TBI should be taken into consideration in designing the pertinent therapeutics.}, }
@article {pmid40362406, year = {2025}, author = {Krivonos, DV and Fedorov, DE and Konanov, DN and Vvedensky, AV and Sonets, IV and Korneenko, EV and Speranskaya, AS and Ilina, EN}, title = {Pike: OTU-Level Analysis for Oxford Nanopore Amplicon Metagenomics.}, journal = {International journal of molecular sciences}, volume = {26}, number = {9}, pages = {}, doi = {10.3390/ijms26094168}, pmid = {40362406}, issn = {1422-0067}, support = {24-15-00419//Russian Science Foundation/ ; }, mesh = {*Metagenomics/methods ; Fungi/genetics/classification ; *Nanopore Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Algorithms ; Metagenome ; *Nanopores ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {The Oxford Nanopore platform and nanopore sequencing are gaining increasing popularity in modern metagenomic research. However, there is a limited set of dedicated tools for analyzing this type of data. The tools used for nanopore amplicon sequencing data analysis often provide only taxonomy annotation without OTU sequence assembly. Conversely, tools that facilitate OTU assembly are constrained in their analysis to long reads, such as the V1-V9 regions of 16S rRNA for bacterial community studies or the full-length ITS cluster (ITS1-5.8S-ITS2) for fungal community studies. In other cases, researchers propose their own solutions without dedicated tools. In this paper, we present Pike, a novel tool for analyzing Oxford Nanopore amplicon sequencing data. Pike allows analysis without amplicon size limitations and allows de novo assembly of OTU sequences. In our research, we created mock communities of fungi and bacteria, which we then used to demonstrate the efficiency of our algorithm. Furthermore, we validated the algorithm using externally available data. We also compared our approach with similar ones to show its applicability.}, }
@article {pmid40361215, year = {2025}, author = {Ma, Y and Jiang, J and Yang, Z and Li, Y and Bai, H and Liu, Z and Zhang, S and Zhi, Z and Yang, Q}, title = {Changes of gastric microflora and metabolites in patients with chronic atrophic gastritis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {537}, pmid = {40361215}, issn = {1479-5876}, support = {No.21377724D//Hebei Provincial Department of Science and Technology/ ; No. 18//National Administration of Traditional Chinese Medicine Science and Technology/ ; 246W7701D//Provincial Science and Technology Plan of Hebei Province/ ; }, mesh = {Humans ; *Gastritis, Atrophic/microbiology/metabolism ; Chronic Disease ; Middle Aged ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Metabolome ; *Stomach/microbiology ; Metabolomics ; *Microbiota ; Bacteria/genetics/metabolism ; Adult ; Aged ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Chronic atrophic gastritis (CAG) is related to the body's microbial and metabolic systems. Combined studies of microbiome and metabolomics can clarify the mechanisms of disease occurrence and progression. We used 16S rRNA sequencing, metagenomics sequencing and metabolomics sequencing to depict the landscapes of bacterium and metabolites, construct correlation networks of different bacterium and metabolites describe potential pathogenic mechanisms of chronic atrophic gastritis.<br><br>METHODS: The gastric juices of 30 non-atrophic gastritis (NAG) patients and 30 CAG patients were collected. Gastric microflora was analyzed by 16S rRNA sequencing and metagenomics sequencing. Gastric metabolites were analyzed by LC-MS analysis. Different bioinformatics methods were used to analyze the data of microbiome and metabolome, and to analyze the relationship between them.<br><br>RESULTS: In atrophic gastritis, bacteria diversity decreased. The genera with a mean decrease in Gini greater than 1.5 included peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides. KEGG pathway included renal cell carcinoma, proximal tubule bicarbonate reclamation, citrate cycle and aldosterone synthesis and secretion with significant enrichment of differential metabolites. Peptostreptococcus, fusobacterium, prevotella and sphingomonas were in pivot positions of the correlation network of differential metabolites and differential bacterium. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism were enriched in chronic atrophic gastritis based on the metagenomic sequencing data.<br><br>CONCLUSION: Peptostreptococcus, fusobacterium, prevotella, sphingomonas and bacteroides were the essential features that distinguish atrophic gastritis from non-atrophic gastritis, and caused disease by altering various metabolic pathways. Viral carcinogenesis, glycine serine and threonine metabolism, RNA polymerase, galactose metabolism and retinol metabolism may be related to the occurrence and progression of CAG.}, }
@article {pmid40360994, year = {2025}, author = {Zhai, R and Zhao, C and Chang, L and Liu, J and Zhao, T and Jiang, J and Zhu, W}, title = {The gut-liver axis plays a limited role in mediating the liver's heat susceptibility of Chinese giant salamander.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {475}, pmid = {40360994}, issn = {1471-2164}, support = {31900327//National Natural Science Foundation of China/ ; 2023NSFSC1153//Natural Science Foundation of Sichuan Province of China/ ; }, mesh = {Animals ; *Liver/metabolism ; *Gastrointestinal Microbiome ; *Caudata/physiology/genetics/microbiology ; Heat-Shock Response ; Transcriptome ; Gene Expression Profiling ; Energy Metabolism ; Larva ; }, abstract = {The Chinese giant salamander (CGS, Andrias davidianus), a flagship amphibian species, is highly vulnerable to high temperatures, posing a significant threat under future climate change. Previous research linked this susceptibility to liver energy deficiency, accompanied by shifts in gut microbiota and reduced food conversion rates, raising questions about the role of the gut-liver axis in mediating heat sensitivity. This study investigated the responses of Chinese giant salamander larvae to a temperature gradient (10-30 °C), assessing physiological changes alongside histological, gut metagenomic, and tissue transcriptomic analyses. Temperatures above 20 °C led to mortality, which resulted in delayed growth. Histological and transcriptomic data revealed metabolic exhaustion and liver fibrosis in heat-stressed salamanders, underscoring the liver's critical role in heat sensitivity. While heat stress altered the gut microbiota's community structure, their functional profiles, especially in nutrient absorption and transformation, remained stable. Both gut and liver showed temperature-dependent transcriptional changes, sharing some common variations in actins, heat shock proteins, and genes related to transcription and translation. However, their energy metabolism exhibited opposite trends: it was downregulated in the liver but upregulated in the gut, with the gut showing increased activity in the pentose phosphate pathway and oxidative phosphorylation, potentially countering metabolic exhaustion. Our findings reveal that the liver of the larvae exhibits greater thermal sensitivity than the gut, and the gut-liver axis plays a limited role in mediating thermal intolerance. This study enhances mechanistic understanding of CGS heat susceptibility, providing a foundation for targeted conservation strategies in the face of climate change.}, }
@article {pmid40360555, year = {2025}, author = {Baek, JW and Lim, S and Park, N and Song, B and Kirtipal, N and Nielsen, J and Mardinoglu, A and Shoaie, S and Kim, JI and Son, JW and Koh, A and Lee, S}, title = {Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {78}, pmid = {40360555}, issn = {2055-5008}, support = {2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; 2021R1C1C1006336, 2021M3A9G8022959, RS-2024-00419699//National Research Foundation of Korea/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; HR22C141105//the Korea Health Industry Development Institute/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; 2024-ER2108-00, 2024-ER0608-00//Korea National Institute of Health/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; GIST-MIT research Collaboration grant//GIST Research Institute/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome/drug effects/genetics ; *Drug Resistance, Bacterial ; Metagenome ; *Microbiota/drug effects ; Microbial Sensitivity Tests ; Metagenomics ; }, abstract = {In recent years, the overuse of antibiotics has led to the emergence of antimicrobial-resistant (AMR) bacteria. To evaluate the spread of AMR bacteria, the reservoir of AMR genes (resistome) has been identified in environmental samples, hospital environments, and human populations, but the functional role of AMR bacteria and their persistence within individuals has not been fully investigated. Here, we performed a strain-resolved in-depth analysis of the resistome changes by reconstructing a large number of metagenome-assembled genomes from the gut microbiome of an antibiotic-treated individual. Interestingly, we identified two bacterial populations with different resistome profiles: extensively acquired antimicrobial-resistant bacteria (EARB) and sporadically acquired antimicrobial-resistant bacteria, and found that EARB showed broader drug resistance and a significant functional role in shaping individual microbiome composition after antibiotic treatment. Our findings of AMR bacteria would provide a new avenue for controlling the spread of AMR bacteria in the human community.}, }
@article {pmid40360028, year = {2025}, author = {Fang, B and Liu, YF and Wei, HX and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ}, title = {Enhancing methanogenesis from long-chain fatty acids (LCFA) and enrichment of novel bacteria with resuscitation-promoting factors.}, journal = {Bioresource technology}, volume = {432}, number = {}, pages = {132663}, doi = {10.1016/j.biortech.2025.132663}, pmid = {40360028}, issn = {1873-2976}, abstract = {Long-chain fatty acids (LCFA) are important intermediate metabolites in lipid hydrolysis during anaerobic digestion for biogas production. High LCFA loads inhibit microbial activity by toxicity, impairing the coupling of β-oxidation and methanogenesis, thus reducing LCFA degradation efficiency. This study employed and tested seven stimulants, including the resuscitation-promoting factors (Rpf and YeaZ), the quorum-sensing molecules (cAMP, and AHLs), the chemical stimulants (pyruvate), the growth promoter (fumarate), and yeast extract + peptone (YP) for enhancement of methanogenic degradation of LCFA. The results indicate that the chemical stimulants and resuscitation-promoting factors enhanced maximum methane-production rate 1.58 to 2.20 fold versus the NS, reducing the lag phase by 1.46-9.76 days. Analysis of the microbial community composition revealed that the quorum sensing factors only increased species richness, while Rpf, YeaZ fumarate, and YP stimulated the growth of core members of the communities. Metagenomic analysis detected three previously unreported LCFA-degrading bacterial taxa, Marinisomatota, Thermoanaerobaculaceae and Pelomonas. Particularly, Rpf and YeaZ significantly enriched LCFA-degrading bacteria such as Syntrophomonadaceae, Leptospiraceae, and Marine Group B within the core species, while YeaZ also stimulated methanogenic bacteria, possibly due to resuscitating dormant microbes from unfavorable conditions. Syntrophic interactions between LCFA degraders and non-degraders, rather than methanogen abundance, govern methanogenic LCFA degradation. These results demonstrate that the use of stimulants is an effective approach to enhance LCFA degradation and provide a new pathway for energy recovery.}, }
@article {pmid40359864, year = {2025}, author = {Fan, M and Li, H and Liu, C and Du, L and Xu, Y and Chen, Y}, title = {Insights into the molecular mechanism on high salt tolerance of electroactive microorganisms collaborated by biochar supported cerium dioxide.}, journal = {Journal of environmental management}, volume = {386}, number = {}, pages = {125679}, doi = {10.1016/j.jenvman.2025.125679}, pmid = {40359864}, issn = {1095-8630}, abstract = {Electroactive microorganisms are a promising approach for treating high-salinity organic wastewater, however, they are highly susceptible to salt stress, which can compromise their metabolic activity. In this paper, biochar supported nano-cerium dioxide catalyst (BC-CeO2) was prepared to strengthen electroactive microorganisms in high salt environment. It was found that BC-CeO2 significantly improved the bioelectrochemical and metabolic activity of microorganisms in high salt environment (600 mM NaCl) compared with the Control. At the initial stage of the reaction, the maximum power density of microbial fuel cells (MFCs) reached 343.21 mW/m[2], and the degradation efficiency of norfloxacin (NOR) was 64.8 %, which was 1.7 times that of the Control. The analysis of microbial antioxidant properties demonstrated that BC-CeO2 could significantly increase the activities of superoxide dismutase (SOD) and catalase (CAT), effectively enhancing the ability of microorganisms to scavenge reactive oxygen species produced by salt stress. Metagenomic analysis revealed that the abundance of KEGG pathways conducive to microbial growth and metabolism under BC-CeO2 was relatively high, such as biosynthesis of amino acids (ko01230), microbial metabolism in diverse environments (ko01120) and so on. The enrichment of salt tolerant genes further illustrated the strengthening effect of BC-CeO2 on microbial adaptation to high salt environment, including genes related to NADH ubiquinone oxidoreductase, Na[+]/H[+] antiporter, intracellular small molecule compatible substance synthesis and transport related enzyme system and K[+] transporter related genes. Furthermore, the activity changes of Na[+]/K[+]-ATPase, which regulates cell permeability, in different environments also confirmed this point. This paper provides an effective strategy for enhancing the treatment of high-salt organic wastewater by electroactive microorganisms.}, }
@article {pmid40359746, year = {2025}, author = {Bansal, M and Santhiya, D and Sharma, JG}, title = {Simulated dump yard microbes drive significant biodegradation of polypropylene and polyvinyl chloride microplastics.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138545}, doi = {10.1016/j.jhazmat.2025.138545}, pmid = {40359746}, issn = {1873-3336}, abstract = {Bacterial culture isolates were used to demonstrate the breakdown of polypropylene (PPs) and polyvinyl chloride (PVCs) microplastics for the first time. Using metagenomics and phylogenetic analysis, bacterial isolates were discovered from a simulated dump yard. PPs and PVCs were broken down using bacterial isolates found to be Acinetobacter baumannii and mixed culture species with a Bacillus sp. dominance. After 50 days of activity, the dry weight of microplastics decreased by 33.3 % (PPs) and 27.1 % (PVCs) due to the breakdown process aided by Acinetobacter baumannii. Weight reductions of 20.3 % for PPs and 18.2 % for PVCs have been observed in mixed bacterial cultures, respectively. Microplastics' thermal stability and transition properties changed, according to experiments like DTG NMR, Raman, and WCA. FTIR analysis captured the structural changes in PPs and PVCs. SEM, TEM, and cell hydrophobicity tests showed that microplastics were biodegrading. GC-MS identified the released byproducts, which included carboxylic acids, alkanes, esters, and aromatic chemicals. Based on these findings, it can be concluded that bacterial isolates are effective in degrading PPs and PVCs and may help create sustainable methods of handling plastic trash.}, }
@article {pmid40359745, year = {2025}, author = {Yang, T and Gong, X and Xu, A and Wang, B and Huang, Z and Wang, C and Gao, D}, title = {Integrated evaluation for advanced removal of nitrate using novel solid carbon biochar/corncob/PHBV composite: Insight into electron transfer and metabolic pathways.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138549}, doi = {10.1016/j.jhazmat.2025.138549}, pmid = {40359745}, issn = {1873-3336}, abstract = {This study developed a novel Biochar/Corncob/PHBV (BCP) composite material, integrating the electron transfer capability of biochar, the cost-effectiveness of corncob, and the sustained carbon release performance of PHBV. The BCP system achieved a maximum nitrate removal efficiency of 97.3 %, significantly outperforming the single PHBV system (91.05 %), while effectively reducing nitrous oxide and other greenhouse gas emissions. It also demonstrated stable carbon release and enhanced electron transfer capabilities, contributing to a more sustainable denitrification process. The physical and chemical characterization of BCP confirmed that its superior performance is attributed to the uniformly distributed functional groups (e.g., CO and -COOH) on the surface and its porous structure, which facilitated electron transfer and microbial adhesion. Metagenomic and microbial analyses further revealed that BCP enriched functional genera such as Cellulomonas and Chryseobacterium and significantly increased the abundance of key functional genes related to nitrate reduction (e.g., NaR and NiR), enhancing organic matter decomposition and microbial nitrogen transformation. Beyond improving nitrate removal efficiency compared to PHBV, the BCP material offers practical engineering value by addressing carbon source limitations in long-term wastewater treatment applications. Its enhanced electron transfer and microbial enrichment suggest strong potential for application in constructed wetlands, biofilters, and other decentralized wastewater treatment systems. The study demonstrates that the BCP composite is not only a viable alternative to traditional PHBV but also a cost-effective and environmentally friendly material with broad applicability in nitrogen pollution control.}, }
@article {pmid40359589, year = {2025}, author = {Silva, MKP and Nicoleti, VYU and Rodrigues, BDPP and Araujo, ASF and Ellwanger, JH and de Almeida, JM and Lemos, LN}, title = {Exploring deep learning in phage discovery and characterization.}, journal = {Virology}, volume = {609}, number = {}, pages = {110559}, doi = {10.1016/j.virol.2025.110559}, pmid = {40359589}, issn = {1096-0341}, abstract = {Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The discovery of novel bacteriophages using large-scale metagenomic data has been accelerated by the accessibility of deep learning (Artificial Intelligence), the increased computing power of graphical processing units (GPUs), and new bioinformatics tools. This review addresses the recent revolution in bacteriophage research, ranging from the adoption of neural network algorithms applied to metagenomic data to the use of pre-trained language models, such as BERT, which have improved the reconstruction of viral metagenome-assembled genomes (vMAGs). This article also discusses the main aspects of bacteriophage biology using deep learning, highlighting the advances and limitations of this approach. Finally, prospects of deep-learning-based metagenomic algorithms and recommendations for future investigations are described.}, }
@article {pmid40359177, year = {2025}, author = {, }, title = {Editorial Note: Extensive culturomics of 8 healthy samples enhances metagenomics efficiency.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0324350}, doi = {10.1371/journal.pone.0324350}, pmid = {40359177}, issn = {1932-6203}, }
@article {pmid40359062, year = {2025}, author = {Jules, E and Decker, C and Bixler, BJ and Ahmed, A and Zhou, ZC and Arora, I and Tafesse, H and Dakanay, H and Bombin, A and Wang, E and Ingersoll, J and Bifulco, K and Frediani, JK and Parsons, R and Sullivan, J and Greenleaf, M and Waggoner, JJ and Martin, GS and Lam, WA and Piantadosi, A}, title = {Respiratory Virus Detection and Sequencing from SARS-CoV-2-Negative Rapid Antigen Tests.}, journal = {Emerging infectious diseases}, volume = {31}, number = {13}, pages = {39-44}, doi = {10.3201/eid3113.241191}, pmid = {40359062}, issn = {1080-6059}, mesh = {Humans ; *SARS-CoV-2/genetics ; Genome, Viral ; COVID-19/diagnosis/virology ; *Respiratory Tract Infections/virology/diagnosis ; Phylogeny ; Antigens, Viral ; *Viruses/genetics/isolation &amp; purification/classification ; }, abstract = {Genomic epidemiology offers insight into the transmission and evolution of respiratory viruses. We used metagenomic sequencing from negative SARS-CoV-2 rapid antigen tests to identify a wide range of respiratory viruses and generate full genome sequences. This process offers a streamlined mechanism for broad respiratory virus genomic surveillance.}, }
@article {pmid40358997, year = {2025}, author = {Connan, C and Fromentin, S and Benallaoua, M and Alvarez, AS and Pons, N and Quinquis, B and Morabito, C and Nazare, JA and Borezée-Durant, E and ,  and Haimet, F and Ehrlich, SD and Valeille, K and Cavezza, A and Blottière, H and Veiga, P and Almeida, M and Doré, J and Benamouzig, R}, title = {Associations Among Diet, Health, Lifestyle, and Gut Microbiota Composition in the General French Population: Protocol for the Le French Gut - Le Microbiote Français Study.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e64894}, doi = {10.2196/64894}, pmid = {40358997}, issn = {1929-0748}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; France ; *Life Style ; Feces/microbiology ; *Diet ; Adult ; Prospective Studies ; *Health Status ; Female ; Male ; Metagenomics/methods ; }, abstract = {BACKGROUND: Over the past 2 decades, the gut microbiota has emerged as a key player in human health, being involved in many different clinical contexts. Yet, many aspects of the relationship with its host are poorly documented. One obstacle is the substantial variability in wet-laboratory procedures and data processing implemented during gut microbiota studies, which poses a challenge of comparability and potential meta-analysis.<br><br>OBJECTIVE: The study protocol described here aimed to better understand the relationship between health, dietary habits, and the observed heterogeneity of gut microbiota composition in the general population. "Le French Gut - Le microbiote fran&#xe7;ais" aimed to collect, sequence, and analyze 100,000 fecal samples from French residents using a high-quality shotgun metagenomic pipeline, complemented with comprehensive health, lifestyle, and dietary metadata.<br><br>METHODS: "Le French Gut&#xa0;- Le microbiote fran&#xe7;ais" is a prospective, noninterventional French national study involving individuals, the creation of a biological collection (feces), and the exploitation of data from questionnaires and the National Health Data System (Syst&#xe8;me National des Donn&#xe9;es de Sant&#xe9;). This national study is open to all metropolitan French adult residents, excluding those who have undergone a colectomy or digestive stoma, or who have had a colonoscopy or taken antibiotics in the last 3 months. This is a home-based trial in which volunteers complete a questionnaire with insights about their health and habits, and in which stool samples are self-collected. Data analysis is structured into 6 work packages, each focusing on a specific aspect of the gut microbiome, including its composition and associations with lifestyle, quality of life, and health.<br><br>RESULTS: This paper outlines the study protocol, with recruitment having started in September 2022 and expected to continue until the end of December 2025. As of January 2025, a total of 20,000 participants have been enrolled. The first scientific publications based on the data analysis are expected by mid-2025.<br><br>CONCLUSIONS: "Le French Gut" aims to provide a reference database and new ecosystem tools for understanding the relationship between the gut microbiota, its host, and diet. We expect to be able to find new signatures or targets and promote the design of innovative preventive strategies, personalized nutrition, and precision medicine.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT05758961; https://clinicaltrials.gov/study/NCT05758961.<br><br>DERR1-10.2196/64894.}, }
@article {pmid40358144, year = {2025}, author = {Mukherjee, SD and Suryavanshi, M and Knight, J and Lange, D and Miller, AW}, title = {Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0091324}, doi = {10.1128/msphere.00913-24}, pmid = {40358144}, issn = {2379-5042}, abstract = {The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multiple urologic and cardiometabolic diseases. The current study employed multiple amplicon-based and shotgun metagenomic methodologies, alongside comparative phylogenetic analyses, to interrogate evolutionary radiation surrounding microbial oxalate degradation within the human gut microbiome. In conservative genome-based estimates, over 30% of gut microbial species harbored at least one oxalate-handling gene, with the specific pathways used dependent on bacterial phylum. Co-occurrence analyses revealed interactions between specialist genes that can metabolize oxalate or its by-products, but not multi-functional genes that can act in more than one oxalate-related pathway. Specialization was rare at the genome level. Amplicon-based metagenomic sequencing of the oxalate-degrading gene, formyl-CoA transferase (frc), coupled with molecular clock phylogenetic analyses are indicative of rapid evolutionary divergence, constrained by phylum. This was corroborated by paired analyses of non-synonymous to synonymous substitutions (dN/dS ratios), which pointed toward neutral to positive selection. Sequence similarity network analyses of frc sequences suggest extensive horizontal gene transferring has occurred with the frc gene, which may have facilitated rapid divergence. The frc gene was primarily allocated to the Pseudomonodota phylum, particularly the Bradyrhizobium genus, which is a species capable of utilizing oxalate as a sole carbon and energy source. Collectively evidence provides strong support that, for oxalate metabolism, evolutionary selection occurs at the gene level, through horizontal gene transfer, rather than at the species level.IMPORTANCEA critical function of the gut microbiota is to neutralize dietary toxins, such as oxalate, which is highly prevalent in plant-based foods and is not degraded by host enzymes. However, little is known about the co-evolutionary patterns of plant toxins and the mammalian gut microbiota, which are expected to exhibit features of an evolutionary arms race. In the current work, we present molecular evidence that microbial genes for oxalate degradation are highly prevalent in humans, potentially driven by extensive horizontal gene transfer events. Phylogenetic analyses reveal that oxalate-degrading genes are under a positive selection pressure and have historically undergone rapid diversification events, which has led to diverse ecological strategies for handling oxalate by gut bacteria. Collectively, data shed light on potential evolutionary relationships between the diet and the gut microbiota that occur relatively independently of the mammalian host.}, }
@article {pmid40357419, year = {2025}, author = {Liu, H and Xu, T and Fu, H and Dai, B and Xie, Y}, title = {Application of Metagenomic Next-Generation Sequencing in HIV-Infected Patients with Bloodstream Infections.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {2389-2399}, pmid = {40357419}, issn = {1178-6973}, abstract = {BACKGROUND: Bloodstream infections (BSI) are common complications in HIV-infected patients and are prone to septic shock and death. This study aimed to analyze the application of blood metagenomic next-generation sequencing (mNGS) in HIV-infected patients with BSI.<br><br>METHODS: Fifty-four HIV-infected patients with suspected BSI were hospitalized at the First Affiliated Hospital of the Zhejiang University School of Medicine between August 2020 and June 2023. Blood mNGS and blood culture (BC) results were retrospectively reviewed and compared to the application value of BSI.<br><br>RESULTS: The mNGS was more sensitive for detecting pathogens (82.4% versus 35.3%; P < 0.05), and when combining blood mNGS with culture results, the sensitivity increased to 88.2%. The detection rate of mNGS for blood-mixed infection was significantly higher than that of BC (P < 0.05). Among the positive results for fungi and bacteria detected by mNGS, 13.5% of the pathogenic microorganisms were consistent with the results of BC.<br><br>CONCLUSION: The mNGS combined with BC can improve pathogen detection sensitivity and the comprehensive identification of pathogenic microorganisms in HIV-infected patients with BSI.}, }
@article {pmid40357399, year = {2025}, author = {Xing, ZC and Guo, HZ and Zhen, P and Ao, T and Hu, M}, title = {Clinical application of metagenomic next-generation sequencing in etiologic diagnosis of severe pneumonia in adults.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1561468}, pmid = {40357399}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Aged ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adult ; COVID-19/diagnosis/virology ; Risk Factors ; *Pneumonia/diagnosis/microbiology/mortality ; Aged, 80 and over ; Bacteria/genetics/isolation &amp; purification/classification ; SARS-CoV-2/isolation &amp; purification ; Bronchoalveolar Lavage Fluid/microbiology/virology ; }, abstract = {OBJECTIVE: To analyze the clinical characteristics and risk factors for death of severe pneumonia (SP) in adults and explore the application value of metagenomic next-generation sequencing in the detection of pathogens.<br><br>METHODS: A total of 132 adult patients with SP admitted from May 2021 to October 2023 were selected. Data on gender, age, smoking, underlying diseases, laboratory tests and prognosis were collected. BALF samples were sent for mNGS, smear-stained microscopy and culture. Meanwhile, conventional methods were used for pathogen detection of blood, urine and throat swab specimens. The detection efficiencies of different methods were compared and the associated pathogen profiles were analyzed.<br><br>RESULTS: Among the 132 patients, there were 92 males and 40 females, with a total of 52 deaths. Age&#x2265;65 years, heart failure, renal insufficiency, positive of COVID-19, use of vasoactive drugs, use of mechanical ventilation and use of CRRT were statistically different between the survivors and non-survivors. Heart failure (OR=4.751) and use of mechanical ventilation (OR=11.914) were risk factors of SP mortality. The bacteria detected were mainly Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa. The fungi detected were mainly Candida and Aspergillus. The viruses detected were mainly COVID-19 and influenza virus. The positive rate of mNGS was higher than conventional methods in both bacteria, fungus and virus (82.58% vs 63.64%, 50.76% vs 37.88% and 67.42% vs 37.88%, respectively) (P<0.05). The sensitivity and accuracy of mNGS in bacterial detection were significantly higher than traditional methods (P<0.05). Compared to culture, mNGS detected more Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae and Escherichia coli, and had a significant advantage in the detection of Mycobacterium tuberculosis complex, Nontuberculous mycobacterial, Legionella pneumophila, Chlamydia psittaci, Pneumocystis jirovecii and Aspergillus. Moreover, mNGS can better indicate mixed infections of bacteria, viruses, or fungi.<br><br>CONCLUSION: Elderly people with chronic diseases were the main group of severe pneumonia in adults. The pathogenic microorganisms that caused SP are complex, and mixed infection is common. mNGS enhanced the effectiveness of pathogen detection, makes up for the shortcomings of conventional methods, especially in identifying unexpected pathogens, and provides a new means for early targeted anti-infection treatment.}, }
@article {pmid40357303, year = {2025}, author = {Fu, C and Sun, Y and Chen, C}, title = {First reported Tannerella forsythia infection in a patient with extensive bronchiectasis: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1571506}, pmid = {40357303}, issn = {2296-858X}, abstract = {Tannerella forsythia infection was common in oral diseases but less reported in lung diseases. This report presents a patient with bronchiectasis who was infected by Tannerella forsythia and subsequently hospitalized with symptoms including fever, progressive cough, sputum production, and shortness of breath. A chest computed tomography (CT) scan revealed multiple bilateral pulmonary bronchiectasis with signs of infection. Metagenomic next-generation sequencing (mNGS) of the bronchoalveolar lavage fluid primarily detected Tannerella forsythia. Treatment with Piperacillin-tazobactam and ornidazole resulted in a favorable outcome. This case first reported a patient with extensive bronchiectasis infected by Tannerella forsythia and provided an effective treatment.}, }
@article {pmid40357282, year = {2025}, author = {Wu, A and Gai, W and Guo, Y and Zhou, C and Xu, Y and Zhang, X and Wang, H}, title = {Clinical features of Talaromyces marneffei infection and colonization in HIV-negative patients: the role of mNGS in diagnosis.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1579522}, pmid = {40357282}, issn = {2296-858X}, abstract = {BACKGROUND: Talaromycosis, caused by Talaromyces marneffei (T. marneffei), has become more common in HIV-negative and immunocompetent patients. The fungus colonizes the body through dormant spores, causing opportunistic infections. Early diagnosis is challenging. This study aims to analyze the clinical features, diagnosis, treatment, and prognosis of T. marneffei infections.<br><br>METHODS: Patients diagnosed with T. marneffei infection or colonization at the People's Hospital of Ningbo University between August 2022 and July 2024 were included. Demographic characteristics, clinical data, diagnostic approaches, and treatment outcomes were analyzed.<br><br>RESULTS: Seven patients were diagnosed with T. marneffei infection, and three with colonization. Productive cough and fever were the predominant symptoms in all patients. Nodules, cavitary lesions, and pleural effusions on chest imaging were observed exclusively in infected patients. The positivity rates for metagenomic next-generation sequencing (mNGS) and conventional microbiological testing were 100 and 10%, respectively. Of the seven infected patients, three had a single infection with T. marneffei, and four had co-infection with T. marneffei and Mycobacterium avium complex. All patients were treated with monotherapy or combination therapy using voriconazole. All but one recovered.<br><br>CONCLUSION: Early diagnosis and combination therapy are critical for T. marneffei infection. mNGS complements traditional methods, facilitating accurate diagnosis and guiding targeted treatment.}, }
@article {pmid40356662, year = {2025}, author = {Vallejo-Espín, D and Galarza-Mayorga, J and Lalaleo, L and Calero-Cáceres, W}, title = {Beyond clinical genomics: addressing critical gaps in One Health AMR surveillance.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1596720}, pmid = {40356662}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) poses an escalating global threat that demands comprehensive surveillance approaches beyond traditional clinical contexts. Although next-generation sequencing (NGS), particularly whole-genome sequencing (WGS), has revolutionized AMR surveillance, current implementation predominantly targets clinical isolates, largely neglecting critical environmental and animal reservoirs. Consequently, significant gaps persist in our understanding of AMR dynamics across diverse ecosystems. This Perspective emphasizes the urgent need to adopt an integrated genomic framework, combining isolate-based WGS with shotgun metagenomics within a cohesive One Health strategy. Such an integrated approach would significantly enhance the detection, tracking, and containment of resistance determinants, facilitating proactive rather than reactive AMR management. Achieving this vision requires global standardization of sequencing methods, harmonization of bioinformatics pipelines, and strengthened cross-sectoral collaboration to ensure timely interventions against AMR threats worldwide.}, }
@article {pmid40356641, year = {2025}, author = {Xing, Y and Xie, Y and Wang, X}, title = {Enhancing soil health through balanced fertilization: a pathway to sustainable agriculture and food security.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1536524}, pmid = {40356641}, issn = {1664-302X}, abstract = {Sustainable soil health management is pivotal for advancing agricultural productivity and ensuring global food security. This review comprehensively evaluates the effects of mineral-organic fertilizer ratios on soil microbial communities, enzymatic dynamics, functional gene abundance, and holistic soil health. By integrating bioinformatics, enzyme activity assays, and metagenomic analyses, we demonstrate that balanced fertilization significantly enhances microbial diversity, community stability, and functional resilience against environmental stressors. Specifically, the synergistic application of mineral and organic fertilizers elevates β-glucosidase and urease activities, accelerating organic matter decomposition and nutrient cycling while modulating microbial taxa critical for nutrient transformation and pathogen suppression. Notably, replacing 20-40% of mineral fertilizers with organic alternatives mitigates environmental risks such as greenhouse gas emissions and nutrient leaching while sustaining crop yields. This dual approach improves soil structure, boosts water and nutrient retention capacity, and increases microbial biomass by 20-30%, fostering long-term soil fertility. Field trials reveal yield increases of 25-40% in crops like rice and maize under combined fertilization, alongside enhanced soil organic carbon (110.6%) and nitrogen content (59.2%). The findings underscore the necessity of adopting region-specific, balanced fertilization strategies to optimize ecological sustainability and agricultural productivity. Future research should prioritize refining fertilization frameworks through interdisciplinary approaches, addressing soil-crop-climate interactions, and scaling these practices to diverse agroecosystems. By aligning agricultural policies with ecological principles, stakeholders can safeguard soil health-a cornerstone of environmental sustainability and human wellbeing-while securing resilient food systems for future generations.}, }
@article {pmid40356191, year = {2025}, author = {Charalambous, H and Brown, C and Vogazianos, P and Katsaounou, K and Nikolaou, E and Stylianou, I and Papageorgiou, E and Vraxnos, D and Aristodimou, A and Chi, J and Costeas, P and Shammas, C and Apidianakis, Y and Antoniades, A}, title = {Dysbiosis in the Gut Microbiome of Pembrolizumab-Treated Non-Small Lung Cancer Patients Compared to Healthy Controls Characterized Through Opportunistic Sampling.}, journal = {Thoracic cancer}, volume = {16}, number = {9}, pages = {e70075}, pmid = {40356191}, issn = {1759-7714}, support = {//Investigator-Initiated Studies Program of Merck Sharp &amp; Dohme Corp/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced/microbiology/pathology ; Male ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology/microbiology ; Female ; *Lung Neoplasms/drug therapy/pathology/microbiology ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology/adverse effects ; Middle Aged ; Aged ; Prospective Studies ; Case-Control Studies ; *Antineoplastic Agents, Immunological/therapeutic use ; }, abstract = {BACKGROUND: The gut microbiome influences the host immune system, cancer development and progression, as well as the response to immunotherapy during cancer treatment. Here, we analyse the composition of the gut bacteriome in metastatic Non-Small Cell Lung Cancer (NSCLC) patients receiving Pembrolizumab immunotherapy within a prospective maintenance trial through opportunistic sampling during treatment.<br><br>METHODS: The gut microbiome profiles of NSCLC patients were obtained from stool samples collected during Pembrolizumab treatment and analysed with 16S rRNA metagenomics sequencing. Patient profiles were compared to a group of healthy individuals of matching ethnic group, age, sex, BMI and comorbidities.<br><br>RESULTS: A significant decrease in the treated patients was observed in two prominent bacterial families of the phylum Firmicutes, Lachnospiraceae and Ruminoccocaceae, which comprised 31.6% and 21.8% of the bacteriome in the healthy group but only 10.9% and 14.2% in the treated patient group, respectively. Species within the Lachnospiraceae and Ruminococcaceae families are known to break down undigested carbohydrates generating short chain fatty acids (SCFA), such as butyrate, acetate and propionate as their major fermentation end-products, which have been implicated in modifying host immune responses. In addition, a significant increase of the Bacteroidacaeae family (Bacteroidetes phylum) was observed from 10.7% in the healthy group to 23.3% in the treated patient group. Moreover, and in agreement with previous studies, a decrease in the Firmicutes to Bacteroidetes ratio in the metastatic NSCLC Pembrolizumab-treated patients was observed.<br><br>CONCLUSION: The observed differences indicate dysbiosis and a compromised intestinal health status in the metastatic NSCLC Pembrolizumab-treated patients. This data could inform future studies of immunotherapy treatment responses and modulation of the gut microbiome to minimise dysbiosis prior or concurrent to treatment.<br><br>TRIAL REGISTRATION: SWIPE Trial (NCT02705820).}, }
@article {pmid40356165, year = {2025}, author = {Park, C and Park, J and Chang, D and Kim, S}, title = {Development of reference-based model for improved analysis of bacterial community.}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116380}, doi = {10.1016/j.foodres.2025.116380}, pmid = {40356165}, issn = {1873-7145}, mesh = {RNA, Ribosomal, 16S/genetics ; *Probiotics ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; DNA, Bacterial/genetics ; Polymerase Chain Reaction/methods ; }, abstract = {Probiotic bacteria play a vital role in maintaining gut microbial homeostasis and are widely used in various commercial products. Although 16S rRNA amplicon-based next-generation sequencing (NGS) is commonly used to analyze probiotic products, biases can arise from various 16S rRNA amplification regions, sequencing platforms, and library kits. In this study, a reference-based bias correction model was developed to correct sequencing biases. The model was validated using eight mock communities and 12 commercial products, which were analyzed across multiple NGS platforms and various 16S rRNA regions. Specific primer-probe assays were developed for accurate bacterial quantification, and their specificity was validated and used in conjunction with droplet digital PCR (ddPCR) to establish initial bacterial ratios within communities. Analysis of the mock communities revealed platform- and region-specific biases, with specific species consistently over- or under-represented. Similarly, commercial product analyses have shown biased outcomes owing to varying sequencing protocols. The correction model, based on PCR efficiencies from the reference communities, successfully corrected biased ratios across different amplification regions and platforms to achieve results that closely matched the proportions predicted by ddPCR. The model effectively corrected the biases arising from the different polymerases. Notably, partial references containing approximately 40 % of the species achieved correction results that were comparable to those of the complete references. This approach demonstrates the potential for improving microbiome analysis accuracy within predictable ranges, and could serve as a model for addressing sequencing bias in metagenomic research.}, }
@article {pmid40356145, year = {2025}, author = {Wang, S and Zheng, C and Bu, C and Guo, D and Zhang, C and Xie, Q and Pan, J and Sun, J and Chen, W and Jiang, S and Zhai, Q}, title = {Role of sn-2 palmitate on the development of the infant gut microbiome: A metagenomic insight.}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116488}, doi = {10.1016/j.foodres.2025.116488}, pmid = {40356145}, issn = {1873-7145}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Infant Formula/chemistry ; Infant ; Feces/microbiology ; *Metagenomics/methods ; Milk, Human/chemistry ; Female ; Male ; Breast Feeding ; *Palmitates/pharmacology ; Infant, Newborn ; Phylogeny ; }, abstract = {The infant gut microbiome, which develops from birth, has profound and lasting effects on human health. Its establishment in early life is influenced by events such as delivery mode and feeding type. This study examined the effects of formula milk enriched with sn-2 palmitate on the gut microbiota of healthy term infants. We conducted a 16-week comparative analysis of three feeding groups: infants receiving high sn-2 palmitate formula (n = 30), regular vegetable oil formula (n = 32), and breast milk (n = 30). Using shotgun metagenomic sequencing of fecal samples, we performed a comprehensive assessment of the gut microbiota. While overall microbial composition and diversity were comparable across groups, the functional profile of the microbiome in infants receiving sn-2 palmitate-enriched formula more closely resembled that of breastfed infants compared to the control formula group. This similarity extended to microbial species interactions, virulence gene abundance, and metabolic pathway expression patterns. In addition, sn-2 palmitate promoted the proliferation of Bifidobacterium breve and enhanced the robustness of the gut microbial ecology. Notably, the phylogenetic analysis of B. breve strains in the sn-2 palmitate group showed closer alignment with the breastfed group compared to the control group. These findings suggest that sn-2 palmitate-enriched formula may confer gut microbiota functional benefits that more closely resemble those of breast milk compared to control formula milk. This study provides scientific evidence for the development of future functional infant formulas.}, }
@article {pmid40356136, year = {2025}, author = {Luo, Y and Tang, R and Huang, Y}, title = {Differences in structure, antioxidant capacity and gut microbiota modulation of red raspberry pectic polysaccharides extracted by different methods.}, journal = {Food research international (Ottawa, Ont.)}, volume = {211}, number = {}, pages = {116474}, doi = {10.1016/j.foodres.2025.116474}, pmid = {40356136}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Rubus/chemistry ; *Antioxidants/pharmacology/chemistry ; *Pectins/chemistry/pharmacology ; Prebiotics/analysis ; *Polysaccharides/chemistry/pharmacology ; *Fruit/chemistry ; Humans ; *Plant Extracts/chemistry/pharmacology ; }, abstract = {Red raspberries are associated with various health benefits, with pectic polysaccharides as their primary component and potential key contributor to these effects. This study aimed to evaluate the antioxidant and prebiotic potential of four red raspberry pectic polysaccharides (RP)-EN-RP (enzyme-assisted extraction), AC-RP (acid-assisted extraction), AL-RP (alkali-assisted extraction), and US-RP (ultrasound-assisted extraction)-and to elucidate the relationship between their structure and function. AC-RP and US-RP contained higher proportions of homogalacturonan (HG) at 50.92 % and 53.10 %, respectively, while EN-RP and AL-RP exhibited higher proportions of rhamnogalacturonan-I (RG-I) at 63.89 % and 43.37 %, respectively. All four polysaccharides demonstrated significant antioxidant and prebiotic properties. AL-RP exhibited the strongest DPPH radical scavenging activity, while US-RP showed the highest hydroxyl radical scavenging ability. These pectic polysaccharides were highly fermentable, significantly modulating gut microbiota composition and promoting the production of propionic acid, particularly EN-RP and AL-RP. Compared to the blank group, RP intervention significantly enriched Bacteroides, Phocaeicola, Bifidobacterium, Limosilactobacillus, and Paraprevotella. Carbohydrate-active enzyme genes in metagenomes revealed that glycoside hydrolases played a vital role in the degradation and utilization of red raspberry polysaccharides. Furthermore, correlation analysis indicated that a higher RG-I proportion and an elevated Rha/GalA ratio enhanced the abundance of certain beneficial microbial species and increased propionic acid production. These findings advance the understanding of the structure-function relationship of natural pectic polysaccharides and highlight their potential for tailoring gut microbiota and promoting health through precise dietary interventions.}, }
@article {pmid40355758, year = {2025}, author = {Saeedi Saravi, SS and Pugin, B and Constancias, F and Shabanian, K and Spalinger, M and Thomas, A and Le Gludic, S and Shabanian, T and Karsai, G and Colucci, M and Menni, C and Attaye, I and Zhang, X and Allemann, MS and Lee, P and Visconti, A and Falchi, M and Alimonti, A and Ruschitzka, F and Paneni, F and Beer, JH}, title = {Gut microbiota-dependent increase in phenylacetic acid induces endothelial cell senescence during aging.}, journal = {Nature aging}, volume = {}, number = {}, pages = {}, pmid = {40355758}, issn = {2662-8465}, support = {#310030_21A053//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; #CRSK-3_229134//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; #21A053//Novartis Stiftung f&#xfc;r Medizinisch-Biologische Forschung (Novartis Foundation for Medical-Biological Research)/ ; }, abstract = {Endothelial cell senescence is a key driver of cardiovascular aging, yet little is known about the mechanisms by which it is induced in vivo. Here we show that the gut bacterial metabolite phenylacetic acid (PAA) and its byproduct, phenylacetylglutamine (PAGln), are elevated in aged humans and mice. Metagenomic analyses reveal an age-related increase in PAA-producing microbial pathways, positively linked to the bacterium Clostridium sp. ASF356 (Clos). We demonstrate that colonization of young mice with Clos increases blood PAA levels and induces endothelial senescence and angiogenic incompetence. Mechanistically, we find that PAA triggers senescence through mitochondrial H2O2 production, exacerbating the senescence-associated secretory phenotype. By contrast, we demonstrate that fecal acetate levels are reduced with age, compromising its function as a Sirt1-dependent senomorphic, regulating proinflammatory secretion and redox homeostasis. These findings define PAA as a mediator of gut-vascular crosstalk in aging and identify sodium acetate as a potential microbiome-based senotherapy to promote healthy aging.}, }
@article {pmid40355744, year = {2025}, author = {Schreiber, S and Waetzig, GH and López-Agudelo, VA and Geisler, C and Schlicht, K and Franzenburg, S and di Giuseppe, R and Pape, D and Bahmer, T and Krawczak, M and Kokott, E and Penninger, JM and Harzer, O and Kramer, J and von Schrenck, T and Sommer, F and Zacharias, HU and ,  and Millet Pascual-Leone, B and Forslund, SK and Heyckendorf, J and Aden, K and Hollweck, R and Laudes, M and Rosenstiel, P}, title = {Nicotinamide modulates gut microbial metabolic potential and accelerates recovery in mild-to-moderate COVID-19.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, pmid = {40355744}, issn = {2522-5812}, support = {EXC 2167: CD-1, CD-2, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: RTF-VI//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; miTARGET (RU5042)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SO1141/10-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB1470, SFB1449//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; miTARGET (RU5042)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: CD-1, CD-2, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167: CD-2, RTF-VI, TI-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, e:Med Network iTREAT 01ZX2202A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; e:Med CKDNapp 01ZX1912A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, e:Med Network iTREAT 01ZX2202A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; e:Med Juniorverbund "Try-IBD" 01ZX1915A and 01ZX2215, e:Med Network iTREAT 01ZX2202A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; K126408//Christian-Albrechts-Universit&#xe4;t zu Kiel (Christian-Albrechts-University Kiel)/ ; }, abstract = {Cellular NAD[+] depletion, altered tryptophan metabolism and gut microbiome dysbiosis are associated with disease progression and unfavourable clinical outcomes in COVID-19. Here, we show that supplementing tryptophan metabolism with nicotinamide alleviates COVID-19 symptoms. We evaluate a 4-week intervention with a novel nicotinamide formulation (1,000 mg) in a prospective, double-blind, randomized, placebo-controlled trial in 900 symptomatic outpatients with PCR-proven COVID-19. In the primary analysis population of participants at risk for severe COVID-19, 57.6% of those receiving nicotinamide and 42.6% receiving placebo recover from their performance drop at week 2 (P = 0.004). Nicotinamide is also beneficial for returning to normal activities (P = 0.009). Effects on gut metagenomic signatures parallel clinical efficacy, suggesting that nicotinamide influences COVID-19-associated faecal microbiome changes. After 6 months, responders to nicotinamide in acute COVID-19 show fewer post-COVID symptoms than placebo responders (P = 0.010). No relevant safety signals are observed. Overall, our results show that nicotinamide leads to faster recovery of physical performance and modulates COVID-19-associated faecal microbiome changes.}, }
@article {pmid40355385, year = {2025}, author = {Wang, L and Chen, Y and Wang, Q and Wang, F}, title = {Microbial imbalances linked to early pregnancy loss: a comparative analysis of vaginal microbiota.}, journal = {The journal of maternal-fetal &amp; neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {38}, number = {1}, pages = {2496787}, doi = {10.1080/14767058.2025.2496787}, pmid = {40355385}, issn = {1476-4954}, mesh = {Humans ; Female ; Pregnancy ; *Vagina/microbiology ; Case-Control Studies ; *Abortion, Spontaneous/microbiology ; Adult ; *Microbiota ; Young Adult ; }, abstract = {OBJECTIVE: To explore the role and related functions of vaginal microbiota in early pregnancy loss.<br><br>METHODS: This study was a case-control study with a comparison group (reference group). We recruited 178 women, including 73 who had experienced at least one early clinical pregnancy loss and 105 patients with one live birth and no history of pregnancy loss. Data on demographics, disease history, menstrual and reproductive history was collected. The case group patients were sampled immediately upon presenting with pregnancy loss at their first visit. The reference group patients underwent samples when they chose to participate voluntarily. All vaginal discharge was performed DNA Preparation and Metagenomics Sequencing. DNA extraction was performed using the phenol/trichloromethane method and the DNA fragments were then size-selected to 300-700 bp using magnetic beads. The selected fragments were repaired and ligated with indexed adaptors. The captured DNA was amplified again by PCR and circularized to create a single-stranded circular (ssCir) library. The ssCir library was subsequently amplified through rolling circle amplification (RCA) to produce DNA nanoballs (DNBs). The DNBs were then loaded onto a flow cell and sequenced using the DNBSEQ Platform. Nonparametric tests, including Kruskal-Wallis and Wilcoxon tests, were employed. Relative abundance between groups was compared, and differential species selection was performed using the LEfSe software with linear discriminant analysis.<br><br>RESULTS: 1. PCoA analysis based on Bray-Curtis distances at the species level revealed a difference between the groups (p = 0.011). At the genus level, &#x3b1;-diversity, assessed using the Shannon, Simpson, and Inverse Simpson indices, indicated higher bacterial richness and diversity in the control group (Shannon: mean 0.554 vs. 0.383, p = 0.0044; Simpson: mean 0.254 vs. 0.179, p = 0.0043; Inverse Simpson: mean 1.636 vs. 1.414, p = 0.0043); At the genus level, 107 microbial genera were identified, 18 of which displayed statistically significant differences. At the species level, 23 microbial species showed significant differences between the two groups. 2. We analyzed the differences in the most abundant phyla, genera, and species, with a particular focus on the top 20 most abundant genera and species. Firmicutes and Proteobacteria were significantly more prevalent among patients with pregnancy loss (PL). Among the top 20 most abundant genera, Streptococcus and Porphyromonas were significantly more abundant in patients with PL, whereas Bifidobacterium was significantly more prevalent in the reference group. Among the 20 most abundant species, Lactobacillus crispatus was significantly more prevalent in patients with PL, whereas common in the control group. 3. Principal Coordinates Analysis (PCoA) of Bray-Curtis distances, highlight their distinct clustering patterns, suggesting a notable difference between the metabolic pathways of the two groups. Key pathways with a negative correlation to PL include those related to amino acid biosynthesis, lipid metabolism, and nucleotide biosynthesis.<br><br>CONCLUSION: Our study highlights the association between vaginal microbiota dysbiosis and EPL, identifying specific microbial taxa that may contribute to pregnancy loss. These findings underscore the importance of the vaginal microbiome in reproductive health and open up new avenues for research into microbiome-based diagnostics and therapies. By integrating microbial, immune, and environmental data, future research has the potential to uncover the mechanisms underlying EPL and develop targeted interventions to improve pregnancy outcomes.}, }
@article {pmid40355358, year = {2025}, author = {Zhang, WL and Zu, YL and Huang, ZH and Li, Z and Gui, RR and Wang, J and Wang, XJ and Wang, HL and Fan, XX and Song, YP and Fang, BJ and Zhou, J}, title = {[BK virus nephropathy after allogeneic hematopoietic stem cell transplantation: a case report and literature review].}, journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi}, volume = {46}, number = {3}, pages = {273-275}, doi = {10.3760/cma.j.121090-20240810-00298}, pmid = {40355358}, issn = {0253-2727}, mesh = {Humans ; Male ; *Hematopoietic Stem Cell Transplantation/adverse effects ; BK Virus ; Young Adult ; *Polyomavirus Infections ; *Kidney Diseases/virology/etiology ; *Tumor Virus Infections ; Transplantation, Homologous ; }, abstract = {A 20-year-old male patient with T-lymphoblastic lymphoma/leukemia received 9/10 human leukocyte antigen-compatible unrelated peripheral blood stem cell transplantation. He was transplanted with 5.91×10(8) mononuclear cells/kg and 2.88×10(6) CD34(+) cells/kg, and neutrophil engraftment was obtained at +11 days and platelet engraftment at +9 days. After transplantation, he presented with repeatedly increased serum creatinine levels, BK virus (BKV) -associated hemorrhagic cystitis, and BKV viremia. BK virus nephropathy was diagnosed based on renal biopsy and metagenomic next-generation sequencing. After adjusting the immunosuppressant, intravenous immunoglobulin, and donor lymphocyte infusion treatment, the patient's renal function deteriorated progressively, and he eventually died of multiple organ failure at +289 days.}, }
@article {pmid40354774, year = {2025}, author = {Hu, T and He, S and Gao, Z and Feng, L and Jiang, J and Zhao, Q and Wei, L}, title = {Micro-mechanism of rhamnolipid promoting acid production during anaerobic digestion: protein structures, metagenomics and molecular dynamics simulations.}, journal = {Water research}, volume = {283}, number = {}, pages = {123795}, doi = {10.1016/j.watres.2025.123795}, pmid = {40354774}, issn = {1879-2448}, abstract = {The addition of rhamnolipid (RL) is a promising strategy to enhance volatile fatty acids (VFAs) production in anaerobic digestion (AD) systems. However, the microscopic mechanisms underlying this enhancement remain poorly understood. This study investigates the micro-mechanisms by which RL promotes VFAs production, integrating protein structural analysis, metagenomics, and molecular dynamics simulations. Experimental results revealed that adding RL at 0.08 g/g TS significantly increased VFAs production to 11,441.8 mg COD/L. Protein structural analysis revealed disruption of amide I-related C = O groups and amide II-related CN and NH bonds, indicating the release or structural alteration of sludge proteins. Metagenomic analysis indicated an increase in the abundance of microbial communities and related genes, suggesting that RL enhanced the activity of acid-producing microorganisms and related metabolic pathways. Furthermore, molecular docking and molecular dynamics simulations indicated that RL spontaneously aggregated and absorbed acetate kinase (AK), altering its conformation and reducing structural compactness, which made acetyl phosphate (AcP) more accessible to the binding site of AK. RL reduced the energy barrier associated with the polar solvation interactions, increasing the contributions of key residues (LYS176 and GLU234) to the binding free energy, which enhanced the binding affinity of AK-AcP complex. This study provides a comprehensive molecular basis for how RL promotes VFAs production in AD, offering a promising strategy for optimizing acid production.}, }
@article {pmid40354675, year = {2025}, author = {Zhi, N and Chang, X and Zha, L and Zhang, K and Wang, J and Gui, S}, title = {Platycodonis radix polysaccharides suppress progression of high-fat-induced obesity through modulation of intestinal microbiota and metabolites.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {142}, number = {}, pages = {156653}, doi = {10.1016/j.phymed.2025.156653}, pmid = {40354675}, issn = {1618-095X}, abstract = {BACKGROUND: Obesity is a prevalent chronic condition worldwide, posing a significant risk to public health. Polysaccharides derived from Platycodonis Radix (PR) have been identified as the primary bioactive compounds in combating obesity, although the underlying molecular mechanisms remain inadequately understood.<br><br>PURPOSE: The purpose of the research is to analyze the potential anti-obesity influnces within PR polysaccharides (PG: PG1 and PG2) by analyzing their impact on gut microbiota (GM) composition, SCFA and BA metabolism, and the regulation of associated gene and protein expression.<br><br>STUDY DESIGN AND METHODS: In this research, 7-week-old male C57BL/6 mice were assigned to a HFD or a control chow diet for 90 days to evaluate the therapeutic effects of PG intervention. Metagenomic analysis was performed to assess GM alterations, while GC-MS and LC-MS were used to quantify SCFA and BA concentrations in cecal contents, respectively. Furthermore, the effects of PG on SCFA- and BA-associated metabolic pathways were examined through qRT-PCR and WB.<br><br>RESULTS: PG1 demonstrated superior efficacy compared to PG2 in reducing HFD-induced obesity and associated metabolic disturbances. High-dose PG1 treatment effectively inhibited weight gain, dyslipidemia, inflammation, liver damage, and fat deposition caused by the HFD. Additionally, PG1 treatment primarily promoted the abundance of SCFA-producing bacteria, enhanced the expression of GPR41 and GPR43 genes, significantly elevated levels of GLP-1 and PYY, and improved circulating leptin and adiponectin levels. The intervention with PG1 notably enhanced the relative abundances of bacteria involved in the production of secondary BAs, such as Lachnospiraceae_NK4A136 and Eubacterium coprostanoligenes. This augmentation facilitated the transformation of primary BAs into secondary forms, diminished the relative expression of intestinal FXR and FGF15, and reduced FGFR4 levels. Consequently, this led to an upregulation of hepatic CYP7A1, accelerating liver cholesterol metabolism and the synthesis of new BAs.<br><br>CONCLUSION: Supplementation with PG1 protects mice from obesity induced by an HFD. The observed protective effects of PG1 appear to be primarily mediated through the activation of the GM-SCFA-GPR pathway and the inhibition of the GM-BA-FXR-FGF15 signaling pathway.}, }
@article {pmid40354439, year = {2025}, author = {Llarena, AK and Haverkamp, THA and Gulliksen, WS and Herstad, K and Holst-Jensen, A and Skjerve, E and Rannem, L and Rodriguez-Campos, S and Øines, &#xd8;}, title = {DNA extraction protocols for animal fecal material on blood spot cards.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0313808}, doi = {10.1371/journal.pone.0313808}, pmid = {40354439}, issn = {1932-6203}, mesh = {Animals ; *Feces/microbiology/chemistry ; Dogs ; Cattle ; Metagenomics/methods ; Horses ; Swine ; Sheep ; *DNA/isolation &amp; purification ; *DNA, Bacterial/isolation &amp; purification/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Collecting fecal samples using dry preservatives is an attractive option in large epidemiological studies as they are easy to use, cheap and independent of cold chain logistics. Here, we test four DNA extraction methods with the aim of identifying an efficient procedure to extract high-quality DNA from fecal material of canine, sheep, equine, bovine, and pig collected on dry blood spot cards, with the goal of generating good quality shotgun metagenomics datasets. Further, the suitability of Illumina shotgun metagenomic sequencing at 20 million paired-end (PE) read depth per sample was assessed on its ability to successfully characterize the taxonomic and functional aspects of the resulting fecal microbiome.<br><br>METHODS: DNA was extracted from pig feces and mock communities collected on blood spot cards using four DNA extraction methods; two different methods of the QIAsymphony&#xae; PowerFecal&#xae; Pro DNA Kit, the ZymoBIOMICS&#x2122; DNA Miniprep Kit, and the MagNA Pure 96 DNA and Viral NA Small Volume Kit. Possible extraction bias was controlled by amplicon sequencing of mock communities. Fecal samples from canine, sheep, equine, bovine, and pig were thereafter subjected to the best performing DNA extraction method and shotgun metagenomic sequencing to determine sequencing efforts for functional and taxonomic analysis.<br><br>RESULTS: The four DNA extraction methods demonstrated similar community composition in the sequenced bacterial mock community. The QIAsymphony&#xae; PowerFecal&#xae; Pro DNA Kit was identified as the DNA extraction method of choice, and the resulting DNA was subjected to shotgun metagenomic sequencing with 20million PE reads. We found that higher number of reads increased the richness of observed genera between 100,000 and 5 million reads, after which higher sequencing effort did not increase the richness of the metagenomes. As for functional analysis, the number of low abundance functions in the metagenomes of the animals' feces increased with sequencing depth above 20 million PE reads.<br><br>CONCLUSION: Our experiments identified several methods suitable for extracting DNA from feces collected on blood spot cards. The QIAGEN's Blood and Tissue kit on the QiaSymphony platform fulfilled the criteria of high yield, quality, and unbiased DNA, while maintaining high throughput for shotgun metagenomic sequencing. A sequencing depth of 20 million PE reads proved adequate for taxonomic estimations and identifying common functional pathways. Detecting rarer traits, however, requires more sequencing effort.}, }
@article {pmid40353658, year = {2025}, author = {Laso-Pérez, R and Rivas-Santisteban, J and Fernandez-Gonzalez, N and Mundy, CJ and Tamames, J and Pedrós-Alió, C}, title = {Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation.}, journal = {mBio}, volume = {}, number = {}, pages = {e0074925}, doi = {10.1128/mbio.00749-25}, pmid = {40353658}, issn = {2150-7511}, abstract = {In the Arctic, phytoplankton blooms are recurring phenomena occurring during the spring-summer seasons and influenced by the strong polar seasonality. Bloom dynamics are affected by nutrient availability, especially nitrogen, which is the main limiting nutrient in the Arctic. This study aimed to investigate the changes in an Arctic microbial community using omics approaches during a phytoplankton bloom focusing on the nitrogen cycle. Using metagenomic and metatranscriptomic samples from the Dease Strait (Canada) from March to July (2014), we reconstructed 176 metagenome-assembled genomes. Bacteria dominated the microbial community, although archaea reached up to 25% of metagenomic abundance in early spring, when Nitrososphaeria archaea actively expressed genes associated with ammonia oxidation to nitrite (amt, amo, nirK). The resulting nitrite was presumably further oxidized to nitrate by a Nitrospinota bacterium that highly expressed a nitrite oxidoreductase gene (nxr). Since May, the constant increase in chlorophyll a indicated the occurrence of a phytoplankton bloom, promoting the successive proliferation of different groups of chemoorganotrophic bacteria (Bacteroidota, Alphaproteobacteria, Gammaproteobacteria). These bacteria showed different strategies to obtain nitrogen, whether it be from organic or inorganic sources, according to the expression patterns of genes encoding transporters for nitrogen compounds. In contrast, during summer, the chemolithotrophic organisms thriving during winter reduced their relative abundance and the expression of their catabolic genes. Based on our functional analysis, we see a transition from a community where nitrogen-based chemolitotrophy plays a relevant role to a chemoorganotrophic community based on the carbohydrates released during the phytoplankton bloom, where different groups seem to specialize in different nitrogen sources.IMPORTANCEThe Arctic is one of the environments most affected by anthropogenic climate change. It is expected that the rise in temperature and change in ice cover will impact the marine microbial communities and the associated biogeochemical cycles. In this regard, nitrogen is the main nutrient limiting Arctic phytoplankton blooms. In this study, we combine genetic and expression data to study the nitrogen cycle at the community level over a time series covering from March to July. Our results indicate the importance of different taxa (from archaea to bacteria) and processes (from chemolithoautotrophy to incorporation of different nitrogen sources) in the cycling of nitrogen during this period. This study provides a baseline for future research that should include additional methodologies like biogeochemical analysis to fully understand the changes occurring on these communities due to global change.}, }
@article {pmid40352947, year = {2025}, author = {Zhong, QL and Xiong, JQ}, title = {A Globally Distributed Cyanobacterial Nitroreductase Capable of Conferring Biodegradation of Chloramphenicol.}, journal = {Research (Washington, D.C.)}, volume = {8}, number = {}, pages = {0692}, pmid = {40352947}, issn = {2639-5274}, abstract = {Cyanobacteria play pivotal roles in global biogeochemical cycles and aquatic ecosystems due to their widespread distribution and significant contributions to primary production. Yet, the interactions between cyanobacteria and antibiotics remain unclear. This study revealed that Synechocystis sp., a cyanobacterial species, removed 94.27% of 0.1 mg l[-1] chloramphenicol (CAP) through enzyme-mediated degradation. While cytochrome P450 enzymes (CYP450s) were found unnecessary for CAP removal, a gene encoding cyanobacterial nitroreductase was significantly up-regulated (7.85-fold) under CAP exposure. The purified nitroreductase exhibited strong binding affinity to CAP (K d = 2.9 nM) and a Michaelis constant (K m) of 104.0 μM. By engineering a bacterial strain with nitroreductase, 94.43% of 0.1 mg l[-1] CAP was removed within 2 h. Metagenomic and metatranscriptomic analyses showed that nitroreductase genes and transcripts are globally distributed across diverse microbial phyla. These findings uncover a novel enzyme for CAP degradation and advance sustainable biotechnologies to mitigate antibiotic pollution, addressing critical environmental challenges in aquaculture and other industries globally.}, }
@article {pmid40351504, year = {2025}, author = {Wilkhoo, HS and Islam, AW and Wilkhoo, HS and Hussain, S and Singh, B and Kadam, SR}, title = {Clinical Insights and Advancements in Human Metapneumovirus Management and Prognosis.}, journal = {Discoveries (Craiova, Romania)}, volume = {13}, number = {1}, pages = {e204}, pmid = {40351504}, issn = {2359-7232}, abstract = {Human metapneumovirus is a respiratory pathogen that infects children, the elderly, and immunocompromised individuals. Despite its global prevalence, underdiagnosis persists because of clinical overlap with other respiratory viruses. The current approach is mostly supportive, with oxygen therapy and hydration being crucial interventions. Ribavirin contains antiviral properties but has little clinical application. Vaccine development is moving forward, with prospects including live-attenuated, subunit-based, and virus-like particle vaccines. Molecular diagnostics, such as RT-PCR and metagenomic sequencing, have increased detection rates, which aids epidemiological monitoring. Monoclonal antibodies targeting the fusion (F) protein are being studied for passive immunity, while immunomodulatory treatments such as corticosteroids and intravenous immunoglobulins may help treat severe cases. Emerging treatments include fusion inhibitors and pan-pneumovirus vaccinations that protect against HMPV and RSV. Future research should concentrate on optimizing antiviral methods, increasing vaccination trials, and improving surveillance to detect outbreaks. A multidisciplinary approach that combines virology, immunology, and epidemiology is required to reduce HMPV's effect and improve patient outcomes. This review serves as a comprehensive literature about HMPV which provides all the crucial clinical perspectives and the latest advancements in management, antivirals, patient prognosis as well and diagnostic modalities.}, }
@article {pmid40351315, year = {2025}, author = {Li, S and Sun, Y and Cao, S and Guo, T and Tong, X and Zhang, Z and Sun, J and Yang, Y and Wang, Q and Li, D and Min, L}, title = {Asparagopsis taxiformis mitigates ruminant methane emissions via microbial modulation and inhibition of methyl-coenzyme M reductase.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1586456}, pmid = {40351315}, issn = {1664-302X}, abstract = {INTRODUCTION: Asparagopsis taxiformis (A. taxiformis) has shown great potential to mitigate methane (CH4) emissions in recent years. This study aims to evaluate the impact of A. taxiformis on methane emissions and to fill the knowledge gap regarding its mechanisms of action in affecting CH4 metabolism and rumen fermentation.<br><br>METHODS: The experimental design consisted of a control group (CON) and test groups supplemented with 2% (Low), 5% (Mid), and 10% (High) of dried and freeze-dried treatment A. taxiformis, respectively, for 48&#x202f;h of in vitro rumen fermentation. The optimal combination strategy for mitigating CH4 emissions was confirmed by analyzing nutrient degradation, CH4 production and rumen fermentation parameters, and the mechanism of action was analyzed by metagenomic and metabolomic approaches.<br><br>RESULTS AND DISCUSSION: The results showed that freeze-dried treatment had better potential to mitigate CH4 emissions than dried treatment, and supplementation of freeze-dried treatments at Low, Mid, and High groups significantly reduced CH4 production by 32.44%, 98.53%, and 99.33%, respectively. However, the High group exhibited a huge negative impact on rumen fermentation. Therefore, subsequent analyses focused on the Low and Mid groups to explore the underlying mechanisms. Metagenomics analyses showed that supplementation of freeze-dried treatment with the Mid-level supplementation significantly increased the relative abundance of propionate-producing bacteria such as Prevotella, Ruminobacter, and Succinivibrio, while inhibited acetate-producing bacteria such as Ruminococcus, altered the pattern of volatile fatty acid (VFA) synthesis in the rumen, and reduced H2 availability for methanogenesis and promoted propionate production, indirectly alleviating CH4 production. Moreover, by suppressing the relative abundance of Methanobrevibacter, CH4 production in the rumen was directly suppressed. Furthermore, KEGG pathway analysis showed that A. taxiformis significantly inhibited the abundance of K00399, methyl-coenzyme M reductase alpha subunit, which directly inhibited CH4 synthesis. Metabolomics analysis of A. taxiformis supplementation significantly enriched ketoglutarate, malate, isocitrate, and melatonin, which may have reduced the release of rumen fermented H2, thereby mitigating CH4 emissions. In summary, freeze-dried treatment A. taxiformis at the 5% supplementation level achieved the optimal balance between CH4 mitigation and rumen fermentation efficiency.}, }
@article {pmid40350519, year = {2025}, author = {Schultz, J and Jamil, T and Sengupta, P and Sivabalan, SKM and Rawat, A and Patel, N and Krishnamurthi, S and Alam, I and Singh, NK and Raman, K and Rosado, AS and Venkateswaran, K}, title = {Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {117}, pmid = {40350519}, issn = {2049-2618}, support = {BAS/1/1096-01-01//KAUST Baseline Grant/ ; PPR-ROSES-2006//National Aeronautical and Space Administration/ ; }, mesh = {*Spacecraft ; United States National Aeronautics and Space Administration ; *Bacteria/genetics/isolation &amp; purification/classification ; United States ; Biofilms/growth &amp; development ; Space Flight ; *Extremophiles/genetics/isolation &amp; purification/classification ; *Genome, Bacterial ; Humans ; Microbiota/genetics ; Genomics ; Metagenome ; Phylogeny ; }, abstract = {BACKGROUND: Human-designed oligotrophic environments, such as cleanrooms, harbor unique microbial communities shaped by selective pressures like temperature, humidity, nutrient availability, cleaning reagents, and radiation. Maintaining the biological cleanliness of NASA's mission-associated cleanrooms, where spacecraft are assembled and tested, is critical for planetary protection. Even with stringent controls such as regulated airflow, temperature management, and rigorous cleaning, resilient microorganisms can persist in these environments, posing potential risks for space missions.<br><br>RESULTS: During the Phoenix spacecraft mission, genomes of 215 bacterial isolates were sequenced and based on overall genome-related indices, 53 strains belonging to 26 novel species were recognized. Metagenome mapping indicated less than 0.1% of the reads associated with novel species, suggesting their rarity. Genes responsible for biofilm formation, such as BolA (COG0271) and CvpA (COG1286), were predominantly found in proteobacterial members but were absent in other non-spore-forming and spore-forming species. YqgA (COG1811) was detected in most spore-forming members but was absent in Paenibacillus and non-spore-forming species. Cell fate regulators, COG1774 (YaaT), COG3679 (YlbF, YheA/YmcA), and COG4550 (YmcA, YheA/YmcA), controlling sporulation, competence, and biofilm development processes, were observed in all spore-formers but were missing in non-spore-forming species. COG analyses further revealed resistance-conferring proteins in all spore-formers (n&#x2009;=&#x2009;13 species) and eight actinobacterial species, responsible for enhanced membrane transport and signaling under radiation (COG3253), transcription regulation under radiation stress (COG1108), and DNA repair and stress responses (COG2318). Additional functional analysis revealed that Agrococcus phoenicis, Microbacterium canaveralium, and Microbacterium jpeli contained biosynthetic gene clusters (BGCs) for &#x3b5;-poly-L-lysine, beneficial in food preservation and biomedical applications. Two novel Sphingomonas species exhibited&#xa0;for&#xa0;zeaxanthin, an antioxidant beneficial for eye health. Paenibacillus canaveralius harbored genes for bacillibactin, crucial for iron acquisition. Georgenia phoenicis had BGCs for alkylresorcinols, compounds with antimicrobial and anticancer properties used in food preservation and pharmaceuticals.<br><br>CONCLUSION: Despite stringent decontamination and controlled environmental conditions, cleanrooms harbor unique bacterial species that form biofilms, resist various stressors, and produce valuable biotechnological compounds. The reduced microbial competition in these environments enhances the discovery of novel microbial diversity, contributing to the mitigation of microbial contamination and fostering biotechnological innovation. Video Abstract.}, }
@article {pmid40350492, year = {2025}, author = {Ding, Y and Ke, J and Hong, T and Zhang, A and Wu, X and Jiang, X and Shao, S and Gong, M and Zhao, S and Shen, L and Chen, S}, title = {Microbial diversity and ecological roles of halophilic microorganisms in Dingbian (Shaanxi, China) saline-alkali soils and salt lakes.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {287}, pmid = {40350492}, issn = {1471-2180}, support = {STEP 2024QZKK02010//Supported by the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2208085MC39//Natural Science Foundation of Anhui Province, China/ ; }, mesh = {China ; *Lakes/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; *Archaea/classification/genetics/isolation &amp; purification ; Phylogeny ; DNA, Archaeal/genetics ; Salinity ; *Biodiversity ; Alkalies/analysis ; Soil/chemistry ; High-Throughput Nucleotide Sequencing ; Sodium Chloride ; Sequence Analysis, DNA ; Bacteria/classification/genetics ; }, abstract = {Halophilic microorganisms abound in numerous hypersaline environments, such as salt lakes, salt mines, solar salterns, and salted seafood. In the northwest of Dingbian county (Shaanxi province, China), there exists a belt of hypersaline habitats extending from the west to the north consisting of saline-alkali soil and salt lakes. Theoretically, such a hypersaline environment has a high probability of containing abundant halophilic archaea communities. Nevertheless, there is nearly no systematic research on halophilic archaea in this area. Here, we employed a combination of culture-dependent and culture-independent methods to analyze the collected samples. The high-throughput sequencing results of the archaeal 16S rRNA gene indicated that the richness of halophilic archaea in saline-alkali soils was significantly higher than that in salt lakes. In saline-alkali soils, the Natronomonas genus of archaea was more predominant compared to other genera, while in salt lakes, the Halonotius, Halorubrum, and Haloarcula genera of archaea had relatively higher abundances. However, the dominant families of halophilic archaea in both environments were mainly Haloferacaceae (30.96-72%), Halomicrobiaceae (17-53.19%) and Nanosalinaceae (1-19.08%). Based on the outcomes of pure culture experiments, a total of 26 genera and 98 strains were identified. Among the identified halophilic microorganisms, the predominant species were Halorubrum and Fodinibius, accounting for 33.67% and 13.27%, respectively. The remainder were mostly low-abundance groups within the community, and 22 potential novel taxa were discovered. Additionally, metagenomic technology was employed in our research. The analysis results demonstrated that the microorganisms in this area possess metabolic pathways capable of degrading various pollutants such as atrazine, methane, and dioxins, suggesting that some microorganisms in this area play a positive role in environmental remediation. This study roughly reveals the diversity composition and dominant species of halophilic archaea in these hypersaline environments and provides a scientific basis for the possible ecological functions of microorganisms in this area during long-term survival. It also offers scientific evidence for the development and utilization of halophilic microbial resources and ecological protection.}, }
@article {pmid40350460, year = {2025}, author = {Zhang, X and Zhong, R and Wu, J and Tan, Z and Jiao, J}, title = {Dietary selection of distinct gastrointestinal microorganisms drives fiber utilization dynamics in goats.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {118}, pmid = {40350460}, issn = {2049-2618}, support = {32372829, 31972992//National Natural Science Foundation of China/ ; 2023JJ10047//Hunan Provincial Natural Science Foundation of China/ ; 2022RC1158//The Science and Technology innovation Program of Hunan Province/ ; 2023382//Youth Innovation Promotion Association CAS/ ; }, mesh = {Animals ; *Goats/microbiology ; *Dietary Fiber/metabolism ; *Gastrointestinal Microbiome ; Rumen/microbiology/metabolism ; Animal Feed/analysis ; Metagenomics/methods ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fibrobacter/metabolism/genetics/isolation &amp; purification ; Ruminococcus/metabolism/genetics/isolation &amp; purification ; Diet/veterinary ; Cecum/microbiology/metabolism ; Cellulose/metabolism ; Fatty Acids, Volatile/metabolism ; Polysaccharides/metabolism ; *Gastrointestinal Tract/microbiology ; }, abstract = {BACKGROUND: Dietary fiber is crucial to animal productivity and health, and its dynamic utilization process is shaped by the gastrointestinal microorganisms in ruminants. However, we lack a holistic understanding of the metabolic interactions and mediators of intestinal microbes under different fiber component interventions compared with that of their rumen counterparts. Here, we applied nutritional, amplicon, metagenomic, and metabolomic approaches to compare characteristic microbiome and metabolic strategies using goat models with fast-fermentation fiber (FF) and slow-fermentation fiber (SF) dietary interventions from a whole gastrointestinal perspective.<br><br>RESULTS: The SF diet selected fibrolytic bacteria Fibrobacter and Ruminococcus spp. and enriched for genes encoding for xylosidase, endoglucanase, and galactosidase in the rumen and cecum to enhance cellulose and hemicellulose utilization, which might be mediated by the enhanced microbial ATP production and cobalamin biosynthesis potentials in the rumen. The FF diet favors pectin-degrading bacteria Prevotella spp. and enriched for genes encoding for pectases (PL1, GH28, and CE8) to improve animal growth. Subsequent SCFA patterns and metabolic pathways unveiled the favor of acetate production in the rumen and butyrate production in the cecum for SF goats. Metagenomic binning verified this distinct selection of gastrointestinal microorganisms and metabolic pathways of different fiber types (fiber content and polysaccharide chemistry).<br><br>CONCLUSIONS: These findings provide novel insights into the key metabolic pathways and distinctive mechanisms through which dietary fiber types benefit the host animals from the whole gastrointestinal perspective. Video Abstract.}, }
@article {pmid40350266, year = {2025}, author = {Ohyama, Y and Miura, T and Furukawa, M and Shimamura, M and Asami, Y and Yamazoe, A and Uchino, Y and Kawasaki, H}, title = {A HPLC-based Method for Counting the Genome Copy Number of Cells Allows the Production of a High-quality Mock Community of Bacterial Cells.}, journal = {Microbes and environments}, volume = {40}, number = {2}, pages = {}, doi = {10.1264/jsme2.ME24076}, pmid = {40350266}, issn = {1347-4405}, mesh = {Chromatography, High Pressure Liquid/methods ; *Bacteria/genetics/isolation &amp; purification/classification ; Humans ; *Microbiota/genetics ; *Genome, Bacterial ; Metagenomics/methods ; Reproducibility of Results ; }, abstract = {Improving the reliability of a metagenomic sequencing ana-lysis requires the use of control samples, known as mock communities. Therefore, mock communities must be prepared with high accuracy and reproducibility, which is particularly challenging for cellular mock communities. In the present study, we prepared a cellular mock community consisting of bacterial strains representative of the human and surrounding environmental microbiomes to demonstrate the suitability of a HPLC-based method that measures the genome number of cells. This method proved to be more accurate and reproducible for preparing cellular mock communities than traditional cell counting-based enumeration methods.}, }
@article {pmid40350102, year = {2025}, author = {El-Son, MAM and Elbahnaswy, S and Khormi, MA and Aborasain, AM and Abdelhaffez, HH and Zahran, E}, title = {Harnessing the Fish Gut Microbiome and Immune System to Enhance Disease Resistance in Aquaculture.}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {110394}, doi = {10.1016/j.fsi.2025.110394}, pmid = {40350102}, issn = {1095-9947}, abstract = {The increasing global reliance on aquaculture is challenged by disease outbreaks, exacerbated by antibiotic resistance, and environmental stressors. Traditional strategies, such as antibiotic treatments and chemical interventions, are becoming less effective, necessitating a shift toward microbiota-based disease control. The fish gut microbiome is a key determinant of immune homeostasis and pathogen resistance. However, previous reviews lack integration of microbiome engineering, machine learning, and next-generation sequencing in fish health strategies. This review encompasses recent advancements in microbiome research, including dietary strategies such as prebiotics, probiotics, synbiotics, and phytogenic feed additives. It synthesizes the latest metagenomic insights, microbiota modulation techniques, and AI-driven disease prediction models. It presents a novel conceptual framework for disease control using microbiome-based approaches in aquaculture. Additionally, we explore emerging methodologies, including microbiota transplantation and synthetic probiotics, to develop precision microbiome interventions. By bridging existing knowledge gaps, this review provides actionable insights into sustainable aquaculture practices through microbiome-driven disease resistance.}, }
@article {pmid40349998, year = {2025}, author = {Patel, M and Patel, K}, title = {Emerging Insights of Staphylococcus spp. in Human mastitis.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107685}, doi = {10.1016/j.micpath.2025.107685}, pmid = {40349998}, issn = {1096-1208}, abstract = {Human mastitis represents a prevalent and intricate condition that significantly challenges breastfeeding women, often exacerbated by pathogenic bacteria such as Staphylococcus aureus. A deep understanding of the interplay between human mastitis, the breast milk microbiome, and causative agents is imperative. This understanding must focus on the bacterium's virulence and resistance genes, which critically influence the severity and persistence of mastitis. Current methods for detecting these genes, including Polymerase Chain Reaction (PCR), 16S rRNA gene sequencing, shotgun metagenomic sequencing, multiplex PCR, whole genome sequencing (WGS), loop-mediated isothermal amplification (LAMP), CRISPR-based assays, and microarray technology, are vital in elucidating bacterial pathogenicity and resistance profiles. However, advanced attention is required to refine diagnostic techniques, enabling earlier detection and more effective therapeutic approaches for human mastitis. The involvement of Staphylococcus aureus in human infection should be a prime focus, especially in women's health, which deals directly with neonates. Essential virulence genes in Staphylococcus species are instrumental in infection mechanisms and antibiotic resistance, serving as potential targets for personalized treatments. Thus, this review focuses on Staphylococcus aureus induced mastitis, examining its virulence factors and detection techniques to advance diagnostic and therapeutic strategies.}, }
@article {pmid40349794, year = {2025}, author = {Dai, Y and Wang, B and Zhang, M and Li, W and Wang, L and Zou, Y and Peng, Y}, title = {Thermal activation of peroxymonosulfate for enhanced volatile fatty acids production and phosphorus release during anaerobic fermentation of iron-rich sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132653}, doi = {10.1016/j.biortech.2025.132653}, pmid = {40349794}, issn = {1873-2976}, abstract = {Heat-peroxymonosulfate (PMS) pre-treatment was simultaneously used for phosphorus (P) release and volatile fatty acids (VFAs) production in this study. Maximum P concentrations increased from 10.3 ± 0.4 mg/L in PMS-0 to 246.1 ± 1.6 mg/L in PMS-0.8, with 41.4 % of total P released. VFAs production on day 5 increased from 2409.1 ± 30.8 mg chemical oxygen demand (COD)/L in PMS-0 to 2995.4 ± 86.5 mg COD/L in PMS-0.8. Metagenomic analysis showed that an increase in PMS dosage was detrimental to P release during polyphosphate hydrolysis by polyphosphate-accumulating organisms; functional genes involved in S cycling increased, suggesting that sulfate reduction was a critical cause of P release from iron-rich sludge during anaerobic fermentation (AF). These results provide important insights for the improvement of P release efficiency and acid production during AF, enhancing the potential for resource recovery from iron-rich sludge.}, }
@article {pmid40349588, year = {2025}, author = {Zhang, S and Li, X and Li, X and Fu, Y and Chen, L and Wang, W and Lin, Q and Lou, H and Yao, Y and Chen, W and Zhong, C and Ye, J and Yao, Y and Guo, H and Yu, Y and Zhou, H}, title = {Optimisation and clinical validation of a metagenomic third-generation sequencing approach for aetiological diagnosis in bronchoalveolar lavage fluid of patients with pneumonia.}, journal = {EBioMedicine}, volume = {116}, number = {}, pages = {105752}, doi = {10.1016/j.ebiom.2025.105752}, pmid = {40349588}, issn = {2352-3964}, abstract = {BACKGROUND: Metagenomic Third Generation Sequencing (mTGS), based on nanopore technology, has emerged as a promising tool for the rapid diagnosis of pneumonia pathogens. However, this technology currently lacks standardised technical protocols, quality control measures, and comprehensive performance evaluations for the simultaneous detection of bacteria, fungi, and viruses in clinical settings.<br><br>METHODS: We optimised the mTGS workflow by refining key parameters (cell wall lysis, fragment size selection, host DNA depletion, and sequencing depth) using reference samples and bronchoalveolar lavage fluid (BALF) from eight patients with pneumonia. These optimisations formed the basis for a standardised mTGS protocol. To assess the clinical diagnostic value of the optimised mTGS, a multicentre prospective cohort study involving 313 pneumonia-suspected patients was conducted. Each BALF sample was tested using conventional microbiological testing (CMTs), metagenomic next-generation sequencing (mNGS), pre-optimised mTGS, and optimised mTGS.<br><br>FINDINGS: The optimised mTGS protocol, based on the refined cell wall lysis, fragment size selection, no host DNA depletion, and 800 MB sequencing depth, achieved a tenfold increase in sensitivity compared with pre-optimised mTGS for detecting the species of Bacillus subtilis, Mycobacterium tuberculosis, Mycobacterium avium, Cryptococcus neoformans, and Human papillomavirus in reference samples. In the prospective cohort, 274 patients with a confirmed diagnosis of pneumonia were identified, yielding 376 distinct microbes. The mTGS identified more microbes than CMTs (314 vs. 115), with a 45.30% increase in sensitivity (84.70% vs. 39.40%, P < 0.01, Chi-square test/Fisher's exact test). Compared with pre-optimised mTGS, the sensitivity of optimised mTGS increased by 32.51% (84.70% vs. 52.19%, P < 0.01, Chi-square test/Fisher's exact test). mTGS showed comparable performance to mNGS (84.70% vs. 79.90%, P = 0.14,Chi-square test/Fisher's exact test), both significantly outperforming CMTs. mNGS was more sensitive for detecting Non-tuberculous mycobacteria, Pneumocystis jirovecii, and Aspergillus spp., while mTGS demonstrated higher sensitivity for M. tuberculosis, Chlamydia psittaci, and Streptococcus pneumoniae. The overall diagnostic agreement between mTGS and clinical diagnosis was 81.80%.<br><br>INTERPRETATION: We optimised and validated a standardised mTGS protocol that significantly improved the ability to detect pathogens in the BALF of patients with pneumonia. Optimised mTGS demonstrated comparable performance to mNGS, making it a promising tool for the aetiological diagnosis of pneumonia.<br><br>FUNDING: The Research and Development Programme of Zhejiang Province (2023C03068, 2024C03187), the National Natural Science Foundation of China (82272338), the Key R&amp;D Plan of the Ministry of Science and Technology (China) of China (2022YFC2504502).}, }
@article {pmid40349412, year = {2025}, author = {Ren, P and You, C and Chen, P and Mei, X and Yang, T and Xu, Y and Wang, X and Shen, Q and Wei, Z}, title = {Organic amendments derived from Chinese herb residues enhance soil ecosystem multifunctionality by enriching key microorganisms.}, journal = {Microbiological research}, volume = {298}, number = {}, pages = {128213}, doi = {10.1016/j.micres.2025.128213}, pmid = {40349412}, issn = {1618-0623}, abstract = {Ecosystem multifunctionality (EMF), a key metric reflecting soil health, has been proven to be positively influenced by organic amendments. Chinese herb residues (CHR), rich in bioactive compounds and with lower ecological risks, are regarded as a promising source for organic amendments. Therefore, we conducted a greenhouse experiment with four treatments: no fertilizer (CK), chemical fertilizer (CF), single application of CHR-OA (OA), and partially replacing chemical fertilizers with CHR-OA (OA-CF), aiming to explore the regulatory mechanism of CHR-OA addition to EMF. A total of 19 ecosystem functions, covering plant growth, pathogen suppression, soil physicochemical properties, and microbial diversity, were used to calculate EMF. The results showed that most of the above ecosystem functions were improved by adding CHR-OA, with the OA-CF possessing the highest EMF, followed by OA. Additionally, Lysobacter was enriched as a key genus. Further analysis revealed that Lysobacter drove EMF by influencing bacterial Simpson index, plant height, and root length, and this conclusion was confirmed in greenhouse verification experiments. Through this study, we have gained a clearer understanding of the prominent ecosystem functions provided by CHR-OA and the regulatory mechanism of EMF.}, }
@article {pmid40349120, year = {2025}, author = {Jiang, S and Huang, S and Zhang, Z and Ma, W and Han, Z and Song, Y and Huo, D and Cui, W and Zhang, J}, title = {Gut microbiota drives structural variation of exogenous probiotics to enhance colonization.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2503371}, doi = {10.1080/19490976.2025.2503371}, pmid = {40349120}, issn = {1949-0984}, mesh = {*Probiotics/pharmacology ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; *Lactobacillus plantarum/genetics/growth &amp; development ; Gastrointestinal Tract/microbiology ; Bile Acids and Salts ; Metagenomics ; }, abstract = {Probiotics encounter colonization resistance from native gut microbiomes, affecting their effectiveness. Genetic engineering of probiotics lacks universal applicability, as gut microbiotas are highly individualized. Here, we employed probiotic Lactiplantibacillus plantarum HNU082 (Lp082) to test whether Lp082 gut-adapted mutants can resolve colonization resistance in a new gut environment. Relying on culture-based methods and metagenomics, two distinct evolutionary clades of Lp082 in mice gut were observed, where one clade, which acquired more mutations, exhibited a longer survival time. However, these Lp082 isolates carrying many single nucleotide variants (SNVs) still exhibited phenotypic inconsistencies, with 13 strains of enhanced acid resistance. Thus, nanopore sequencing was proposed to identify structural variations (SVs). Among them, 12 strains had the Cro/C1-type HTH DNA-binding domain insertion, which enhanced growth and reproduction under bile salt stress, thereby increasing colonization time and quantity in the gut. The gut domestication process can drive probiotics to undergo many SNVs and SVs, thereby enhancing their colonization ability, which provides new insights into the colonization mechanisms and offers an ecology-based strategy.}, }
@article {pmid40348945, year = {2025}, author = {Chen, J and Liu, J and Liu, S and Li, Z and Gao, C and Wang, Z and Huang, S and Jiang, Z and Yang, H}, title = {Multiomics reveals the synergistic response of gut microbiota and spider A. ventricosus to lead and cadmium toxicity.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {114}, number = {5}, pages = {77}, pmid = {40348945}, issn = {1432-0800}, support = {32001205//National Natural Science Foundation of China/ ; 2023JJ30299//Natural Science Foundation of Hunan Province/ ; 2019JJ50236//Natural Science Foundation of Hunan Province/ ; }, mesh = {Animals ; *Cadmium/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Lead/toxicity ; *Spiders/physiology/drug effects ; Metagenomics ; Multiomics ; }, abstract = {The potential crosstalk between the host and gut microbiota (GM) under heavy metal compound pollution remains unexplored. Herein, using comprehensive analysis of metagenomics, metabolomics, behavioral analysis, and cell morphology to investigate the causal relationship between GM and host responses to cadmium (Cd) and lead (Pb) toxicities. Results indicate that Pb and Cd pollution, alone or together, hinder spider predatory behavior and change the composition and function of GM. Combined exposure reduces protein and exogenous compound metabolism, while single exposure affects energy and lipid metabolism. Gut microbiota helps spider antioxidant activity by increasing glutathione, lipoic acid, and L-cysteine. Oxidative damage, increased Enterobacteriaceae (Salmonella), and lipopolysaccharide (LPS) may harm the midgut barrier. Upregulation of choline and acetylcholine, and downregulation of spermidine, may initiate neurotoxicity. Inhibiting actinomycetes might boost sodium gallate for detoxifying single contaminants. Combined pollution detoxification may involve downregulation of indole synthesis metabolic bacteria, tryptophan, indole metabolites, cytochrome P450 (CYP450), and an increase in Desulfobulbia could remove heavy metals and reduce oxidative stress. Combined pollution has a synergistic effect, making the toxicity of multiple pollutants greater than their individual effects, impacting metal resistance genes (MRGs), and antibiotic resistance ontology (AROs) which used for classifying and describing antibiotic resistance, midgut barrier integrity, oxidative stress, and detoxification. The results help to elucidate the interplay of GM and host's reactions, and aid in monitoring and bioremediation of heavy metal pollution.}, }
@article {pmid40348632, year = {2025}, author = {Lotankar, M and Houttu, N and Benchraka, C and Lahti, L and Laitinen, K}, title = {Links between gut microbiota with specific serum metabolite groups in pregnant women with overweight or obesity.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {}, number = {}, pages = {104095}, doi = {10.1016/j.numecd.2025.104095}, pmid = {40348632}, issn = {1590-3729}, abstract = {BACKGROUND AND AIM: Gut microbiota may regulate metabolism but is incompletely characterized in pregnancy. Our objective was to investigate the relations using omics techniques.<br><br>METHODS AND RESULTS: In a cross-sectional setting, fecal and serum samples of 361 healthy pregnant women with overweight or obesity were analyzed with a combinatorial approach of metagenomics and targeted NMR-based metabolomics, with statistical and machine learning techniques to identify and analyze the extent to which the gut microbiota composition and predicted functions would be reflected in the serum metabolome. We identified five biclusters, each of which consisted of a set of gut microbial species and serum metabolites with correlated abundance profiles. Two of the biclusters included metabolites that have been linked to the cardiovascular health; one was linked with factors known to increase the risk i.e., various sizes of lipoprotein subclasses (VLDL and LDL), subclasses of relative lipoprotein lipid concentrations (VLDL, IDL, and LDL), apolipoprotein B, and an inflammation marker, glycoprotein acetylation. These metabolites were associated with abundances of species such as, Enterocloster bolteae and Ruminococcus gnavus. The second bicluster included metabolites linked with a reduced cardiovascular risk, such as different sizes of HDL (high-density lipoprotein), subclasses for relative lipoprotein lipid concentrations and mean diameter for HDL particles, and fatty acid ratios. These metabolites were associated with abundances of species, such as Bacteroides cellulosilyticus and Alistipes finegoldii. We did not observe any biclusters between predicted pathways and serum metabolites.<br><br>CONCLUSION: Overall, we identified five biclusters of co-abundant gut bacteria and serum metabolites , of which two were linked to pro-atherogenic and anti-atherogenic properties.<br><br>TRIAL REGISTRATION: www.<br><br>CLINICALTRIALS: Gov: NCT01922791.}, }
@article {pmid40348492, year = {2025}, author = {Quigley, EMM}, title = {Microbial Influences on Irritable Bowel Syndrome.}, journal = {Gastroenterology clinics of North America}, volume = {54}, number = {2}, pages = {351-365}, doi = {10.1016/j.gtc.2024.12.003}, pmid = {40348492}, issn = {1558-1942}, mesh = {*Irritable Bowel Syndrome/microbiology ; Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; Metabolomics ; Metagenomics ; Dysbiosis ; }, abstract = {Since the description of postinfection irritable bowel syndrome (IBS), a role for gut microbes in the pathogenesis of IBS has been proposed. Molecular microbiological tools have now been applied to IBS, though data are largely derived from fecal samples with attendant limitations. Metagenomics, metabolomics, and other 'omics facilitate a comprehensive picture of the microbiome and its metabolic activity. Has a microbial signature characteristic of IBS been identified? The answer is no; this should not be a surprise given the heterogeneity of the phenotype and each individual's microbiome profile.}, }
@article {pmid40348264, year = {2025}, author = {Hu, Z and Li, Z and Xu, Y and He, F and Zhang, J and Li, T}, title = {MgFe-LDHs/Vallisneria natans combined system for simultaneous elimination of endogenous N and P pollution in eutrophic water: Performance, synergetic mechanism, and metagenomics analysis.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121798}, doi = {10.1016/j.envres.2025.121798}, pmid = {40348264}, issn = {1096-0953}, abstract = {Eutrophication is the main factor for the degradation of lake ecosystems. More than exogenous input, endogenous N and P nutrients are responsible for it. Although the P passivation technology with functional materials is common for alleviating endogenous P pollution, will it have the same effect for endogenous N removal? In this study, a novel MgFe-LDHs/Vallisneria natans (V. natans) combined system was established for effective eliminating endogenous N and P simultaneously. During remediation periods, MgFe-LDHs/V. natans combined system with the most obvious improvement for overlying water quality that was reflected by DO, ORP, and SS, and TP, TN, and NH4[+]-N removal efficiency were up to 99%. In sediments, TP and TN removal rate was approximately 68% and 63%, where the reduction of Org-P and NH4[+]-N accounted for the majority of it, respectively. Under stimulation of MgFe-LDHs, NH4[+]-N assimilation in V. natans could be promoted through improving the metabolizing enzymes activity. In turn, V. natans contributed to Org-P mineralization by secreting organic acid, further facilitating IP enrichment on MgFe-LDHs. Additionally, owing to the synergism between V. natans allelopathy and MgFe-LDHs, the symbiotic relationship between microbial communities was much closer and more stable, the expression of functional genes that relate to denitrification, assimilatory nitrate reduction, phosphorylation and organophosphorus mineralization processes were up-regulated prominently. That is, microorganisms acted synergistically were important for endogenous N and P elimination performance. This study proposed a high-efficiency and environmentally friendly materials/plants combined remediation technology for eutrophication, especially those where with much high endogenous N and P loading.}, }
@article {pmid40348210, year = {2025}, author = {Lin, Z and Zhang, P and Shi, D and Zhang, Y and Wu, W and Tang, Q and Wang, Q and Wang, S}, title = {Association between the gut microbiota and cystitis: A two-sample mendelian randomization study combined with the GEO database.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107683}, doi = {10.1016/j.micpath.2025.107683}, pmid = {40348210}, issn = {1096-1208}, abstract = {BACKGROUND: Disturbances within the intestinal microbiota have emerged as a significant factor contributing to systemic inflammation, thereby rendering distant anatomical sites more vulnerable to various illnesses, including inflammatory conditions in the urinary tract such as cystitis. However, the causal relationship between dysbiosis of the gut microbiota and cystitis remains unclear. We sought to elucidate the causal relationship between the intestinal microbiota and cystitis employing Mendelian randomization (MR), offering insights into novel preventive and therapeutic strategies for managing cystitis.<br><br>METHOD: Summary statistics for the Genome-Wide Association Study (GWAS) of cystitis were sourced from the R5 release dataset provided by the FinnGen consortium, which included 8,081 cystitis cases and 195,140 controls. Single Nucleotide Polymorphisms (SNPs) that showed strong associations with 196 microbial taxa (encompassing 18,340 individuals) were selected as instrumental variables. To analyse the causal relationships between cystitis and gut microbiota, we employed four MR analysis methods: random effects, inverse variance weighting, weighted medians, and MR-Egger regression. Sensitivity analyses were performed using the Cochran's Q test, funnel plots, leave-one-out analyses, and the MR-Egger intercept test. We conducted metagenomic analysis of fecal samples from 7 patients with cystitis and 7 healthy controls to validate the findings from our MR results. To further elucidate the biological mechanisms, we conducted positional mapping of the extracted SNPs associated with the significant taxa. Additionally, we curated differentially expressed genes (DEGs) from three datasets about cystitis obtained from the Gene Expression Omnibus (GEO). Finally, we intersected the DEGs with the mapped genes to identify common genes of cystitis.<br><br>RESULTS: Our analysis revealed significant associations between specific gut microbiota and cystitis. IVW results revealed that four gut microorganisms, specifically, the genus RuminococcaceaeUCG011, genus Sutterella, family Porphyromonadaceae, and family Veillonellaceae (P&#x2009;<&#x2009;0.05), contributed to a reduction in the incidence of cystitis. Similarly, four cystitis-related bacteria, namely, the genus Marvinbryantia, the genus Odoribacter, the genus Ruminiclostridium6, and the genus Sellimonas, are thought to play a significant role in elevating the risk of cystitis (P&#x2009;<&#x2009;0.05). The metagenomic analysis revealed significant differences in the abundance of the genera Sutterella and Odoribacter in patients with cystitis compared to healthy controls. Additionally, we mapped causal SNPs to genes and identified 62 genes. Bioinformatics analysis reveals 161 common DEGs in cystitis. Through MR and bioinformatics analysis, we identified two common genes-ICAM1 and HP-as potential targets for cystitis.<br><br>CONCLUSION: Our research identified genetic connections between eight components of gut microbiota and two genes related to cystitis. These results offer important insights for subsequent studies into the complex relationship between gut microbiota and cystitis.}, }
@article {pmid40347608, year = {2025}, author = {Ahmed, I and Zhuang, Z and Zhang, D and Li, P and Zhang, B}, title = {Temperature-driven dynamics of intracellular and extracellular antibiotic resistance genes during aerobic composting: Insights from qPCR and metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138519}, doi = {10.1016/j.jhazmat.2025.138519}, pmid = {40347608}, issn = {1873-3336}, abstract = {The widespread use of antibiotics in animal farming has accelerated the dissemination of antibiotic resistance genes (ARGs). Aerobic composting is an effective method for managing animal manure, yet its effects on intracellular (iARGs) and extracellular ARGs (eARGs) under different temperature regimes including control (LT), gradual increase temperature (GT), and initially enriched temperature (HT) remain unclear. This study investigated the dynamics of iARGs and eARGs across these temperature gradients during composting. Initial composting substrate harbored higher levels of iARGs than eARGs. After composting, ARG rebound was primarily driven by eARG enrichment. On day 40, iARGs decreased by 3.1 logs in HT, 1.2 logs in LT, and 1 log in GT, while eARGs decreased by 0.9 log only in HT but increased in LT and GT. Initially phyla Firmicutes and Proteobacteria were dominated, the microbial community shifted to Bacteroidetes in LT, Actinobacteria in GT, and retained Firmicutes dominance in HT on day 40. Metagenomic analysis revealed that 68 % ARG reduction was associated with plasmid-borne ARGs, with reductions of 83.4 % in HT, 68.2 % in GT, and 51.6 % in LT, whereas non-plasmid ARGs were reduced by up to 75 % across all treatments. Notably, plasmid conjugation was significantly inhibited under HT and GT conditions.}, }
@article {pmid40347566, year = {2025}, author = {Jiang, J and Wu, H and Yuan, Y}, title = {Comparative analysis of different Phyllostachys species on gut microbiome and fecal metabolome in giant pandas (Ailuropoda melanoleuca).}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {55}, number = {}, pages = {101529}, doi = {10.1016/j.cbd.2025.101529}, pmid = {40347566}, issn = {1878-0407}, abstract = {The influences of different bamboo species on the microbiome and metabolome of giant pandas (Ailuropoda melanoleuca) remain understudied. The aim of this study was to investigate the effects of different Phyllostachys species on the gut microbial communities and fecal metabolite profiles in giant pandas. Metagenome and metabolome were performed on the feces of giant pandas fed with different Phyllostachys species (P. edulis, P. iridescens, P. glauca, and P. violascens). The results of metagenome showed that dietary with P. glauca could notably decrease the microbial Shannon index. The relative abundances of both Cellulosilyticum and Pseudomonas were enhanced after dietary with P. iridescens, suggesting P. iridescens could enhance the cellulose-degrading function in giant pandas. However, dietary with P. glauca or P. violascens could increase the relative abundances of certain pathogenic bacteria (Escherichia, Shigella, and Klebsiella). Metabolomics analysis further revealed that all experimental groups exhibited notably elevated levels of fecal flavonoids and fatty acids. In addition, the correlation analysis showed that certain nutrients of bamboo leaves (mainly crude protein and Cu) were significantly correlated with several differential gut bacteria and fecal metabolites. Based on the present results, P. iridescens might be a substitute for the routinely used Phyllostachys species (P. edulis) in the captive management of giant pandas. The results have revealed that bamboo species is an important factor affecting the gut microbiota and fecal metabolites in giant pandas. Our results could provide important information about bamboo species-induced alterations on the microbiome and metabolome in giant pandas.}, }
@article {pmid40347421, year = {2025}, author = {Akinbi, GO and Lin, Q and Fiola, TE and Rathore, RS and Badisa, VLD and Mwashote, B and Chen, G and Ibeanusi, V}, title = {Ecosystem assessment to support innovative advancements in soil sustainability in the major land resource areas of Mississippi through geochemical and metagenomics studies.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {40347421}, issn = {1614-7499}, support = {NR204423XXXXC125-F1-SA1-21//U.S. Department of Agriculture/ ; }, abstract = {In the present study, the ecosystem of Roebuck (RF) and Nesbit blueberry plantation (NBP) farms in Mississippi state, USA that differed by type of fertilizer treatment was assessed using soil samples through geophysical-chemical parameters and metagenomics studies. Soil geophysical-chemical parameters such as pH, moisture, organic content, nutrients, and toxic metal concentrations were measured. Metagenomic analysis was performed to identify the bacterial communities in the soil samples. The results revealed that the pH of the NBP farm (organic fertilizer) was lower than that of the RF farm (chemical fertilizer). The NBP soil samples exhibited higher moisture and organic contents than the RF soil samples. The tested heavy metal concentrations in both farm soil samples were within the limits recommended by the EPA (United States Environmental Protection Agency). Different concentrations of nutrients were observed between these two farms soil samples. RF soil indicated greater species richness and a more balanced distribution of species abundances. Proteobacteria, Bacteroidota, and Actinobacteriota were the most abundant phyla observed in RF soil, whereas Proteobacteria, Acidobacteriota, and Actinobacteriota were the most abundant phyla observed in NBP soil. This study clearly demonstrated the effects of fertilizer type on the soil through variations in geophysical-chemical parameters, which subsequently changed the microbial communities. This study suggests that organic fertilizer application could be an effective method for sustainable soil quality as the organic fertilized soils exhibited higher moisture and organic content that promotes plant growth.}, }
@article {pmid40347034, year = {2025}, author = {Song, L and He, W and Lu, H and Jiang, J and Ding, PH and He, F}, title = {Submucosal Microbiome in Peri-Implantitis: A Comparative Metagenomic Analysis.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.13407}, pmid = {40347034}, issn = {1600-0765}, support = {82470973;82271026;82170953//the National Natural Science Foundation of China/ ; 2024M762880//the Postdoctoral Science Foundation of China/ ; }, abstract = {Through metagenomic sequencing, this study reveals significant microbial and functional differences between peri-implant health and peri-implantitis, identifying pathogenic species, virulence genes, and antibiotic resistance markers that may contribute to disease progression.}, }
@article {pmid40346812, year = {2025}, author = {Pryor, JC and Nieva, C and Talley, NJ and Eslick, GD and Duncanson, K and Burns, GL and Hoedt, EC and Keely, S}, title = {Microbial-derived peptidases are altered in celiac disease, non-celiac gluten sensitivity, and functional dyspepsia: a systematic review and re-analysis of the duodenal microbiome.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2500063}, doi = {10.1080/19490976.2025.2500063}, pmid = {40346812}, issn = {1949-0984}, mesh = {Humans ; *Celiac Disease/microbiology/enzymology ; *Gastrointestinal Microbiome ; *Glutens/metabolism ; *Duodenum/microbiology ; *Dyspepsia/microbiology ; *Peptide Hydrolases/metabolism/genetics ; *Bacteria/enzymology/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dietary gluten triggers symptoms in patients with gluten-related disorders (GRDs) including celiac disease (CeD), non-celiac gluten sensitivity (NCGS), and subsets of patients with functional dyspepsia (FD). The gastrointestinal microbiota is altered in these patients when compared to healthy individuals. As the microbiota is crucial for the hydrolysis of gluten, we hypothesized that the capacity of the microbiota to digest gluten is reduced in these conditions. We systematically reviewed and re-analyzed published datasets to compare gastrointestinal microbiomes of GRD patients and identify signals explaining gluten responses. A systematic search of five databases was conducted to identify studies where the microbiota of CeD, NCGS, or FD patients was analyzed by 16S rRNA amplicon or shotgun metagenomic sequencing and compared to control populations. Where available, raw duodenal microbiota sequence data were re-analyzed with a consistent bioinformatic pipeline. Thirty articles met the inclusion criteria for this systematic review. Microbiota diversity metrics were not impacted by the diseases; however, genera including Streptococcus, Neisseria, and Lactobacillus were commonly altered in GRD patients. Re-analysis of duodenal 16S rRNA data was possible for five included articles but did not identify any consistent differentially abundant taxa. Predicted functional analysis of the microbiome revealed that peptidases including aminopeptidase, proline iminopeptidase, and Xaa-Pro dipeptidase are altered in CeD, NCGS, and FD, respectively. These microbial-derived peptidases hydrolyze bonds in proline-rich gluten peptides. While the gastrointestinal microbiota in patients with GRDs differ from controls, no distinct phenotype links them. However, alterations to the predicted functional capacity of the microbiome to produce gluten-hydrolyzing enzymes suggest that inappropriate digestion of gluten by the microbiome impacts host responses to dietary gluten in these conditions. These findings have implications for therapeutic management of GRDs, as treatment with gluten-degrading enzymes or tailored probiotics could improve disease outcomes by enhancing gluten digestion into non-reactive peptides.}, }
@article {pmid40346542, year = {2025}, author = {Gao, H and Xu, L and Liu, Y and Wang, X and Zhu, S and Lin, H and Gao, Y and Mao, D and Lu, X and Luo, Y}, title = {Whole genome comparisons reveal gut-to-lung translocation of Escherichia coli and Burkholderia cenocepacia in two cases of ventilator-associated pneumonia in ICU patients.}, journal = {Respiratory research}, volume = {26}, number = {1}, pages = {178}, pmid = {40346542}, issn = {1465-993X}, support = {2022BKY015//the Tianjin Graduate Research and Innovation Projects/ ; 42377426//the National Natural Science Foundation of China/ ; 18ZXDBSY00100//the Tianjin Science and Technology Plan Project/ ; 21JCYBJC01200//the Tianjin Municipal Natural Science Foundation/ ; 2023220//the Research Project on Integrated Traditional Chinese and Western Medicine of Tianjin Municipal Health Commission/ ; 2020YFC1806904//the National Key R&amp;D Program of China/ ; 41831287//the Key Projects of the National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Escherichia coli/genetics/isolation &amp; purification/pathogenicity ; Animals ; *Pneumonia, Ventilator-Associated/microbiology/diagnosis/genetics ; Mice ; *Burkholderia cenocepacia/genetics/isolation &amp; purification/pathogenicity ; *Gastrointestinal Microbiome/genetics ; Male ; *Intensive Care Units/trends ; Female ; *Bacterial Translocation/physiology/genetics ; *Lung/microbiology ; Middle Aged ; Aged ; *Whole Genome Sequencing/methods ; *Genome, Bacterial ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Identifying the sources of pathogenic bacteria causing ventilator-associated pneumonia (VAP) in intensive care unit (ICU) patients is crucial for developing effective prevention and treatment strategies. However, the scarcity of reported cases with confirmed sources limits the ability to evaluate and manage VAP, which remains a major challenge for healthcare systems globally.<br><br>METHODS: Pathogens were isolated from endotracheal aspirate (ETA) samples of VAP patients using conventional culture techniques. Whole-genome comparisons, based on average nucleotide identity (ANI), were performed to identify genetically identical strains by comparing pulmonary isolate genomes with gut metagenome-derived bacterial genomes. Mouse models of pneumonia and colitis were used to validate the translocation of pathogenic bacteria from the gut to the lungs. Metagenomic analysis was performed to characterize the gut microbiome and resistome.<br><br>RESULTS: Pathogenic isolates were obtained from the ETA samples of seven VAP patients, with one isolate per sample. Among these, Escherichia coli (Ec1) and Burkholderia cenocepacia (Bc1) from two patients were genetically identical to strains in their respective gut microbiota, with ANI values above 99%, indicating gut-to-lung translocation. The Ec1 strain demonstrated increased resistance to cefazolin while remaining susceptible to gentamicin, amikacin, and kanamycin, compared to previously reported pneumonia-associated E. coli strains. The Bc1 strain showed elevated resistance to macrolides, chloramphenicols, and tetracyclines relative to pneumonia-associated B. cenocepacia strains. Metagenomic analysis revealed a highly individualized gut microbiota composition among VAP patients. Notably, the translocated bacteria were not dominant within their gut microbiota. Additionally, these patients showed a marked increase in the total abundance of antibiotic resistance genes (ARGs) in their gut microbiota. The translocation ability of the Ec1 strain was validated in a mouse pneumonia model, where it caused more severe lung damage. Furthermore, elevated levels of Escherichia-Shigella were detected in the lung tissues of colitis mice, suggesting that gut-to-lung bacterial translocation may occur in a severely inflamed host, potentially leading to pneumonia.<br><br>CONCLUSIONS: This study demonstrates the gut-to-lung translocation of E. coli and B. cenocepacia, highlighting their role in the development and progression of VAP in ICU patients. These findings provide valuable insights for implementing targeted prevention and treatment strategies for VAP in ICU settings.}, }
@article {pmid40346475, year = {2025}, author = {Yuan, T and Ren, W and Zhang, J and Mahmood, M and Jia, Z and Zhang, S and Wang, M and Liang, S and Yuan, F and Liu, Y}, title = {Synergistic effect of grassland plants and beneficial rhizosphere bacteria helps plants cope with overgrazing stress.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {614}, pmid = {40346475}, issn = {1471-2229}, support = {32060407//Natural Science Foundation of China/ ; 2021ZD00804//Major Special Foundation of Science and Technology Plan of Inner Mongolia/ ; }, mesh = {*Rhizosphere ; Soil Microbiology ; *Grassland ; Plant Roots/microbiology ; *Poaceae/microbiology/physiology/growth &amp; development ; Stress, Physiological ; Plant Growth Regulators/metabolism ; }, abstract = {BACKGROUND: Overgrazing (OG) is an important driver of grassland degradation and productivity decline. Highly effective synergy between plants and rhizosphere growth-promoting rhizobacteria (PGPR) may be a major way for grassland plants to effectively cope with OG stress. There have been few reports providing solid evidence on how this synergy occurs.<br><br>RESULT: This study combined with multi-omics analysis and the interaction effect of specific root exudate with PGPR B68, aiming to reveal the synergistic effect and regulatory mechanism of L. chinensis and PGPR under overgrazing stress. The results showed that Leymus chinensis plants with OG history can recruit the beneficial Phyllobacterium sp. B68 by regulating specific root exudate compounds(such as amino acid L-leucyl-L-alanine and alkaloid cordycepin). These compounds enhanced B68 rhizosphere colonization by promoting B68 chemotaxis and biofilm formation. The pot study experiments indicated that the bacterial isolates used as bio inoculants increased L. chinensis growth (mainly including plant height and biomass) by significantly increasing the chlorophyll content, RuBisCO activity, soluble sugar, plant hormones and nutrient content. Metagenomics results show that B68 inoculation significantly altered rhizosphere soil bacterial community composition and function. Additionally, B68 systemically upregulated the expression level of genes involved in plant hormone signaling, nutrient and sugar transporters, nitrogen metabolism, cell division, cell wall modification and photosynthesis to promote plant growth. The above results indicate that the PGPR B68 recruited by the root exudates of L. chinensis under OG helps the plant adapt to stress by promoting nutrient uptake and transport, maintaining hormone homeostasis, and enhancing the expression of genes related to plant growth and nutrient metabolism.<br><br>CONCLUSION: This study provides new insights into the positive interactions between grassland plants and rhizosphere bacteria under OG stress, offering valuable knowledge for developing new fertilizers and better management practices for degraded rangeland restoration and sustainable agriculture development.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40346456, year = {2025}, author = {Cao, M and Huang, L and Zhang, R}, title = {Community-acquired pneumonia associated with influenza co-infection caused by fusobacterium necrophorum: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {686}, pmid = {40346456}, issn = {1471-2334}, mesh = {Humans ; *Community-Acquired Infections/microbiology/drug therapy/diagnosis ; *Influenza, Human/complications/diagnosis/drug therapy/microbiology ; *Fusobacterium Infections/drug therapy/microbiology/diagnosis/complications ; Anti-Bacterial Agents/therapeutic use ; *Coinfection/microbiology/drug therapy/diagnosis ; *Fusobacterium necrophorum/isolation &amp; purification/genetics/drug effects ; *Pneumonia, Bacterial/microbiology/drug therapy/diagnosis ; Male ; Adult ; Community-Acquired Pneumonia ; }, abstract = {BACKGROUND: Fusobacterium necrophorum is a rare pathogen associated with community-acquired pneumonia (CAP), particularly among healthy adults. This case report presents a rare documented case of CAP caused by F. necrophorum in a young individual, providing valuable insights for the diagnosis and treatment of similar cases.<br><br>CASE PRESENTATION: The patient was initially diagnosed with influenza, and subsequently developed CAP caused by F. necrophorum. Despite one week of outpatient treatment with moxifloxacin, the symptoms persisted, leading to hospitalisation. Treatment with piperacillin tazobactam/imipenem and doxycycline, which target atypical pathogens, did not result in improvement after admission. Conventional diagnostic methods failed to identify the causative pathogen; however, metagenomic next-generation sequencing of bronchoalveolar lavage fluid confirmed it to be F. necrophorum. The patient showed significant improvement after ten days of targeted treatment with ornidazole and imipenem/piperacillin tazobactam, and was discharged.<br><br>CONCLUSION: Uncommon pathogens, such as F. necrophorum, should be considered as potential culprits in young individuals with CAP when conventional cultures yield negative results but there is a strong suspicion of infection, especially if initial antibiotic therapy is ineffective.}, }
@article {pmid40346111, year = {2025}, author = {Song, W and Yang, Q and Lv, H and Lv, Y and Jiang, Y and Qu, J and Li, Y}, title = {Prospective multicenter study identifying prognostic biomarkers and microbial profiles in severe CAP using BALF, blood mNGS, and PBMC transcriptomics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {16252}, pmid = {40346111}, issn = {2045-2322}, support = {No. 82200005//National Natural Science Foundation of China/ ; No. 82470002//National Natural Science Foundation of China/ ; 2023ZD0506200//National Key Research and Development Program of China/ ; SHDC2020CR5010//the three-year action plan of Shanghai Shenkang Hospital Development Center/ ; shslczdzk02202//Shanghai Municipal Key Clinical Specialty/ ; 2017ZZ02014//Shanghai Top-Priority Clinical Key Disciplines Construction Project/ ; 20dz2261100//Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases/ ; }, mesh = {Humans ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; *Biomarkers/blood ; Prospective Studies ; Prognosis ; Middle Aged ; Aged ; *Transcriptome ; *Leukocytes, Mononuclear/metabolism/microbiology ; High-Throughput Nucleotide Sequencing ; *Pneumonia/microbiology/genetics ; Severity of Illness Index ; Metagenomics/methods ; Adult ; Gene Expression Profiling ; }, abstract = {To identify potential biomarkers associated with the prognosis and severity of severe community-acquired pneumonia (SCAP), we conducted a multi-center prospective study from January 1, 2022, to December 31, 2023, enrolling 14 mild CAP and 75 SCAP patients in Shanghai, China. Patients underwent bronchoalveolar lavage fluid (BALF) and blood metagenomic next-generation sequencing (mNGS) as well as peripheral blood mononuclear cell (PBMC) transcriptomics. Among the 75 SCAP patients, 32 died within 30 days, with older age, a history of allergies, and comorbidities like cerebrovascular disease linked to worse outcomes. BALF mNGS showed greater microbial diversity, revealing a higher prevalence of pathogens, including Acinetobacter baumannii, Klebsiella pneumoniae, and Candida albicans, compared to mild CAP patients. RNA sequencing identified 431 differentially expressed genes in deceased SCAP patients, with significant alterations in immune pathways. Notably, microbial markers such as Pneumocystis jirovecii and viral markers like Human cytomegalovirus were associated with poor outcomes. Transcriptomic biomarkers, including otoferlin (OTOF), MS4A4A, and SIGLEC1, were identified as potential prognostic indicators for SCAP severity. GSEA and traditional GO/KEGG analyses identified key immune and metabolic pathways in SCAP (death) patients, including upregulation of complement activation, oxidative phosphorylation, nitrogen metabolism, while downregulation of adaptive immune response, hematopoietic cell lineage, and antigen processing pathways. These findings underscore the superiority of BALF mNGS over blood mNGS for pathogen detection, revealing microbial differences and transcriptomic alterations between mild and severe cases while identifying prognostic markers for SCAP treatment strategies.}, }
@article {pmid40345996, year = {2025}, author = {Eyssautier-Chuine, S and Besaury, L and Vaillant-Gaveau, N and Villaume, S and Habrant, A and Franco Castillo, I and Rondeau, M and Aggad, D and Gommeaux, M and Fronteau, G and Mitchell, SG}, title = {Controlling Lampenflora in Heritage Sites: In Situ Testing of POM-ILs in the Pommery Champagne Cellar.}, journal = {ChemPlusChem}, volume = {}, number = {}, pages = {e202500043}, doi = {10.1002/cplu.202500043}, pmid = {40345996}, issn = {2192-6506}, abstract = {Artificial lighting, essential for geotouristic purposes in subterranean sites, has facilitated the growth of colored photosynthetic organisms (lampenflora) on two monumental 19th-century bas-reliefs of the Pommery Champagne cellar - a UNESCO-protected heritage site - causing significant aesthetic and physical deterioration. To sustainably preserve these stone artworks, biocidal polyoxometalate-ionic liquids (POM-ILs) were tested alongside the commercial biocide Preventol RI80® on three trial zones, cleaned and colonized areas of a wall, and clean stone samples positioned on a testing station within the cellar. After one year, untreated control areas exhibited growth/regrowth of green biofilms, whereas surfaces treated with POM-ILs or Preventol RI80® remained biofilm-free. Measurements of colorimetry and chlorophyll fluorescence confirmed the effectiveness of both biocides in controlling photosynthetic microorganisms. However, confocal fluorescence microscopy highlighted a reduced long-term inhibition by Preventol RI80® compared to POM-ILs, despite the latter being applied at lower concentrations. Metagenomic analysis validated the performance of POM-ILs, showing a notable decrease in microbial richness and diversity in treated areas. While both products effectively inhibited phototrophs and fungi, their efficacy against Pseudomonadota was limited, due to microbial adaptation via antibiotic resistance genes. This study underscores the potential of POM-ILs as a sustainable alternative for preserving cultural heritage against microbial colonization.}, }
@article {pmid40345059, year = {2025}, author = {Yao, H and Romans-Casas, M and Vassilev, I and Rinta-Kanto, JM and Puig, S and Rissanen, AJ and Kokko, M}, title = {Selective butyrate production from CO2 and methanol in microbial electrosynthesis - influence of pH.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {165}, number = {}, pages = {109000}, doi = {10.1016/j.bioelechem.2025.109000}, pmid = {40345059}, issn = {1878-562X}, abstract = {Methanol assisted microbial electrosynthesis (MES) enables butyrate production from carbon dioxide and methanol using external electricity. However, the effects of operational parameters on butyrate formation remain unclear. By running three flat plate MES reactors with fed-batch mode at three controlled pH values (5.5, 6 and 7), the present study investigated the influence of pH on methanol assisted MES by comparing the process performance, microbial community structure, and genetic potential. The highest butyrate selectivity (87 % on carbon basis) and the highest butyrate production rate of 0.3 g L[-1] d[-1] were obtained at pH 6. At pH 7, a comparable butyrate production rate was achieved, yet with a lower selectivity (70 %) accompanied with acetate production. Butyrate production rate was considerably hindered at pH 5.5, reaching 0.1 g L[-1] d[-1], while the selectivity reached was up to 81 %. Methanol and CO2 consumption increased with pH, along with more negative cathodic potential and more negative redox potential. Furthermore, pH affected the thermodynamical feasibility of involved reactions. The results of metagenomic analyses suggest that Eubacterium callanderi dominated the microbial communities at all pH values, which was responsible for methanol and CO2 assimilation via the Wood-Ljungdahl pathway and was likely the main butyrate producer via the reverse β-oxidation pathway.}, }
@article {pmid40344981, year = {2025}, author = {Lin, F and Tang, W and Zeng, L and Peng, L and Li, Z and Fang, Z}, title = {A rare case of severe pneumonia caused by leptospirosis complicated with Jarisch-Herxheimer reaction.}, journal = {Diagnostic microbiology and infectious disease}, volume = {113}, number = {1}, pages = {116891}, doi = {10.1016/j.diagmicrobio.2025.116891}, pmid = {40344981}, issn = {1879-0070}, abstract = {BACKGROUND: Leptospirosis, a zoonotic disease caused by Leptospira species, presents significant diagnostic challenges due to its diverse clinical manifestations. Jarisch-Herxheimer reaction (JHR), an acute inflammatory response triggered by antibiotic therapy, can complicates disease management. Reports of leptospirosis with JHR remain rare, emphasizing the need for early diagnosis and appropriate treatment.<br><br>CASE PRESENTATION: An 80-year-old male presented with severe pneumonia, septic shock, and acute respiratory distress syndrome (ARDS). Diagnosis of leptospirosis was confirmed through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, identifying Leptospira species. The patient was treated with piperacillin-tazobactam and supportive care, leading to full recovery.<br><br>CONCLUSIONS: This case highlights the importance of mNGS in diagnosing rare infections and the need for vigilance in managing JHR. Clinicians should consider leptospirosis in patients with unexplained severe pneumonia and systemic inflammation.}, }
@article {pmid40344830, year = {2025}, author = {Hou, X and Gu, J and Chen, J and Ullah, H and Mamtimin, T and Wang, X and Li, X and Jiang, Y and Fan, J and Han, H and Li, X}, title = {Identification and functional characterization of a novel CaSrpA enzyme for selenite reduction and selenium nanoparticle formation.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138486}, doi = {10.1016/j.jhazmat.2025.138486}, pmid = {40344830}, issn = {1873-3336}, abstract = {Selenite reductases are widely distributed across various oxidoreductase families (e.g., ThxR, OYE, and FccA enzymes) [1]. The ability of short-chain dehydrogenase/reductase (SDR) family enzymes for selenite reduction remains unknown. Using metagenomic and metatranscriptomic analyses, 40 putative selenite reductases were identified from selenium-rich regions based on catalytic domain homology and transcriptional upregulation. These enzymes mainly belong to the SDR family and metalloenzymes. Enzyme activity analysis indicated that CaSrpA possessed the ability (Vmax, 18.85 μM/min/g) to reduce selenite to selenium nanoparticles (SeNPs). Phylogenetic analysis showed that CaSrpA was clustered in the clade of SDR enzymes, with the typical Rossmann fold. CaSrpA also oxidized S-1-phenylethanol to phenylacetone (Vmax, 15.4 μM/min/mg), sharing 53 % sequence similarity with the alcohol dehydrogenase RasADH. Molecular docking and structural superposition identified sixteen key residues associated with CaSrpA activity. Site-directed mutagenesis revealed that over 14 mutants exhibited a 30-90 % reduction in relative activity. Mutant M206A enhanced catalytic efficiency towards selenite by 2.4-fold and S-1-phenylethanol by 5.4-fold via a lid-opening mechanism. Molecular dynamics simulation elucidated that the mutant M206A utilized lid opening mechanism to accommodate more substrate and co-factor for catalysis via altering the conformation of the α7-α8 loop. This study helps understand the intrinsic connection between the SDR family and selenite-reducing capability, broadening the repertoire of selenite reductases.}, }
@article {pmid40344797, year = {2025}, author = {Chen, Y and Liu, Q and Xu, XW}, title = {Spatio-temporal variability of nitrogen-cycling potentials in particle-attached and free-living microbial communities in the Yangtze River estuary and adjacent regions.}, journal = {Marine pollution bulletin}, volume = {217}, number = {}, pages = {118121}, doi = {10.1016/j.marpolbul.2025.118121}, pmid = {40344797}, issn = {1879-3363}, abstract = {Particle-attached (PA) and free-living (FL) microorganisms regulate coastal biogeochemical cycles, yet their roles in nitrogen transformation remain unclear. To address this knowledge gap, we seasonally sampled PA and FL from seawater along salinity gradients in the Yangtze River estuary (YRE) and adjacent regions to investigate the spatio-temporal variability of microbial communities, abundances of nitrogen-cycling genes, and key microbial groups affiliated with the nitrogen cycle in PA and FL. Compared to FL, the composition, structure and diversity of PA exhibited more pronounced variations in response to salinity and [NO3[-]]. Metagenomic analyses indicated a predominant role of denitrification in both PA and FL, with greater abundances of genes involved in most nitrogen transformation processes observed in the estuarine region. The potential for the nitrogen cycle in PA was relatively lower in May, while greater in FL, potentially due to competition for nitrogen substrates between PA and phytoplankton during spring. PERMANOVA and Mantel tests showed that gene abundances exhibited spatio-temporal dynamics and were associated with species and environmental factors. Gene-affiliated taxa identification and the Weighted Correlation Network Analysis revealed that the differences in environmental factors and taxa responsible for the nitrogen transformation drove spatio-temporal variations of the nitrogen cycle between PA and FL, and implied the significance of their interaction in nitrogen fates in coastal ecosystem. Gammaproteobacteria and Betaproteobacteria were highly affiliated with nitrogen-cycling genes, while Nitrososphaeria played an important role in nitrification and denitrification. This study offered practical insights for mitigating eutrophication through targeted regulation of microbial-mediated nitrogen fluxes.}, }
@article {pmid40344252, year = {2025}, author = {Crawford, MS and Ulu, A and Ramirez, BM and Santos, AN and Chatterjee, P and Canale, V and Manz, S and Lei, H and Soriano, SM and Nordgren, TM and McCole, DF}, title = {Respiratory Exposure to Agriculture Dust Extract Alters Gut Commensal Species and Key Metabolites in Mice.}, journal = {Journal of applied toxicology : JAT}, volume = {}, number = {}, pages = {}, doi = {10.1002/jat.4808}, pmid = {40344252}, issn = {1099-1263}, support = {2R01DK091281/NH/NIH HHS/United States ; 1R01AI153314/NH/NIH HHS/United States ; 1R01DK130373/NH/NIH HHS/United States ; R00ES025819/NH/NIH HHS/United States ; R01HL158926/NH/NIH HHS/United States ; T34GM062756/NH/NIH HHS/United States ; U54OH007550//The University of California, Davis-Western Center for Agricultural Health and Safety/ ; //University of California Presidential Postdoctoral Fellowship Program/ ; //National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK)/ ; }, abstract = {Exposure to agricultural dust containing antimicrobial-resistant pathogens poses significant health risks for workers in animal agriculture production. Beyond causing severe airway inflammation, pollutants are linked to intestinal diseases. Swine farm dust is rich in ultrafine particles, gram-positive and gram-negative bacteria, and bacterial components such as lipopolysaccharides (LPS; endotoxins). In our previous study, we demonstrated that intranasal exposure of male and female C57BL/6J mice to 12.5% hog dust extract (HDE, containing 22.1-91.1 EU/mL) for 3 weeks resulted in elevated total cell and neutrophil counts in bronchoalveolar lavage fluid and increased intestinal permeability compared to saline controls. Now, we report that 16S and metagenomic analyses of Week 3 stool samples from HDE-treated mice indicate a reduced abundance of the beneficial species Akkermansia muciniphila and Clostridium sp. ASF356 and Lachnospiraceae bacterium. Bacterial alpha diversity showed increased species evenness in fecal samples from HDE-treated mice (Pielou's evenness, p = 0.047, n = 5-6/group). Metabolomic analysis also indicated significant reductions in key metabolites involved in energy metabolism, including riboflavin (p = 0.027, n = 11) and nicotinic acid (p = 0.049, n = 11), as well as essential amino acids, such as inosine (p = 0.043, n = 11) and leucine (p = 0.018, n = 11). While HDE exposure does not robustly alter overall microbial abundance or community structure, it leads to specific reductions in beneficial bacterial species and critical metabolites necessary for maintaining intestinal homeostasis by supporting energy metabolism, gut barrier function, microbiota balance, and immune regulation. The results of this study underscore the potential risks for gut health posed by inhalation of agricultural dust.}, }
@article {pmid40344212, year = {2025}, author = {Zhao, Y and Song, L and Li, HY and Liu, SX and Mao, FF and Li, XJ and Ding, PH}, title = {Metagenomic Insights Into the Subgingival Microbiome in Periodontal Health and Different Grades of Periodontitis.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.13408}, pmid = {40344212}, issn = {1600-0765}, support = {//Postdoctoral Science Foundation of China/ ; //National Natural Science Foundation of China/ ; //the Science Fund for Distinguished Young Scholars of Zhejiang Province/ ; //National Key Research and Development Program of China/ ; //Key Research and Development Program of Zhejiang Province/ ; //Fundamental Research Funds for the Central Universities/ ; }, abstract = {AIM: This cross-sectional study compared the subgingival microbiome in periodontal health (PH) and periodontitis, focusing on distinguishing Stage III Grade B periodontitis (PD-S3gB) and Stage III Grade C periodontitis (PD-S3gC) as defined by the 2018 Classification of Periodontitis.<br><br>METHODS: Subgingival samples from subjects with PH, PD-S3gB, and PD-S3gC were analyzed using metagenomic sequencing. Taxonomic and functional annotations were performed, followed by analyses of microbial diversity, differential abundance, interspecies networks, predictive modeling, and functional pathway enrichment.<br><br>RESULTS: Significant differences in both alpha and beta diversity were observed between PH and periodontitis. Several periodontal pathogens were more abundant in disease states, with Capnocytophaga granulosa and Capnocytophaga sp. CM59 enriched in PD-S3gC compared to PD-S3gB. The PD-S3gC group also exhibited a more complex microbial network with increased interspecies connectivity. An 11-species diagnostic model effectively distinguished PH, PD-S3gB, and PD-S3gC. Furthermore, pathways related to motility, chemotaxis, and methane metabolism were significantly enriched in periodontitis.<br><br>CONCLUSION: Distinct structural and functional differences in the subgingival microbiome characterize periodontal health and periodontitis. Periodontitis with a rapid rate of progression is marked by specific pathogen overgrowth and enhanced microbial interactions, supporting the development of microbiome-based diagnostics and personalized therapies.<br><br>TRIAL REGISTRATION: Chinese Clinical Trial Registration: ChiCTR2000039426.}, }
@article {pmid40343892, year = {2025}, author = {Kiige, JK and Kavoo, AM and Mwajita, MR and Mogire, D and Ogada, S and Wekesa, TB and Kiirika, LM}, title = {Metagenomic characterization of bacterial abundance and diversity in potato cyst nematode suppressive and conducive potato rhizosphere.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0323382}, doi = {10.1371/journal.pone.0323382}, pmid = {40343892}, issn = {1932-6203}, abstract = {Potato (Solanum tuberosum L.) is an important food crop in Kenya, providing a source of nutrition and income for many farmers. However, potato cyst nematodes (PCN) cause significant damage to potato plants, leading to substantial economic losses and threatening the nation's food security. Understanding the composition and functional potential of bacterial communities in the soil is important for developing sustainable biological control strategies against PCN and improving soil health. This cross-sectional purposive study examined the bacterial communities associated with PCN-suppressive and conducive potato rhizosphere from two major potato-producing counties in Kenya. We analyzed 180 soil samples from symptomatic and asymptomatic potato plants using shotgun metagenomics, followed by functional analysis to identify genes and metabolic pathways relevant to soil and plant health. Taxonomic classification revealed Enterobacteriaceae and Pseudomonadaceae as the most dominant bacterial families present. Within these families, the genera Pseudomonas and Enterobacter were highly abundant, both known for their plant growth-promoting traits, including biological control of soil pathogens and nutrient solubilization. KEGG and Pfam database analysis revealed pathways associated with nutrient cycling, transport systems, and metabolic functions. The abundance of iron-acquisition, chemotaxis, and diverse transport genes across analyzed samples suggests the presence of beneficial bacterial communities. This study provides the first report on bacterial ecology in PCN-infested rhizosphere in Kenya and its implications for soil health and PCN management.}, }
@article {pmid40343328, year = {2025}, author = {McLamb, F and Vazquez, A and Olander, N and Vasquez, MF and Feng, Z and Malhotra, N and Bozinovic, L and Najera Ruiz, K and O'Connell, K and Stagg, J and Bozinovic, G}, title = {Comparative Three-Barcode Phylogenetics and Soil Microbiomes of Planted and Wild Arbutus Strawberry Trees.}, journal = {Plant direct}, volume = {9}, number = {5}, pages = {e70078}, doi = {10.1002/pld3.70078}, pmid = {40343328}, issn = {2475-4455}, abstract = {Taxonomic identification of closely related plants can be challenging due to convergent evolution, hybridization, and overlapping geographic distribution. To derive taxonomic relationships among planted and wild Arbutus plants across a large geographic range, we complemented three standard plastid barcodes rbcL, matK, and trnH-psbA with soil and fruit chemistry, soil microbiome, and plant morphology analyses. Soil and plant sampling included planted Arbutus from manicured sites in Southern California, USA, wild plants from Southern and Northern California, and wild populations from Mediterranean island of Hvar, Croatia. We hypothesized that phenotypic variation within and between sites correlates with plants' genotype and geographic distribution. Similar fruit chemistry corresponds to geographical proximity and morphological resemblance, while bulk soil bacterial content defines three distinct clusters distinguishing planted versus wild trees and continent of origin. The soil microbiome of wild California Arbutus was characterized by an abundance of Nitrobacter, while the presence of Candidatus Xiphinematobacter was high in wild Hvar samples and most planted samples, but low in all wild California samples. Although all three barcodes resolved four main groups, the position of samples varies across barcodes. The rbcL phylogram is relatively unbalanced, suggesting slower diversification among wild California populations and exhibiting greater resolution than other barcodes among planted individuals. While our data demonstrate an overall agreement among standard plant barcodes relative to geo-distribution and plant morphology, sustained efforts on cost-effective global plant DNA barcode library standardization for closely related and geographically overlapping plants is recommended.}, }
@article {pmid40343031, year = {2025}, author = {Tan, MH and Bangre, O and Rios-Teran, CA and Tiedje, KE and Deed, SL and Zhan, Q and Rasyidi, F and Pascual, M and Ansah, PO and Day, KP}, title = {Metagenomic analysis reveals extreme complexity of Plasmodium spp. infections in high transmission in West Africa.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.04.29.25326533}, pmid = {40343031}, abstract = {Mixed-species, mixed-strain Plasmodia infections are known to occur in humans in malaria endemic areas. To date, the true extent of this complexity has not been explored in high- burden countries of sub-Saharan Africa. Here we take a metagenomic lens to infections obtained by sampling variable blood volumes from residents living in high, seasonal transmission in northern Ghana. We identified significantly higher prevalence of Plasmodium spp. and inter-/intra-species complexity in larger blood volumes. Overall, malaria infections displayed high levels of metagenomic complexity comprising single-, double-, and triple- species infections with varying levels of complexity for P. falciparum, P. malariae, P. ovale curtisi, and P. ovale wallikeri. We present evidence of individuals with greater susceptibility to highly-complex infections that cannot be explained by age or location. The implications of these findings to malaria epidemiology and control are illustrated by a geographic scaling exercise to district and region levels in Ghana.}, }
@article {pmid40342956, year = {2025}, author = {Yang, Z and Liu, Q and Hu, Y and Geng, S and Ni, JX}, title = {Application of Metagenomic and Targeted Next-Generation Sequencing in Diagnosis of Pulmonary Tuberculosis in Bronchoalveolar Lavage Fluid.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {2229-2241}, doi = {10.2147/IDR.S514090}, pmid = {40342956}, issn = {1178-6973}, abstract = {PURPOSE: To explore the application value of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in the diagnosis of pulmonary tuberculosis (PTB) in bronchoalveolar lavage fluid (BALF).<br><br>PATIENTS AND METHODS: Data from 202 patients with suspected PTB at Wuhan Central Hospital (Jan 2022 - Jan 2024) were retrospectively analyzed. BALF samples were collected and examined using mNGS and tNGS, comparing their sensitivity to traditional methods like acid-fast staining, TB culture, and TB-DNA. Mixed microbial species were identified from the BALF using mNGS and tNGS, and the pros and cons of tNGS were evaluated against mNGS.<br><br>RESULTS: Of the 202 patients evaluated, 94 were diagnosed with PTB. The BALF mNGS and tNGS exhibited a sensitivity of 77.66% and a specificity of 100%, with positive and negative predictive values of 100% and 83.72%, respectively, outperforming conventional diagnostic methods. It was possible to compare the AUC values of the ROC curves of the BALF mNGS and tNGS with the corresponding values of the other three assay methods (0.89 vs 0.56, p < 0.05), MTB culture (0.89 vs 0.71, p < 0.05), and TB-DNA (0.89 vs 0.68, p < 0.05). Additionally, these techniques identified mixed microbial species in 52.13% of the BALF samples. Although both mNGS and tNGS demonstrated similar diagnostic rates, tNGS proved to be faster, more cost-effective, and incorporated a tuberculosis-specific wall-breaking technology, thereby suggesting greater clinical utility.<br><br>CONCLUSION: BALF mNGS and tNGS technologies quickly and accurately detect PTB patients with greater sensitivity and specificity than traditional MTB methods. While both mNGS and tNGS demonstrate enhanced capacity for polymicrobial detection, the clinical significance of co-detected microorganisms requires integration with clinical context to differentiate colonization from active infection. Compared to mNGS, tNGS provides distinct advantages in clinical utility.}, }
@article {pmid40342698, year = {2025}, author = {Kang, X and Shao, M and Jiang, J and He, L and Lu, Y and Song, J and Xu, J and Fan, Z}, title = {The Gut Microbiome of the Asiatic Toad (Bufo gargarizans) Reflects Environmental Changes and Human Activities.}, journal = {Ecology and evolution}, volume = {15}, number = {5}, pages = {e71394}, doi = {10.1002/ece3.71394}, pmid = {40342698}, issn = {2045-7758}, abstract = {Amphibians are extremely sensitive to environmental changes, and their gut microbiome may have different responses to environmental changes. Here, metagenomic sequencing was used to investigate the intestinal microbiota of the Asiatic toad (Bufo gargarizans) from three different habitats (city areas, transition areas, and wild areas) of Sichuan Province, China. The results showed that Proteobacteria, Firmicutes, and Fusobacteria were the main bacteria in the gut of B. gargarizans. There were significant differences in the composition and function of the gut microbiome among the samples from the three different habitats. Enterobacteriaceae showed significant changes in the three habitats and occupied a high relative abundance in the city areas, especially for Citrobacter. Especially, antibiotic resistance genes (ARGs) and virulence factors (VFs) were significantly increased in city areas. We performed de novo assembly of the metagenome-assembled genomes (MAGs). In total, 322 nonredundant MAGs were reconstructed, 304 of which might be potential novel genomes. Among the 13 species-level genome bins (SGBs) belonging to Enterobacteriaceae, the one belonging to Citrobacter portucalensis annotated the most types of ARGs and VFs. Phylogenetic and functional analyses of the assembled C. portucalensis MAG and public genome data were carried out, suggesting that it may play a potential role in intestinal diseases in amphibians. Our study revealed the differences in the gut microbiome of B. gargarizans across different habitats and suggests that amphibian intestinal microbiota could serve as environmental indicators to reflect environmental changes and human activities. The reconstructed MAGs expanded our understanding of the gut microbiota in amphibians, which may serve as a substantial reservoir for microbiome resources.}, }
@article {pmid40342619, year = {2025}, author = {Sakiyama, Y and Yuan, JH and Yoshimura, A and Takeuchi, M and Maki, Y and Mori, T and Takei, J and Ando, M and Hiramatsu, Y and Nozuma, S and Higuchi, Y and Yonezawa, H and Kirishima, M and Suzuki, M and Kano, T and Tarisawa, M and Hashiguchi, S and Kunii, M and Sato, S and Takahashi-Iwata, I and Hashiguchi, A and Matsuura, E and Izumo, S and Tanimoto, A and Takashima, H}, title = {Brain biopsy and metagenomic sequencing enhance aetiological diagnosis of encephalitis.}, journal = {Brain communications}, volume = {7}, number = {3}, pages = {fcaf165}, doi = {10.1093/braincomms/fcaf165}, pmid = {40342619}, issn = {2632-1297}, abstract = {Identifying the aetiology of CNS diseases, regardless of their infectious or non-infectious nature, is often intricate. Next-generation sequencing (NGS) has emerged as a powerful tool for sensitive and unbiased screening of tissue or body fluid specimens. This study aimed to investigate the underlying aetiology of patients with suspected infectious CNS diseases. Between April 2013 and October 2021, we collected brain tissue samples from 33 patients diagnosed with encephalitis or encephalitis-like CNS diseases, obtained via biopsy or autopsy, and underwent metagenomic NGS (mNGS) in conjunction with pathological evaluations. Moreover, we employed PCR-based assays and pathogen-specific immunostaining to corroborate the presence of pathogens within the tissue samples. Among the 33 patients, mNGS elucidated pathogen-specific genomic sequences in 7 cases (21.2%), including halobacteria (archaea), Balamuthia mandrillaris, Epstein-Barr virus, Toxoplasma gondii and herpes simplex virus. Additionally, brain tissue mNGS ruled out known pathogens, identifying 14 cases (42.4%) of non-infectious CNS diseases, which included neoplastic, autoimmune/inflammatory and amyloid angiopathy conditions. The adjustment of therapeutic strategies based on these findings led to improvements in clinical symptoms, imaging outcomes and patient prognosis. Brain biopsy serves as both a direct pathological research target and a valuable source of samples for unbiased high-throughput sequencing. Our study illustrates the reliability of mNGS on brain tissue, which significantly improves the diagnostic rate for suspected encephalitis or encephalitis-like diseases of unknown aetiology. These findings underscore the importance of mNGS in guiding more precise and effective therapeutic interventions for patients in clinical practice.}, }
@article {pmid40342595, year = {2025}, author = {Sun, Y and Cai, Q and Li, T and Chen, J and Fang, Y}, title = {Genome assembly of Klebsiella michiganensis based on metagenomic next-generation sequencing reveals its genomic characteristics in population genetics and molecular epidemiology.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1546594}, doi = {10.3389/fmicb.2025.1546594}, pmid = {40342595}, issn = {1664-302X}, abstract = {INTRODUCTION: Klebsiella michiganensis, a significant member of the Klebsiella oxytoca complex, has emerged as a potential pathogen in clinical settings. Despite extensive research on the Klebsiella pneumoniae complex, the pathogenicity and drug resistance of the K. oxytoca complex remain understudied, particularly regarding the reconstruction of whole genomes from metagenomic next-generation sequencing (mNGS) data.<br><br>METHODS: In this study, bronchoalveolar lavage fluid (BALF) from a 55-year-old woman with a suspected right lung infection in Anhui Province, China, was analyzed using mNGS.<br><br>RESULTS: Three distinct assembly strategies were employed to reconstruct the genome of K. michiganensis, leading to the identification of a novel ST452 strain, KMLRT2206. Comprehensive genomic analysis of this strain and 206 clinical isolates (genomes downloaded from public databases) revealed the population structure, distribution of drug resistance genes, and virulence factors of K. michiganensis. The results demonstrated significant genetic diversity, with the species divided into three major clades, each exhibiting distinct patterns of drug resistance and virulence genes. Notably, 38.6% of the strains harbored the bla OXY-1-1 gene, highlighting a potential threat of drug resistance. While virulence gene distribution was not correlated with sequence type (ST), significant differences were observed among clades.<br><br>CONCLUSION: This study underscores the value of mNGS combined with optimized assembly strategies for accurate species identification within the K. oxytoca complex, providing critical insights for clinical pathogen detection and epidemiological surveillance.}, }
@article {pmid40341642, year = {2025}, author = {Humińska-Lisowska, K and Michałowska-Sawczyn, M and Kosciolek, T and Łabaj, PP and Kochanowicz, A and Mieszkowski, J and Proia, P and Cięszczyk, P and Zielińska, K}, title = {Gut microbiome and blood biomarkers reveal differential responses to aerobic and anaerobic exercise in collegiate men of diverse training backgrounds.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {16061}, pmid = {40341642}, issn = {2045-2322}, support = {2018/29/N/NZ7/02800//Narodowe Centrum Nauki/ ; 2018/29/N/NZ7/02800//Narodowe Centrum Nauki/ ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome/physiology ; *Biomarkers/blood ; *Exercise/physiology ; Young Adult ; Feces/microbiology ; Exercise Test ; Athletes ; Anaerobiosis ; Adult ; }, abstract = {The gut microbiome influences physiological responses to exercise by modulating inflammatory markers and metabolite production. Athletes typically exhibit greater microbial diversity, which may be associated with improved performance, but the mechanisms linking different exercise modalities to the gut microbiome are not fully understood. In this study, blood and stool samples were collected from endurance athletes, strength athletes, and non-athletic controls performing two maximal exercise tests (the anaerobic Wingate test and the aerobic Bruce Treadmill Test) to integrate serum biomarker data with gut bacterial metagenomic profiles. While most biochemical markers showed similar post-exercise trends across groups, SPARC (secreted protein acidic and rich in cysteine) and adiponectin levels showed modality-specific responses. Strength-trained participants showed unique microbiome-biomarker associations after the Wingate test. In addition, baseline enrichment of certain bacterial taxa, including Clostridium phoceensis and Catenibacterium spp., correlated with reduced Bruce Treadmill test response in strength-trained individuals. These findings, while requiring further validation, indicate the complex interplay between exercise type, training background, and the gut microbiome, and suggest that specific microbial species may help shape recovery and adaptation.}, }
@article {pmid40341309, year = {2025}, author = {Coimbra, A and D'arc, M and Moreira, FRR and Cosentino, MAC and Schiffler, FB and Miranda, TDS and Mouta, R and Girardi, DL and Wanderkoke, V and Medeiros, G and Francisco, TM and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and Santos, AFD}, title = {Fecal Virome of Southeastern Maned Sloth (Bradypus crinitus) (Pilosa: Bradypodidae).}, journal = {Genetics and molecular biology}, volume = {48}, number = {2}, pages = {e20240183}, doi = {10.1590/1678-4685-GMB-2024-0183}, pmid = {40341309}, issn = {1415-4757}, abstract = {We report a viral metagenomic analysis of fecal samples from Bradypus crinitus (Pilosa: Bradypodidae), a recently described sloth species that occurs in the Atlantic Forest of Espírito Santo and Rio de Janeiro states, Southeast Brazil. Through Illumina sequencing, we generated a total of 2,065,344 raw reads, of which 945,386 reads (45.77%) passed the quality and size filter. The highest proportion of them was assigned to Eukarya, followed by Bacteria and only a small proportion to Virus. However, we identified 24 viral families using distinct taxonomic assignment tools, including phages and vertebrate viruses, such as retroviruses and papillomaviruses. Also, we identified four bacterial genus already associated with disease in sloths. Our study sheds light on the microbiome of a previously unexplored species, further contributing to the comprehension of metagenomic global diversity.}, }
@article {pmid40341174, year = {2025}, author = {Kalwasińska, A and Królikiewicz, I and Tirkey, SR and Szabó, A and Kumar, SB}, title = {Enhanced understanding of nitrogen fixing bacteria through DNA extraction with polyvinylidene fluoride membrane.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {16079}, pmid = {40341174}, issn = {2045-2322}, support = {101038072//European Commission/ ; 101038072//European Commission/ ; }, mesh = {*Polyvinyls/chemistry ; Triticum/microbiology ; *DNA, Bacterial/isolation &amp; purification/genetics ; Rhizosphere ; Soil Microbiology ; *Nitrogen-Fixing Bacteria/genetics/isolation &amp; purification/classification ; Metagenomics/methods ; Nitrogen Fixation ; Fluorocarbon Polymers ; }, abstract = {The rhizobiota, particularly nitrogen-fixing bacteria, play a crucial role in plant functioning by providing essential nutrients and defense against pathogens. This study investigated the diversity of nitrogen-fixing bacteria in a relatively understudied habitat: technosoils developed from industrial soda production. To analyze the bacterial diversity in the rhizosphere soils of wheat (Triticum aestivum L.) and aster (Tripolium pannonicum Jacq.), regions of the nifH gene were amplified and sequenced from the resident bacterial communities. A polyvinylidene fluoride (PVDF) membrane was employed for metagenomic DNA extraction, enhancing the detection of nitrogen-fixing bacteria. Prior to standard DNA extraction, an enrichment step was conducted in nitrogen-free JMV medium at 26 °C for 24 h, with a modification that replaced soil with the PVDF membrane. This approach enabled a more comprehensive analysis of the rhizosphere bacterial community, revealing that unique amplicon sequence variants (ASVs) in aster and wheat membrane samples accounted for a notable proportion of all ASVs in the dataset (8.5% and 23%, respectively) that were not captured using the standard method. Additionally, our findings demonstrated higher alpha diversity of nitrogen-fixing bacteria in the wheat rhizosphere compared to the aster rhizosphere. In wheat, the dominant genus was Insolitispirillum (38.80%), followed by unclassified genera within Gammaproteobacteria (9.76%) and Rhodospirillaceae (4.74%). In contrast, the aster rhizosphere was predominantly occupied by Azotobacter (95.69%).}, }
@article {pmid40340931, year = {2025}, author = {Niu, BB and Xu, JJ and Li, JA and Zhu, LD}, title = {Case report: Cervical suppurative lymphadenitis caused by burkholderia multivorans in a healthy child.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {678}, pmid = {40340931}, issn = {1471-2334}, support = {ZR2024QH132//Natural Science Foundation of Shandong Province/ ; }, mesh = {Humans ; Male ; *Lymphadenitis/microbiology/diagnosis/drug therapy/pathology ; Child, Preschool ; Anti-Bacterial Agents/therapeutic use ; *Burkholderia Infections/diagnosis/microbiology/drug therapy ; Neck/pathology/microbiology ; Lymph Nodes/pathology/microbiology ; Meropenem/therapeutic use ; }, abstract = {BACKGROUND: Cervical suppurative lymphadenitis in children is commonly caused by Staphylococcus aureus or Streptococcus pyogenes. However, cases caused by Burkholderia multivorans (BM) are rare. The clinical presentation lacks specificity, making it difficult for clinicians to recognize, which may delay diagnosis and treatment.<br><br>CASE PRESENTATION: We report a case of a 5-year-old boy admitted with recurrent fever and neck swelling. Initial treatment with meropenem and linezolid was ineffective, and symptoms persisted after 24 days of conservative therapy. Aspiration of pus yielded negative culture results. Definitive diagnosis was achieved through surgical biopsy of cervical lymph nodes, pathological examination, and metagenomic next-generation sequencing (mNGS), which identified BM as the causative pathogen. The patient was successfully treated with a combination of trimethoprim-sulfamethoxazole and meropenem. The cervical lesion exhibited granulomatous inflammation and was managed with adjunctive vacuum-assisted closure (VAC) therapy, resulting in complete wound healing without recurrence.<br><br>CONCLUSIONS: This study aims to raise awareness among all specialists about BM as a potential causative agent in cervical suppurative lymphadenitis. Early recognition and timely intervention can reduce misdiagnosis and missed diagnoses, improving patient outcomes.}, }
@article {pmid40340823, year = {2025}, author = {Shen, Y and An, Z and Gao, L and Gu, M and Xia, S and Ding, Q and Li, Y and Cao, S and Li, J and Huang, J and Zhong, J and Chen, K and Wang, X and Wang, H}, title = {Integrated multi-omics analysis and functional validation uncovers RPL26 roles in regulating growth traits of Asian water buffaloes (Bubalus bubalis).}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {456}, pmid = {40340823}, issn = {1471-2164}, support = {2021YFD1200404//National Key R &amp; D Program of China/ ; ZR2023QC252//Shandong Provincial Natural Science Foundation/ ; }, mesh = {Animals ; *Buffaloes/genetics/growth &amp; development/metabolism ; *Ribosomal Proteins/genetics/metabolism ; Quantitative Trait Loci ; Transcriptome ; Genomics ; Metabolomics ; Metabolome ; Multiomics ; }, abstract = {BACKGROUND: Asian water buffaloes (Bubalus bubalis) in the Yangtze River Basin of China are the important meat provider for local residents because of its outstanding body size. Several previous studies have highlighted their genetic basis of growth characteristics, but the crucial genes regulating growth traits via multi-layer omics are still rarely investigated.<br><br>RESULTS: We conducted a comprehensive multi-omics analysis integrating blood and muscle transcriptome, plasma metabolome, rumen fluid metagenome, and genome of Haizi water buffaloes. Of note, ribosomal protein L26 (RPL26) located in the evolutionary selection regions associated with body sizes is the top differentially expressed gene (DEG) in both blood and muscle tissues. Further metabolomics and metagenomics identified growth-related molecular biomarkers (myristicin and Bacteroidales) and microbiological composition (Bacteroides and Prevotella). Leveraging cattle quantitative trait loci (QTLs) and genotype-tissue expression (CattleGTEx) databases, we found the significant correlations of QTL_180979 on RPL26 and two identified cis-eQTLs in muscle tissue in the upstream of RPL26 with weight gain. The follow-up cell assay validations confirmed the regulation roles of RPL26 in cell cycle, apoptosis, and differentiation, where the low RPL26 expressions enhanced the antiapoptotic ability and promoted the differentiation of myoblasts into myotubes markedly.<br><br>CONCLUSIONS: Our study illustrates RPL26 roles in regulating growth traits via both integrated multi-omics analysis and functional validations that suggests the further applications of RPL26 for growth trait selection of water buffaloes.}, }
@article {pmid40340756, year = {2025}, author = {Laue, HE and Willis, AD and Wang, F and MacDougall, MC and Xu, Y and Karagas, MR and Madan, JC and Fleisch, AF and Lanphear, BP and Cecil, KM and Yolton, K and Chen, A and Buckley, JP and Braun, JM}, title = {Early-life and concurrent predictors of the healthy adolescent microbiome in a cohort study.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {50}, pmid = {40340756}, issn = {1756-994X}, support = {K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; K99/R00ES034086 , P01ES011261, R01ES0272244, R01ES025214//National Institute of Environmental Health Sciences,United States/ ; R35GM133420/GM/NIGMS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; UL1TR001425/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Adolescent ; Female ; Male ; Child ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cohort Studies ; Metagenomics/methods ; }, abstract = {BACKGROUND: The microbiome of adolescents is poorly understood, as are factors influencing its composition. We aimed to describe the healthy adolescent microbiome and identify early-life and concurrent predictors of its composition.<br><br>METHODS: We performed metagenomic sequencing of 247 fecal specimens from 167 adolescents aged 11-14&#xa0;years participating in the Health Outcomes and Measures of the Environment (HOME) Study, a longitudinal pregnancy and birth cohort (Cincinnati, OH). We described common features of the adolescent gut microbiome and applied self-organizing maps (SOMs)-a machine-learning approach-to identify distinct microbial profiles (n&#x2009;=&#x2009;4). Using prospectively collected data on sociodemographic characteristics, lifestyle, diet, and sexual maturation, we identified early-life and concurrent factors associated with microbial diversity and phylum relative abundance with linear regression models and composition with Kruskal-Wallis and Fisher's exact tests.<br><br>RESULTS: We found that household income and other sociodemographic factors were consistent predictors of the microbiome, with higher income associated with lower diversity and differential relative abundances of Firmicutes (increased) and Actinobacteria (decreased). Sexual maturation, distinct from chronological age, was related to higher diversity in females and differences in phylum relative abundances and compositional profiles in both males and females.<br><br>CONCLUSIONS: Our study suggests that adolescence is a unique window for gut microbial composition and that it may be shaped by both early-life and concurrent exposures, highlighting its potential in future epidemiologic research.}, }
@article {pmid40340623, year = {2025}, author = {Deng, J and Zhang, J and Su, M and Li, J and Su, Y and Zhong, Q and Hu, J and Chen, Y and Liao, S and Lin, D and Guo, X}, title = {Fusobacterium mortiferum and its metabolite 5-aminovaleric acid promote the development of colorectal cancer in obese individuals through Wnt/β-catenin pathway by DKK2.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2502138}, doi = {10.1080/19490976.2025.2502138}, pmid = {40340623}, issn = {1949-0984}, mesh = {*Colorectal Neoplasms/metabolism/microbiology/genetics/pathology ; Animals ; Humans ; Mice ; Gastrointestinal Microbiome ; *Fusobacterium/metabolism ; *Wnt Signaling Pathway/drug effects ; *Obesity/microbiology/metabolism/complications ; *Intercellular Signaling Peptides and Proteins/metabolism/genetics ; Male ; Female ; Cell Line, Tumor ; Cell Proliferation ; Mice, Inbred C57BL ; }, abstract = {Colorectal cancer (CRC) is one of the most prevalent cancers worldwide, with high incidence and mortality rates. An increasing body of research suggests that obesity is a significant risk factor for the development of CRC. Moreover, recent findings have highlighted the close association between the gut microbiota and both obesity and CRC. Despite this, the specific mechanisms by which the gut microbiota influences obesity and CRC remain unclear. This study aims to explore the role of the gut bacterium Fusobacterium mortiferum and its metabolite 5-aminovaleric acid (5-AVA) in the development of obesity and CRC. Our study found that the metabolite 5-aminovaleric acid produced by Fusobacterium mortiferum significantly inhibits the expression of the tumor suppressor DKK2. This inhibition leads to enhanced proliferation of CRC cells. Furthermore, we discovered that Fusobacterium mortiferum and 5-AVA can activate the Wnt/β-catenin signaling pathway by inhibiting DKK2, thereby promoting tumor growth. This finding was validated in CRC mouse models and in vitro experiments. Additional mechanistic studies revealed that 5-AVA interacts with the demethylase KDM6B, affecting the demethylation process of DKK2 and subsequently activating the Wnt/β-catenin signaling pathway. Our study retrospectively collected fecal samples from patients who underwent gastrointestinal endoscopy at the Sixth Affiliated Hospital of Sun Yat-sen University over the past five years. Participants were stratified into a healthy control group and an adenoma group based on the outcomes of their colonoscopies. Following this, we conducted metagenomic analysis to identify differential bacteria, and based on the results, we performed bacterial cultivation and metabolomic profiling. The roles of the targeted bacteria and their metabolites were further validated through animal models and cellular assays, employing techniques such as Western Blot, qPCR, immunohistochemistry, molecular docking simulations, and gene overexpression studies. This study uncovers the potential carcinogenic effects of Fusobacterium mortiferum and 5-AVA in the development of obesity and CRC. Our research emphasizes the complex interplay between the gut microbiota and host metabolism and suggests new directions for future research to explore how modulation of the gut microbiota could prevent and treat CRC.}, }
@article {pmid40340466, year = {2025}, author = {Javornik Cregeen, S and Tisza, MJ and Hanson, B and Cook, M and Surathu, A and Schneider, R and Wu, J and Short, K and Domakonda, K and Hopkins, L and Ross, MC and Petrosino, JF and Deegan, J and Stadler, LB and Boerwinkle, E and Maresso, A}, title = {Sequencing-Based Detection of Measles in Wastewater: Texas, January 2025.}, journal = {American journal of public health}, volume = {}, number = {}, pages = {e1-e5}, doi = {10.2105/AJPH.2025.308146}, pmid = {40340466}, issn = {1541-0048}, abstract = {Measles is a potentially deadly viral infection spread via respiratory droplets from infected individuals. Outbreaks occur when vaccine coverage drops below the threshold of herd, or community, immunity. Using a sequencing-based approach, we report the prospective (January 7, 2025) detection of measles in nucleic acid extracts from 2 wastewater treatment plants in Houston, Texas, with a population of more than 218 000 residents. The sequencing data from 2 samples contained 53 unique reads mapping to 11 different regions of the measles virus genome with a 99.4% match to genotype B3. Importantly, no detections were observed from 821 previous samples from the same city spanning nearly 3 years of monitoring. The findings were confirmed using droplet digital polymerase chain reaction. A concomitant investigation identified 2 unvaccinated measles-positive travelers living within the same sewershed as the wastewater detection event. This work suggests that sequencing-based wastewater analysis is valuable as a comprehensive early detection warning system that facilitates more targeted epidemiological investigation. (Am J Public Health. Published online ahead of print May 8, 2025:e1-e5. https://doi.org/10.2105/AJPH.2025.308146).}, }
@article {pmid40340458, year = {2025}, author = {Bay, L and Barnes, CJ and Fritz, BG and Ravnborg, N and Ruge, IF and Halling-Sønderby, A-S and Søeborg, SR and Langhoff, KH and Lex, C and Hansen, AJ and Thyssen, JP and Bjarnsholt, T}, title = {Unique dermal bacterial signature differentiates atopic dermatitis skin from healthy.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0015625}, doi = {10.1128/msphere.00156-25}, pmid = {40340458}, issn = {2379-5042}, abstract = {UNLABELLED: Gaining a deeper understanding of the variation in skin microbiota across habitats and layers provides critical insights into the complex host-microbial interactions that drive inflammatory skin diseases. Our study investigated dermal versus epidermal microbiota in lesional and non-lesional skin of 37 adult atopic dermatitis (AD) patients and 37 healthy controls. Skin biopsies were partitioned into epidermal and dermal compartments, while serial tape strips collected the superficial epidermis. Bacterial communities were analyzed by cultivation, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, confocal laser scanning microscopy, and metagenomic sequencing. We found that the effects of AD were evident across skin layers. The natural variation between skin layers and habitats diminishes in AD-affected skin, intensifying the impact of the microenvironment and host factors. A remarkably distinct dermal bacterial community was discovered among AD patients, being more conserved and providing a clearer difference between skin habitats, while the epidermis varied substantially. Importantly, comparisons between AD patients and controls revealed more genera differed when studying the dermal samples than the epidermal ones. Staphylococcus, Corynebacterium, and Cutibacterium genera differed with AD status across all samples, but Prevotella and Mitsuokella only differed in the dermis. In the dry and moist dermis, this translated into 14 and 61 gene pathways significantly varying with AD status, including many related to the biosynthesis of menaquinones (vitamin K2). These results suggest dermal sampling would allow for the role of the skin microbiome within AD pathogenesis to be better resolved since these communities are simpler and less prone to environmental contamination.<br><br>IMPORTANCE: This study sheds light on the profound impact of skin microbiota's complex composition and distribution in atopic dermatitis (AD). The distinctive bacterial profile and activity, especially within the dermal skin compartment, vividly mirrored the cutaneous conditions in this inflamed microenvironment. The striking similarity in bacterial communities across different skin habitats in atopic skin underscores the high influence of atopic dermatitis-the genetic predisposition to an amplified immune response. This finding suggests that the dermal bacterial profile could be a valuable tool for longitudinally monitoring changes during the disease's relapsing phases, allowing for a precise categorization of patients into specific AD endotypes. Broadening the focus throughout the entire eczema-affected skin paves the way for treatments capable of modulating dermal biological factors, offering more effective management of AD. By further centering the interest in host-microbial interactions, we can refine personalized treatments, ultimately improving the lives of millions suffering from atopic dermatitis.}, }
@article {pmid40340444, year = {2025}, author = {Richtsmeier, P and Nedielkov, R and Haring, M and Yücel, O and Elsner, L and Lülf, RH and Wöhlbrand, L and Rabus, R and Moeller, H and Philipp, B and Mueller, FM}, title = {7β-Hydroxysteroid dehydratase Hsh3 eliminates the 7-hydroxy group of the bile salt ursodeoxycholate during degradation by Sphingobium sp. strain Chol11 and other Sphingomonadaceae.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0018525}, doi = {10.1128/aem.00185-25}, pmid = {40340444}, issn = {1098-5336}, abstract = {Bile salts are steroids with distinctive hydroxylation patterns that are produced and excreted by vertebrates. In contrast to common human bile salts, ursodeoxycholate (UDCA) has a 7-hydroxy group in β-configuration and is used in large amounts for the treatment of diverse gastrointestinal diseases. We isolated the 7β-hydroxysteroid dehydratase Hsh3 that is involved in UDCA degradation by Sphingobium sp. strain Chol11. Hsh3 eliminates the 7β-hydroxy group as water, leading to a double bond in the B-ring. This is similar to 7α-hydroxysteroid dehydratases in this and other strains, but Hsh3 is evolutionarily different from these. Purified Hsh3 accepted steroids with and without side chains as substrates and had minor activity with 7α-hydroxy groups. The deletion mutant strain Chol11 Δhsh3 had impacted growth with UDCA and accumulated a novel compound. The compound was identified as 3',5-dihydroxy-H-methyl-hexahydro-5-indene-1-one-propanoate, consisting of steroid rings C and D with a C3-side chain carrying the former 7β-hydroxy group, indicating that Hsh3 activity is important especially for the later stages of bile salt degradation. Hsh3 homologs were found in other sphingomonads that were also able to degrade UDCA as well as in environmental metagenomes. Thus, Hsh3 adds to the bacterial enzyme repertoire for degrading a variety of differently hydroxylated bile salts.IMPORTANCEThe bacterial degradation of different bile salts is not only important for the removal of these steroidal compounds from the environment but also harbors interesting enzymes for steroid biotechnology. The 7β-hydroxy bile salt ursodeoxycholate (UDCA) naturally occurs in high concentration in the feces of black bears and has important pharmaceutical relevance for the treatment of different liver-related diseases, for which it is administered in high and increasing amounts. Additionally, it is present in the bile salt pool of humans in trace amounts. While UDCA degradation is environmentally important, the enzyme Hsh3 modifies the hydroxy group that confers the medically relevant properties and thus might be interesting for microbiome analyses and biotechnological applications.}, }
@article {pmid40339985, year = {2025}, author = {Xavier, RGC and Santana, CH and de Castro, YG and Carvalho, RDO and da Silva, TF and Azevedo, V and Aburjaile, FF and Dorneles, EMS and Santos, RL and Silva, ROS}, title = {Metagenomic and 16S rRNA analysis of culture-negative uterine samples identifies Brucella spp. in a female dog with pyometra.}, journal = {Topics in companion animal medicine}, volume = {}, number = {}, pages = {100981}, doi = {10.1016/j.tcam.2025.100981}, pmid = {40339985}, issn = {1946-9837}, abstract = {Canine pyometra is the most prevalent reproductive disease in female dogs and involves a complex interplay of hormonal and microbial factors. Although Enterobacteriaceae are known to be the main cause of pyometra, up to 25% of samples remain negative when classic culture methods are used. The lack of growth in conventional media raises the intriguing possibility that non-cultivable microorganisms participate in the disease. Our study aimed to address this knowledge gap by investigating the microbiota in culture-negative uterine samples from dogs with pyometra. The purulent uterine contents of dogs with pyometra (n=79) were subjected to bacterial culture. Most of the samples showed bacterial growth of Escherichia coli (48/79, 60.7%) or other bacterial species (25/79, 31.8%). Samples that tested negative using the classic culture method (6/79=7.5%) were further analyzed using 16S rRNA gene sequencing, high-throughput 16S rRNA sequencing, and shotgun metagenomics. Only three of these provided DNA of sufficient quality for further analysis, which revealed a mixture of Haemophilus/Aggregatibacter and Fusobacterium/Porphyromonas in two uterine content. In the third sample, Brucella spp. was identified as the main genus. This study suggests that pathogens that are not easily isolated by classical culture methods, including zoonotic species, may be present in the uterus of dogs with pyometra.}, }
@article {pmid40339893, year = {2025}, author = {Zhang, L and Wang, S and Jia, Y and Liu, Z and Yao, J and Chen, Y}, title = {Alterations in microbial communities and antibiotic resistance genes pre- and post-sludge bulking in a wastewater treatment plant.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126391}, doi = {10.1016/j.envpol.2025.126391}, pmid = {40339893}, issn = {1873-6424}, abstract = {Sludge bulking is a common issue in wastewater treatment plants (WWTPs) that can disrupt microbial communities and potentially impact the abundance and spread of antibiotic resistance genes (ARGs) within treatment systems. This study employed high-throughput 16S rRNA gene sequencing and metagenomic sequencing to examine the changes in microbial communities and ARGs in a WWTP during non-bulking and bulking periods. The results indicated that bacterial diversity decreased in bulking sludge while maintaining a high removal efficiency of conventional pollutants. Significant differences were detected at the bacterial genus level between non-bulking and bulking sludge (p < 0.05). The proliferation of Candidatus_Microthrix contributed to sludge bulking, while Micropruina improved sludge settleability. When treating wastewater with the same water quality and quantity, anaerobic/anoxic/oxic (A[2]/O) exhibited the highest resistance to sludge bulking, followed by Bardenpho and the Carrousel oxidation ditch. The abundance of ARGs in bulking sludge (28.15-43.63 ppm) was lower than that in non-bulking sludge (51.72-59.01 ppm). The ARGs removal efficiency reached 96.24% and 94.34% during bulking and non-bulking periods, respectively. Network analysis revealed that Candidatus_Microthrix was positively correlated with aadS and tetX, and norank_f_Saprospiraceae exhibited positive correlations with vanRO and ANT(3'')-Iia. These findings provide valuable insights into the impacts of sludge bulking on WWTP performance and ARGs dynamics, informing evidence-based policies for sustainable wastewater treatment.}, }
@article {pmid40339368, year = {2025}, author = {Zhang, X and Liu, T and Sun, W and Zhang, C and Jiang, X and You, X and Wang, X}, title = {The fate and ecological risk of typical diamide insecticides in soil ecosystems under repeated application.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138440}, doi = {10.1016/j.jhazmat.2025.138440}, pmid = {40339368}, issn = {1873-3336}, abstract = {Diamide insecticides are the third most widely used class of pesticides worldwide. However, the long-term impacts of repeated diamide applications on soil ecosystems remain unclear. This study investigated chlorantraniliprole (CLP) and cyantraniliprole (CYP) effects on soil ecosystems through simulated repeated exposures. Results showed both exhibited slow degradation in the soil, with repeated applications extending their persistence, particularly for CLP. Both significantly inhibited soil alkaline nitrogen and organic matter accumulation, while reducing urease and sucrase activities, with CLP exerting stronger inhibitory effects. Metagenomic analysis indicated that CLP and CYP notably reduced soil microbial diversity. Additionally, the two insecticides altered the soil microbial community structure and inhibited carbon-nitrogen metabolic pathways. Further analysis revealed that CLP treatment significantly decreased the relative abundances of Mesorhizobium and Marmoricola, whereas CYP treatment primarily reduced Clostridium_sensu_stricto_1. All of these genera exhibited significant positive correlations with key metabolic pathways in soil carbon and nitrogen cycling. Notably, the relative abundance of Sphingomonas increased significantly following CLP and CYP treatments, demonstrating potential degradation capabilities. Overall, both CLP and CYP posed ecological risks to soil ecosystems, with CLP exhibiting more severe impacts. These findings revealed the need for strengthened scientific management in actual production.}, }
@article {pmid40339316, year = {2025}, author = {Cuzman, OA and Raio, A and Galeotti, M and Striova, J and Chaban, A and Innocenti, S and Penoni, S and de Luca, F and Cantini, B and Petrocchi, D}, title = {Pink discoloration due to pigmented Archaea on the walls of the so-called Michelangelo's "secret room" (Medici Chapel, Florence, Italy).}, journal = {The Science of the total environment}, volume = {981}, number = {}, pages = {179494}, doi = {10.1016/j.scitotenv.2025.179494}, pmid = {40339316}, issn = {1879-1026}, abstract = {Pink discolorations are often observed on heritage buildings mainly in areas affected by salt weathering, where the development of halotolerant and halophilic microorganisms is favored. Part of these extremophilic microorganisms contains carotenoids, reason for which their colonization becomes visible by naked eye on large surfaces. This work investigates the pink alteration of the walls with drawings attributed to Michelangelo, located in the basement room of the Medici Chapel (Florence, Italy). The results of in-depth multidisciplinary investigations are discussed in the context of a thorough literature review on pink alterations of heritage buildings. For the first time, we combined culture-based approaches with metagenomic analyses that revealed the pink pigmented archaea Halalkalicoccus sp. as dominant, pointing their role in the pink discoloration present on the wall. Raman spectroscopy was exploited for the characterization of the biogenic pigments and Fourier Transform infrared spectroscopy and scanning electron microscopy to analyze the salt formations present on the walls.}, }
@article {pmid40339249, year = {2025}, author = {Shi, Z and Zeng, W and Liu, Z and Yao, F and Guo, J and Chen, Y and Qin, Z and Zhang, J}, title = {Invasive apple snails with their core microbes are underestimated hotspots for disseminating antibiotic resistance genes and virulence factors in aquatic habitats.}, journal = {Journal of environmental management}, volume = {385}, number = {}, pages = {125575}, doi = {10.1016/j.jenvman.2025.125575}, pmid = {40339249}, issn = {1095-8630}, abstract = {Antibiotic resistance in pathogens is a threat to human health. The invasive apple snail (Pomacea canaliculata), widely distributed and linked to human activities, is a potential vector for human pathogens. However, its role in spreading antibiotic resistance genes (ARGs) is poorly understood. This study assessed the microbiological risk of this snail by sampling from five interconnected habitats: feces of invasive apple snails and native snails, ditch water, sediment, and soil. Using metagenomic and 16S rRNA sequencing, we analyzed the microbial communities and quantified the ARGs and virulence factors (VFs). Results showed that invasive apple snails carried significantly higher levels of ARGs and VFs compared with the native snails and environmental samples. ARGs and VFs were primarily found co-occurring in Aeromonas and Citrobacter freundii, with Aeromonas identified as the core microbe selected by invasive apple snails. Furthermore, the abundance and community dissimilarity of Aeromonas positively correlated with those of ARGs and VFs, both directly and indirectly through mobile genetic elements. This suggests Aeromonas may play a key role in disseminating ARGs and VFs across habitats. Overall, this study highlights the invasive apple snail as a significant vector for ARGs and virulent pathogens, providing critical insights for risk assessment and targeted management within the One Health framework.}, }
@article {pmid40338610, year = {2025}, author = {Gan, X and Yu, Q and Hu, X and Qian, Y and Mu, X and Li, H}, title = {Metagenomic and metatranscriptomic analysis reveals the enzymatic mechanism of plant polysaccharide degradation through gut microbiome in plateau model animal (Ochotona curzoniae).}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf045}, pmid = {40338610}, issn = {1574-6968}, abstract = {Herbivorous animals can obtain energy by decomposing plant polysaccharides through gut microbiota, but the mechanism of gut microbiota decomposing plant polysaccharides in high-altitude model animals is still unclear. Plateau pika (Ochotona curzoniae) is a key model animal native to the Qinghai-Tibet Plateau with a high intake of grass. Thus, Plateau pika is an excellent animal model for studying how herbivorous animals digest and metabolize grass polysaccharides. Here, we used 16S rDNA, 16S rRNA, metagenomic and metatranscriptomic sequencing to characterize gut microbial composition, gene potential and expressed function in pikas from different altitudes. Unlike total bacteria, Oscillospira and Ruminococcus were main active bacterial genera in pika's gut. The metabolic pathways of cellulose and hemicellulose were up-regulated in the middle and high-altitude groups, those genes encoding polysaccharide enzymes were enriched. Notably, the proportion of lignin metabolic genes expressed in pika's gut was the highest, followed by cellulase and hemicellulase genes. According to comparative metagenomics of different animals, the number and relative abundance of cellulase and hemicellulase genes in pika's gut were at higher level compared with steer, etc. These results indicated that plateau pika obtained sufficient energy from grass-based diet by increasing the expression of related metabolic enzymes.}, }
@article {pmid40338446, year = {2025}, author = {Mei, S and Deng, Z and Meng, FY and Guo, QQ and Tao, HY and Zhang, L and Xi, C and Zhou, Q and Tian, XF}, title = {Sini Powder Alleviates Stress Response and Suppresses Hepatocellular Carcinoma Development by Restoring Gut Microbiota.}, journal = {Chinese journal of integrative medicine}, volume = {}, number = {}, pages = {}, pmid = {40338446}, issn = {1993-0402}, abstract = {OBJECTIVES: To explore the underlying pharmacological mechanisms and its potential effects of Chinese medicine herbal formula Sini Powder (SNP) on hepatocellular carcinoma (HCC).<br><br>METHODS: The active components of SNP and their in vivo distribution were identified using ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Construction of component-target-disease networks, protein-protein interaction network, Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis, and molecular docking were employed to analyze the active components and anti-HCC mechanisms of SNP. Cell viability assay and wound healing assay were utilized to confirm the effect of SNP-containing serum (2.5%, 5.0%, 10%, 20%, and 40%), isoprenaline or propranolol (both 10, 100, and 1,000 &#xb5; mol/L) on proliferation and migration of HepG 2 or Huh7 cells. Meanwhile, the effect of isoprenaline or propranolol on the &#x3b2; 2 adrenergic receptor (ADRB2) mRNA expression on HepG2 cells were measured by real-time quantitative reverse transcription (RT-qPCR). Mice with subcutaneous tumors were either subjected to chronic restraint stress (CRS) followed by SNP administration (364 mg/mL) or directly treated with SNP (364 mg/mL). These two parallel experiments were performed to validate the effects of SNP on stress responses. Stress-related proteins and hormones were quantified using RT-qPCR, enzyme-linked immunosorbent assay, and immunohistochemistry. Metagenomic sequencing was performed to confirm the influence of SNP on the gut microbiota in the tumor-bearing CRS mice.<br><br>RESULTS: The distribution of the 12 active components of SNP was confirmed in various tissues and feces. Network pharmacology analysis confirmed the anti-HCC effects of the 5 active components. The potential anti-HCC mechanisms of SNP may involve the epidermal growth factor receptor (EGFR), proto-oncogene tyrosine-protein kinase Src (SRC) and signal transducer and activator of transcription 3 (STAT3) pathways. SNP-containing serum inhibited the proliferation of HepG2 and Huh7 cells at concentrations of 2.5% and 5.0%, respectively, after 24 h of treatment. Furthermore, SNP suppressed tumor progression in tumor-bearing mice exposed to CRS. SNP treatment also downregulated the expressions of stress-related proteins and pro-inflammatory cytokines, primarily by modulating the gut microbiota. Specifically, the abundance of Alistipes and Prevotella, which belong to the phylum Bacteroidetes, increased in the SNP-treated group, whereas Lachnospira, in the phylum Firmicutes, decreased.<br><br>CONCLUSION: SNP can combat HCC by alleviating stress responses through the regulation of gut microbiota.}, }
@article {pmid40338094, year = {2025}, author = {Tanaka, M and Toyonaga, T and Nakagawa, F and Iwamoto, T and Hasegawa, Y and Komatsu, A and Sumiyoshi, N and Shibuya, N and Minemura, A and Ariyoshi, T and Matsumoto, A and Oka, K and Shimoda, M and Saruta, M}, title = {Dietary 3-Aminobenzoic Acid Enhances Intestinal Barrier Integrity and Attenuates Experimental Colitis.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00406.2024}, pmid = {40338094}, issn = {1522-1547}, support = {21K15985//Kaken Pharmaceutical (Kaken)/ ; }, abstract = {Disruption of intestinal epithelial integrity and increased permeability is central to the pathogenesis of ulcerative colitis (UC). In this study, we identified 3-aminobenzoic acid (3-ABA), a dietary component abundant in azuki beans, soybeans and chickpeas as a regulator of epithelial permeability and inflammation in the colon. Screening 119 gut microbial metabolites revealed the ability of 4-ABA, a structural isomer of 3-ABA, to enhance barrier function in Caco2 cells. Further analysis of structural isomers identified 3-ABA as the most effective, significantly increasing transepithelial electrical resistance and reducing epithelial permeability. Using liquid chromatography-mass spectrometry, 3-ABA was detected in dietary beans and human fecal samples. Fecal 3-ABA levels were significantly lower in UC patients compared to healthy individuals. Metagenomic and functional prediction analyses revealed dysbiosis in UC patients, characterized by an enrichment of bacterial genes involved in ABA degradation. Gene expression analysis of 3-ABA-stimulated Caco2 cells demonstrated upregulation of tight junction molecules, such as CLDN1 and TJP1, enhancing epithelial barrier integrity. In a dextran sodium sulfate-induced colitis mouse model, rectal 3-ABA administration ameliorated colitis by enhancing epithelial barrier function and reducing inflammation. These findings highlight 3-ABA's potential as a dietary therapeutic agent for UC, offering a novel strategy to enhance intestinal integrity and mitigate inflammation.}, }
@article {pmid40337776, year = {2025}, author = {Li, Y and Li, C and Fang, Y and Zhang, L and Ying, X and Ren, R and Zang, Y and Ying, D and Zhu, S and Liu, J and Cao, X}, title = {Comprehensive Analysis of Pathogen Diversity and Diagnostic Biomarkers in Patients with Suspected Pulmonary Tuberculosis Through Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {2215-2227}, pmid = {40337776}, issn = {1178-6973}, abstract = {BACKGROUND: This study aimed to investigate the co-infecting pathogens and lung microbiomes in patients with clinically confirmed pulmonary tuberculosis (TB) and explore potential diagnostic biomarkers to differentiate between varied infection patterns.<br><br>METHODS: We conducted a retrospective cohort study by analyzing 198 bronchoalveolar lavage fluid (BALF) samples collected from patients with suspected pulmonary TB. All BALF samples were sequenced using metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: A total of 63 pathogens were detected in all samples. The TB group exhibited a higher diversity of pathogens (n=51) than the Non-TB group (n=37). The analysis revealed that TB patients had significantly higher pathogen counts (P=0.014), and specific microorganisms, such as Mycobacterium tuberculosis complex (MTBC), MTB, Streptococcus infantis, and Campylobacter curvus, were significantly enriched. Furthermore, the abundance of MTBC was negatively correlated with hemoglobin levels (R=-0.17, P=0.015) and positive correlated with C-reactive protein (CRP) levels (R=0.16, P=0.029). The random forest model combined eight differential microbes and five clinical parameters, yielding an area under the curve (AUC) of 0.86 for differentiating TB from Non-TB cohorts, whereas subgroup differentiation yielded an AUC of 0.571, demonstrating the potential for targeted diagnostics in pulmonary infections.<br><br>CONCLUSION: Our findings highlight the complexity of co-infection patterns in pulmonary TB and emphasize the potential of integrating microbial and clinical markers to improve diagnostic accuracy. This study provides valuable insights into the role of the lung microbiome in TB and informs future research on targeted therapies for this disease.}, }
@article {pmid40336613, year = {2025}, author = {Yusuf, A and Li, M and Zhang, SY and Odedishemi-Ajibade, F and Luo, RF and Wu, YX and Zhang, TT and Yunusa Ugya, A and Zhang, Y and Duan, S}, title = {Harnessing plant-microbe interactions: strategies for enhancing resilience and nutrient acquisition for sustainable agriculture.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1503730}, pmid = {40336613}, issn = {1664-462X}, abstract = {The rhizosphere, a biologically active zone where plant roots interface with soil, plays a crucial role in enhancing plant health, resilience, and stress tolerance. As a key component in achieving Sustainable Development Goal 2, the rhizosphere is increasingly recognized for its potential to promote sustainable agricultural productivity. Engineering the rhizosphere microbiome is emerging as an innovative strategy to foster plant growth, improve stress adaptation, and restore soil health while mitigating the detrimental effects of conventional farming practices. This review synthesizes recent advancements in omics technologies, sequencing tools, and synthetic microbial communities (SynComs), which have provided insights into the complex interactions between plants and microbes. We examine the role of root exudates, composed of organic acids, amino acids, sugars, and secondary metabolites, as biochemical cues that shape beneficial microbial communities in the rhizosphere. The review further explores how advanced omics techniques like metagenomics and metabolomics are employed to elucidate the mechanisms by which root exudates influence microbial communities and plant health. Tailored SynComs have shown promising potential in enhancing plant resilience against both abiotic stresses (e.g., drought and salinity) and biotic challenges (e.g., pathogens and pests). Integration of these microbiomes with optimized root exudate profiles has been shown to improve nutrient cycling, suppress diseases, and alleviate environmental stresses, thus contributing to more sustainable agricultural practices. By leveraging multi-disciplinary approaches and optimizing root exudate profiles, ecological engineering of plant-microbiome interactions presents a sustainable pathway for boosting crop productivity. This approach also aids in managing soil-borne diseases, reducing chemical input dependency, and aligning with Sustainable Development Goals aimed at global food security and ecological sustainability. The ongoing research into rhizosphere microbiome engineering offers significant promise for ensuring long-term agricultural productivity while preserving soil and plant health for future generations.}, }
@article {pmid40335921, year = {2025}, author = {Jia, S and Mi, H and Su, Y and Liu, Y and Ming, Z and Lin, J}, title = {Changes of intestinal microbiome and its relationship with painful diabetic neuropathy in rats.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {281}, pmid = {40335921}, issn = {1471-2180}, support = {22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; 22SXQT0125//Bureau of Science and Technology Nanchong Municipality/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; CBY22-ZDA09//School-level Key Scientific Research Project of North Sichuan Medical College/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Diabetic Neuropathies/microbiology/pathology ; Rats ; Male ; Rats, Sprague-Dawley ; Diabetes Mellitus, Experimental/microbiology/complications ; Interleukin-1beta/metabolism ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Tumor Necrosis Factor-alpha/metabolism ; Diabetes Mellitus, Type 2/microbiology/complications ; Colon/pathology/microbiology ; Spinal Cord/pathology/metabolism ; }, abstract = {OBJECTIVE: To analyze the gut bacterial microbiome in rats with painful diabetic neuropathy (PDN) compared to normal rats.<br><br>METHODS: Type 2 diabetes was induced in rats via a high-fat and high-sugar diet combined with a low dose of streptozotocin. Glucose metabolism and insulin sensitivity were evaluated using intraperitoneal glucose tolerance tests and insulin tolerance tests. The progression of peripheral neuropathy was assessed using the mechanical withdrawal threshold and thermal withdrawal latency. Histopathological analysis of rat colon tissues was performed using hematoxylin-eosin staining to observe morphological changes. The expression levels of pro-inflammatory cytokines TNF-&#x3b1; and IL-1&#x3b2; in spinal cord tissues were measured using enzyme-linked immunosorbent assay (ELISA). Fecal samples were then collected for metagenomic sequencing and analysis.<br><br>RESULT: Behavioral tests revealed reduced mechanical withdrawal threshold and thermal withdrawal latency in PDN rats. Histological analysis showed significant colonic mucosal damage and inflammatory cell infiltration, suggesting impaired intestinal barrier function. Elevated TNF-&#x3b1; and IL-1&#x3b2; levels in spinal cord tissues further highlight peripheral inflammation's role in PDN. Sequencing analysis revealed significant differences in gut microbiota composition between PDN and control rats, with altered Bacillota/Bacteroidota ratios and increased Lactobacillus abundance. Functional annotation analysis, based on the KEGG, EggNOG, and CAZy databases, indicated significant enrichment of metabolic pathways related to carbohydrate and amino acid metabolism, energy metabolism, and cell structure biogenesis in PDN rats. Cluster analysis identified higher functional clustering in Metabolism and Genetic Information Processing pathways in PDN rats.<br><br>CONCLUSION: This study demonstrates that PDN leads to altered gut microbiota composition, disrupted metabolic pathways, and increased inflammation, contributing to the pathological progression of diabetic neuropathy. This study provides new insights into the interplay between gut microbiota and diabetic neuropathy, offering potential avenues for therapeutic interventions targeting microbiome and metabolism.}, }
@article {pmid40335750, year = {2025}, author = {Deepali, D and Tejoprakash, N and Sudhakara Reddy, M}, title = {Diversity of Bacterial Communities in Seleniferous Soils and Their Impact on Plant Growth and Selenium Toxicity.}, journal = {Current microbiology}, volume = {82}, number = {6}, pages = {285}, pmid = {40335750}, issn = {1432-0991}, mesh = {*Selenium/toxicity/metabolism ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism/drug effects ; *Soil/chemistry ; *Zea mays/growth &amp; development/microbiology/drug effects ; Biodiversity ; *Microbiota ; Plant Roots/microbiology/growth &amp; development ; *Soil Pollutants/toxicity ; Phylogeny ; }, abstract = {The present study aimed to investigate the diversity of bacterial communities in seleniferous soils using Illumina Mi-Seq Next-Generation Sequencing. This study also compared seleniferous soils (SE) with non-seleniferous (NS) soils to evaluate Selenium (Se) impact on microbial communities and soil properties. Metagenomic analysis identified Proteobacteria as the predominant phylum in both environments, with SE soils exhibiting a higher dominance (48%) than NS soils (31%). The most dominant operational taxonomic unit (OTU) across both soil types belonged to the genus Bacillus. Se altered microbial community composition, increasing the abundance of the Bacillaceae family (30%) and Pseudomonadaceae family (25%) compared to NS soil. Bacillus was the dominant genus in the SE environment indicating its tolerance to selenium. Diversity indices indicated that control soils had higher species richness, while SE soils exhibited a more stressed microbial structure. A consortium of bacterial isolates (Proteus terrae Se3, Halopseudomonas formosensis Se5, and Corynebacterium glutamicum Se38) was inoculated in maize plants cultivated in natural seleniferous soils. Plants inoculated with bacterial consortium grew more healthy and had greater biomass in their roots, shoots, and seeds. Bacterial inoculation results in lesser selenium accumulation in the roots, shoots and seeds of maize plants compared to non-inoculated plants. These results suggest that bacterial species from seleniferous soils may be employed as biofertilizers to enhance plant growth and help plants tolerate Se toxicity in seleniferous soils.}, }
@article {pmid40335687, year = {2025}, author = {Zhang, J and Feng, X and Li, M and Liu, Y and Liu, M and Hou, LJ and Dong, HP}, title = {Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40335687}, issn = {1476-4687}, abstract = {Research on the morphology, physiology and genomics of Asgard archaea has provided valuable insights into the evolutionary history of eukaryotes[1-3]. A previous study suggested that eukaryotes are nested within Heimdallarchaeia[4], but their exact phylogenetic placement within Asgard archaea remains controversial[4,5]. This debate complicates understanding of the metabolic features and timescales of early eukaryotic ancestors. Here we generated 223 metagenome-assembled nearly complete genomes of Asgard archaea that have not previously been documented. We identify 16 new lineages at the genus level or higher, which substantially expands the known phylogenetic diversity of Asgard archaea. Through sophisticated phylogenomic analysis of this expanded genomic dataset involving several marker sets we infer that eukaryotes evolved before the diversification of all sampled Heimdallarchaeia, rather than branching with Hodarchaeales within the Heimdallarchaeia. This difference in the placement of eukaryotes is probably caused by the previously underappreciated chimeric nature of Njordarchaeales genomes, which we find are composed of sequences of both Asgard and TACK archaea (Asgard's sister phylum). Using ancestral reconstruction and molecular dating, we infer that the last Asgard archaea and eukaryote common ancestor emerged before the Great Oxidation Event and was probably an anaerobic H2-dependent acetogen. Our findings support the hydrogen hypothesis of eukaryogenesis, which posits that eukaryotes arose from the fusion of a H2-consuming archaeal host and a H2-producing protomitochondrion.}, }
@article {pmid40335510, year = {2025}, author = {Zhi, J and Liang, Y and Zhao, W and Qiao, J and Zheng, Y and Peng, X and Li, L and Wei, X and Wang, W}, title = {Oral microbiome-derived biomarkers for non-invasive diagnosis of head and neck squamous cell carcinoma.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {74}, pmid = {40335510}, issn = {2055-5008}, support = {82403470//National Natural Science Foundation of China/ ; 82401333//National Natural Science Foundation of China/ ; 21JCYBJC01570//Tianjin Municipal Science and Technology Committee/ ; 24JCQNJC01170//Tianjin Municipal Science and Technology Project/ ; TJWJ2023XK013//Tianjin Municipal Health Commission/ ; TJYXZDXK-046A//Tianjin Municipal Health Commission/ ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Squamous Cell Carcinoma of Head and Neck/diagnosis/microbiology ; *Microbiota ; Male ; Cross-Sectional Studies ; Middle Aged ; Female ; *Head and Neck Neoplasms/diagnosis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Metagenomics ; Dysbiosis/microbiology ; *Mouth/microbiology ; Adult ; Biomarkers/analysis ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Machine Learning ; Biomarkers, Tumor ; }, abstract = {Mounting evidence suggests that sustained microbial dysbiosis is associated with the development of multiple cancers, while the species-level bacterial taxa and metabolic dysfunction of oral microbiome in patients with head and neck squamous cell carcinoma (HNSCC) remains unclear. In this cross-sectional study, comprehensive metagenomic and 16S rRNA amplicon sequencing analyses of oral swab samples from 172 patients were performed. Unsupervised clustering algorithms of relative microbial abundance profiles revealed three distinctive microbiome clusters. Based on the metagenomic and 16S rRNA amplicon sequencing data, machine learning-based methods were used to construct the HNSCC diagnostic classifier, which exhibited high area under the curve values of 0.78-0.89. Our study provided the first exhaustive metagenomic and 16S rRNA amplicon sequencing analyses to date, revealing that microbial-metabolic dysbiosis is a potential risk factor for HNSCC progression and therefore providing a robust theoretical basis for potential diagnostic and therapeutic strategies for HNSCC patients.}, }
@article {pmid40335465, year = {2025}, author = {Romano, S and Wirbel, J and Ansorge, R and Schudoma, C and Ducarmon, QR and Narbad, A and Zeller, G}, title = {Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4227}, pmid = {40335465}, issn = {2041-1723}, support = {BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/E/F/000PR10356//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; SEG 9093//European Molecular Biology Organization (EMBO)/ ; EMBO ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; 395357507 - SFB 1371//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Parkinson Disease/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Humans ; *Machine Learning ; Metagenome ; }, abstract = {There is strong interest in using the gut microbiome for Parkinson's disease (PD) diagnosis and treatment. However, a consensus on PD-associated microbiome features and a multi-study assessment of their diagnostic value is lacking. Here, we present a machine learning meta-analysis of PD microbiome studies of unprecedented scale (4489 samples). Within most studies, microbiome-based machine learning models accurately classify PD patients (average AUC 71.9%). However, these models are study-specific and do not generalise well across other studies (average AUC 61%). Training models on multiple datasets improves their generalizability (average LOSO AUC 68%) and disease specificity as assessed against microbiomes from other neurodegenerative diseases. Moreover, meta-analysis of shotgun metagenomes delineates PD-associated microbial pathways potentially contributing to gut health deterioration and favouring the translocation of pathogenic molecules along the gut-brain axis. Strikingly, microbial pathways for solvent and pesticide biotransformation are enriched in PD. These results align with epidemiological evidence that exposure to these molecules increases PD risk and raise the question of whether gut microbes modulate their toxicity. Here, we offer the most comprehensive overview to date about the PD gut microbiome and provide future reference for its diagnostic and functional potential.}, }
@article {pmid40335388, year = {2025}, author = {Dwivedi, SL and Vetukuri, RR and Kelbessa, BG and Gepts, P and Heslop-Harrison, P and Araujo, ASF and Sharma, S and Ortiz, R}, title = {Exploitation of rhizosphere microbiome biodiversity in plant breeding.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.04.004}, pmid = {40335388}, issn = {1878-4372}, abstract = {Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.}, }
@article {pmid40335001, year = {2025}, author = {Li, G and Liu, R and Chen, Y and Liang, H and Liang, Y and Li, X and Ke, Y and Lin, B and Zhong, J and Guo, X and Che, J and Luo, J}, title = {Evolutionary dynamics and codon bias analysis of canine circovirus: Insights into global spread and host adaptability.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {108369}, doi = {10.1016/j.ympev.2025.108369}, pmid = {40335001}, issn = {1095-9513}, abstract = {Circoviruses are relatively new pathogens, and new circoviruses are constantly being discovered, with a growing range of hosts. Recently, canine circovirus (CanineCV) was reported to infect cats and badgers, further broadening its host range. Previous studies on the evolution and dissemination of CanineCV were fragmented. Here, when conducting a metagenomic analysis of shelter dogs, we identified a canine circovirus positivity rate of 32.4% and obtained three new viral strains. Furthermore, we integrated publicly available viral sequences and employed multiple bioinformatic software tools to analyze the evolution, codon usage bias, recombination, origin, spatiotemporal distribution and host adaptability of CanineCV. In this study, CanineCV could be divided into five distinct phylogenetic clades, named as China-I, China-II, Cosmopolitan, EA, and SEA clades. The extensive inter-clade recombination was observed, which plays an important role in viral evolution, while based on existing sequence information, CanineCV most likely originated in Norway from Vulpes vulpes in 1950.7. Notably, CanineCV exhibits greater adaptability to human hosts compared to previously documented hosts, as indicated by host adaptability indices, suggesting that this virus may possess zoonotic potential. In summary, our study elucidates the phylogeography and evolutionary dynamics of CanineCV and underscores the importance of investigating its potential for zoonotic transmission.}, }
@article {pmid40334798, year = {2025}, author = {Zhu, X and Chen, L and Yang, P and Luo, S and Teng, M and Zhu, W and Li, Y and Zhao, D and Wang, N and Chen, X and Cheng, M and Tu, H and Huang, W and Yang, F and Wang, L and Liu, X and Ning, K}, title = {Microbiome catalog and dynamics of the Chinese liquor fermentation process.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132620}, doi = {10.1016/j.biortech.2025.132620}, pmid = {40334798}, issn = {1873-2976}, abstract = {Fermented food remains poorly understood, largely due to the lack of knowledge about microbes in food fermentation. Here, this study constructed Moutai Fermented Grain Catalog (MTFGC), a representative liquor fermented by one of the most complex fermentations. MTFGC comprised 8,379,551 non-redundant genes and 5,159 metagenome-assembled genomes, with 20% species and 20% genes being novel. Additionally, 25,625 biosynthetic gene clusters (BGCs) and 28 BGC-enriched species were identified. Moreover, the microbial community assembly was deterministic, with significant species and gene changes in early fermentation stages, while stabilizing in later stages. Further BGC-knockout experiments verified Bacillus licheniformis, a BGC-enriched species, employed its BGCs for synthesizing the aroma-related lipopeptide lichenysin. This study has established the largest genetic resource for fermented food, uncovering its uniqueness and high metabolic potential. These findings facilitate the transition potential from traditional fermentation to precision-driven synthetic biology in food systems.}, }
@article {pmid40254113, year = {2025}, author = {Bartáková, V and Bryjová, A and Polačik, M and Alila, DO and Nagy, B and Watters, B and Bellstedt, D and Blažek, R and Žák, J and Reichard, M}, title = {Phylogenomics and population genomics of Nothobranchius in lowland Tanzania: species delimitation and comparative genetic structure.}, journal = {Molecular phylogenetics and evolution}, volume = {208}, number = {}, pages = {108357}, doi = {10.1016/j.ympev.2025.108357}, pmid = {40254113}, issn = {1095-9513}, mesh = {Animals ; Tanzania ; *Phylogeny ; Polymorphism, Single Nucleotide ; *Genetics, Population ; Genetic Variation ; Sequence Analysis, DNA ; Metagenomics ; Killifishes ; }, abstract = {Annual killifishes of the genus Nothobranchius are widespread across East Africa, with a particularly high biodiversity in lowland Tanzania. While they are typically found in ephemeral pools, the pools vary greatly in size, connectivity and inundation patterns. It was previously suggested that main river channels formed significant barriers to Nothobranchius dispersal. Here, we study the distribution of genetic lineages in an equatorial part of their range where main river channels that may act as barriers occur and closely related lineages frequently coexist in secondary contact zones. We used single-nucleotide polymorphism (SNP) dataset from double-digest restriction site-associated DNA (ddRAD) sequencing to investigate how genetic diversity is structured in Nothobranchius species from the coastal lowlands of Tanzania. Our analyses resolved some uncertain phylogenetic relationships within the N. melanospilus and N. guentheri species groups and placed N. flammicomantis outside the Coastal clade. Rather than a shared intraspecific genetic diversity pattern across four coexisting and widely distributed species, we found highly diverse patterns of intra-specific genetic structure among N. eggersi, N. janpapi, N. melanospilus and N. ocellatus. Populations of Nothobranchius species from the humid coastal lowlands of Tanzania are therefore structured, but not constrained by barriers formed by river channels or by basins - in contrast to Nothobranchius species from the dry part of their distribution. Some of the genetic relationships determined call for a re-evaluation of taxonomic delimitations.}, }
@article {pmid40333210, year = {2025}, author = {Trujillo, HA and Komeili, A}, title = {Revealing the diversity of bacterial and archaeal organelles via comparative genomics.}, journal = {Molecular biology of the cell}, volume = {36}, number = {5}, pages = {pe4}, doi = {10.1091/mbc.E20-08-0564}, pmid = {40333210}, issn = {1939-4586}, mesh = {*Archaea/genetics/metabolism ; Genomics/methods ; *Bacteria/genetics/metabolism ; *Organelles/genetics/metabolism ; Metagenomics/methods ; Magnetosomes/genetics/metabolism ; Genome, Archaeal ; }, abstract = {Like eukaryotes, bacteria and archaea rely on intracellular organelles to manage biological activities. Despite their prevalence, the understanding of the diversity of these organelles and the molecular mechanisms governing their function remain limited. In this review, we examine the potential of genomics and metagenomics to augment classical approaches for the study and discovery of microbial organelles. First, we highlight how the intimate interplay between model system studies and metagenomics have been critical in illuminating the function, diversity, and ancient evolutionary origins of the lipid-bounded magnetosome organelles of magnetotactic bacteria. We next discuss the central role of open genome databases and mechanistic studies in identification and characterization of protein-bounded encapsulin organelles with novel roles in sulfur metabolism and other cellular processes. Finally, we focus on the mostly uncultured Asgard archaea superphylum, whose metagenomes are challenging our views on organelle evolution and eukaryogenesis.}, }
@article {pmid40333159, year = {2025}, author = {Gao, Y and Lou, Y and Hui, Y and Chen, H and Sang, H and Liu, F}, title = {Characterization of the Gut Microbiota in Patients with Psoriasis: A Systematic Review.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/pathogens14040358}, pmid = {40333159}, issn = {2076-0817}, support = {22LCYY-QH10//Jinling Hospital/ ; }, mesh = {Humans ; *Psoriasis/microbiology/therapy ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; *Dysbiosis/microbiology/therapy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Background: Psoriasis is a prevalent and persistent inflammatory disorder with systemic manifestations. Emerging evidence implicates the gut microbiota in regulating inflammatory responses, metabolic pathways, and immune homeostasis. This review synthesizes current evidence on gut microbiota dysbiosis in psoriasis and evaluates the therapeutic potential of probiotics and fecal microbiota transplantation (FMT) in disease management. Method: Following PRISMA guidelines, we systematically reviewed studies investigating gut microbiome profiles in psoriasis through the MEDLINE, EMBASE, and Web of Science databases (January 2015-December 2024). Included studies utilized 16S rRNA gene sequencing or metagenomic analyses for microbial characterization. Results: Comparative analyses revealed distinct gut microbiota patterns in psoriasis patients compared with healthy controls, although specific microbial signatures exhibited inconsistencies across studies. Notably, interventions modulating gut microbiota composition-particularly probiotic supplementation-demonstrated measurable improvements in psoriasis severity scores and inflammatory markers. Conclusions: Gut microbiome modulation represents a promising therapeutic strategy for psoriasis; however, current evidence highlights the need for standardized microbial analysis methodologies and larger longitudinal studies to establish causality. Future research should prioritize the functional characterization of microbiota-host interactions to optimize therapeutic applications.}, }
@article {pmid40333137, year = {2025}, author = {McHugh, JW and Challener, DW and Tabaja, H}, title = {Change of Heart: Can Artificial Intelligence Transform Infective Endocarditis Management?.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/pathogens14040371}, pmid = {40333137}, issn = {2076-0817}, mesh = {Humans ; *Artificial Intelligence ; *Endocarditis/diagnosis/therapy/diagnostic imaging ; Echocardiography ; Machine Learning ; Disease Management ; }, abstract = {Artificial intelligence (AI) has emerged as a promising adjunct in the diagnosis and management of infective endocarditis (IE), a disease characterized by diagnostic complexity and significant morbidity. Machine learning (ML) models such as SABIER and SYSUPMIE have demonstrated strong predictive accuracy for early IE diagnosis, embolic risk stratification, and postoperative mortality, surpassing traditional clinical scoring systems. In imaging, AI-enhanced echocardiography and advanced modalities like FDG-PET/CT offer improved sensitivity, specificity, and reduced inter-observer variability, potentially transforming clinical decision making. Additionally, AI-powered microbiological techniques, including MALDI-TOF mass spectrometry combined with ML and neural network-based metagenomic classifiers, show promise in rapidly identifying pathogens and predicting antimicrobial resistance. Despite encouraging early results, widespread adoption faces barriers, including data limitations, interpretability issues, ethical concerns, and the need for robust validation. Future directions include leveraging generative AI as clinical consultative tools, provided their capabilities and limitations are carefully managed. Ultimately, collaborative efforts addressing these challenges could transform IE care, enhancing diagnostic accuracy, clinical outcomes, and patient safety.}, }
@article {pmid40333054, year = {2025}, author = {Matos, JSS and Demoliner, M and Gularte, JS and Filippi, M and de Abreu Góes Pereira, VM and da Silva, MS and Weber, MN and de Barros, MP and Spilki, FR}, title = {Virome of Terrestrial Mammals and Bats from Southern Brazil: Circulation of New Putative Members of the Togaviridae Family and Other Findings.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/pathogens14040310}, pmid = {40333054}, issn = {2076-0817}, support = {405786/2022-0//CNPQ/ ; }, mesh = {Animals ; Brazil/epidemiology ; *Chiroptera/virology ; *Virome ; *Mammals/virology ; Phylogeny ; Metagenomics ; Humans ; }, abstract = {The surveillance of wildlife viromes is essential for identifying zoonotic threats within the One Health framework. This study analyzed rectal and oral swabs from 88 individuals representing 13 species as felids, wild rodents, marsupials and non-human primates in Southern Brazil using metagenomic sequencing. Akodon montensis (n = 15 individuals) and Coendou spinosus (n = 4) harbored Chikungunya virus (ChikV, Togaviridae), marking its first detection in these hosts. Molossus molossus (n = 17) presented Coronaviridae and Orthoherpesviridae, while Eptesicus furinalis (n = 1) also carried Coronaviridae. A broad virome diversity, including Togaviridae and Adenoviridae members, was identified in Didelphis albiventris (n = 43), with significant relevance to human health. Additional species, such as Callithrix jacchus (n = 1), Leopardus guttulus (n = 1), Myocastor coypus (n = 1), Monodelphis iheringi (n = 1), Thaptomys nigrita (n = 1), Sooretamys angouya (n = 1), Brucepattersonius iheringi (n = 1), and Lasiurus blossevillii (n = 1), contributed to insights into viral reservoirs. These results underscore the importance of virome studies in regions harboring high biodiversity, emphasizing genomic surveillance as a vital tool for monitoring zoonotic viruses and safeguarding global health.}, }
@article {pmid40332920, year = {2025}, author = {Liu, H and Chen, W and Fang, X and Li, D and Xiong, Y and Xie, W and Chen, Q and You, Y and Lin, C and Wang, Z and Wang, J and Chen, D and Li, Y and Cai, P and Nie, C and Hong, Y}, title = {Impact of Ectropis grisescens Warren (Lepidoptera: Geometridae) Infestation on the Tea Plant Rhizosphere Microbiome and Its Potential for Enhanced Biocontrol and Plant Health Management.}, journal = {Insects}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/insects16040412}, pmid = {40332920}, issn = {2075-4450}, support = {2023XQ019//Key Technological Innovation and Industrialization Project/ ; 2022J011198//Project of Fujian Provincial Department of Science and Technology/ ; 2024J01917//Project of Fujian Provincial Department of Science and Technology/ ; 2024J01916//Project of Fujian Provincial Natural Science Fund/ ; N2023Z007//Nanping Academy of Resource Industrialization Chemistry Project/ ; N2023J004//Key Project of the Nanping Natural Fund/ ; 202410397010//National College Student Innovation and Entrepreneurship Project/ ; }, abstract = {The root-associated microbiome significantly influences plant health and pest resistance, yet the temporal dynamics of its compositional and functional change in response to Ectropis grisescens Warren (Lepidoptera: Geometridae) infestation remain largely unexplored. The study took samples of leaves, roots, and rhizosphere soil at different times after the plants were attacked by E. grisescens. These samples were analyzed using transcriptomic and high-throughput sequencing of 16S rRNA techniques. The goal was to understand how the plant's defense mechanisms and the microbial community around the roots changed after the attack. Additionally, bacterial feedback assays were conducted to evaluate the effects of selected microbial strains on plant growth and pest defense responses. By conducting 16S rRNA sequencing on the collected soil samples, we found significant shifts in bacterial communities by the seventh day, suggesting a lag in community adaptation. Transcriptomic analysis revealed that E. grisescens attack induced reprogramming of the tea root transcriptome, upregulating genes related to defensive pathways such as phenylpropanoid and flavonoid biosynthesis. Metagenomic data indicated functional changes in the rhizosphere microbiome, with enrichment in genes linked to metabolic pathways and nitrogen cycling. Network analysis showed a reorganization of core microbial members, favoring nitrogen-fixing bacteria like Burkholderia species. Bacterial feedback assays confirmed that selected strains, notably Burkholderia cepacia strain ABC4 (T1) and a nine-strain consortium (T5), enhanced plant growth and defense responses, including elevated levels of flavonoids, polyphenols, caffeine, jasmonic acid, and increased peroxidase (POD) and superoxide dismutase (SOD) activities. This study emphasizes the potential of utilizing root-associated microbial communities for sustainable pest management in tea cultivation, thereby enhancing resilience in tea crops while maintaining ecosystem balance.}, }
@article {pmid40332799, year = {2025}, author = {Bai, C and Duan, Y and Zhao, C and Yan, L and Suthisut, D and Lü, J and Bai, Y and Zeng, F and Zhang, M}, title = {Abundance of the Dominant Endosymbiont Rickettsia and Fitness of the Stored-Product Pest Liposcelis bostrychophila (Psocoptera: Liposcelididae).}, journal = {Insects}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/insects16040349}, pmid = {40332799}, issn = {2075-4450}, support = {32172260//National Natural Science Foundation of China/ ; }, abstract = {Endosymbiotic bacteria are key factors that regulate the biological traits of Liposcelis bostrychophila. This study employed metagenomic methods to analyze the dominant species of symbiotic microorganisms associated with L. bostrychophila. By controlling the environmental temperature, we were able to manipulate the abundance of endosymbionts and establish populations with high, medium, and low levels of these bacteria. This allowed us to examine the fitness parameters of L. bostrychophila under different levels of endosymbiont abundance. The experimental results revealed that L. bostrychophila hosts 51 genera of symbiotic microorganisms, with Rickettsia being the dominant genus, accounting for 84.11% to 98.16% of the total share. Environmental temperature significantly affected the abundance of Rickettsia, with notable differences observed during the adult stage of L. bostrychophila. A temperature gradient of 28 °C, 35 °C, and 37 °C was established, allowing for the classification of populations based on Rickettsia abundance into three categories: high-abundance populations (LBhp), medium-abundance populations (LBmp), and low-abundance populations (LBlp). The abundance of Rickettsia had a significant impact on the fitness of L. bostrychophila. Specifically, a high abundance of Rickettsia contributed positively to population fitness by increasing egg production, prolonging egg hatching time, enhancing lifespan, and improving both survival and reproductive rates. Therefore, the endosymbiont Rickettsia plays a crucial role in the growth and development of L. bostrychophila. In the future, our research will help further uncover the interactions between Rickettsia and its host, providing new perspectives for pest control and offering a better understanding of insect biology and ecology.}, }
@article {pmid40331433, year = {2025}, author = {Meyer, F and Robertson, G and Deng, ZL and Koslicki, D and Gurevich, A and McHardy, AC}, title = {CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf369}, pmid = {40331433}, issn = {1362-4962}, support = {//NFDI4Microbiota consortium/ ; 460129525//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Finding appropriate software and parameter settings to process shotgun metagenome data is essential for meaningful metagenomic analyses. To enable objective and comprehensive benchmarking of metagenomic software, the community-led initiative for the Critical Assessment of Metagenome Interpretation (CAMI) promotes standards and best practices. Since 2015, CAMI has provided comprehensive datasets, benchmarking guidelines, and challenges. However, benchmarking had to be conducted offline, requiring substantial time and technical expertise and leading to gaps in results between challenges. We introduce the CAMI Benchmarking Portal-a central repository of CAMI resources and web server for the evaluation and ranking of metagenome assembly, binning, and taxonomic profiling software. The portal simplifies evaluation, enabling users to easily compare their results with previous and other users' submissions through a variety of metrics and visualizations. As a demonstration, we benchmark software performance on the marine dataset of the CAMI II challenge. The portal currently hosts 28 675 results and is freely available at https://cami-challenge.org/.}, }
@article {pmid40331220, year = {2025}, author = {Wang, Y and Wei, C and Chen, Z and Zhou, M and Huang, L and Chen, C}, title = {Characterization of the diversity, genomic features, host bacteria, and distribution of crAss-like phages in the pig gut microbiome.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1582122}, pmid = {40331220}, issn = {2297-1769}, abstract = {Phages play an important role in shaping the gut microbiome. CrAss-like phages, which are key members of the gut virome, show high abundance in the human gut and have attracted increasing interest. However, few studies have been found in pigs, and the distribution of crAss-like phages across broader pig populations remains unknown. Here, we obtained 1,251 pig crAss-like phage genomes from 403 metagenomes publicly available and a pig gut virome dataset constructed by ourselves. These crAss-like phage genomes were further clustered into 533 virus operational taxonomic units (vOTUs). Phylogenetic analysis revealed that crAss-like phages in pig guts were distributed across four well-known family-level clusters (Alpha, Beta, Zeta, and Delta) but were absent in the Gamma and Epsilon clusters. Genomic structure analysis identified 149 pig crAss-like phage vOTUs that utilize alternative genetic codes. Gene blocks encoding replication and assembly proteins varied across crAss-like phage clusters. Approximately 64.73% of crAss-like phage genes lacked functional annotations, highlighting a gap in understanding their functional potential. Numerous anti-CRISPR protein genes were identified in crAss-like phage genomes, and CAZymes encoded by these phages were primarily lysozymes. Host prediction indicated that bacterial hosts of pig crAss-like phages primarily belonged to Prevotella, Parabacteroides, and UBA4372. We observed that interactions between crAss-like phages and Prevotella copri might have a possible effect on fat deposition in pigs. Finally, all detected vOTUs exhibited low prevalence across pig populations, suggesting heterogeneity in crAss-like phage compositions. This study provides key resources and novel insights for investigating crAss-like phage-bacteria interactions and benefits research on the effects of crAss-like phages on pig health and production traits.}, }
@article {pmid40330784, year = {2025}, author = {Krivonos, D and Pavlenko, A and Lukina-Gronskaya, A and Korneenko, E and Speranskaya, A and Ilina, E}, title = {Case Report: Fatal case of dual infection Metapneumovirus complicated by Streptococcus pyogenes.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1576583}, pmid = {40330784}, issn = {2296-858X}, abstract = {Human Metapneumovirus (hMPV) is a common cause of acute respiratory viral infection in humans, typically occurring in children and causing no serious complications. However, the severity of the disease can be exacerbated by certain bacterial pathogens that lead to severe illness and even death. This report details a fulminant case of dual infection with hMPV and group A Streptococcus (Streptococcus pyogenes) in a three-year-old child. The whole genome sequencing of isolated clinical S. pyogenes strains was conducted, followed by an analysis of the genomic characteristics of the pathogen. Also, potential viral and bacterial pathogens were identified by qPCR and 16S rRNA metagenomic sequencing in any autopsy materials obtained from the patient. Children who had contact with the patient and began to exhibit symptoms of a cold were also tested and confirmed to have uncomplicated hMPV infection. The S. pyogenes strain has been found to contain five genes for various streptococcal exotoxins (speA, speB, speJ, speG and smeZ). In addition, the speA gene is situated in close proximity to the prophage, which may suggest that it is encoded and transferred specifically by the bacteriophage. We hypothesize that it was the cumulative effects of different streptococcal exotoxins that led to the patient's death.}, }
@article {pmid40330742, year = {2025}, author = {Liu, C and Cai, Y and Yuan, K and Lu, M and Deng, Y and Chen, X and Ye, L and Cui, S and Lyu, J and Ling, Y}, title = {Confirmation of Tuberculous Meningitis Using Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {2209-2214}, pmid = {40330742}, issn = {1178-6973}, abstract = {BACKGROUND: Tuberculous meningitis (TBM) remains a significant clinical challenge due to limitations in traditional diagnostic methods, such as cerebrospinal fluid (CSF) analysis and tuberculosis culture, which often have long turnaround times and low sensitivity and specificity. This case report highlights the pivotal role of metagenomic next-generation sequencing (mNGS) in enhancing clinical knowledge for the diagnosis and management of TBM, supplementing insights into its clinical presentation and treatment.<br><br>CASE PRESENTATION: A 56-year-old male patient was admitted to the hospital with a chief complaint of "unconsciousness for 4 days". Following five days of antimicrobial therapy, the patient showed significant improvement with no fever or headache, but exhibited a suspicious left-sided Babinski sign (+). MRI revealed evidence of cerebral infarction, while spiral CT imaging showed hydrocephalus accompanied by interstitial cerebral edema. A lumbar puncture revealed elevated intracranial pressure, increased protein levels in CSF, reduced glucose and chloride concentrations, and negative results for CSF smear, CSF culture, and blood culture. T-SPOT testing was positive, and mNGS of CSF detected Mycobacterium tuberculosis (M. tuberculosis) Based on clinical and etiological findings, a diagnosis of tuberculous meningitis was confirmed. The patient was treated with quadruple anti-tuberculosis therapy combined with linezolid, resulting in clinical improvement. He was subsequently transferred to a specialized chest hospital for further management.<br><br>CONCLUSION: The patient's condition improved after 5 days of treatment. TBM is notoriously challenging to diagnose and treat. Traditional diagnostic methods, such as smear microscopy and tuberculosis culture, often yield low positive rates, delaying timely diagnosis and intervention. Early detection, accurate diagnosis, and prompt treatment are crucial for improving patient outcomes. mNGS of CSF has proven to be a powerful tool in TBM diagnosis, enabling early and precise identification of the pathogen, thereby facilitating timely treatment and reducing TBM-related mortality.}, }
@article {pmid40330288, year = {2025}, author = {Bhowmik, S and Hajra, A and Bandyopadhyay, D}, title = {Genetic insights in infectious diseases: Insights from a case report and implications for personalized medicine.}, journal = {World journal of clinical cases}, volume = {13}, number = {13}, pages = {101438}, pmid = {40330288}, issn = {2307-8960}, abstract = {The relationship between genetics and infectious diseases is important in shaping our understanding of disease susceptibility, progression, and treatment. Recent research shows the impact of genetic variations, such as heme-oxygenase promoter length, on diseases like malaria and sepsis, revealing both protective and inconclusive effects. Studies on vaccine responses highlight genetic markers like human leukocyte antigens, emphasizing the potential for personalized immunization strategies. The ongoing battle against drug-resistant tuberculosis (TB) illustrates the complexity of genomic variants in predicting resistance, highlighting the need for integrated diagnostic tools. Additionally, genome-wide association studies reveal antibiotic resistance mechanisms in bacterial genomes, while host genetic polymorphisms, such as those in solute carrier family 11 member 1 and vitamin D receptor, demonstrate their role in TB susceptibility. Advanced techniques like metagenomic next-generation sequencing promise detailed pathogen detection but face challenges in cost and accessibility. A case report involving a highly virulent Mycobacterium TB strain with the pks1 gene further highlights the need for genetic insights in understanding disease severity and developing targeted interventions. This evolving landscape emphasizes the role of genetics in infectious diseases, while also addressing the need for standardized studies and accessible technologies.}, }
@article {pmid40330019, year = {2025}, author = {Fang, P and Wen, Y and Deng, W and Liang, R and He, P and Wang, C and Fan, N and Huo, K and Zhao, K and Li, C and Bai, Y and Ma, Y and Hu, L and Guan, Y and Yang, S}, title = {Investigation of dynamic microbial migration patterns in the respiratory tract.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1542562}, pmid = {40330019}, issn = {2235-2988}, mesh = {Humans ; *Respiratory Tract Infections/microbiology ; Prospective Studies ; Male ; Female ; Middle Aged ; *Microbiota ; Sputum/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Respiratory System/microbiology ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Oropharynx/microbiology ; Bayes Theorem ; *Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: The role of the respiratory microbiome in lung diseases is increasingly recognized, with the potential migration of respiratory pathogens being a significant clinical consideration. Despite its importance, evidence elucidating this phenomenon remains scarce.<br><br>METHODS: This prospective study collected clinical samples from patients with suspected lower respiratory tract infections (LRTI), including oropharyngeal swabs (OPS), sputum, and bronchoalveolar lavage fluid (BALF). Metagenomic next-generation sequencing (mNGS) was employed to analyze respiratory microbial diversity, complemented by Bayesian source tracking and sequence alignment analyses to explore pathogen migration patterns.<br><br>RESULTS: A cohort of 68 patients was enrolled, with 56 diagnosed with LRTI and 12 with non-infectious respiratory conditions. A statistically significant disparity in respiratory microbiome diversity was observed between infected and non-infected groups (p < 0.05). Intriguingly, no significant variations in microbial community structure, including alpha and beta diversity, were detected across different respiratory tract sites within individuals. The Bayesian source tracking analysis revealed a pronounced migration pattern among pathogens compared to the overall microbial community, with migration ratios of 51.54% and 1.92%, respectively (p < 0.05). Sequence similarity analysis further corroborated these findings, highlighting a notable homology among specific migrating pathogens.<br><br>CONCLUSION: This study represents a pioneering effort in deducing pathogen migration patterns through microbial source tracking analysis. The findings provide novel insights that could significantly advance clinical diagnostics and therapeutic strategies for respiratory infections.}, }
@article {pmid40330015, year = {2025}, author = {Manimaran, A and Desingu, PA and Kumaresan, A and Singh, P and Subramanya, K and Dodamani, P and Dineshbhai, PA}, title = {The metagenomic and whole-genome metagenomic detection of multidrug-resistant bacteria from subclinical mastitis-affected cow's milk in India.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1549523}, pmid = {40330015}, issn = {2235-2988}, mesh = {Animals ; India ; *Milk/microbiology ; Cattle ; *Drug Resistance, Multiple, Bacterial/genetics ; Female ; *Mastitis, Bovine/microbiology ; *Metagenomics/methods ; *Genome, Bacterial ; *Bacteria/genetics/isolation &amp; purification/drug effects/classification ; Whole Genome Sequencing ; Virulence Factors/genetics ; Humans ; }, abstract = {Multidrug-resistant (MDR) bacteria in farm animal products threaten human health by causing zoonotic infections. The complete genome sequences of MDR bacteria from subclinical mastitis-affected cow's milk have not yet been comprehensively documented in India. In this study, using a bacterial metagenomic sequencing approach, we detected the nearly complete genome sequences of Pseudomonas veronii and Staphylococcus xylosus from subclinical mastitis-affected cow's milk. Furthermore, we sequenced the nearly complete genome sequences of Escherichia coli, Klebsiella pneumoniae, Staphylococcus hominis, and S. xylosus from subclinical mastitis-affected cow's milk using a whole-genome metagenomic sequencing method. Our analysis subsequently revealed that the complete genome sequences of the identified bacteria contained MDR genes and genes for multiple virulence factors. These MDR bacteria may pose a public health risk through exposure to milkers, milk handlers, and farm workers or through the handling and consumption of unpasteurized milk.}, }
@article {pmid40329854, year = {2025}, author = {Buddle, S and Torres, O and Morfopoulou, S and Breuer, J and Brown, JR}, title = {The use of metagenomics to enhance diagnosis of Encephalitis.}, journal = {Expert review of molecular diagnostics}, volume = {}, number = {}, pages = {}, doi = {10.1080/14737159.2025.2500655}, pmid = {40329854}, issn = {1744-8352}, abstract = {INTRODUCTION: Encephalitis has a broad etiology, including infectious and auto-immune causes. In infectious encephalitis the breadth of causative organisms results in incomplete testing and low diagnostic yields.Metagenomics sequences all DNA and RNA allows untargeted detection of all organisms in a single specimen; this is of particular use in diagnosis of encephalitis with a broad etiology.<br><br>AREAS COVERED: We review the literature and discuss metagenomics workflows, host depletion and pathogen enrichment methods, bioinformatics analysis and potential analysis of the host transcriptome to aid diagnosis. We discuss the clinical use of metagenomics for diagnosis of neurological infection including time to result, cost, quality assurance, patient cohorts in whom metagenomics adds the most value, recommended specimen types, limitations and review published cases in which metagenomics has been used to diagnose encephalitis.<br><br>EXPERT OPINION: There is good evidence for the utility of metagenomics to diagnose infection in encephalitis. Due to infections with rare, unexpected or novel pathogens, metagenomics adds most value to diagnosis in immunocompromised patients and the greatest diagnostic yield is in brain biopsies. Technical advances are needed to reduce the complexity, cost and time to result which will enable wider adoption in clinical laboratories and use as a first line test.}, }
@article {pmid40329496, year = {2025}, author = {Rose, S and Johnson, H and Cartozzo, C and Swall, J and Simmons, T and Singh, B}, title = {Testing the efficacy of surface swab sampling to determine postmortem submersion interval (PMSI), using the microbiome colonization of skeletal remains.}, journal = {Journal of forensic sciences}, volume = {}, number = {}, pages = {}, doi = {10.1111/1556-4029.70039}, pmid = {40329496}, issn = {1556-4029}, abstract = {Postmortem interval (PMI) estimation contributes valuable information in the medicolegal investigation of decomposed human remains, and estimating the postmortem submersion interval (PMSI) can specifically aid investigations involving victims discovered in aquatic environments. Microbial succession-driven models in long-term decomposition studies have utilized the abundant colonizing bacterial community of skeletal remains to estimate the PMSI using bone powder. This study investigates the use of bone surface swabbing as an effective alternative method that minimizes time and resources required for bone sampling and also provides a highly replicable method for decomposition studies. Skeletal porcine (Sus scrofa) remains were caged and submerged in both lentic and lotic environments (Henley Lake in White Hall and James River at the Rice Rivers Center in Charles City, respectively) in Central Virginia from November 2017 to November 2018. Bone surface swabs and water samples were analyzed at 500 accumulated degree days (ADD) intervals, from baseline (0 ADD) to 4500 ADD. Variable region 4 (V4) of 16S rDNA was amplified and sequenced using the Illumina MiSeq Sequencing platform and analyzed using Mothur (v.1.39.5) and R (v.4.04). Analysis of Molecular Variance (AMOVA) indicated a significant difference in bacterial community structure among and between the swab, bone, and water samples (p < 0.001, F = 7.92331), and among and between lake and river samples (p < 0.001, F = 9.38829). PMSI models were constructed using random forest models for lake swabs (R[2] = 0.83, RMSE = 623.24) and river swabs (R[2] = 0.83, RMSE = 580.2). Swab samples from both aquatic environments predicted PMSI, albeit slightly less accurately than those previously reported from bone powder (lake: R[2] = 0.96, 334.1; river: R[2] = 0.94, 498.47).}, }
@article {pmid40329426, year = {2025}, author = {Ren, L and Yang, J and Xiao, Y and Guo, L and Rao, J and Wu, C and Wang, X and Wang, Y and Zhang, L and Zhang, L and Jiang, X and Zhong, J and Zhong, J and Yang, W and Wang, C and Wang, J and Li, M}, title = {Transmission of the human respiratory microbiome and antibiotic resistance genes in healthy populations.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {115}, pmid = {40329426}, issn = {2049-2618}, support = {2020-I2M-2-013//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2019PT310029//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2022YFA1304300//National Key R&amp;D Program of China/ ; 2022YFA1304300//National Key R&amp;D Program of China/ ; NSFC82221004//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Microbiota/genetics ; Female ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Male ; Adult ; Metagenomics/methods ; *Oropharynx/microbiology ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Family Characteristics ; Young Adult ; Metagenome ; }, abstract = {BACKGROUND: The human microbiome is transmissible between individuals, including pathogens and commensals with metabolic and immune-modulating effects, which could influence susceptibility, severity, and outcomes of both infection and non-infection diseases. However, limited studies of respiratory microbiome transmission within populations have been conducted. Herein, we performed species- and strain-level metagenomic analyses on oropharyngeal (OP) swabs from 1046 healthy urban dwellers across 13 districts, including 111 households with at least two cohabitants, to elucidate the transmission dynamics of the respiratory microbiome within households and communities.<br><br>RESULTS: We found that geographic districts accounted for the greatest variation in the OP microbiome, with unrelated individuals from the same district showing greater microbiome similarity and higher strain-sharing rates than those from different districts. Cohabitants, especially spouses and siblings, exhibited similar microbial abundances and shared more strains, with 16.7% (IQR 0.0-33.3%) of strains shared among cohabitants, compared to 0.0% (IQR 0.0-11.1%) in non-cohabiting pairs (p&#x2009;<&#x2009;0.05). Both respiratory commensals and opportunistic pathogens were shared among cohabitants. In contrast, no evidence of vertical transmission was detected between mother-offspring pairs. Additionally, the OP microbiome contained diverse antibiotic resistance genes (ARGs), with 15.0% linked to mobile genetic elements (MGEs) or plasmids; the flanking sequences of these ARGs were more conserved across species than those of non-MGE-associated ARGs, suggesting horizontal transfer of ARGs among respiratory microorganisms.<br><br>CONCLUSIONS: In summary, we characterized the transmissible nature of the OP microbiome and the risk of ARG dissemination among respiratory microorganisms. These findings underscore the role of respiratory microbes and ARGs exchange in shaping the microbiome of healthy populations and emphasize their relevance to public health strategies for respiratory health management. Video Abstract.}, }
@article {pmid40329425, year = {2025}, author = {Vigneron, A and Cloarec, LA and Brochier-Armanet, C and Flandrois, JP and Troussellier, M and Bernard, C and Agogué, H and Oger, PM and Hugoni, M}, title = {Genomic characterisation of novel extremophile lineages from the thalassohaline lake Dziani Dzaha expands the metabolic repertoire of the PVC superphylum.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {48}, pmid = {40329425}, issn = {2524-6372}, support = {project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; project MARWEL, ANR-21-CE20-0049//Agence Nationale de la Recherche/ ; project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; }, abstract = {BACKGROUND: Extreme environments are useful systems to investigate limits of life, microbial biogeography and ecology, and the adaptation and evolution of microbial lineages. Many novel microbial lineages have been discovered in extreme environments, especially from the Planctomycetota-Verrucomicrobiota-Chlamydiota (PVC) superphyla. However, their evolutionary history and roles in ecosystem functioning and microbiome assemblage are poorly understood.<br><br>RESULTS: Applying a genome-centric approach on an 8-year metagenomic timeseries produced from the hypersaline and hyperalkaline waters of Lake Dziani Dzaha (Mayotte), we recovered 5 novel PVC extremophilic candidate lineages from the biosphere of the lake. Sibling to Elusimicrobia and Omnitrophota, these lineages represented novel halophilic clades, with global distributions bounded to soda lakes and hypersaline hydrosystems. Genome mining of these newly defined clades revealed contrasted, but ecologically relevant, catabolic capabilities involved in the carbon, hydrogen and iron/electron cycles of the Dziani Dzaha ecosystem. This also includes extracellular electron transfer for two of them, suggesting metal reduction or potential electron exchanges with other members of the lake community. By contrast, a putative extracellular giant protein with multiple carbohydrate binding domains and toxin-like structures, as observed in virulence factors, was identified in the genome of another of these clades, suggesting predatory capabilities.<br><br>CONCLUSIONS: Our results provided genomic evidences for original metabolism in novel extremophile lineages of the PVC superphyla, revealing unforeseen implications for members of this widespread and diverse bacterial radiation in aquatic saline ecosystems. Finally, monitoring the in-situ distribution of these lineages through the timeseries reveals the drastic effects of environmental perturbations on extreme ecosystem biodiversity.}, }
@article {pmid40329403, year = {2025}, author = {Huang, Y and Cheng, S and Shi, J and He, P and Ma, Y and Yang, R and Zhang, X and Cao, Y and Lei, Z}, title = {Enhancing Holstein steers growth performance: oregano essential oil's impact on rumen development, functionality and microorganism.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {44}, pmid = {40329403}, issn = {2524-4671}, support = {GSA-XMLZ-2021-01//Beef Cattle Quality Fattening Project of Gansu Province/ ; GSSLCSX-2020-1//Major Science and Technology Special Project of Gansu Province/ ; 2024CYZC-36//Industry Support Project of Gansu Province/ ; }, abstract = {BACKGROUND: Dietary supplementation with oregano essential oil (OEO), a natural plant extracts, is an effective and acceptable method to improve growth, beef quantity and quality, but the undergoing mechanism in rumen has not yet been reported in Holstein steers. This study investigated the effects of oregano essential oil (OEO) on growth performance, fermentation parameters, digestive enzymes activity, rumen development and microbiota in Holstein steers. Eighteen steers were randomly divided into two groups (n = 9) and fed either a basal diet (CCK) or the same diet supplemented with 20 g/(d·head) OEO (CEO) for 270 days.<br><br>RESULTS: OEO increased the rumen contents of volatile fatty acids (VFA, acetate (P&#x2009;=&#x2009;0.011), propionate (P&#x2009;=&#x2009;0.008), butyrate (P&#x2009;=&#x2009;0.018)) and digestive enzymes activity (cellulase (P&#x2009;=&#x2009;0.018), protease and &#x3b2;-glucosidase (P&#x2009;<&#x2009;0.001)), and improved rumen development (papillae width (P&#x2009;=&#x2009;0.008) and micropapillary density (P&#x2009;=&#x2009;0.001)), which reasons contribute to increase body weight (BW, P&#x2009;=&#x2009;0.022), average daily gain (ADG, P&#x2009;=&#x2009;0.021), carcass weight (P&#x2009;=&#x2009;0.001), dressing percentage (P&#x2009;<&#x2009;0.001), and net meat production (P&#x2009;=&#x2009;0.001) of steers. Meanwhile, metagenomic and metabolomic analysis revealed OEO significantly reduced abundance of rumen microorganisms, especially methanogenic archaea and viruses while beneficial bacteria (Bifidobacterium) and virulence factors were not affected. KEGG analysis revealed that OEO significantly reduces the host risk of disease, improves the digestive system, and reduces the energy basic metabolism level. A correlation analysis indicated fourteen kinds key microbiome and six downregulated metabolites interfere with each other and together influence the growth performance of steers.<br><br>CONCLUSION: These results suggest that feed with 20&#xa0;g/(d&#xb7;head) OEO in steers diets could improve growth performance, and reduces virus abundance and disease risk. And the findings provide fundamental insights into OEO, as an alternative source of natural bioactive compounds, how effect on rumen development, composition and function of microorganisms.}, }
@article {pmid40329386, year = {2025}, author = {Hou, L and Zhao, Z and Steger-Mähnert, B and Jiao, N and Herndl, GJ and Zhang, Y}, title = {Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {114}, pmid = {40329386}, issn = {2049-2618}, support = {42206098//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 42125603//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; MELRS2327//State Key Laboratory of Marine Environmental Science/ ; I4978-B//Austrian Science Fund/ ; }, mesh = {*Snow/microbiology ; Gammaproteobacteria/metabolism/genetics/classification ; Metagenomics/methods ; Metagenome ; *Seawater/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Phytoplankton/microbiology/metabolism ; Multiomics ; }, abstract = {BACKGROUND: Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.<br><br>RESULTS: Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).<br><br>CONCLUSIONS: Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.}, }
@article {pmid40329334, year = {2025}, author = {Lu, D and Kalantar, KL and Glascock, AL and Chu, VT and Guerrero, ES and Bernick, N and Butcher, X and Ewing, K and Fahsbender, E and Holmes, O and Hoops, E and Jones, AE and Lim, R and McCanny, S and Reynoso, L and Rosario, K and Tang, J and Valenzuela, O and Mourani, PM and Pickering, AJ and Raphenya, AR and Alcock, BP and McArthur, AG and Langelier, CR}, title = {Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID platform.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {46}, pmid = {40329334}, issn = {1756-994X}, support = {5R01HL155418//NIH/NHLBI/ ; 5R01HL155418//NIH/NHLBI/ ; 5R01HL155418//NIH/NHLBI/ ; PJT-156214/CAPMC/CIHR/Canada ; PJT-156214/CAPMC/CIHR/Canada ; PJT-156214/CAPMC/CIHR/Canada ; David Braley Chair in Computational Biology//McMaster University/ ; }, mesh = {Humans ; *Cloud Computing ; *Drug Resistance, Bacterial/genetics ; Software ; Whole Genome Sequencing ; *Bacteria/genetics/drug effects ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next-generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences.<br><br>RESULTS: To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and single-isolate whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes from Illumina data. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and single-isolate WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections.<br><br>CONCLUSIONS: In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and single-isolate WGS data. Its development represents an important step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.}, }
@article {pmid40329323, year = {2025}, author = {Duarte, B and Feijão, E and Cruz-Silva, A and Pascoal, P and Nunes, M and Pereira, M and Figueiredo, A and Dias, RP and Tanner, SE and Fonseca, VF}, title = {Reveal your microbes, and i'll reveal your origins: geographical traceability via Scomber colias intestinal tract metagenomics.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {43}, pmid = {40329323}, issn = {2524-4671}, support = {http://doi.org/10.54499/UIDB/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.11260.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UI/BD/153050/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, abstract = {The commercial demand for small pelagic fish, such as Atlantic chub mackerel (Scomber colias), renders them susceptible to provenance fraud. Scomber colias specimens intestinal tract bacteriome from five distinct fishing areas along the Portuguese Atlantic coastline were analyzed by 4th-generation sequencing. Bacteria diversity indices and differential abundance revealed dissimilarities in operational taxonomic unit (OTU) abundance among specimens from distinct fishing sites. Random forest-based model yielded an 85% accuracy rate in attributing sample provenance based on intestinal tract bacteriome OTU relative abundance. Further refinement of microbial features using Indicator Species Analysis, Linear Discriminant Analysis Effect Size (LEfSe) and OTU Gini scores enabled the identification of 3-5 bacterial OTU location biomarkers per fishing site. The intestinal tract bacteriome revealed sequences linked to pathogenic bacteria, particularly in specimens from Center-North and Center-South fishing areas. While this doesn't imply active pathogens, it highlights potential public health concerns and complements efforts to improve seafood microbiological quality and traceability.}, }
@article {pmid40328980, year = {2025}, author = {Liébana-García, R and López-Almela, I and Olivares, M and Romaní-Pérez, M and Manghi, P and Torres-Mayo, A and Tolosa-Enguís, V and Flor-Duro, A and Bullich-Vilarrubias, C and Rubio, T and Rossini, V and Segata, N and Sanz, Y}, title = {Gut commensal Phascolarctobacterium faecium retunes innate immunity to mitigate obesity and metabolic disease in mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40328980}, issn = {2058-5276}, abstract = {The gut microbiota may protect against obesity and chronic metabolic conditions by regulating the immune response to dietary triggers. Yet the specific bacteria that control the overactivation of the immune system in obesity and their mode of action remain largely unknown. Here we surveyed 7,569 human metagenomes and observed an association between the gut symbiont Phascolarctobacterium faecium and non-obese adults regardless of nationality, sex or age. In a mouse model of diet-induced obesity, we confirmed the specificity of P. faecium DSM 32890 anti-obesogenic properties compared with other species of the same genus. P. faecium reversed the inflammatory phenotype associated with obesity. Specifically, P. faecium promoted polarization of alternatively activated macrophages (M2), which reversed the obesity-induced increase in gut-resident type 1 innate lymphoid cells. This resulted in mitigation of glucose intolerance, adiposity and body weight gain irrespective of treatment with live or pasteurized bacteria. The metabolic benefits were independent of the adaptive immune system, but they were abolished by an inhibitor of M2 polarization in mice. P. faecium directly promoted M2-macrophage polarization through TLR2 signalling and these effects seemed to be independent of gut microbiota changes. Overall, we identify a previously undescribed gut commensal bacterium that could help mitigate obesity and metabolic comorbidities by retuning the innate immune response to hypercaloric diets.}, }
@article {pmid40328944, year = {2025}, author = {Kim, Y and Worby, CJ and Acharya, S and van Dijk, LR and Alfonsetti, D and Gromko, Z and Azimzadeh, PN and Dodson, KW and Gerber, GK and Hultgren, SJ and Earl, AM and Berger, B and Gibson, TE}, title = {Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.}, journal = {Nature microbiology}, volume = {10}, number = {5}, pages = {1184-1197}, pmid = {40328944}, issn = {2058-5276}, support = {R35GM143056//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R21AI154075//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R35GM149270//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01DK121822//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U19AI110818//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R35GM141861//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Microbiota/genetics ; Feces/microbiology ; Female ; *Metagenomics/methods ; Bayes Theorem ; Longitudinal Studies ; Escherichia coli/genetics/isolation &amp; purification/classification ; Infant ; Algorithms ; Enterococcus faecalis/genetics/isolation &amp; purification/classification ; Adult ; *Bacteria/genetics/classification/isolation &amp; purification ; }, abstract = {The ability to detect and quantify microbiota over time from shotgun metagenomic data has a plethora of clinical, basic science and public health applications. Given these applications, and the observation that pathogens and other taxa of interest can reside at low relative abundance, there is a critical need for algorithms that accurately profile low-abundance microbial taxa with strain-level resolution. Here we present ChronoStrain: a sequence quality- and time-aware Bayesian model for profiling strains in longitudinal samples. ChronoStrain explicitly models the presence or absence of each strain and produces a probability distribution over abundance trajectories for each strain. Using synthetic and semi-synthetic data, we demonstrate how ChronoStrain outperforms existing methods in abundance estimation and presence/absence prediction. Applying ChronoStrain to two human microbiome datasets demonstrated its improved interpretability for profiling Escherichia coli strain blooms in longitudinal faecal samples from adult women with recurring urinary tract infections, and its improved accuracy for detecting Enterococcus faecalis strains in infant faecal samples. Compared with state-of-the-art methods, ChronoStrain's ability to detect low-abundance taxa is particularly stark.}, }
@article {pmid40328731, year = {2025}, author = {Wei, C and Xu, X and Zhang, J and Wang, X and Han, T and Zhang, Y and Pan, S and Ming, Z and Li, R and Lou, F and Cheng, Y and Xu, H and Sun, X and Geng, G and Pan, Y and Liu, Q and Qi, H and Yan, X and Dang, K and Zhou, J and Sun, C and Li, Y}, title = {Timing of unsaturated fat intake improves insulin sensitivity via the gut microbiota-bile acid axis: a randomized controlled trial.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4211}, pmid = {40328731}, issn = {2041-1723}, support = {Key Program 82030100//National Natural Science Foundation of China (National Science Foundation of China)/ ; Joint Fund Project U24A20768//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {The timing of dietary total fat intake influences glucose homeostasis, however, the impact of unsaturated fat (USFA) intake has yet to be explored. This 12-week, double-blind, randomized, controlled, 2 × 2 factorial-designed feeding trial investigated the effects of timing (lunch or dinner) and types of dietary USFA (high monounsaturated fat or polyunsaturated fat diet) intake on glucose metabolism in seventy prediabetes participants (mean age, 57 years). Sixty participants with completed fecal samples were included in the final analysis (n = 15 for each group). Postprandial serum glucose was first primary outcome, postprandial insulin levels and insulin sensitivity indices were co-primary outcomes Secondary outcomes were continuous glucose levels, serum fatty acid profile, gut microbiome (metagenomic sequencing) and fecal metabolites. Results showed no significant differences in postprandial glucose between groups. However, USFA intake at lunch (vs. dinner) improved insulin sensitivity and reduced postprandial insulin and serum free saturated fatty acid (Ptiming < 0.05, Ptype > 0.05, Pinteraction > 0.05), which was associated with alterations in gut microbiome and bile acid metabolism, regardless of USFA type. In summary, these results suggest that advancing timing of USFA intake improves insulin sensitivity through the gut microbiome and bile acid metabolism. Trial registration: ChiCTR2100045645.}, }
@article {pmid40328237, year = {2025}, author = {Teitelbaum, J and Madan, S and Patel, S and Coyle, C and Chiu, CY and Thwe, PM and Uehara, M and Jermyn, R and Hemmige, V}, title = {Chagas Meningoencephalitis Diagnosed in Heart Transplant Patient Using Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.24-0553}, pmid = {40328237}, issn = {1476-1645}, abstract = {Chagas meningoencephalitis can present in immunocompromised patients after organ transplantation. We present the first reported instance in which metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid diagnosed Chagas meningoencephalitis in a patient. The diagnosis of Chagas in this case underscores the role of mNGS in identifying rare or unexpected pathogens.}, }
@article {pmid40328153, year = {2025}, author = {Chu, Y and Dong, X and Fang, S and Gan, L and Lee, X and Zhou, L}, title = {Viruses in human-impacted estuarine ecotones: Distribution, metabolic potential, and environmental risks.}, journal = {Water research}, volume = {282}, number = {}, pages = {123750}, doi = {10.1016/j.watres.2025.123750}, pmid = {40328153}, issn = {1879-2448}, abstract = {Estuaries, as dynamic ecological interfaces between marine and terrestrial systems, are characterized by high productivity and intricate microbial communities. Viruses exert critical regulatory effects on microbial processes, influencing ecological functions and contributing to environmental dynamics in estuarine ecosystems. Despite their significance, the diversity and ecological roles of estuarine viruses remain insufficiently understood. This study explored the viral biogeographic patterns, metabolic potential, and influencing factors in 30 subtropical estuaries in China. Few estuarine viruses (< 22 %) exhibited homology with known viruses, and the low overlap of virus clusters with other environments highlights their novelty and habitat specificity. Mantel tests and random forest analysis identified salinity, temperature, nutrients, and pollutants as key factors influencing viral composition and functional profiles. In addition, correlation analysis between virus and host confirmed significant virus-host interactions, while functional analyses highlighted the role of environmental conditions and horizontal gene transfer in shaping auxiliary metabolic genes linked to elemental biogeochemical cycles, particularly phosphorus, sulfur, and nitrogen. The detection of antibiotic resistance genes (ARGs) and virulence factors (VFs) within viral genomes underscores the role of viruses as reservoirs of ARGs and VFs in these ecosystems. These results demonstrate the profound influence of abiotic and host factors on viral community structures in subtropical estuarine ecotones and underscore the ecological significance of metabolic genes in biogeochemical cycling. By clarifying these interactions, this study advances the understanding of viral contributions to ecosystem functioning and biogeochemical dynamics in estuarine environments.}, }
@article {pmid40328090, year = {2025}, author = {Xia, Y and Lan, Y and Xu, Y and Liu, F and Chen, X and Luo, J and Xu, H and Liu, Y}, title = {Effects of microplastics and tetracycline induced intestinal damage, intestinal microbiota dysbiosis, and antibiotic resistome: metagenomic analysis in young mice.}, journal = {Environment international}, volume = {199}, number = {}, pages = {109512}, doi = {10.1016/j.envint.2025.109512}, pmid = {40328090}, issn = {1873-6750}, abstract = {Microplastics (MPs) and antibiotic tetracycline (TC) are widespread in the environment and constitute emerging combined contaminants. Young individuals are particularly vulnerable to agents that disrupt intestinal health and development. However, the combined effects of MPs and TC remain poorly understood. In this study, we developed a young mouse model exposed to polystyrene MPs, either alone or in combination with TC for 8 weeks to simulate real-life dietary exposure during early life. Our findings revealed that concurrent exposure to MPs and TC caused the most severe intestinal barrier dysfunction driven by inflammatory activation and oxidative imbalance. Moreover, exposure to MPs and TC reduced the abundance of potential probiotics while promoting the growth of opportunistic pathogens. Metagenomic analysis further indicated that co-exposure to MPs and TC enhanced the abundance of bacteria carrying either antibiotic resistance genes (ARGs) or virulence factor genes (VFGs), contributing to the widespread dissemination of potentially harmful genes. Finally, a strong positive correlation was observed between microbiota dysbiosis, ARGs, and VFGs. In general, this study highlighted the hazards of MPs and antibiotics to intestinal health in young mice, which provided a new perspective into the dynamics of pathogens, ARGs, and VFGs in early-life intestinal environments.}, }
@article {pmid40328065, year = {2025}, author = {Ye, Y and Yan, X and Jiang, Y and Wang, S and Liu, D and Ren, Y and Li, D and Ngo, HH and Guo, W and Cheng, D and Jiang, W}, title = {Optimized feeding schemes of heterotrophic anodic denitrification coupled with cathodic phosphate recovery from wastewater using a microbial fuel cell.}, journal = {The Science of the total environment}, volume = {981}, number = {}, pages = {179590}, doi = {10.1016/j.scitotenv.2025.179590}, pmid = {40328065}, issn = {1879-1026}, abstract = {Enhanced water quality standards and increasing resource scarcity have prompted extensive research into low-cost nitrogen removal and phosphate recovery from wastewater. Microbial fuel cells (MFCs) offer a viable solution by simultaneously removing nitrogen, recovering phosphorus, and generating electrical energy. This study employed MFCs to achieve simultaneous nitrogen removal and phosphorus recovery, investigating the impact of different feeding schemes. The experimental results indicated that replacing the entire anode chamber solution and recycling the anode effluent to the cathode chamber effectively prevented the accumulation of nitrifying bacteria while achieving the highest pollutant removal performance. Under closed circuit conditions, the system consistently maintained low nitrite concentrations, achieving an average nitrate removal efficiency of 68.09 ± 1.86 % and phosphate recovery efficiency of 83.46 ± 5.30 %. Furthermore, this feeding scheme facilitated microbial growth and reproduction while also improving operational convenience. The study utilized metagenomics and other technologies to comprehensively analyze the system's operation mechanism and reasons for its excellent performance.}, }
@article {pmid40327993, year = {2025}, author = {Grafakou, ME and Pferschy-Wenzig, EM and Aziz-Kalbhenn, H and Kelber, O and Moissl-Eichinger, C and Bauer, R}, title = {Bidirectional interactions between St. John´s wort and gut microbiome: Potential implications on gut-brain-axis.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {187}, number = {}, pages = {118111}, doi = {10.1016/j.biopha.2025.118111}, pmid = {40327993}, issn = {1950-6007}, abstract = {Emerging evidence highlights the role of gut microbiome in mental health disorders, including depression, raising the question whether the action of antidepressants could be mediated, at least in part, via the microbiome-gut-brain axis. To explore this, we subjected a St. John's wort extract (STW 3-VI), clinically proven to be effective in mild to moderate depression, to a model of the upper and lower intestinal tract, including static in vitro predigestion followed by ex vivo incubation with human microbiota samples. To cover the interindividual diversity of gut microbiome composition, fecal samples from ten healthy volunteers were used. Although unchanged levels of most annotated compounds were observed during simulated upper intestinal tract digestion, incubation with fecal microbiota led to a significant change of the chemical profile of the extract. While hyperforins remained stable, flavonoids and hypericins were rapidly biotransformed, suggesting that they may act as prodrugs. Several metabolites were formed, many of which are known to be involved in gut-brain communication. Differential abundance analysis revealed significant changes in microbiome composition, particularly for taxa known to be potentially associated with depression. Among others, the Firmicutes/Bacteroidetes ratio, known to be lowered in depressive patients, was increased. Functional profiling revealed modulation of pathways involved in gut-brain communication, such as tyrosine and tryptophan metabolism. These bidirectional interactions suggest for the first time the gut microbiome as a potential mediator of the pharmacological effects of St. John's wort extracts via the microbiome-gut-brain axis.}, }
@article {pmid40327934, year = {2025}, author = {Yu, Y and Huang, W and Tang, S and Xiang, Y and Yuan, L and Yin, H and Dang, Z}, title = {Degradation mechanisms of isodecyl diphenyl phosphate (IDDP) and bis-(2-ethylhexyl)-phenyl phosphate (BEHPP) using a novel microbially-enriched culture.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138453}, doi = {10.1016/j.jhazmat.2025.138453}, pmid = {40327934}, issn = {1873-3336}, abstract = {Organophosphate esters (OPEs) pose significant environmental concerns due to their widespread presence, potential toxicity, and persistence. This study investigated the degradation of the isodecyl diphenyl phosphate (IDDP) and bis-(2-ethylhexyl)-phenyl phosphate (BEHPP) using a novel enrichment culture, which could degrade 85.4 % and 78.2 % of 1 mg/L IDDP and BEHPP after 192 h and 172 h, respectively, under extremely low bacterial dosage (the initial OD600 nm= 0.0075, biomass was approximately 1 mg/L). The identification of intermediate products suggested that the degradation reactions likely included hydrolysis, hydroxylation, methylation, carboxylation, and glycosylation. Metagenomic analysis highlighted the crucial role of enzymes in degrading IDDP and BEHPP, including phosphatase, phosphodiesterase, cytochrome P450, and hydroxylase. Pure strains Burkholderia cepacia ZY1, Sphingopyxis terrae ZY2, and Amycolatopsis ZY3 were isolated, and their efficient individual degradation abilities were confirmed. These efficiencies were lower compared to the enrichment culture, emphasizing the importance of microbial interactions for effective degradation. The pathways identified for these strains illustrated their involvement in different degradation steps, reinforcing the synergy between different degraders. Molecular dynamics simulations provided insights into the interactions between alkaline phosphatase (ALP), cytochrome P450 (CYP450), and hydroxylase with OPEs. These enzymes demonstrated a strong binding capacity with both BEHPP and IDDP, exhibiting distinct binding site preferences that may contribute to varied metabolic pathways. These findings comprehensively reveal the transformation mechanisms of OPEs.}, }
@article {pmid40327666, year = {2025}, author = {Yang, X and Zhang, Y and Xu, Y and Xu, Y and Zhang, M and Guan, Q and Hu, W and Tun, HM and Xia, Y}, title = {Microbial Disturbances Caused by Pesticide Exposure and Their Predictive Implications for Gestational Diabetes Mellitus.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c01076}, pmid = {40327666}, issn = {1520-5851}, abstract = {Previous studies have suggested that pesticide exposure and gut microbiome alterations are associated with gestational diabetes mellitus (GDM) risk. Understanding the complex interactive effect of these factors on GDM is essential. In a cohort of 852 pregnant women, we assessed pesticide levels in serum and analyzed the gut microbiota using 16S rRNA and shotgun metagenomic sequencing. We explored the interactions between pesticides and gut microbiota, assessed their roles in GDM development, and proposed a predictive model based on identified biomarkers. We identified an environmental risk score (ERS), denoting the pesticide mixture level significantly associated with GDM, with the gut microbiota, particularly involving the Dorea branch, playing a crucial mediating role. In addition, we found an interactive effect of pesticide exposure and gut microbiota on GDM risk. Notably, low Prevotella enrichment combined with high ERS arisen from pesticide levels led to a 10.36-fold increased GDM risk. The identified pesticide and gut microbial biomarkers achieved high predictive accuracy for GDM (AUC: 0.833, 95% CI: 0.748-0.918). Collectively, maternal pesticide exposure may induce disrupted microbiome-dependent glycemic alteration, necessitating future assessment of clinical implications. Potential GDM markers can serve as targets for therapeutic intervention caused by pesticides, leading to prevention.}, }
@article {pmid40327160, year = {2025}, author = {Li, N and Gao, G and Zhang, T and Zhao, C and Zhao, Y and Zhang, Y and Sun, Z}, title = {Co-variation of Host Gene Expression and Gut Microbiome in Intestine-Specific Spp1 Conditional Knockout Mice.}, journal = {Current microbiology}, volume = {82}, number = {6}, pages = {282}, pmid = {40327160}, issn = {1432-0991}, support = {32325040//National Natural Science Foundation of China/ ; 2022BINCMCF007//Nutrition and Care of Maternal &amp; Child Research Fund Project" of Biostime Institute of Nutrition &amp; Care/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Osteopontin/genetics/metabolism ; Mice, Knockout ; Lipid Metabolism/genetics ; *Intestines/microbiology ; Mice, Inbred C57BL ; Transcriptome ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Osteopontin, which is a highly phosphorylated and glycosylated acidic secreted protein encoded by the secreted phosphoprotein 1 (Spp1) gene, plays a crucial role in immune regulation, inflammatory responses, and cell adhesion. However, its impact on intestinal gene expression and gut microbiota remains underexplored. In this study, we developed an Spp1 conditional knockout mouse model to investigate alterations in the intestinal transcriptome and microbiome, with particular emphasis on changes in gene expression and predicted metabolic pathways. Our findings demonstrated that Spp1 gene conditional knockout significantly modified the expression of genes involved in immune regulation and lipid metabolism. Moreover, metagenomic analysis revealed marked shifts in gut microbial diversity and predicted the metabolic pathways associated with digestion, absorption, and lipid metabolism. These results suggest that Spp1 is instrumental in maintaining gut microbial equilibrium and in regulating host lipid metabolism and immune responses. This study offers new insights into the role of Spp1 in host-microbiota interactions and the potential foundations for developing related therapeutic strategies.}, }
@article {pmid40327041, year = {2025}, author = {Hao, Q and Wang, O and Gong, X and Liu, F and Zhang, Y and Xie, Z and Tang, J and Sang, Y and Li, F and Liu, F}, title = {Cadmium-Induced Responses and Tolerance Mechanisms of Aerobic Methanotrophs in Rice Paddy Soils.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c00031}, pmid = {40327041}, issn = {1520-5851}, abstract = {Paddy fields are major sources of atmospheric methane and are at risk of cadmium (Cd) contamination. Aerobic methanotrophs, which serve as biological methane sinks, play a key role in methane cycling, but their responses to Cd stress remain poorly understood. Here, we examined the relationship between Cd pollution levels and aerobic methane oxidation potential in paddy soils. We evaluated methanotrophic enrichments under Cd exposure, applied metagenomic sequencing to identify functional microbes, and investigated Cd tolerance mechanisms in pure culture. Aerobic methane oxidation rates were positively correlated with Cd levels in paddy soils from South China, with Methylocystis and Methylomonas emerging as dominant genera possessing diverse Cd tolerance genes. Notably, interspecific differences in Cd tolerance were observed among methanotrophic strains. The faster-growing Methylomonas sp., endowed with more robust antioxidant defenses and extracellular polymeric substances synthesis genes, exhibited Cd resistance through markedly enhanced loosely bound extracellular polymeric substances production, in contrast to the Cd-sensitive Methylobacter sp. Gene knockout experiments confirmed the essential roles of glutathione synthase, glutathione peroxidase, and exosortase in exopolysaccharide extrusion for Cd detoxification. These findings advance our understanding of the methane cycle in Cd-contaminated rice paddies and suggest potential strategies to mitigate methane emissions while addressing Cd detoxification.}, }
@article {pmid40326928, year = {2025}, author = {Wang, R and Deng, P and Hu, X and Shen, C and Dong, X and Hu, K and Li, R}, title = {Optimizing Watershed Land Use to Achieve the Benefits of Lake Carbon Sinks while Maintaining Water Quality.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c00190}, pmid = {40326928}, issn = {1520-5851}, abstract = {Greenhouse gas emissions and water quality decline are two major issues currently affecting lakes worldwide. Determining how to control both greenhouse gas emissions and water quality decline is a long-term challenge. We compiled data on the annual average carbon dioxide (CO2) flux and water quality parameters for 422 global lakes, revealing that 82.42% of the lakes act as carbon sources and that 66.56% have experienced water quality deterioration. Carbon sources and eutrophication trends were observed for lakes from the 1990s to 2020s, with further deterioration expected over the next 80 years. Unmanaged land use change in lake watersheds could exacerbate the CO2 flux into lakes and water quality degradation. In this study, a watershed land use planning (WLUP) framework was established, and a 24.83% reduction in the CO2 flux into lake water, a 5.07% reduction in chlorophyll a (Chl-a), a 4.70% reduction in total phosphorus, and a 12.92% increase in Secchi depth were achieved. The WLUP framework identifies Asia and Europe as the regions experiencing the greatest demands for land use transformation, where optimization leads to the most significant improvements. Metagenomic analysis revealed that forests enhance carbon fixation and that grasslands reduce carbon degradation and phosphorus metabolism in lake watersheds, explaining and supporting the possibility of WLUP. This work provides a win-win solution for improving CO2 fluxes and water quality in global lakes to mitigate the effects of climate change and promote lake protection.}, }
@article {pmid40326765, year = {2025}, author = {Lindner, BG and Graham, KE and Phaneuf, JR and Hatt, JK and Konstantinidis, KT}, title = {SourceApp: A Novel Metagenomic Source Tracking Tool that can Distinguish between Fecal Microbiomes Using Genome-To-Source Associations Benchmarked Against Mixed Input Spike-In Mesocosms.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c03603}, pmid = {40326765}, issn = {1520-5851}, abstract = {Methodologies utilizing metagenomics are attractive to fecal source tracking (FST) aims for assessing the presence and proportions of various fecal inputs simultaneously. Yet, compared to established culture- or PCR-based techniques, metagenomic approaches for these purposes are rarely benchmarked or contextualized for practice. We performed shotgun sequencing experiments (n = 35) of mesocosms constructed from the water of a well-studied recreational and drinking water reservoir spiked with various fecal (n = 6 animal sources, 3 wastewater sources, and 1 septage source) and synthetic microbiome spike-ins (n = 1) introduced at predetermined cell concentrations to simulate fecal pollution events of known composition. We built source-associated genome databases using publicly available reference genomes and metagenome assembled genomes (MAGs) recovered from short- and long-read sequencing of the fecal spike-ins, and then created an associated bioinformatic tool, called SourceApp, for inferring source attribution and apportionment by mapping the metagenomic data to these genome databases. SourceApp's performance varied substantially by source, with cows being underestimated due to under sampling of cow fecal microbiomes. Parameter tuning revealed sensitivity and specificity near 0.90 overall, which exceeded all alternative tools. SourceApp can assist researchers with analyzing and interpreting shotgun sequencing data and developing standard operating procedures on the frontiers of metagenomic FST.}, }
@article {pmid40326511, year = {2025}, author = {Zhu, Y and Liu, Q and Alffenaar, JW and Wang, S and Cao, J and Dong, S and Zhou, X and Li, X and Li, X and Xiong, H and Zhu, L and Hu, Y and Wang, W}, title = {Gut Microbiota in Patients with Tuberculosis Associated with Different Drug Exposures of Antituberculosis Drugs.}, journal = {Clinical pharmacology and therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1002/cpt.3687}, pmid = {40326511}, issn = {1532-6535}, support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-03//Shanghai New Three-year Action Plan for Public Health/ ; 82073612//National Natural Science Foundation of China/ ; }, abstract = {Interindividual variability in drug exposure can significantly influence treatment outcomes and may lead to drug concentration-related side effects during tuberculosis (TB) treatment. Although the gut microbiota is known to affect drug metabolism, its impact on anti-TB drugs has not been thoroughly explored. This study sought to elucidate the relationship between pre-treatment gut microbiota and drug exposure levels among patients with pulmonary TB. Two cohorts were analyzed: a discovery cohort (N = 99) and a validation cohort (N = 32), both comprising patients undergoing anti-TB therapy with rifampicin, isoniazid, pyrazinamide, and ethambutol. The gut microbiota patterns of participants from the discovery cohort and the validation cohort were profiled by 16S rRNA gene sequencing and metagenomics, respectively. Analyses of both cohorts robustly established a positive association between pre-treatment microbial diversity and drug exposure, as well as significant differences in gut microbiota composition across various drug exposure groups. At the species level, Faecalibacterium prausnitzii was positively associated with drug exposure to rifampicin. Moreover, functional analysis revealed that starch and sucrose metabolism and secondary bile acid biosynthesis were more abundant in the high drug exposure group. To identify biomarkers capable of stratifying patients based on their drug exposure levels, 11 taxa, represented by Faecalibacterium, were selected in the discovery cohort (AUC = 0.992) and were confirmed in the validation cohort with high predictive accuracy (AUC = 0.894). This study demonstrated a correlation between microbial dysbiosis and reduced exposure to anti-TB medications. Optimizing treatment by regulating gut microbiota to improve drug exposure levels requires further validation through larger scale multicenter clinical trials.}, }
@article {pmid40326136, year = {2025}, author = {Wu, B and Wang, J and Zhang, LN and Tang, W and Chen, KL}, title = {[Value of Pathogenic Detection by Next-Generation Sequencing in Bronchoalveolar Lavage Fluid on Children with Hematological Malignancies].}, journal = {Zhongguo shi yan xue ye xue za zhi}, volume = {33}, number = {2}, pages = {569-574}, doi = {10.19746/j.cnki.issn.1009-2137.2025.02.039}, pmid = {40326136}, issn = {1009-2137}, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Hematologic Neoplasms/microbiology/complications ; Child ; Child, Preschool ; Infant ; Retrospective Studies ; Male ; Female ; Adolescent ; *High-Throughput Nucleotide Sequencing ; *Pneumonia/diagnosis/microbiology ; }, abstract = {OBJECTIVE: To investigate the application value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in etiological diagnosis of children with hematological malignancies complicated with pneumonia.<br><br>METHODS: We retrospectively analyzed the clinical data of children with hematological malignancies who underwent BALF mNGS pathogenic detection due to pneumonia. All patients underwent mNGS detection of bronchoalveolar lavage fluid as well as traditional methods(including sputum culture, bronchoalveolar lavage fluid culture, blood culture, serological detection of pathogens, etc.). By analyzing the results of mNGS and traditional methods, we compared key indicators such as the positive rate, etiological distribution.<br><br>RESULTS: A total of 26 children with hematological malignancies enrolled in the study, including 12 males and 14 females, with a median age of 4.9 (1.8-14.9) years, underwent bronchoalveolar lavage (BAL) 35 times. A total of 17 pathogenic microorganisms were detected in BALF mNGS, including 9 cases of bacterial infection, 10 cases of viral infection, 3 cases of fungal infection, 2 cases of mycoplasma infection and 8 cases of mixed infection, and the most commonly detected bacteria, viruses and fungi were streptococcus pneumoniae, cytomegalovirus and pneumocystis jirovecii, respectively. The positive rate of mNGS detection (91.43%) was significantly higher than that of traditional methods detection (20%, P <0.001). A total of 25 cases were adjusted according to BALF mNGS results.<br><br>CONCLUSION: The application of BALF mNGS technology can improve the detection rate of the pathogens in children with hematological malignancies complicated with pneumonia, initially revealed the pathogen spectrum of pulmonary infection in this group, and effectively guide clinical medication, improve treatment outcomes.}, }
@article {pmid40325896, year = {2025}, author = {Ikegwuoha, NPP and Hanekom, T and Booysen, E and Jason, C and Parker-Nance, S and Davies-Coleman, MT and van Zyl, LJ and Trindade, M}, title = {Fimsbactin Siderophores From a South African Marine Sponge Symbiont, Marinomonas sp. PE14-40.}, journal = {Microbial biotechnology}, volume = {18}, number = {5}, pages = {e70155}, doi = {10.1111/1751-7915.70155}, pmid = {40325896}, issn = {1751-7915}, support = {//South African Medical Research Council (Self-Initiated grant)/ ; 87326//DSI/NRF SARChI research chair in Microbial Genomics/ ; 312184//European Union PharmaSea Consortium/ ; 129660//National Research Foundation/ ; }, mesh = {*Siderophores/chemistry/metabolism/genetics/isolation &amp; purification ; Multigene Family ; Animals ; Biosynthetic Pathways/genetics ; *Porifera/microbiology ; Symbiosis ; Hydroxamic Acids/metabolism/chemistry ; }, abstract = {Low iron levels in marine habitats necessitate the production of structurally diverse siderophores by many marine bacterial species for iron acquisition. Siderophores exhibit bioactivities ranging from chelation for iron reduction in hemochromatosis sufferers to antimicrobial activity either in their own right or when coupled to known antibiotics for targeted delivery or for molecular imaging. Thus, marine environments are a sought-after resource for novel siderophores that could have pharmaceutical or industrial application. The fimsbactins A-F (1-6) are mixed catechol-hydroxamate siderophores that have only been reported to be produced by Acinetobacter species with the fimsbactin biosynthetic gene clusters (BGCs) widespread among species within this genus. Here, we identified a putative fimsbactin BGC from an uncharacterized marine isolate, Marinomonas sp. PE14-40. Not only was the gene synteny not conserved when comparing the pathway from Marinomonas sp. PE14-40 to the fimsbactin BGC from Acinetobacter sp., but five of the core biosynthetic genes found in the canonical fimsbactin BGC are located elsewhere on the genome and do not form part of the core cluster in Marinomonas sp. PE14-40, with four of these, fbsBCDL, colocalized. Through ESI-MS/MS analysis of extracts from Marinomonas sp. PE14-40, the known fimsbactin analogues 1 and 6 were identified, as well as two new fimsbactin analogues, 7 and 8, containing a previously unreported L-lysine-derived hydroxamate moiety, N1-acetyl-N1-hydroxycadaverine. Feeding experiments using stable isotope-label L-lysine provided further evidence of the N1-acetyl-N1-hydroxycadaverine moiety in 7 and 8. The study demonstrates functional conservation in seemingly disparate biosynthetic pathways and enzyme promiscuity's role in producing structurally diverse compounds.}, }
@article {pmid40325616, year = {2025}, author = {Xu, HY and Jiang, MT and Yang, YF and Huang, Y and Yang, WD and Li, HY and Wang, X}, title = {Microalgae-Based Fucoxanthin Attenuates Rheumatoid Arthritis by Targeting the JAK-STAT Signaling Pathway and Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c12474}, pmid = {40325616}, issn = {1520-5118}, abstract = {Fucoxanthin, an abundant carotenoid in marine algae, has garnered attention for its diverse health benefits, including anti-inflammatory and anticancer properties. Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by joint inflammation and damage. This study investigated the therapeutic potential of fucoxanthin extracted from Phaeodactylum tricornutum in collagen-induced RA. Our results demonstrated that fucoxanthin significantly alleviated RA symptoms, including weight loss, joint swelling, and decreased appetite. Histological analysis revealed that fucoxanthin mitigated synovial inflammation, cartilage damage, and bone erosion. Mechanistically, transcriptomic analysis and cell experiments indicated that fucoxanthin suppressed the JAK-STAT signaling pathway by downregulating the expression of inflammatory cytokines, such as IL-6 and IL-1β. Furthermore, metagenomic analysis suggested that fucoxanthin restored the altered gut microbiota composition associated with RA. These findings highlight the therapeutic potential of fucoxanthin from P. tricornutum in the management of RA by targeting multiple pathways, including inflammation and gut microbiota.}, }
@article {pmid40325428, year = {2025}, author = {Liu, H and Zhu, Y and Huang, Y and Jiang, H}, title = {The application of metagenomic next generation sequencing in diagnosing tuberculous otitis media: a case report and review of the literature.}, journal = {Journal of medical case reports}, volume = {19}, number = {1}, pages = {207}, pmid = {40325428}, issn = {1752-1947}, support = {LQ24H130002//Natural Science Foundation of Zhejiang Province/ ; 2024C03238//Key Research and Development Program of Zhejiang Province/ ; }, mesh = {Humans ; Female ; Middle Aged ; *Otitis Media/diagnosis/microbiology/drug therapy ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Tuberculosis/diagnosis/drug therapy/microbiology ; Antitubercular Agents/therapeutic use ; Tomography, X-Ray Computed ; Mastoidectomy ; }, abstract = {BACKGROUND: Tuberculous otitis media is a chronic Mycobacterium tuberculosis infection of the middle ear tissues. Diseases with varied and insidious clinical features can make diagnosis difficult and delay treatment.<br><br>CASE PRESENTATION: Here, we document a case of tuberculous otitis media in a 46-year-old ethnic Han woman that manifested as nonspecific chronic otitis media. A mastoidectomy and tympanoplasty were performed for the initial diagnosis of cholesteatoma. The histopathology of the tissue specimen revealed granuloma formation with necrosis. Staining for acid-fast bacilli and the polymerase chain reaction method for Mycobacterium tuberculosis yielded negative results. However, the chest computed tomography scan demonstrated a pulmonary miliary nodule. Next, metagenomic next-generation sequencing was applied and the Mycobacterium tuberculosis was identified. The patient recovered after receiving antituberculous treatment.<br><br>CONCLUSION: This report highlights the application of novel diagnostic tools such as metagenomic next-generation sequencing as a supplementary method for the diagnosis of tuberculous otitis media in highly suspected patients.}, }
@article {pmid40325409, year = {2025}, author = {Herbert, J and Thompson, S and Beckett, AH and Robson, SC}, title = {Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {47}, pmid = {40325409}, issn = {2524-6372}, support = {Expanding Excellence in England (E3)//Research England/ ; Expanding Excellence in England (E3)//Research England/ ; Expanding Excellence in England (E3)//Research England/ ; }, abstract = {INTRODUCTION: Metagenomics, the genomic analysis of all species present within a mixed population, is an important tool used for the exploration of microbiomes in clinical and environmental microbiology. Whilst the development of next-generation sequencing, and more recently third generation long-read approaches such as nanopore sequencing, have greatly advanced the study of metagenomics, recovery of unbiased material from microbial populations remains challenging. One promising advancement in genomic sequencing from Oxford Nanopore Technologies (ONT) is adaptive sampling, which enables real-time enrichment or depletion of target sequences. As sequencing technologies continue to develop, and advances such as adaptive sampling become common techniques within the microbiological toolkit, it is essential to evaluate the benefits of such advancements to metagenomic studies, and the impact of methodological choices on research outcomes.<br><br>AIM AND METHODS: Given the rapid development of sequencing tools and chemistry, this study aimed to demonstrate the impacts of choice of DNA extraction kit and sequencing chemistry on downstream metagenomic analyses. We first explored the quality and accuracy of 16S rRNA amplicon sequencing for DNA extracted from the ZymoBIOMICS Microbial Community Standard, using a range of commercially available DNA extraction kits to understand the effects of different kit biases on assessment of microbiome composition. We next compared the quality and accuracy of metagenomic analyses for two nanopore-based ligation chemistry kits with differing levels of base-calling error; the older and more error-prone (~&#x2009;97% accuracy) LSK109 chemistry, and newer more accurate (~&#x2009;99% accuracy) LSK112 Q20&#x2009;+&#x2009;chemistry. Finally, we assessed the impact of the nanopore sequencing chemistry version on the output of the novel adaptive sampling approach for real-time enrichment of the genome for the yeast Saccharomyces cerevisiae from the microbial community.<br><br>RESULTS: Firstly, DNA extraction kit methodology impacted the composition of the yield, with mechanical bead-beating methodologies providing the least biased picture due to efficient lysis of Gram-positive microbes present in the community standard, with differences in bead-beating methodologies also producing variation in composition. Secondly, whilst use of the Q20&#x2009;+&#x2009;nanopore sequencing kit chemistry improved the base-calling data quality, the resulting metagenomic assemblies were not significantly improved based on common metrics and assembly statistics. Most importantly, we demonstrated the effective application of adaptive sampling for enriching a low-abundance genome within a metagenomic sample. This resulted in a 5-7-fold increase in target enrichment compared to non-adaptive sequencing, despite a reduction in overall sequencing throughput due to strand-rejection processes. Interestingly, no significant differences in adaptive sampling enrichment efficiency were observed between the older and newer ONT sequencing chemistries, suggesting that adaptive sampling performs consistently across different library preparation kits.<br><br>CONCLUSION: Our findings underscore the importance of selecting a DNA extraction methodology that minimises bias to ensure an accurate representation of microbial diversity in metagenomic studies. Additionally, despite the improved base-calling accuracy provided by newer Q20&#x2009;+&#x2009;sequencing chemistry, we demonstrate that even older ONT sequencing chemistries can achieve reliable metagenomic sequencing results, enabling researchers to confidently use these approaches depending on their specific experimental needs. Critically, we highlight the significant potential of ONT's adaptive sampling technology for targeted enrichment of specific genomes within metagenomic samples. This approach offers broad applicability for enriching target organisms or genetic elements (e.g., pathogens or plasmids) or depleting unwanted DNA (e.g., host DNA) in diverse sample types from environmental and clinical studies. However, researchers should carefully weigh the benefits of adaptive sampling against the potential trade-offs in sequencing throughput, particularly for low-abundance targets, where strand rejection can lead to pore blocking. These results provide valuable guidance for optimising adaptive sampling in metagenomic workflows to achieve specific research objectives.}, }
@article {pmid40325330, year = {2025}, author = {Panicucci, C and Casalini, S and Fiorito, G and Rinaldi, AB and Biagioli, V and Cangelosi, D and Brolatti, N and Principi, E and Baratto, S and Pedemonte, M and Morando, S and Riva, A and Venturino, C and Striano, P and Uva, P and Bruno, C}, title = {Exploratory Analysis of Gut Microbiota Profile in Duchenne Muscular Dystrophy (DMD) Patients with Intellectual Disability.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {40325330}, issn = {1559-1182}, abstract = {This study investigates the differences in gut microbiota composition between DMD patients with (DMD +) and without (DMD -) intellectual disability (ID) and its potential role in cognitive outcomes. In this study, we assessed the gut microbiota in 50 genetically confirmed DMD patients (median age 13.1 years) using 16S rRNA gene sequencing. Cognitive assessment was performed using the Wechsler Intelligence Scales, with ID defined as an IQ < 70. Stool samples were analyzed, and statistical methods were used to assess alpha- and beta-diversity. Thirty-four percent of patients had ID. No significant differences were found in alpha-diversity or in the Firmicutes/Bacteroidetes ratio. However, beta-diversity analysis revealed significant differences between DMD + and DMD - groups, including, in DMD + , an increased abundance of Propionibacterium and Bifidobacterium, and a reduction in Bulleidia. These bacteria are involved in metabolic pathways that can influence neurological health through the gut-brain axis, particularly via the production of short-chain fatty acids. While these preliminary findings suggest a possible association between gut microbiota profile and cognitive impairment in DMD, further research is needed to explore a causal relationship and consider microbiota-targeted therapeutic strategies.}, }
@article {pmid40325116, year = {2025}, author = {Yiminniyaze, R and Zhang, Y and Zhu, N and Zhang, X and Wang, J and Li, C and Wumaier, G and Zhou, D and Xia, J and Li, S and Dong, L and Zhang, Y and Zhang, Y and Li, S}, title = {Characterizations of lung cancer microbiome and exploration of potential microbial risk factors for lung cancer.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {15683}, pmid = {40325116}, issn = {2045-2322}, support = {82241028//National Clinical Key Specialty Project Foundation/ ; 82270058//National Natural Science Foundation of China/ ; 22Y11900600//Shanghai Year 2022 Science and Technology Innovation Action Plan Medical Innovation Research Special Project/ ; }, mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; Risk Factors ; *Microbiota/genetics ; Middle Aged ; Aged ; Lung/microbiology/pathology ; High-Throughput Nucleotide Sequencing ; Adult ; Shewanella/isolation &amp; purification/genetics ; }, abstract = {Recent studies have indicated that the lung microbiome may contribute to the development and progression of lung cancer, although the precise mechanisms remain to be fully elucidated. This study sought to delineate the microbial composition within lung cancer tissues and identify potential microbial risk factors. Tissue samples were collected from patients newly diagnosed with pulmonary opacities, and metagenomic next-generation sequencing was employed to analyze these samples. Tissue samples were collected from 130 patients with pulmonary opacities, categorized into lung cancer (50 cases), pulmonary infection (53 cases), and non-infectious pulmonary diseases (27 cases). The non-infectious group served as the primary control. The diversity of the lung microbiome in lung cancer tissues was found to be comparable to that observed in non-infectious benign pulmonary conditions. Specific phyla and genera exhibited increased abundance in lung cancer tissues. Additionally, correlations were established between certain microorganisms and clinical characteristics associated with lung cancer. Multivariate binary logistic regression analysis revealed that age and Shewanella were independent risk factors for lung cancer development. This study suggests that the composition of the lung microbiome differs significantly between individuals with lung cancer and those with benign pulmonary conditions, with certain microbes such as Shewanella potentially serving as risk factors for lung cancer progression.}, }
@article {pmid40324989, year = {2025}, author = {Gibbs, AJ and Fuentes, S and Adams, I and Hajizadeh, M and Ben Mansour, K and Guy, PL and Fribourg, C and Ziebell, H and Kreuze, J and Fox, A and Jones, RAC}, title = {A phylogeny of the tymoviruses, sensu stricto, and its global interpretation in space and time.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-01-25-0061-RE}, pmid = {40324989}, issn = {0191-2917}, abstract = {Maximum likelihood (ML) phylogenies of 109 tymoviruses, including three obtained directly from metagenomes, were calculated from all three open reading frames separately, but the concatenated sequences of their replicase and coat protein genes gave the most representative trees. ML phylogenies were also calculated from all recorded tymomvirus coat protein genes, and from datasets of the turnip yellow mosaic virus cluster, and separately of tomato yellow blotch, Andean potato latent and Andean potato mild mosaic viruses. These phylogenies showed that the basal divergence of tymoviruses occurred in a population infecting Eurasian brassicas (rosids), and more recently, one of the basal lineages diversified and adapted to infect some solanaceous (asterid) plants and crops of Central and South America. Heterochronous dating of the phylogenies failed, but heuristic comparisons based on patristic distances, branching patterns and external events suggested that the 'most recent common ancestor' of all known tymoviruses existed before the last Ice Age. Some lineages reached the Americas about 15,000 years ago. However, most spread of the few tymoviruses now found on more than one continent occurred during the past two centuries. The only recombinants were two sequences of Chiltepin yellow mosaic virus both with Nemesia ring necrosis virus as minor parent. Population genetic analysis found significant evidence of population contraction in the tymovirus populations infecting asterid hosts in the Americas. It also found the replicase and coat protein genes were significantly negatively selected. By contrast, the overlapping movement protein genes were positively selected which may help them adapt to new host species, including infecting economically significant crops. This knowledge about tymoviruses is important to plant biosecurity authorities.}, }
@article {pmid40324646, year = {2025}, author = {Shen, H and Wang, D and Huang, Y and Yang, Y and Ji, S and Zhu, W and Liu, Q}, title = {2,3,7,8-tetrachlorodibenzofuran modulates intestinal microbiota and tryptophan metabolism in mice.}, journal = {Life sciences}, volume = {373}, number = {}, pages = {123679}, doi = {10.1016/j.lfs.2025.123679}, pmid = {40324646}, issn = {1879-0631}, abstract = {Persistent organic pollutants (POPs) are known to disrupt gut microbiota composition and host metabolism, primarily through dietary exposure. In this study, we investigate the impact of 2,3,7,8-tetrachlorodibenzofuran (TCDF) on gut microbiota and host metabolic processes. RNA-seq analysis revealed that TCDF exposure significantly affected tryptophan metabolism, lipid metabolic pathways, and immune system function. Metagenomic and metabolomic analyses further showed that TCDF reduced the abundance of Mucispirillum schaedleri and levels of two key tryptophan metabolites, indole-3-carboxaldehyde (3-IAld) and Indole acrylic acid (IA). Supplementation with 3-IAld and IA alleviated TCDF-induced liver toxicity in mouse, as evidenced by reduced Cyp1a1 expression, and mitigated intestinal inflammation, reflected by lower pro-inflammatory cytokines (Ifn-γ and Il-1β) in the colon. Additionally, 3-IAld and IA supplementation enhanced intestinal barrier function, as demonstrated by increased Mucin 2 (MUC2) expression in the gut mucosa of mouse. These findings suggest that TCDF exposure disrupts the gut microbiome and host metabolic balance, and highlight the potential therapeutic role of tryptophan-derived metabolites in mitigating environmental pollutant-induced damage.}, }
@article {pmid40324616, year = {2025}, author = {Zhao, X and Chen, Y and Hu, J and Wang, H and Ye, Z and Zhang, J and Meng, J and Li, J and Dahlgren, RA and Zhang, S and Gao, H and Chen, Z}, title = {Efficacy of nitrate and biochar@birnessite composite microspheres for simultaneous suppression of As(III) mobilization and greenhouse gas emissions in flooded paddy soils.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121757}, doi = {10.1016/j.envres.2025.121757}, pmid = {40324616}, issn = {1096-0953}, abstract = {Elevated As(III) pollution and greenhouse gas (GHG) emissions are two primary environmental concerns associated with flooded paddy soils. Herein, a novel biochar@birnessite composite microsphere was engineered using a biochar, birnessite and sodium alginate formulation. The microspheres were applied along with nitrate to examine their efficacy in suppressing As(III) mobilization and GHG emissions in an As-contaminated flooded paddy soil. After a 10-day incubation period, the combined nitrate+microsphere treatment achieved desirable remediation effects versus a nitrate-alone treatment, with mobile As(III) (initially 0.1 mM in flooded layer) completely immobilized and N2O, CH4 and CO2 emissions declining by 89%, 73% and 31%, respectively. As(III) immobilization was ascribed to oxidation/adsorption/coprecipitation by FeOx/MnOx regenerated from successive cycles of Feammox/Mnammox and nitrate-reduction coupled with Fe(II) oxidation (NRFO)/nitrate-reduction coupled with Mn(II) oxidation (NRMO). Moreover, NRFO/NRMO-derived full denitrification displayed high thermodynamic feasibility, leading to full denitrification with the generation of N2 rather than N2O. The co-occurrence of anaerobic oxidation of methane (AOM) driven by biochar-shuttling and coupled reduction of nitrate/FeOx/MnOx fostered anaerobic oxidation of CH4 to CO2. A portion of the resulting CO2 was incorporated into poorly-soluble carbonate minerals leading to lower CO2 emission and soil carbon sequestration. Metagenomic sequencing revealed that the nitrate+microsphere treatment enriched the abundances of key microorganisms linked to As/Fe/Mn oxidation and GHG mitigation (e.g., Geobacter, Streptomyces, Cupriavidus and Chloroflexus). Our findings document the efficacy of nitrate+biochar@birnessite microsphere treatment as an effective remediation strategy to simultaneously mitigate As(III) pollution and GHG emissions in flooded paddy soils.}, }
@article {pmid40323477, year = {2025}, author = {Kiran, NS and Chatterjee, A and Yashaswini, C and Deshmukh, R and Alsaidan, OA and Bhattacharya, S and Prajapati, BG}, title = {The gastrointestinal mycobiome in inflammation and cancer: unraveling fungal dysbiosis, pathogenesis, and therapeutic potential.}, journal = {Medical oncology (Northwood, London, England)}, volume = {42}, number = {6}, pages = {195}, pmid = {40323477}, issn = {1559-131X}, mesh = {Humans ; *Dysbiosis/microbiology ; *Mycobiome ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Inflammation/microbiology ; *Gastrointestinal Neoplasms/microbiology ; Fungi/pathogenicity ; Animals ; }, abstract = {The gastrointestinal mycobiome, comprising diverse fungal species, plays a significant role in gastrointestinal carcinogenesis and inflammatory bowel disease (IBD) pathogenesis. Recent studies have demonstrated that dysbiosis of the gut mycobiome, characterized by an overrepresentation of pathogenic fungi such as Candida albicans and Aspergillus, correlates with increased inflammation and cancer risk. For instance, C. albicans has been shown to induce colonic inflammation through the activation of pattern recognition receptors and the release of pro-inflammatory cytokines, exacerbating IBD symptoms and potentially facilitating tumorigenesis. Additionally, metagenomic analyses have revealed distinct fungal signatures in colorectal cancer tissues compared to adjacent healthy tissues, highlighting the potential of fungi as biomarkers for disease progression. Mechanistically, gut fungi contribute to disease through biofilm formation, mycotoxin secretion (e.g., aflatoxins, candidalysin), pro-inflammatory cytokine induction (e.g., IL-1β, IL-17), and disruption of epithelial barriers-creating a tumor-promoting and inflammation-prone environment. Furthermore, the interplay between fungi and the bacterial microbiome can amplify inflammatory responses, contributing to chronic inflammation and cancer development. Fungal interactions with bacterial communities also play a synergistic role in shaping mucosal immune responses and enhancing disease severity in both cancer and IBD contexts. As research continues to elucidate these complex fungal-host and fungal-bacterial interactions, targeting the gut mycobiome may offer novel therapeutic avenues for managing IBD and gastrointestinal cancers, emphasizing the need for integrated, mechanistically informed approaches to microbiome research.}, }
@article {pmid40323435, year = {2025}, author = {Reynolds, J and Yoon, JY}, title = {Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis.}, journal = {Mikrochimica acta}, volume = {192}, number = {6}, pages = {334}, pmid = {40323435}, issn = {1436-5073}, mesh = {*Machine Learning ; *Microbiota ; Humans ; Spectrometry, Fluorescence/methods ; *Bacteria/isolation &amp; purification/genetics ; }, abstract = {Most microbiota determination (skin, gut, soil, etc.) are currently conducted in a laboratory using expensive equipment and lengthy procedures, including culture-dependent methods, nucleic acid amplifications (including quantitative PCR), DNA microarray, immunoassays, 16S rRNA sequencing, shotgun metagenomics, and sophisticated mass spectrometric methods. In situ and rapid analysis methods are desirable for fast turnaround time and low assay cost. Fluorescence identification of bacteria and their mixtures is emerging to meet this demand, thanks to the recent development in various machine learning methods. High-dimensional spectroscopic or microscopic imaging data can be obtained to identify the bacterial makeup and its implications for human health and the environment. For example, we can classify healthy versus non-healthy skin microbiome, inflammatory versus non-inflammatory gut microbiome, degraded versus non-degraded soil microbiome, etc. This tutorial summarizes the various machine-learning algorithms used in bacteria identification and microbiota determinations. It also summarizes the various fluorescence spectroscopic methods used to identify bacteria and their mixtures, including fluorescence lifetime spectroscopy, fluorescence resonance energy transfer (FRET), and synchronous fluorescence (SF) spectroscopy. Finally, various fluorescence microscopic imaging methods were summarized that have been used to identify bacteria and their mixtures, including epi-fluorescence microscopy, confocal microscopy, two-photon/multi-photon microscopy, and super-resolution imaging methods (STED, SIM, PALM, and STORM). Finally, it discusses how these methods can be applied to microbiota determinations, what can be demonstrated in the future, opportunities and challenges, and future directions.}, }
@article {pmid40323169, year = {2025}, author = {Zhu, D and Galley, J and Pizzini, J and Musteata, E and Douglas, MV and Chazin, WJ and Skaar, EP and Tabor, JJ and Britton, RA}, title = {Microbial Biosensor for Sensing and Treatment of Intestinal Inflammation.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2504364}, doi = {10.1002/advs.202504364}, pmid = {40323169}, issn = {2198-3844}, support = {//Baylor College of Medicine Seed Funding/ ; //Crohn's and Colitis Foundation Litwin Pioneer Award (RAB)/ ; R01AI123278//National Institutes of Health grants/ ; U19AI157981//National Institutes of Health grants/ ; R01AI155586//National Institutes of Health grants/ ; R01AI164587//National Institutes of Health grants/ ; U19AI174999//National Institutes of Health grants/ ; }, abstract = {Synthetic biology has enabled the development of biosensors to detect intestinal inflammation, yet few target the clinically validated biomarker of intestinal inflammation calprotectin with both diagnostic and therapeutic capabilities. Here, an optimized calprotectin biosensor is presented that leverages a zinc uptake regulator (Zur) controlled promoter coupled with a memory circuit to detect and record intestinal inflammation in vivo. The level of biosensor activation strongly correlates with calprotectin levels in the colon of two independent mouse models of colitis. Coupling of the biosensor with the production of the anti-inflammatory cytokine IL10 allowed for the resolution of chemically induced colitis, demonstrating the ability of the biosensor to sense and respond to disease. This work highlights the utility of developing synthetic organisms for the diagnosis and treatment of intestinal disease using clinically validated biomarkers.}, }
@article {pmid40322835, year = {2025}, author = {Luo, Z and Lu, X and Zhang, T and Shi, S and Zhao, R and He, Y and Yao, H and Zhu, W and Zhang, C}, title = {Moxibustion Enhances Ovarian Function by Inhibiting the Th17/IL-17 Pathway and Regulating Gut Microbiota in POI Rats.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {93}, number = {5}, pages = {e70082}, doi = {10.1111/aji.70082}, pmid = {40322835}, issn = {1600-0897}, support = {BE2020624//Natural Science Foundation of Jiangsu Province/ ; }, mesh = {Animals ; Female ; *Moxibustion/methods ; *Gastrointestinal Microbiome/immunology ; Rats ; *Th17 Cells/immunology ; *Interleukin-17/metabolism ; *Primary Ovarian Insufficiency/therapy/immunology/chemically induced ; Rats, Sprague-Dawley ; *Ovary/physiology ; Signal Transduction ; Disease Models, Animal ; }, abstract = {PROBLEM: Premature ovarian insufficiency (POI) is a significant cause of female infertility, severely impacting physical and mental health. Current treatments, primarily hormone replacement therapy, fail to restore ovarian function and may cause adverse effects. Moxibustion, a traditional Chinese medicine therapy, has shown potential in treating POI, but its mechanisms remain unclear. This study investigated the therapeutic effects of moxibustion on POI rats and explored its underlying mechanisms.<br><br>METHOD OF STUDY: A POI rat model was established using cyclophosphamide, and moxibustion was applied daily to the CV4 and SP6 acupoints for 4 weeks. We analyzed hormone levels, estrous cycles, follicle count, and gut microbiota. Transcriptomic and metagenomic sequencing were performed to identify potential pathways. Network pharmacology was used to predict active components and targets.<br><br>RESULTS: Moxibustion restored estrous cycles, improved hormonal imbalances, and increased ovarian reserve function. Network pharmacology identified five active components in moxa, and based on the results of network pharmacology and transcriptome sequencing, we believe that the regulation of the IL-17 pathway is the key mechanism. Further experiments showed moxibustion downregulated the Th17/IL-17 pathway, reduced key proteins such as IL-17R, NF-&#x3ba;B, MMP3, I&#x3ba;B&#x3b1;, IL-1&#x3b2;, MMP9, TRAF6, and Cox2. Flow cytometry confirmed a decrease in Th17 cell proportion. Gut microbiota analysis revealed that moxibustion enhanced microbial diversity and modulated specific bacterial species, which correlated with improved hormone levels.<br><br>CONCLUSION: Moxibustion has a therapeutic effect on POI rats by regulating the Th17/IL17 pathway and gut microbiota, which provides evidence for the clinical application of moxibustion.}, }
@article {pmid40322711, year = {2025}, author = {Kulsum, U and Patankar, C and Biswas, D}, title = {MOSMAP: Mosquito metagenome analysis pipeline.}, journal = {Bioinformation}, volume = {21}, number = {2}, pages = {110-112}, pmid = {40322711}, issn = {0973-2063}, abstract = {MosMAP is a bioinformatics pipeline designed for mosquito metagenome analysis. MosMAP automates essential processes like quality control, taxonomic classification, species abundance estimation and visualization by integrating tools such as Trimgalore, Kraken 2, Bracken and Krona into a user-friendly workflow. Each of these tools is integrated to ensure a smooth and efficient workflow from raw data to interpretable results. The pipeline simplifies complex bioinformatics tasks, making them accessible to researchers with limited computational expertise. MosMAP demonstrated high concordance with standard bioinformatics workflows such as Kraken and Bracken in terms of read retention, taxonomic accuracy and abundance estimation when applied to metagenomes of mosquito collected in Bhopal, India. This accessible pipeline promotes the simplification of meta-genomics, supporting research in microbiology, ecology and vector-borne diseases.}, }
@article {pmid40322468, year = {2025}, author = {Shan, H and Wang, J and Zhang, Q and Ming, Z and Zhang, Y and He, P and Fang, P and Zhang, M and Li, W and Shi, H and Guan, Y and Yang, S}, title = {Pathogen surveillance and risk factors for pulmonary infection in patients with lung cancer: A retrospective single-center study.}, journal = {Open medicine (Warsaw, Poland)}, volume = {20}, number = {1}, pages = {20251180}, pmid = {40322468}, issn = {2391-5463}, abstract = {BACKGROUND: Early and accurate diagnosis of pulmonary infection (PI) is crucial for the timely implementation of appropriate treatment strategies in lung cancer patients.<br><br>METHODS: Metagenomic next-generation sequencing and conventional testing were performed in lung cancer patients with and without PI. The pathogen profiles were analyzed, and risk factors for PI were explored using univariate and multivariate logistic regression models.<br><br>RESULTS: A total of 55 lung cancer patients with PI and 59 non-infected lung cancer patients were included. There were 41 underlying pathogens identified by both methods in lung cancer patients with PI. The coexistence of different pathogen types was common, particularly between fungi and viruses, which was observed in 28.57% of cases. The incidence of Streptococcus pneumoniae and Pneumocystis jirovecii is significantly higher in small-cell lung carcinoma patients compared to that in non-small-cell lung carcinoma patients. Besides, cytomegalovirus, P. jirovecii, and Aspergillus were more likely to be found in advanced-stage patients. Risk factor analysis revealed that Karnofsky Performance Status <90 and chemotherapy were strongly associated with PI in lung cancer patients.<br><br>CONCLUSIONS: This study highlights the complexity of PI in lung cancer patients, emphasizing the need for tailored diagnostic and therapeutic strategies based on cancer type and stage.}, }
@article {pmid40321823, year = {2025}, author = {Yupanqui García, GJ and Badotti, F and Ferreira-Silva, A and da Cruz Ferraz Dutra, J and Martins-Cunha, K and Gomes, RF and Costa-Rezende, D and Mendes-Pereira, T and Delgado Barrera, C and Drechsler-Santos, ER and Góes-Neto, A}, title = {Microbial diversity of the remote Trindade Island, Brazil: a systematic review.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19305}, pmid = {40321823}, issn = {2167-8359}, mesh = {Brazil ; *Soil Microbiology ; *Biodiversity ; *Bacteria/genetics/classification/isolation &amp; purification ; Islands ; *Fungi/genetics/classification/isolation &amp; purification ; *Archaea/genetics/classification/isolation &amp; purification ; Ecosystem ; *Microbiota ; }, abstract = {Trindade Island is a unique volcanic environment in the South Atlantic, characterized by acidic soils, rich organic matter and a high diversity of micro- and macroorganisms. Such diversity can represent a range of ecological niches and functions, potentially offering valuable ecosystem services. This systematic review aimed to synthesize the current knowledge of the island's microbial communities, focusing on their ecological roles and biotechnological potential. Following the PRISMA guidelines, a comprehensive search of the scientific literature was conducted to identify studies that performed DNA sequencing of samples collected on Trindade Island, Brazil. The selected studies used approaches, such as shotgun metagenomics and marker gene sequencing, including samples from microcosm experiments and culture-dependent samples. A total of eight studies were selected, but only six provided detailed taxonomic information, from which more than 850 genera of Bacteria, Archaea, and Fungi were catalogued. Soil communities were dominated by Actinobacteriota, Acidobacteriota, and Ascomycota (Fungi) while marine and coral environments showed high diversity of Pseudomonadota and Cyanobacteria. Microcosm experiments revealed adaptive responses to hydrocarbon contamination, mainly for Alcanivorax and Mortierella (Fungi). Compared to other ecosystems, such as the oligotrophic Galapagos Islands and the sea-restricted Cuatro Cienegas Basin, Cyanobacteria were shown to be more adaptive.}, }
@article {pmid40321713, year = {2025}, author = {De Coninck, L and Hadermann, A and Ingletto, L and Colebunders, R and Gamnsi Njamnshi, K and Njamnshi, AK and Mokili, JL and Siewe Fodjo, JN and Matthijnssens, J}, title = {Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of RNA viruses.}, journal = {Virus evolution}, volume = {11}, number = {1}, pages = {veaf024}, pmid = {40321713}, issn = {2057-1577}, abstract = {Strong epidemiological evidence suggests that onchocerciasis may be associated with epilepsy-hence the name onchocerciasis-associated epilepsy (OAE). However, the pathogenesis of OAE still needs to be elucidated, as recent studies have failed to detect Onchocerca volvulus in the central nervous system of persons with OAE. Therefore, it was suggested that a potentially neurotropic virus transmitted by blackflies could play a role in triggering OAE. To investigate this hypothesis, adult blackflies were collected in an onchocerciasis-endemic area with a high OAE prevalence in the Ntui Health District, Cameroon. A viral particle-based shotgun sequencing approach was used to detect viral sequences in 55 pools of 10 blackflies. A very high abundance of viral reads was detected across multiple (novel) viral families, including viral families associated with human disease. Although no genomes closely related to known neurotropic viruses were found in the blackfly virome, the plethora of novel viruses representing novel species, genera and even families warrant further exploration for their potential to infect vertebrates. These results could serve as a first step for studying the viruses associated with the haematophagous blackfly, which also could be present in their nematode host O. volvulus. Exploring the diversity of viruses in blackflies should be included in the active surveillance of zoonotic diseases.}, }
@article {pmid40321599, year = {2025}, author = {Zhou, Z and Song, Y and Yan, Y and Zheng, Y}, title = {Metagenomic Next-Generation Sequencing Improves the Diagnosis Efficiency of Mixed Periprosthetic Joint Infections.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {2165-2174}, pmid = {40321599}, issn = {1178-6973}, abstract = {PURPOSE: To explore the clinical significance of metagenomic next-generation sequencing (mNGS) in the diagnosis of mixed periprosthetic joint infections (PJI).<br><br>METHODS: The data pertaining to patients suspected of PJI who underwent arthroplasty at our hospital between January 2020 and June 2024 were analyzed. Patients included in the study were subjected to microbial culture and mNGS analyses to evaluate the efficacy of mNGS in diagnosing mixed PJIs.<br><br>RESULTS: Among the 44 PJI patients included, 20 (45.45%) were culture-positive, and 35 (79.55%) were mNGS-positive. Compared to microbial culture, mNGS demonstrated significantly higher sensitivity, negative predictive value, and accuracy (79.55% vs 45.45%, 55.00% vs 35.14%, and 80.70% vs 57.89%, respectively; all&#xa0;P<0.05). However, the specificity of mNGS was significantly lower than culture (84.62% vs 100.00%, P<0.05). For mixed PJIs, the sensitivity of mNGS was notably higher, albeit with lower specificity and positive predictive value compared to microbial culture (72.23% vs 27.27%, 85.19% vs 100.00%, 66.67% vs 100.00%, respectively; all P<0.05). mNGS enables more sensitive detection of co-pathogens in mixed PJI, accelerating targeted therapy and reducing inappropriate broad-spectrum therapy. While its lower specificity requires clinical integration, it clarifies complex diagnoses and streamlines stewardship for improved outcomes.<br><br>CONCLUSION: mNGS is a promising technique for rapidly and accurately detecting co-pathogens in mixed PJI.}, }
@article {pmid40321269, year = {2025}, author = {Tronel, A and Roger-Margueritat, M and Plazy, C and Biennier, S and Craspay, A and Mohanty, I and Cools Portier, S and Laiola, M and Roeselers, G and Mathieu, N and Hupe, M and Dorrestein, PC and Alcaraz, JP and Martin, D and Cinquin, P and Silvent, AS and Giai, J and Proust, M and Soranzo, T and Buelow, E and Le Gouellec, A}, title = {Profiling the human luminal small intestinal microbiome using a novel ingestible medical device.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.04.18.25326056}, pmid = {40321269}, abstract = {The invasive nature of sample collection for studying the small intestinal (SI) microbiome often results in its poor characterization. This study evaluated a novel ingestible medical device (MD) for SI luminal sample collection. A monocentric interventional trial (NCT05477069) was conducted on 15 healthy subjects. Metagenomics, metabolomics and culturomics assessed the MD's effectiveness in characterizing the healthy SI microbiome and identifying potential biomarkers. The SI microbiota differed significantly from the fecal microbiota, displaying high inter-individual variability, lower species richness, and reduced alpha diversity. A combined untargeted and semi-targeted LC-MS/MS metabolomics approach identified a distinct SI metabolic footprint, with bile acids and amino acids being the most abundant classes of metabolites. Host and host/microbe-derived bile acids were particularly abundant in SI samples. The application of a fast culturomics approach to two SI samples enabled species-level characterization, resulting in the identification of 90 bacterial species, including five potential novel species. The present study demonstrates the efficacy of our novel sampling MD in enabling comprehensive SI microbiome analysis through an integrative multi-omics approach, allowing the identification of distinct microbiome signatures between SI and fecal samples.}, }
@article {pmid40320901, year = {2025}, author = {Gervasoni, KN and Iacia, MVMS and Silva, KO and Franco, LG and Mendes, MEF and Neves, TJDC and Sanches, WS and Oliveira, LB and Saito, EA and Vieira, KCO and Pereira, VC and Nai, GA and Winkelstroter, LK}, title = {Protective Effect of Piperine on Indomethacin-Induced Intestinal Damage.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70097}, doi = {10.1002/mnfr.70097}, pmid = {40320901}, issn = {1613-4133}, abstract = {Nonsteroidal antiinflammatory drugs (NSAIDs) are widely prescribed for the treatment of inflammation and chronic pain. Chronic use of NSAIDs is associated with adverse events and organ damage, especially to the gastric mucosa and small intestine. This study evaluates the protective effect of piperine on indomethacin-induced intestinal damage. Eighteen male Mus musculus mice, aged 6-8 weeks, were used. Intestinal damage was induced with indomethacin (10 mg/mL) and cotreatment with piperine (20 mg/mL), both administered orally. After 14 days, the animals were euthanized. Biochemical serological analysis was performed. Intestinal inflammation was assessed based on macroscopic, histopathological, and metagenomic analyses. Histopathological analysis showed a reduction in small intestine inflammation (p < 0.05) and the disappearance of necrosis in the intestinal wall of the large intestine. Crypt and villus measurements showed increased values in the piperine-treated group (p < 0.05). An approximately six-fold increase in aspartate aminotransferase (AST) was observed in the Indomethacin group (p < 0.05). Regarding the intestinal microbiota, an increase in genus diversity was observed in the piperine-treated group (p < 0.05). There was a 50% reduction in micronucleus formation with the administration of piperine 20 mg/kg (p < 0.05). It was concluded that cotreatment with piperine has great potential in mitigating the side effects caused by NSAIDs.}, }
@article {pmid40320531, year = {2025}, author = {Vidaur, L and Guridi, A and Leizaola, O and Marin, J and Rello, J and Sarasqueta, C and Sorarrain, A and Marimón, JM}, title = {Respiratory dysbiosis as prognostic biomarker of disease severity for adults with community-acquired pneumonia requiring mechanical ventilation.}, journal = {Pneumonia (Nathan Qld.)}, volume = {17}, number = {1}, pages = {10}, pmid = {40320531}, issn = {2200-6133}, support = {FIS17/01463//Instituto de Salud Carlos III/ ; FIS17/01463//Instituto de Salud Carlos III/ ; }, abstract = {OBJETIVES: To ascertain the role of the lung microbiome in the development of severe pneumonia and its potential as a biomarker for disease progression.<br><br>METHODS: BAL samples from 34 adults with severe community-acquired pneumonia (CAP) (17 viral, 8 viral coinfected with bacteria and 9 bacterial) admitted to the ICU for acute respiratory failure between 2019 and 2021 were collected within the first 48&#xa0;h of admission to the ICU. The microbiome was characterized via the Ion 16S Metagenomics Kit and the Ion Torrent sequencing platform. Clinical factors, including survival, mechanical ventilation duration, blood biomarkers and organ failure in terms of acute respiratory distress syndrome (ARDS), shock or acute renal failure, were correlated with microbiome characteristics.<br><br>RESULTS: The microbiome diversity in patients with viral pneumonia was significantly greater than that in patients with bacterial or coinfected pneumonia: the Shannon diversity index was 3.75 (Q1-Q3: 2.5-4.1) versus 0.4 (Q1-Q3: 0.2-1.3) and 0.48 (Q1-Q3: 0.3-1.1), respectively (p&#x2009;<&#x2009;0.05). The microbiome diversity index was associated with severity-of-illness (APACHE II), independent of the etiology of pneumonia (B coefficient -1.845; p&#x2009;<&#x2009;0.01). Patients with severe viral CAP who developed ARDS had a lower presence of Proteobacteria, and those who were complicated with ventilator-associated pneumonia had a higher prevalence of Acinetobacter at admission. The mortality of patients with bacterial or coinfected pneumonia was 35%. In coinfected patients, the diversity index was associated with the development of shock.<br><br>CONCLUSION: Patients with severe CAP have low respiratory microbiome diversity, indicating that respiratory microbiome diversity is a potential biomarker of disease severity.}, }
@article {pmid40320520, year = {2025}, author = {Liu, S and Wu, J and Cheng, Z and Wang, H and Jin, Z and Zhang, X and Zhang, D and Xie, J}, title = {Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {111}, pmid = {40320520}, issn = {2049-2618}, support = {2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&amp;D Program of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; }, mesh = {*Microbiota/physiology ; *Stress, Physiological ; *Plants/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil Microbiology ; Droughts ; }, abstract = {BACKGROUND: Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.<br><br>RESULTS: This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.<br><br>CONCLUSIONS: Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.}, }
@article {pmid40320100, year = {2025}, author = {Kogoj, R and Bosilj, M and Šturm, AC and Korva, M and Smrdel, KS and Kvas, E and Pirš, M and Lepen, L and Triglav, T}, title = {Bioinformatic challenges in metagenomic next generation sequencing data analysis while unravelling a case of uncommon campylobacteriosis.}, journal = {Journal of biomedical informatics}, volume = {}, number = {}, pages = {104841}, doi = {10.1016/j.jbi.2025.104841}, pmid = {40320100}, issn = {1532-0480}, abstract = {OBJECTIVE: This study aimed to employ advanced bioinformatics and modern sequencing approaches to solve a diagnostic problem of persistent Campylobacter spp. molecular detection yet negative culture results from four consecutive stool samples of a previously healthy patient with newly diagnosed selective IgA deficiency with prolonged diarrhoea METHODS: Metagenomic next-generation sequencing (mNGS) based on short-paired end reads with basic bioinformatic read classification analysis was used at first. Due to confusing results, advanced bioinformatics involving contigs construction and classification, reference genome mappings and reads filtering with BBSplit, additionally coupled with metagenomic long-reads sequencing and Full-length 16S rRNA metabarcoding were employed to further elucidate the results. Virulence factors were analysed using the Prokka Genome Annotation tool. Modified classical bacteriology methods were finally used for further clarification.<br><br>RESULTS: Short-pair end reads analysis identified several Campylobacter species in all four samples. After advanced bioinformatic approaches were applied, candidatus C. infans was suspected as the putative pathogen. This result was further supported by metagenomic long-reads sequencing and Full-length 16S rRNA metabarcoding. Nevertheless, after modifying the culture conditions based on mNGS results, a mixed culture of candidatus C. infans and C.ureolyticus was obtained. Sequencing of the mixed culture resulted in an 87.48&#x202f;% and 73.47&#x202f;% genome coverage of candidatus C. infans and C. ureolyticus, respectively. In the candidatus C. infans genome more virulence factors hits were found than in the C. ureolyticus genome thus supporting the first as the most probable cause of symptoms.<br><br>CONCLUSION: This study shows the pivotal role and strengths of mNGS in unravelling an unusual case of diarrhoea and demonstrates how mNGS can guide established microbiological methods to improve on current limitations. However, it also emphasises the need for careful interpretation of sequencing data, particularly for closely related bacterial species from clinical samples that are known to support complex microbial communities.}, }
@article {pmid40320026, year = {2025}, author = {Zheng, Y and Yue, Y and Liu, C and Pang, L and Wang, Y and Yang, Z}, title = {The role of riverbed substrates in N2O and CH4 emission: Insights from metagenomic analysis of epilithic biofilms.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121772}, doi = {10.1016/j.envres.2025.121772}, pmid = {40320026}, issn = {1096-0953}, abstract = {Riverbed substrates are critical in N2O and CH4 emission with functional microbes adhering to them. However, the role of substrates remains to be fully understood. This study monitors N2O and CH4 emission and collects epilithic biofilms on riverbed substrates with various diameters and size heterogeneity from 10 sections along a mountain river. Compared with the global range, moderate water-air exchange rates of N2O (-2.34-29.2 μg/m[2]/h) and rapid CH4 emission (-2.58-35.2 mg/m[2]/h) are observed. Based on metagenomic analysis, the abundances of nirS and fmdA genes, which encode catalysts in the denitrification and the hydrogenotrophic methanogenesis process, are found to be significantly higher in the medium diameter group (2-100 mm), implying higher N2O and CH4 emission. Meanwhile, the abundance of nirS and nirK genes, which are key to N2O production, is significantly higher in the low size heterogeneity group, promoting N2O release. In contrast, the abundance of ftr, pta,ackA and ACS genes critical in the methanogenesis processes are significantly lower in the low size heterogeneity group, inhibiting CH4 emission. For N2O production, the nitrification process is found to be dominated by species of Nocardioides and Planctomycetales, denitrification process by species of Tabrizicola and Rhodobacteraceae, and dissimilatory nitrate reduction to ammonium process by Leptospiraceae species. In contrast, CH4 is mainly generated by species of Pirellula and Proteobacteria through hydrogenotrophic, acetoclastic and methylotrophic methanogenesis respectively. A structural equation model indicated that substrate physical properties are equally or even more important as/than the aquatic nutrients concentration for N2O or CH4 emission in mountain rivers.}, }
@article {pmid40319779, year = {2025}, author = {Zhu, J and Li, X and Wang, Y and Gu, X and Wang, H and Ma, J and Huang, Y}, title = {Organic sulfur-driven denitrification pretreatment for enhancing autotrophic nitrogen removals from thiourea-containing wastewater: performance and microbial mechanisms.}, journal = {Water research}, volume = {282}, number = {}, pages = {123753}, doi = {10.1016/j.watres.2025.123753}, pmid = {40319779}, issn = {1879-2448}, abstract = {Thiourea (CH4N2S) is a widely used industrial reagent and is frequently detected in both sewage and industrial wastewater. However, treating thiourea-containing wastewater remains challenging due to its toxicity, high ammonium concentration, and low C/N ratio. In this study, a novel integrated autotrophic-heterotrophic denitrification (IAHD)- completely autotrophic nitrogen removal over nitrite (CANON) process was developed. The degradation pathway of toxic compounds, nitrogen, and sulfur release and transformation, as well as variations in functional genes were comprehensively examined. The results show that by incorporating an IAHD unit, prior to CANON, toxic thiourea was effectively degraded by the recycled nitrate from CANON. The released sulfur and organic carbon served as electron donors facilitating efficient NO3[-]-N reduction. The optimal thiourea/NO3[-]-N ratio for IAHD operation was determined to be 4:1 (m:m), achieving NO3[-] and thiourea removal efficiencies of 90 % and 99 %, respectively. Additionally, NH4[+]-N and SO4[2-]-S concentrations increased by 199.9 mg/L and 201.9 mg/L, respectively. Approximately 53.3 % of thiourea was converted into high-molecular-weight biological metabolites in the IAHD unit, which were subsequently and completely degraded in the CANON unit, where a robust nitrite-shunt and anammox process occurred. 16S rRNA amplicon sequencing revealed that Thiobacillus (with a relative abundance of 39.9 %) was the dominant genera in the IAHD unit, followed by Arenimonas (10.8 %) and norank_o_1013-28-CG33 (12.4 %), indicating that sulfur autotrophic denitrification was the primary pathway for thiourea degradation. Metagenomic analysis further confirmed that thiourea, acting as an electron donor, stimulated the expression of key functional genes involved in denitrification, sulfur oxidation, dissimilatory nitrate reduction, hydrolytic oxidation, and amino acid synthesis and transport pathways. These processes contributed to the active biological transformation of carbon, nitrogen and sulfur in the IAHD unit. This study demonstrates that implementing a prior autotrophic-heterotrophic denitrification unit effectively degrades toxic thiourea, thereby ensuring the subsequent nitrogen removal performance of CANON. This approach offers a new paradigm for the treatment of thiourea-containing wastewater, promoting a more efficient and low-carbon process.}, }
@article {pmid40319631, year = {2025}, author = {Zhao, Z and Gao, B and Henawy, AR and Rehman, KU and Ren, Z and Jiménez, N and Zheng, L and Huang, F and Yu, Z and Yu, C and Zhang, J and Cai, M}, title = {Mitigating the transfer risk of antibiotic resistance genes from fertilized soil to cherry radish during the application of insect fertilizer.}, journal = {Environment international}, volume = {199}, number = {}, pages = {109510}, doi = {10.1016/j.envint.2025.109510}, pmid = {40319631}, issn = {1873-6750}, abstract = {The transfer of antibiotic resistance genes (ARGs) from fertilized soil to vegetables, particularly those consumed raw, causes significant public health risks through the food chain. Black soldier fly larvae can efficiently convert animal manure into organic fertilizer with reduced antibiotic resistance. This study utilized metagenomic sequencing to investigate fields treated with control organic fertilizer (COF), black soldier fly organic fertilizer (BOF), and no fertilizer, with the aim of assessing the transfer risks of ARGs from soil to cherry radish. The results indicated that BOF significantly reduced the richness and abundance of ARGs in both soil and cherry radish compared to COF, reducing 13 ARG subtypes and a 27.6% decrease in ARG abundance in cherry radish. Moreover, a significant positive correlation was observed between mobile genetic elements (MGEs) and virulence factors (VFs) with ARGs, with BOF treatment resulting in a relative abundance reduction of 32.8% and 29.1%, respectively. The complexity of networks involving ARGs with MGEs, VFs, and microbial communities in the BOF treatment was 54.2%, 32.3%, and 32.8% lower, respectively, than the COF treatment. Further analysis of metagenomic-assembled genomes (MAGs) revealed the co-occurrence of ARGs, MGEs, and VFs in cherry radish, indicating the presence of potential pathogenic antibiotic-resistant bacteria (PARB). Notably, the abundance of these PARB in BOF radishes decreased by 45.6% compared to COF. These findings underscore the efficacy of insect fertilizer in mitigating the transfer risks of ARGs to radish, highlighting the significance of sustainable agricultural practices in managing the environmental and health risks associated with ARGs.}, }
@article {pmid40319164, year = {2025}, author = {Fan, Y and Chen, J and Xu, S and Zhou, H and Shang, Y and Tian, X and Wang, B and Zhao, Y and Shan, G and Zhao, Y and Zhang, P and Chen, X}, title = {Bacillus cereus is a key microbial determinant of intractable otitis media with effusion.}, journal = {Communications medicine}, volume = {5}, number = {1}, pages = {150}, pmid = {40319164}, issn = {2730-664X}, abstract = {BACKGROUND: Currently, the mechanisms by which otitis media with effusion (OME) progresses to intractable OME is unclear. Since crosstalk between microbiome and host contributes to many diseases, we hypothesized that similar interactions could occur in the middle ear effusion (MEE) samples from patients with OME and influence intractable OME pathogenesis. This study aimed to evaluate the microbial profile of MEE samples and to determine whether there were microbial differences between the MEE microbiota of patients with intractable OME and those with rapidly cured OME.<br><br>METHODS: MEE samples were collected from 46 OME patients, including 20 from the long course group and 26 from the short course group. Metagenomic sequencing was performed on 30 of these samples, allowing the identification of microbial differences associated with varying disease durations. The difference was verified by further experimental validation, including fluorescence in situ hybridization (FISH) and quantitative polymerase chain reaction (qPCR).<br><br>RESULTS: The alpha diversity indices and overall MEE microbial structure show no significant difference between the long course and short course groups, but species such as Bacillus cereus, Nocardiopsis dassonvillei, and Rothia aeria are significantly more prevalent in the MEE of long course OME patients. qPCR analyses and FISH also confirm the difference in the abundance of Bacillus cereus between the two groups.<br><br>CONCLUSIONS: Bacillus cereus plays a role in the persistence of OME infection and serves as a potential biomarker to predict OME prognosis. Further studies are warranted to explore the value of Bacillus cereus detection in informing early intervention.}, }
@article {pmid40297421, year = {2025}, author = {Mejia, ME and Bowman, S and Lee, J and El-Halwagi, A and Ferguson, K and Maliekel, M and Zhou, Y and Serchejian, C and Robertson, CM and Ballard, MB and Lu, LB and Khan, S and Oladunjoye, OO and Huang, S and Agarwal, SK and Patras, KA}, title = {A cross-sectional analysis of the vaginal microenvironment in rheumatoid arthritis.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {40297421}, support = {F31 AI167538/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; }, abstract = {OBJECTIVE: The human microbiota is implicated in the development and progression of rheumatoid arthritis (RA). Given the increased RA burden in women, and well-known correlations between the vaginal microbiota and local inflammation, we seek to understand the vaginal microenvironment in the context of RA pathology.<br><br>METHODS: Self-collected vaginal swabs and questionnaires on dietary and health practices were obtained from 36 RA and 50 demographically-matched control women, 18-63 years of age. Additionally, medication regimen and disease activity and severity were captured for the RA cohort. Vaginal swabs were subjected to full-length 16S rRNA gene sequencing, multiplex cytokine analyses, and quantification of rheumatoid factor, c-reactive protein, and anti-citrullinated protein antibodies (ACPAs).<br><br>RESULTS: Vaginal microbial richness and genera Peptoniphilus and Prevotella, among other rare taxa, were elevated in RA versus control samples. Vaginal IL-18 and EGF levels were increased in the RA group; IL-18 correlated with multiple microbial features whereas EGF levels were not associated with bacterial composition or other host factors. Within the RA cohort, decreased relative abundance of Streptococcus was associated with joint pathologies, and Lactobacillus gasseri was lower in individuals with serum detection of ACPAs and rheumatoid factor. Vaginal ACPAs were higher in the RA group and positively correlated with Streptococcus and multiple vaginal inflammatory cytokines.<br><br>CONCLUSIONS: We describe vaginal microbial and immunological differences in women with RA, particularly when accounting for diet and menopausal status, disease activity and severity, and medication use. This work opens a new avenue in the multidisciplinary approach to RA patient care.}, }
@article {pmid40318372, year = {2025}, author = {Chu, D and Zhang, H and Wang, Z and Ning, K}, title = {Microbial resources and interactions across three-dimensional space for a freshwater ecosystem.}, journal = {The Science of the total environment}, volume = {980}, number = {}, pages = {179522}, doi = {10.1016/j.scitotenv.2025.179522}, pmid = {40318372}, issn = {1879-1026}, abstract = {Freshwater ecosystems are important natural resources but face serious threats. Nevertheless, they host diverse microorganisms crucial for biosynthetic potential and global biochemical cycles. To fully understand the enrichment and interaction of species and functional resources in freshwater ecosystems, it is essential to profile the microbial resources in the whole three-dimensional space. We profiled 131 metagenomic samples to construct the Honghu Microbial Catalog, comprising 2617 metagenome-assembled genomes, 1718 candidate species, over 60 million non-redundant gene clusters, and 7396 biosynthetic gene clusters. We emphasized surface water may be the primary source of microbial species and ARGs for Honghu Lake. We also found the impact of surface water on groundwater had an "influence sphere". Furthermore, we have identified groundwater as a potential refuge for microbial resources, enriched with CPR bacteria and ARGs. These findings are crucial for the understanding, management, and protection of freshwater ecosystems.}, }
@article {pmid40318358, year = {2025}, author = {Karatas, M and Bloemen, M and Swinnen, J and Roukaerts, I and Gucht, SV and Van Ranst, M and Wollants, E and Matthijnssens, J}, title = {Untapped potential of wastewater for animal and potentially zoonotic virus surveillance: Pilot study to detect non-human animal viruses in urban settings.}, journal = {Environment international}, volume = {199}, number = {}, pages = {109500}, doi = {10.1016/j.envint.2025.109500}, pmid = {40318358}, issn = {1873-6750}, abstract = {INTRODUCTION: Wastewater surveillance has become an essential tool for monitoring viral outbreaks and surveillance of human viruses. While PCR-based methods are most frequently used, more advanced techniques, such as shotgun metagenomics in combination with viral capture methods, have been developed. These capture methods significantly improve the ability to detect nearly all (known) viruses at once in complex samples, including wastewater. In this study, we focus on tracking animal specific and zoonotic viruses in city wastewater using metagenomics combined with hybrid-capture approach.<br><br>METHODS: We collected 6 wastewater samples from Leuven and Brussels, situated in the center of Belgium. Automated wastewater samplers collected 50&#xa0;mL samples every 10&#xa0;min resulting in a 24&#xa0;h composite influent wastewater. All samples were processed using the TWIST comprehensive research panel capture, designed to target over 3,000 human and animal viruses species and 15,000 strains. Sequencing was performed on the AVITI sequencing platform, targeting an average of ten million reads per sample. The sequencing data were analyzed using the EsViritu tool.<br><br>RESULTS: Over 2294 viral genomes or segments were recovered from wastewater samples. Of these, 168 were associated with non-human vertebrate animals, including cats, dogs, pigeons, and rats, spanning 51 virus species. We identified near-complete genomes of clinically relevant animal viruses, such as pigeon circovirus, chicken anemia virus, feline bocaparvovirus 2, canine minute virus, rat coronavirus, canine parvovirus, and porcine circovirus. Additionally, we noted the presence of viruses with known cross-species transmission potential, including porcine torovirus, rosavirus, hepatitis E virus, rat hepatitis virus, and cardiovirus.<br><br>CONCLUSION: The results demonstrate the ability to track a wide range of animal viruses in urban wastewater, potentially forming an early warning system for zoonotic diseases, ultimately being a useful tool for One Health based public health approaches.}, }
@article {pmid40318224, year = {2025}, author = {Maritan, AJ and Clements, CS and Pratte, ZA and Hay, ME and Stewart, FJ}, title = {Sea cucumber grazing linked to enrichment of anaerobic microbial metabolisms in coral reef sediments.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf088}, pmid = {40318224}, issn = {1751-7370}, abstract = {Sea cucumbers have been overharvested world-wide, making assessments of their ecological effects challenging, but recent research demonstrated that sea cucumbers increase coral survival via disease suppression and were therefore important for facilitating reef health. The mechanisms underpinning the sea cucumber-coral interaction therefore are not well understood but are likely mediated through sea cucumber grazing of microbes from reef sediments. We explored how sea cucumber grazing alters the sediment microbiome by leveraging a healthy sea cucumber population on a reef in French Polynesia. We used quantitative PCR, 16S rRNA gene sequencing, and shotgun metagenomics to compare the sediment microbiome in cages placed in situ with or without sea cucumbers. We hypothesized that grazing would lower microbial biomass, change sediment microbiome composition, and deplete sediment metagenomes of anaerobic metabolisms, likely due to aeration of the sediments. Sea cucumber grazing resulted in a 75% reduction in 16S rRNA gene abundances and reshaped microbiome composition, causing a significant decrease of cyanobacteria and other phototrophs relative to ungrazed sediments. Grazing also resulted in a depletion of genes associated with cyanotoxin synthesis, suggesting a potential link to coral health. In contrast to expectations, grazed sediment metagenomes were enriched with marker genes of diverse anaerobic or microaerophilic metabolisms, including those encoding high oxygen affinity cytochrome oxidases. This enrichment differs from patterns linked to other bioturbating invertebrates. We hypothesize that grazing enriches anaerobic processes in sediment microbiomes through removal of oxygen-producing autotrophs, fecal deposition of sea cucumber gut-associated anaerobes, or modification of sediment diffusibility. These results suggest that sea cucumber harvesting influences biogeochemical processes in reef sediments, potentially mediating coral survival by altering the sediment microbiome and its production of coral-influencing metabolites.}, }
@article {pmid40316928, year = {2025}, author = {Zhang, Y and Sun, D and Fang, Y and Feng, Y and Wu, Y and Shen, W and Wu, W and Gao, X and Sun, Y and Ma, X and Gao, F and Zhu, C and Zhou, J and Gu, C}, title = {Uncommon pulmonary manifestation of hepatitis B virus: a case report of secondary organizing pneumonia.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {645}, pmid = {40316928}, issn = {1471-2334}, support = {Z-2014-06-2301//China International Medical Exchange Foundation Xiansheng Clinical Research Special Fund Research Project/ ; 2023-SSGJ-002//Key Construction Disciplines of Provincial and Municipal Co construction of Zhejiang/ ; 2021-GFXK-04//Peak Discipline of Jiaxing First Hospital/ ; 2021AD30177//Science and Technology Project of Jiaxing/ ; }, mesh = {Humans ; Male ; Middle Aged ; *Hepatitis B virus/genetics/isolation &amp; purification ; *Hepatitis B/complications/virology/diagnosis ; Lung/pathology/virology ; DNA, Viral/genetics ; Viral Load ; Organizing Pneumonia ; }, abstract = {BACKGROUND: Hepatitis B virus (HBV) primarily affects the liver, but increasingly, it is recognized for its potential extrahepatic manifestations. This case highlights the importance of considering viral infections in the differential diagnosis of pulmonary nodules.<br><br>CASE PRESENTATION: A 63-year-old man presented with a new mixed ground-glass nodule in the left lower lobe during a routine check-up. He had a history of liver resection for hepatocellular carcinoma, with results negative for hepatitis B virus surface antigen. The HBV viral load in the patient's serum was below the detection limit of quantitative PCR (qPCR). Immunohistological analysis of lung biopsy samples indicated chronic inflammation. However, after a course of intravenous antibiotics, the nodule increased in size, prompting further investigation. Therefore, lung biopsy tissue was subjected to metagenomic next-generation sequencing (mNGS), and HBV DNA was detected. The patient was diagnosed with secondary organizing pneumonia associated with HBV. Then he was treated with prednisone acetate and had remission.<br><br>CONCLUSION: This case underscores the potential for HBV to manifest as pulmonary complications, such as secondary organizing pneumonia. Therefore, in the stage of infectious diseases in patients with a history of hepatocellular carcinoma, HBV needs to be the focus of monitoring, so as to clarify the cause of diagnosis and treatment as soon as possible.<br><br>CLINICAL TRIAL: Not applicable.}, }
@article {pmid40316630, year = {2025}, author = {Aya, V and Pardo-Rodriguez, D and Vega, LC and Cala, MP and Ramírez, JD}, title = {Integrating metagenomics and metabolomics to study the gut microbiome and host relationships in sports across different energy systems.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {15356}, pmid = {40316630}, issn = {2045-2322}, support = {Small grant//Universidad del Rosario/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Energy Metabolism ; Adult ; Athletes ; Young Adult ; *Sports ; Feces/microbiology ; Female ; Lipidomics ; }, abstract = {The gut microbiome plays a critical role in modulating host metabolism, influencing energy production, nutrient utilization, and overall physiological adaptation. In athletes, these microbial functions may be further specialized to meet the unique metabolic demands of different sports disciplines. This study explored the role of the gut microbiome in modulating host metabolism among Colombian athletes by comparing elite weightlifters (n = 16) and cyclists (n = 13) through integrative omics analysis. Fecal and plasma samples collected one month before an international event underwent metagenomic, metabolomic, and lipidomic profiling. Metagenomic analysis revealed significant microbial pathways, including L-arginine biosynthesis III and fatty acid biosynthesis initiation. Key metabolic pathways, such as phenylalanine, tyrosine, and tryptophan biosynthesis; arginine biosynthesis; and folate biosynthesis, were enriched in both athlete groups. Plasma metabolomics and lipidomics revealed distinct metabolic profiles and a separation between athlete types through multivariate models, with lipid-related pathways such as lipid droplet formation and glycolipid synthesis driving the differences. Notably, elevated carnitine, amino acid, and glycerolipid levels in weightlifters suggest energy system-specific metabolic adaptations. These findings underscore the complex relationship between the gut microbiota composition and metabolic responses tailored to athletic demands, laying the groundwork for personalized strategies to optimize performance. This research highlights the potential for targeted modulation of the gut microbiota as a basis for tailored interventions to support specific energy demands in athletic disciplines.}, }
@article {pmid40316568, year = {2025}, author = {Joshi, P and Bhattacharjee, R and Sahu, M and Gajjar, D}, title = {Insights into urinary catheter colonisation and polymicrobial biofilms of Candida- bacteria under flow condition.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {15375}, pmid = {40316568}, issn = {2045-2322}, mesh = {*Biofilms/growth &amp; development ; Humans ; *Urinary Catheters/microbiology ; *Candida/physiology/isolation &amp; purification/growth &amp; development ; Urinary Tract Infections/microbiology ; *Bacteria/growth &amp; development/isolation &amp; purification/genetics ; Catheter-Related Infections/microbiology ; Coinfection/microbiology ; Metagenomics ; Pseudomonas aeruginosa ; Escherichia coli ; Klebsiella pneumoniae ; }, abstract = {Most hospital-acquired urinary tract infections are the result of implanted urinary catheter, with majority of studies focused on a single species colonisation, but recently polymicrobial colonisations are being reported. In this study, indwelling urinary catheters were collected from ICU patients and the colonising microbiome was isolated and identified by the traditional; culturing method and metagenomics. It was observed that majority of catheters were colonised by polymicrobial biofilms, containing both bacterial and fungal isolates making them diverse and complex. However, the metagenomics results were quite surprising showing the presence of multiple organisms of which only 1or 2 showed growth when cultured. Later, in vitro assays were performed by selecting 6 combinations, with each combination containing one Candida spp. - C. albicans or C. tropicalis with one bacteria K. pneumoniae, P. aeruginosa or E. coli. It was observed that polymicrobial biofilms were stronger than mono-microbial biofilms, suggesting their increased surface adhesion. Furthermore, to simulate the dynamic environment in which cells are exposed to a certain level of fluid movement, a flow system was established to imitate the flow generated in colonized urinary catheter. We have observed changes in biofilm architecture, adhesion and thickness under flow conditions compared with static conditions, with a uniformly adhered biofilm with increased thickness of polymicrobial biofilms as compared to mono-species biofilms. The biofilm formed under flow was more viable than the static biofilm with higher number of live cells in flow condition.}, }
@article {pmid40315933, year = {2025}, author = {Cheng, Z and Wang, J and Liu, X and Cao, S}, title = {Accelerated sludge granulation of novel complete ammonium and nitrate removal via denitratation anammox over nitrite process at elevated loading rates.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132610}, doi = {10.1016/j.biortech.2025.132610}, pmid = {40315933}, issn = {1873-2976}, abstract = {The Complete Ammonium and Nitrate Removal via Denitratation Anammox Over Nitrite (CANDAN) process was evaluated for rapid sludge granulation in a lab-scale sequencing batch reactor. Over 119 days under increasing nitrogen loading rates (NLRs), the system finally achieved average 89.2 % total nitrogen removal at 1.93 kg N/m[3]/d NLR, with sludge particle sizes increasing from 215.6 μm to 924.5 μm. Higher NLRs significantly increased extracellular polymeric substances, especially hydrophobic proteins, enhancing sludge hydrophobicity and aggregation. Metagenomic analysis identified Candidatus Brocadia and Thauera as predominant and key microbial genera for nitrogen removal. Furthermore, the upregulation of carbon metabolism under heightened NLRs facilitated the synthesis of hydrophobic amino acids, promoting sludge granulation. These findings demonstrate NLR-driven granulation mechanisms, highlight optimizing NLR as key for accelerating granulation, providing insights to improve start-up and operational efficiency of CANDAN systems.}, }
@article {pmid40315837, year = {2025}, author = {Baker, JS and Qu, E and Mancuso, CP and Tripp, AD and Conwill, A and Lieberman, TD}, title = {Intraspecies dynamics underlie the apparent stability of two important skin microbiome species.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2025.04.010}, pmid = {40315837}, issn = {1934-6069}, abstract = {Adult human facial skin microbiomes are remarkably similar at the species level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 356 metagenomes, we reconstruct on-person evolutionary history to reveal on- and between-person strain dynamics. We find that multiple cells are typically involved in transmission, indicating ample opportunity for migration. Despite this accessibility, family members share only some of their strains. S. epidermidis communities are dynamic, with each strain persisting for an average of only 2 years. C. acnes strains are more stable and have a higher colonization rate during the transition to an adult facial skin microbiome, suggesting this window could facilitate engraftment of therapeutic strains. These previously undetectable dynamics may influence the design of microbiome therapeutics and motivate the study of their effects on hosts.}, }
@article {pmid40315739, year = {2025}, author = {Ma, G and Yang, P and Lu, T and Deng, X and Meng, L and Xie, H and Zhou, J and Xiao, X and Tang, X}, title = {Comparative analysis of oral, placental, and gut microbiota characteristics, functional features and microbial networks in healthy pregnant women.}, journal = {Journal of reproductive immunology}, volume = {169}, number = {}, pages = {104535}, doi = {10.1016/j.jri.2025.104535}, pmid = {40315739}, issn = {1872-7603}, abstract = {AIM: Most studies on pregnant women focus on analyzing individual microbial species at specific body sites. This study aims to explore the characteristics, functions, and microbial networks of the oral, placental, and gut microbiota in healthy pregnant women.<br><br>METHODS: A total of 23 healthy pregnant women were enrolled in this study. We analyzed the microbial composition, functional profiles, and microbial networks of the oral, placental, and gut microbiota using 16S rRNA gene sequencing.<br><br>RESULTS: Our findings revealed significant differences in microbial composition across these three sites. The placental microbiota contained a relatively high proportion of low-abundance microorganisms, which were more diverse and evenly distributed compared to the gut and oral microbiota. The microbial composition at each site displayed distinct characteristics, likely influenced by environmental, physiological, and biological factors. The placental microbiota exhibited a complex network of tightly interconnected genera, whereas the gut microbiota showed sparser connections, with fewer closely related genera compared to the placental and oral microbiota. Functional differences were also observed among the three microbiota, with each playing a unique role in maintaining host health and metabolic balance. While the oral and gut microbiota shared functional similarities, the placental microbiota exhibited distinct functional characteristics.<br><br>CONCLUSIONS: This study provides valuable insights into the microbial communities of healthy pregnant women, offering important data for microbiological research during pregnancy and laying the foundation for future investigations into the roles of these microbial communities in maternal health.}, }
@article {pmid40315479, year = {2025}, author = {Kharey, G and Palace, V and Whyte, L and Greer, C}, title = {Pangenomic analysis of three putative hydrocarbon degrading genera Limnohabitans, Aquabacterium, and Novosphingobium collected from freshwater sources.}, journal = {Genome}, volume = {}, number = {}, pages = {}, doi = {10.1139/gen-2023-0099}, pmid = {40315479}, issn = {1480-3321}, abstract = {A pangenome analysis offers a unique exploration of the metabolic and genetic diversity, range of ecological niches, and evolution of a particular genus or species. However, such pangenomic analyses are uncommon among environmentally relevant genera. Here, we present freshwater pangenomes of 3 environmentally relevant genera, Limnohabitans, Aquabacterium, and Novosphingobium. These genera had been detected in hydrocarbon degrading cultures in previous research by our group. Using pangenomic tools we attempted to characterize the extent of hydrocarbon degradation potential within each pangenome and determine what ecological niche each genus occupies within hydrocarbon degradation. In total 46 Limnohabitans, 10 Aquabacterium, and 32 Novosphingobium freshwater genomes were collected from various databases and compiled into pangenomes. We found that each pangenome harbours downstream hydrocarbon degrading potential and unexpected genetic diversity within its core and accessory pangenomes possibly stemming from geographic and metagenomic data processing influences. This work was the first to explore pangenomes of these environmentally relevant genera.}, }
@article {pmid40315414, year = {2025}, author = {Galperina, A and Lugli, GA and Milani, C and De Vos, WM and Ventura, M and Salonen, A and Hurwitz, B and Ponsero, AJ}, title = {The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut.}, journal = {PLoS computational biology}, volume = {21}, number = {5}, pages = {e1012268}, doi = {10.1371/journal.pcbi.1012268}, pmid = {40315414}, issn = {1553-7358}, abstract = {The growing interest in the role of the gut virome in human health and disease, has led to several recent large-scale viral catalogue projects mining human gut metagenomes each using varied computational tools and quality control criteria. Importantly, there has been to date no consistent comparison of these catalogues' quality, diversity, and overlap. In this project, we therefore systematically surveyed nine previously published human gut viral catalogues. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy between the ressources and suggesting the need for an aggregated resource bringing these viral sequences together. We further expanded these viral catalogues by mining 7,867 infant gut metagenomes from 12 large-scale infant studies collected in 9 different countries. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Using computational inference tools, annotations were obtained for each vOTU representative sequence quality, viral taxonomy, predicted viral lifestyle, and putative host. This project aims to facilitate the reuse of previously published viral catalogues by the research community and follows a modular framework to enable future expansions as novel data becomes available.}, }
@article {pmid40315131, year = {2025}, author = {Donvil, L and Housmans, JAJ and Peeters, E and Vranken, W and Orlando, G}, title = {In-silico identification of archaeal DNA-binding proteins.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf169}, pmid = {40315131}, issn = {1367-4811}, abstract = {MOTIVATION: The rapid advancement of next-generation sequencing technologies has generated an immense volume of genetic data. However, this data is unevenly distributed, with well-studied organisms being disproportionately represented, while other organisms, such as from archaea, remain significantly underexplored. The study of archaea is particularly challenging due to the extreme environments they inhabit and the difficulties associated with culturing them in the laboratory. Despite these challenges, archaea likely represent a crucial evolutionary link between eukaryotic and prokaryotic organisms, and their investigation could shed light on the early stages of life on Earth. Yet, a significant portion of archaeal proteins are annotated with limited or inaccurate information. Among the various classes of archaeal proteins, DNA-binding proteins are of particular importance. While they represent a large portion of every known proteome, their identification in archaea is complicated by the substantial evolutionary divergence between archaeal and the other better studied organisms.<br><br>RESULTS: To address the challenges of identifying DNA-binding proteins in archaea, we developed Xenusia, a neural network-based tool capable of screening entire archaeal proteomes to identify DNA-binding proteins. Xenusia has proven effective across diverse datasets, including metagenomics data, successfully identifying novel DNA-binding proteins, with experimental validation of its predictions.<br><br>AVAILABILITY: Xenusia is available as a PyPI package, with source code accessible at https://github.com/grogdrinker/xenusia, and as a Google Colab web server application at xenusia.ipynb.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid40314681, year = {2025}, author = {Li, X and Su, K and He, Y and Shao, S and Lan, L and Zhang, Q}, title = {Knowledge Mapping of International Microbiota Research: Analyzing Thirty-Year Citation Classics and Exploring Future Expectations.}, journal = {The new microbiologica}, volume = {48}, number = {1}, pages = {46-59}, pmid = {40314681}, issn = {1121-7138}, mesh = {Humans ; *Microbiota ; *Biomedical Research ; Bibliometrics ; Gastrointestinal Microbiome ; }, abstract = {Microbiota research has rapidly emerged as a pivotal field, with over 250,000 publications and more than ten million citations recorded in the Web of Science Core Collection database by 2024. There were 1682 original microbiota citation classics (each receiving 400 citations or more) identified over the past three decades, totaling 1,559,594 citations and averaging 927 citations per paper. Collaborative efforts in the production of these citation classics involved 87 out of 89 participating countries and 2107 out of 2142 institutions. The USA, various European countries, and China emerged as the leading contributors to this burgeoning research area. Jeffrey I. Gordon, Rob Knight, and Curtis Huttenhower were the prominent figures in microbiota research. Author keywords were analyzed, which revealed a notable shift in research focus from environmental microorganisms to human gut microbiota. Advances such as high-throughput 16S rRNA sequencing and metagenomics expanded the scope of investigations into host-microbiota interactions. Current research interests encompass exploring mechanisms underlying gut-X-axis conditions, including inflammatory bowel disease, obesity, diabetes, colorectal cancer, liver diseases, and neurological disorders. Moreover, environmental exposures have been evidenced to alter gut microbiota and metabolites, contributing a novel research direction. Future research direction is also anticipated to delve further into biosynthetic gene engineering technologies aimed at microbial interventions, including probiotics and fecal microbiota transplantation. This study outlines the evolving landscape of microbiota research and provides valuable insights to inform future investigations within the field.}, }
@article {pmid40314024, year = {2025}, author = {Malwe, AS and Longwani, U and Sharma, VK}, title = {XenoBug: machine learning-based tool to predict pollutant-degrading enzymes from environmental metagenomes.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {2}, pages = {lqaf037}, pmid = {40314024}, issn = {2631-9268}, mesh = {*Machine Learning ; *Metagenome ; *Xenobiotics/metabolism ; Biodegradation, Environmental ; *Environmental Pollutants/metabolism ; *Bacteria/enzymology/genetics ; Metagenomics/methods ; }, abstract = {Application of machine learning-based methods to identify novel bacterial enzymes capable of degrading a wide range of xenobiotics offers enormous potential for bioremediation of toxic and carcinogenic recalcitrant xenobiotics such as pesticides, plastics, petroleum, and pharmacological products that adversely impact ecology and health. Using 6814 diverse substrates involved in ∼141 200 biochemical reactions, we have developed 'XenoBug', a machine learning-based tool that predicts bacterial enzymes, enzymatic reaction, the species capable of biodegrading xenobiotics, and the metagenomic source of the predicted enzymes. For training, a hybrid feature set was used that comprises 1603 molecular descriptors and linear and circular fingerprints. It also includes enzyme datasets consisting of ∼3.3 million enzyme sequences derived from an environmental metagenome database and ∼16 million enzymes from ∼38 000 bacterial genomes. For different reaction classes, XenoBug shows very high binary accuracies (>0.75) and F1 scores (>0.62). XenoBug is also validated on a set of diverse classes of xenobiotics such as pesticides, environmental pollutants, pharmacological products, and hydrocarbons known to be degraded by the bacterial enzymes. XenoBug predicted known as well as previously unreported metabolic enzymes for the degradation of molecules in the validation set, thus showing its broad utility to predict the metabolism of any input xenobiotic molecules. XenoBug is available on: https://metabiosys.iiserb.ac.in/xenobug.}, }
@article {pmid40313842, year = {2025}, author = {Lu, X and Du, X and Zhong, D and Li, R and Cao, J and Huang, S and Wang, Y}, title = {Nanopore Environmental Analysis.}, journal = {JACS Au}, volume = {5}, number = {4}, pages = {1570-1590}, pmid = {40313842}, issn = {2691-3704}, abstract = {As global pollution continues to escalate, timely and accurate monitoring is essential for guiding pollution governance and safeguarding public health. The increasing diversity of pollutants across environmental matrices poses a significant challenge for instrumental analysis methods, which often require labor-intensive and time-consuming sample pretreatment. Nanopore technology, an emerging single-molecule technique, presents a promising solution by enabling the rapid identification of multiple targets within complex mixtures with minimal sample preparation. A wide range of pollutants have been characterized using natural biological nanopores or artificial solid-state nanopores, and their distinct advantages include simple sample preparation, high sensitivity, and rapid onsite analysis. In particular, long-read nanopore sequencing has led to dramatic improvements in the analyses of environmental microbial communities, allows species-level taxonomic assignment using amplicon sequencing, and simplifies the assembly of metagenomes. In this Perspective, we review the latest advancements in analyzing chemical and biological pollutants through nanopore sensing and sequencing techniques. We also explore the challenges that remain in this rapidly evolving field and provide an outlook on the potential for nanopore environmental analysis to transform pollution monitoring, risk assessment, and public health protection.}, }
@article {pmid40313750, year = {2025}, author = {Ndione, MHD and Ndiaye, EH and Dieng, M and Diouf, B and Sankhé, S and Diallo, D and Kane, M and Sene, NM and Mbanne, M and Sy, FA and Diop, SMBS and Doukanda, SFM and Sall, AA and Faye, O and Dia, N and Weaver, SC and Faye, O and Diallo, M and Fall, G and Gaye, A and Diagne, MM}, title = {Mosquito-Based Detection of Endogenous Jaagsiekte Sheep Retrovirus in Senegal: Expanding the Scope of Xenosurveillance.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-5951454/v1}, pmid = {40313750}, issn = {2693-5015}, abstract = {Background Mosquitoes are well-known vectors for arthropod-borne viruses, yet their role as passive carriers of non-arthropod-borne viruses remains underexplored. Xenosurveillance, a method that utilizes blood-feeding arthropods to sample host and pathogen genetic material, has emerged as a valuable tool in viral ecology. In this study, we report the first identification of Jaagsiekte Sheep Retrovirus (JSRV)-related sequences in blood-fed mosquitoes collected in Senegal. JSRV, a betaretrovirus responsible for ovine pulmonary adenocarcinoma, is typically found in sheep, but its genetic trace in mosquitoes offers a novel perspective on host-vector contact and surveillance. Our study aimed to investigate whether mosquitoes can serve as sentinels for detecting both pathogens and host-derived markers in complex ecosystems. Methods Mosquitoes were collected between 2016 and 2019 from three ecologically significant regions in Senegal (Louga, Barkedji, and Kedougou). Blood-fed mosquitoes were pooled and subjected to RNA extraction and metagenomic sequencing using Illumina NextSeq550. Sequencing data were analyzed with CZ-ID and BLAST for viral identification. RT-qPCR assays were designed to validate the presence of JSRV-related sequences, targeting conserved regions of the envelope gene and 3' untranslated region. Phylogenetic analysis was conducted using MAFFT and IQ-TREE to compare the detected sequence with global exogenous and endogenous JSRV references. Results A diverse array of viruses across mosquito species, including both arboviruses and non-arthropod-borne viruses. A JSRV-related sequence was detected in a single blood-fed mosquito pool collected in Barkedji (2019). The RT-qPCR assay confirmed JSRV presence, validating the sequencing results. Phylogenetic analysis revealed strong similarity to known endogenous JSRV (enJSRV) sequences integrated in the sheep genome, indicating that the detected material likely originated from host DNA ingested during blood feeding. Discussion This study presents the first report of endogenous retroviral sequences detected in mosquitoes, alongside the identification of actively circulating viruses, highlighting the broader potential of mosquitoes as environmental sentinels. While mosquitoes are not biological vectors for JSRV, their ability to capture both host-derived retroviral material and pathogenic viral genomes through bloodmeals reinforces the value of xenosurveillance for monitoring livestock-vector-environment interactions. These findings contribute to broader efforts in integrated disease surveillance and underscore the utility of combining metagenomics with molecular diagnostics to detect diverse viral signals in high-risk ecological settings.}, }
@article {pmid40313611, year = {2025}, author = {Ren, X and Sun, H and Cheng, Y and Zhang, Y and Gao, D}, title = {Neurocysticercosis detected by targeted next-generation sequencing of cerebrospinal fluid: a case report.}, journal = {Frontiers in neurology}, volume = {16}, number = {}, pages = {1504348}, pmid = {40313611}, issn = {1664-2295}, abstract = {The patient, a middle-aged male with a long history of the disease, had experienced recurrent headaches for 26 years and episodic shaking of the right limb with slurred speech for the past month. He was previously diagnosed with cerebral cysticercosis and had shown improvement after anthelmintic treatment. In recent years, he noted a resurgence of headaches. One month prior, he developed right limb shaking and occasional slurred speech. A clinical neurological examination was unremarkable, but cranial MRI and cerebrospinal fluid sequencing confirmed a diagnosis of cerebral cysticercosis. Anthelmintic treatment was administered, resulting in symptom improvement.}, }
@article {pmid40313603, year = {2025}, author = {Pu, Y and Zhou, X and Cai, H and Lou, T and Liu, C and Kong, M and Sun, Z and Wang, Y and Zhang, R and Zhu, Y and Ye, L and Zheng, Y and Zhu, B and Quan, Z and Zhao, G and Zheng, Y}, title = {Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.}, journal = {Phenomics (Cham, Switzerland)}, volume = {5}, number = {1}, pages = {76-90}, pmid = {40313603}, issn = {2730-5848}, abstract = {UNLABELLED: In gut microbial research, DNA extraction remarkably influences study outcomes and biological interpretations. Rapid advancements in the research scale and technological upgrades necessitate evaluating new methods to ensure reliability and precision in microbial community profiling. We systematically evaluated the performance of eight recent and commonly used extraction methods using a microbial mock community (MMC) and fecal samples from two healthy volunteers, incorporating bacterial, archaeal, and fungal constituents. Performance metrics included nucleic acid assessment, microbial profile assessment, and scalability for large-scale studies, leveraging shotgun metagenomics for in-depth analysis. Despite variations in DNA quantity and quality, all methods yielded sufficient DNA for shotgun metagenomic sequencing. In the MMC microbial profile assessment, the QIAamp PowerFecal pro Kit (PF) and DNeasy PowerSoil HTP kit (PS) methods exhibited higher similarity with the theoretical composition and lower variability across technical replicates compared to other methods. For fecal samples, the extraction method accounted for 21.4% of the overall microbiome variation and significantly affected the abundances of 32% of detected microbial species. Methods using mechanical lysis with small beads, such as PF and PS, demonstrated better efficiency, indicated by increased microbial diversity in extracting DNA from Gram-positive bacteria. Furthermore, the PF and PS methods are notably simple to execute and automation-friendly, though relatively costly. Our study underscores the importance of maintaining consistency in DNA extraction methods for reliable comparative metagenomic analyses. We recommend PF and PS methods as optimal for expansive gut metagenomic research, emphasizing the critical role of mechanical lysis in DNA extraction.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00232-x.}, }
@article {pmid40313600, year = {2025}, author = {Tang, M and Zhang, Z and Lin, L and Niu, J and Meng, G and Wang, W and Wang, J and Wang, Y}, title = {Comparative Analysis of Growth Dynamics and Relative Abundances of Gut Microbiota Influenced by Ketogenic Diet.}, journal = {Phenomics (Cham, Switzerland)}, volume = {5}, number = {1}, pages = {65-75}, pmid = {40313600}, issn = {2730-5848}, abstract = {UNLABELLED: Although the compositional alterations of gut bacteria in ketogenic diet (KD) have been intensively investigated, the causal relationship between this extreme diet and the microbiota changes is not fully understood. Here, we studied the growth dynamics of intestinal bacteria in KD. We used the CoPTR method to calculate the peak-to-trough ratio (PTR) based on metagenomic sequencing data, serving as an indicator of bacterial growth rates. Notably, Akkermansia muciniphila, a bacterium strongly linked to the therapeutic benefits of KD, exhibited one of the highest growth rates, aligning with its markedly elevated abundance. Our findings also revealed discrepancies in the change patterns of CoPTR values and relative abundances for various bacteria across different diet groups, some of which might be attributed to the exceptionally high or low growth rates of specific species. For some of the species demonstrating obvious differences in growth rates between KD and standard diet, we conducted in vitro culture experiments, supplementing them with diverse nutritional sources to elucidate the underlying mechanisms. The integrative analysis of bacterial abundance and growth dynamics can help deepen our understanding of the gut microbiota changes caused by KD and the therapeutic effects of this special diet.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00228-7.}, }
@article {pmid40313461, year = {2025}, author = {Bessa, LJ and Egas, C and Pires, C and Proença, L and Mascarenhas, P and Pais, RJ and Barroso, H and Machado, V and Botelho, J and Alcoforado, G and Mendes, JJ and Alves, R}, title = {Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1543100}, pmid = {40313461}, issn = {2235-2988}, mesh = {Humans ; *Peri-Implantitis/microbiology ; *Saliva/microbiology ; Pilot Projects ; Cross-Sectional Studies ; *Microbiota ; *Dental Implants/microbiology ; Male ; Female ; Biofilms/growth &amp; development ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Metagenomics ; Adult ; }, abstract = {INTRODUCTION: The rising use of dental implants is accompanied by an expected increase in peri-implant diseases, particularly peri-implantitis (PI), which poses a significant threat to implant success and necessitates a thorough understanding of its pathogenesis for effective management.<br><br>METHODS: To gain deeper insights into the role and impact of the peri-implant microbiome in the pathogenesis and progression of PI, we analyzed 100 samples of saliva and subgingival biofilm from 40 participants with healthy implants (HI group) or with co-occurrence of diagnosed PI-affected implants and healthy implants (PI group) using shotgun metagenomic sequencing. We identified the most discriminative species distinguishing healthy from diseased study groups through log ratios and differential ranking analyses.<br><br>RESULTS AND DISCUSSION: Mogibacterium timidum, Schaalia cardiffensis, Parvimonas micra, Filifactor alocis, Porphyromonas endodontalis, Porphyromonas gingivalis and Olsenella uli were associated with the subgingival peri-implant biofilm. In contrast, Neisseria sp oral taxon 014, Haemophilus parainfluenzae, Actinomyces naeslundii, Rothia mucilaginosa and Rothia aeria were more prevalent in the healthy peri-implant biofilm. Functional pathways such as arginine and polyamine biosynthesis, including putrescine and citrulline biosynthesis, showed stronger correlations with PI-affected implants. In contrast, peri-implant health was characterized by the predominance of pathways involved in purine and pyrimidine deoxyribonucleotide de novo biosynthesis, glucose and glucose-1-phosphate degradation, and tetrapyrrole biosynthesis. Our findings reveal that healthy implants in PI-free oral cavities differ significantly in microbial composition and functional pathways compared to healthy implants co-occurring with PI-affected implants, which more closely resemble PI-associated profiles. This pattern extended to salivary samples, where microbial and functional biomarkers follow similar trends.}, }
@article {pmid40313410, year = {2025}, author = {Liu, J and Zhou, Y and Feng, J and Cai, C and Zhang, S}, title = {Comparative metagenomic analysis reveals the adaptive evolutionary traits of siboglinid tubeworm symbionts.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1533506}, pmid = {40313410}, issn = {1664-302X}, abstract = {Tubeworms flourish in marine cold seeps and hydrothermal vents through the establishment of symbiotic relationships with chemosynthetic bacteria. However, the environmental adaptations and evolutionary relationships of tubeworm symbionts across diverse habitats and hosts remain largely unknown. In this study, we characterized the genomes of 26 siboglinid tubeworm symbionts collected from deep-sea hydrothermal vents, cold seeps, and deep-sea mud, including two sequenced in this study and 24 previously published. Phylogenetic analysis classified the 26 symbiont genomes into five distinct clusters at the genus level. The findings highlight the remarkable diversity in symbiont classification, influenced by the habitat and species of tubeworm, with the symbiont genome characteristics of various genera revealing unique evolutionary strategies. Siboglinid symbionts exhibit functional metabolic diversity, encompassing chemical autotrophic capabilities for carbon, nitrogen, and sulfur metabolism, hydrogen oxidation, and a chemoorganotrophic ability to utilize various amino acids, cofactors, and vitamins. Furthermore, the symbiont's homeostatic mechanisms and CRISPR-Cas system are vital adaptations for survival. Overall, this study highlights the metabolic traits of siboglinid symbionts across different genera and enhances our understanding of how different habitats and hosts influence symbiont evolution, offering valuable insights into the strategies that symbionts use to adapt and thrive in extreme environments.}, }
@article {pmid40313389, year = {2025}, author = {Yu, D and Liu, Y and Cai, H and Huang, W and Wu, H and Yang, P}, title = {Metagenomic investigation of bacterial laccases in a straw-amended soil.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19327}, pmid = {40313389}, issn = {2167-8359}, mesh = {*Laccase/genetics/metabolism ; *Metagenomics ; *Soil Microbiology ; Phylogeny ; *Bacteria/enzymology/genetics ; *Soil/chemistry ; Escherichia coli/genetics ; *Bacterial Proteins/genetics/metabolism ; }, abstract = {BACKGROUND: Bacterial laccases play a crucial role in the degradation of lignin and the turnover of soil organic matter. Their advantageous properties make them highly suitable for a wide range of industrial applications. However, the limited identification of these potential enzymes has impeded their full utilization. The straw-amended soil provides materials for the development of bacterial laccases.<br><br>METHODS: Metagenomic sequencing of a straw-amended soil was conducted to explore novel bacterial laccases. The putative bacterial laccases were then screened using profile hidden Markov models for further analysis. The most abundant gene, lacS1, was heterologously expressed in Escherichia coli and the recombinant laccase was purified for enzymatic characterization.<br><br>RESULTS: A total of 322 putative bacterial laccases were identified in the straw-amended soil. Among them, 45 sequences had less than 30% identity to any entries in the Carbohydrate-Active Enzyme database and only 4.66% were more than 75% similar to proteins in the NCBI environmental database, exhibiting their novelty. These enzymes were found across various bacterial orders, demonstrating substantial diversity. Phylogenetic analysis revealed a number of the bacterial laccase sequences clustered with homologs characterized by favorable enzymatic properties. Five full-length representative bacterial laccase genes were obtained by modified thermal asymmetric interlaced PCR. The laccase activity of lacS1 was validated. It was a mesophilic enzyme with alkaline stability and halotolerance, indicating its promise for industrial applications.<br><br>IMPLICATIONS: These findings highlight novel bacterial laccase resources with potential for industrial applications and enzyme engineering.}, }
@article {pmid40313234, year = {2025}, author = {Leibovitzh, H and Fliss Isakov, N and Werner, L and Thurm, T and Hirsch, A and Cohen, NA and Maharshak, N}, title = {A Mushroom Based Prebiotic Supplement Pilot Study Among Patients with Crohn's Disease.}, journal = {Journal of dietary supplements}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/19390211.2025.2498127}, pmid = {40313234}, issn = {1939-022X}, abstract = {Data on a mushroom based prebiotic supplementation in patients with Crohn's disease (CD) in western population is scarce. In this pilot trial, we aimed to assess the clinical efficacy and fecal microbial compositional and functional alterations associated with 'Mycodigest,' a commercial prebiotic supplement composed of three mushroom extracts. Patients with mild to moderate CD were recruited to a single center, randomized, double-blind, placebo-controlled pilot induction trial. Clinical efficacy using the Harvey-Bradshaw index and biochemical response using C-reactive protein and fecal calprotectin were assessed at week 8 post-intervention. Fecal samples were assessed by DNA shotgun metagenomic sequencing. A multivariable linear mixed effects model was used to assess alteration in fecal microbiome composition and function pre- and post-'Mycodigest' intervention. Clinical response was higher in the 'Mycodigest' intervention (N = 10) compared to the placebo (N = 6) group (80 vs. 16.7%, respectively, p = 0.035). There were no differences in terms of biochemical response within each group pre- and post-intervention. Post-'Mycodigest' intervention, 25 species were found to be differentially abundant compared to baseline, including increase in short chain fatty acid producing bacteria, such as Parabacteroides distasonis (Beta coefficient 0.92, 95% Confidence interval [CI] 0.36-1.47) and Faecalimonas umbilicata (Beta coefficient 0.57, 95% CI 0.23-0.90). Two microbial pathways related to the metabolism of isoprenoid compounds were increased post-'Mycodigest' intervention. Mushroom based prebiotic supplementation in subjects with CD resulted in clinical improvement which may be related to post-intervention favorable compositional and functional microbial alterations.}, }
@article {pmid40313154, year = {2025}, author = {Abiola, C and Gwak, JH and Lee, UJ and Adigun, AO and Rhee, SK}, title = {Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {63}, number = {4}, pages = {e2502002}, doi = {10.71150/jm.2502002}, pmid = {40313154}, issn = {1976-3794}, support = {//National Research Foundation of Korea/ ; 2021R1A2C3004015//Ministry of Science and ICT/ ; RS-2023-00213601//Ministry of Science and ICT/ ; 2020R1A6A1A06046235//Ministry of Education/ ; //Korea Institute of Marine Science &amp; Technology Promotion/ ; RS-2024-00436293//Ministry of Oceans and Fisheries/ ; }, mesh = {*Soil Microbiology ; Phylogeny ; *Nitrification ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Ammonia/metabolism ; Oxidation-Reduction ; Soil/chemistry ; Metagenomics ; Filtration ; Nitrites/metabolism ; }, abstract = {Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FF_bin01 and FF_bin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FF_bin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FF_bin01 and FF_bin02 are identified as novel species within the genera "Candidatus Nitrosocosmicus" and Nitrososphaera, respectively, while FF_bin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FF_bin01 and FF_bin02 harbor a gene encoding manganese catalase and FF_bin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.}, }
@article {pmid40313146, year = {2025}, author = {Jeong, H and Choe, Y and Nam, J and Ban, YH}, title = {A guide to genome mining and genetic manipulation of biosynthetic gene clusters in Streptomyces.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {63}, number = {4}, pages = {e2409026}, doi = {10.71150/jm.2409026}, pmid = {40313146}, issn = {1976-3794}, support = {//Ministry of Science and ICT/ ; IITP-2025-RS-2023-00260267//Institute for Information &amp; communications Technology Planning &amp; Evaluation/ ; 202305080001//Kangwon National University/ ; //National Research Foundation of Korea/ ; 2021R1C1C2006260//Ministry of Science and ICT/ ; RS-2023-00301850//Ministry of Education/ ; }, mesh = {*Streptomyces/genetics/metabolism ; *Multigene Family ; *Biosynthetic Pathways/genetics ; *Genome, Bacterial ; Secondary Metabolism/genetics ; Biological Products/metabolism ; *Genomics/methods ; }, abstract = {Streptomyces are a crucial source of bioactive secondary metabolites with significant clinical applications. Recent studies of bacterial and metagenome-assembled genomes have revealed that Streptomyces harbors a substantial number of uncharacterized silent secondary metabolite biosynthetic gene clusters (BGCs). These BGCs represent a vast diversity of biosynthetic pathways for natural product synthesis, indicating significant untapped potential for discovering new metabolites. To exploit this potential, genome mining using comprehensive strategies that leverage extensive genomic databases can be conducted. By linking BGCs to their encoded products and integrating genetic manipulation techniques, researchers can greatly enhance the identification of new secondary metabolites with therapeutic relevance. In this context, we present a step-by-step guide for using the antiSMASH pipeline to identify secondary metabolite-coding BGCs within the complete genome of a novel Streptomyces strain. This protocol also outlines gene manipulation methods that can be applied to Streptomyces to activate cryptic clusters of interest and validate the functions of biosynthetic genes. By following these guidelines, researchers can pave the way for discovering and characterizing valuable natural products.}, }
@article {pmid40312907, year = {2025}, author = {Zheng, CM and Kang, HW and Moon, S and Byun, YJ and Kim, WT and Choi, YH and Moon, SK and Piao, XM and Yun, SJ}, title = {Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer.}, journal = {Investigative and clinical urology}, volume = {66}, number = {3}, pages = {272-280}, doi = {10.4111/icu.20240454}, pmid = {40312907}, issn = {2466-054X}, support = {2020R1I1A3062508/NRF/National Research Foundation of Korea/Korea ; RS-2023-00245919/NRF/National Research Foundation of Korea/Korea ; RS-2024-00342111/NRF/National Research Foundation of Korea/Korea ; 5199990614277/NRF/National Research Foundation of Korea/Korea ; /KHIDI/Korea Health Industry Development Institute/Korea ; }, mesh = {Humans ; *Microbiota/genetics ; *Urinary Bladder Neoplasms/microbiology/urine ; *DNA, Bacterial/isolation &amp; purification/urine ; Male ; Female ; Middle Aged ; *Urine/microbiology ; Aged ; RNA, Ribosomal, 16S ; Reproducibility of Results ; }, abstract = {PURPOSE: This study aimed to evaluate and optimize microbial DNA extraction methods from urine, a non-invasive sample source, to enhance DNA quality, purity, and reliability for urinary microbiome research and biomarker discovery in bladder cancer.<br><br>MATERIALS AND METHODS: A total of 302 individuals (258 with genitourinary cancers and 44 with benign urologic diseases) participated in this study. Urine samples were collected via sterile catheterization, resulting in 445 vials for microbial analysis. DNA extraction was performed using three protocols: the standard protocol (SP), water dilution protocol (WDP), and chelation-assisted protocol (CAP). DNA quality (concentration, purity, and contamination levels) was assessed using NanoDrop spectrophotometry. Microbial analysis was conducted on 138 samples (108 cancerous and 30 benign) using 16S rRNA sequencing. Prior to sequencing on the Illumina MiSeq platform, Victor 3 fluorometry was used for validation.<br><br>RESULTS: WDP outperformed other methods, achieving significantly higher 260/280 and 260/230 ratios, indicating superior DNA purity and reduced contamination, while maintaining reliable DNA yields. CAP was excluded due to poor performance across all metrics. Microbial abundance was significantly higher in WDP-extracted samples (p<0.0001), whereas SP demonstrated higher alpha diversity indices (p<0.01), likely due to improved detection of low-abundance taxa. Beta diversity analysis showed no significant compositional differences between SP and WDP (p=1.0), supporting the reliability of WDP for microbiome research.<br><br>CONCLUSIONS: WDP is a highly effective and reliable method for microbial DNA extraction from urine, ensuring high-quality and reproducible results. Future research should address sample variability and crystal precipitation to further refine microbiome-based diagnostics and therapeutics.}, }
@article {pmid40312727, year = {2025}, author = {Wang, L and Wu, Y and Zhao, ZB and Jia, T}, title = {Small-scale heterogeneity of soil properties in farmland affected fava beans growth through rhizosphere differential metabolites and microorganisms.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {45}, pmid = {40312727}, issn = {2524-6372}, support = {52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Soil heterogeneity has been acknowledged to influence plant growth, with the small-scale soil heterogeneity always being overlooked in practice. It remains unclear how rhizosphere soil biotics and abiotics respond to soil heterogeneity and how rhizosphere interactions influence crop growth.<br><br>RESULTS: In this study, we planted fava beans in a farmland around an e-waste dismantling site, and a distinct boundary (row spacing is 30&#xa0;cm) was observed in the field during the flowering stage, which divided fava beans phenotypes into two distinct groups (Big vs Little) based on the differences in biomass and height. Soil total concentrations of As, B, Co, Cr, Cu, Pb, Sr, Zn, Ni, Cd and soil pH significantly differed in the rhizosphere of fava beans in the two adjacent rows, which were located on either side of the boundary, with a row-spacing of 30&#xa0;cm. Random Forest analysis demonstrated that these differentiated soil properties (soil pH, total As, B, Cd, Co, Cr, Cu, Mo, Ni and Zn) substantially influenced fava beans growth (height and biomass). Metagenomic sequencing showed that microbial taxa were significantly enriched their abundance in rhizosphere soils between the two groups of fava beans, with eukaryotic taxa being more sensitively affected. A total of 20 metabolites including coniferyl alcohol, jasmonic acid, resveratrol, and L-aspartic acid, etc. were significantly correlated with fava beans growth. These metabolites were significantly enriched in 15 metabolic pathways (nucleotide metabolism, pyrimidine metabolism, purine metabolism, biosynthesis of plant secondary metabolites, lysine biosynthesis, etc.). Furthermore, 11 microbial genera involved in these metabolic pathways, and these genera were differentially enriched between the two groups and significantly correlated with fava beans growth.<br><br>CONCLUSIONS: Overall, the integrated analysis of multi-omics revealed that soil properties heterogeneity at small-scale altered the rhizosphere differential microorganisms and metabolites, which functionally influenced fava beans growth and tolerance to environmental stress. Notably, even soil heterogeneity at such a small spatial scale can cause significant differences in plant growth, and the comprehensive explorations utilizing multi-omics techniques provide novel insights to the field management, which is crucial for the survival and sustainable development of humanity.}, }
@article {pmid40312673, year = {2025}, author = {Qin, X and Song, Y and Ding, J and Qin, X and Chen, K and Wang, H}, title = {Symptomatic central nervous system infections in kidney transplant recipients: a 20-years multicenter observational study.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {641}, pmid = {40312673}, issn = {1471-2334}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; Male ; Female ; *Central Nervous System Infections/epidemiology/microbiology/etiology/diagnosis/mortality/cerebrospinal fluid ; Retrospective Studies ; Middle Aged ; Adult ; *Transplant Recipients/statistics &amp; numerical data ; China/epidemiology ; Aged ; Young Adult ; }, abstract = {BACKGROUND: Central nervous system (CNS) infections in kidney transplant recipients (KTRs) remain poorly characterized, with current evidence largely derived from isolated case reports over the past two decades. This multicenter study aims to systematically delineate the epidemiology, clinical profiles, and outcomes of CNS infections in a large KTR cohort.<br><br>METHODS: We conducted a retrospective analysis of 3,602 KTRs across three transplant centers in China (May 2004-July 2024). CNS infections were defined by: 1) neurological symptoms/signs, and 2) microbiological confirmation via cerebrospinal fluid (CSF) analysis, including metagenomic next-generation sequencing (mNGS) and routine microbiologic testing (bacterial and fungal cultures).<br><br>RESULTS: CNS infections were diagnosed in 0.53% of KTRs (19/3602), with symptom onset occurring 2-121&#xa0;months post-transplantation. Etiologies included bacterial (47%, 9/19), viral (32%, 6/19), and fungal (21%, 4/19) pathogens. Notably, 79% of cases (15/19) were exclusively identified by mNGS, whereas conventional cultures failed detection. Presenting symptoms included headache (79%) and altered mental status (42%). Mortality reached 42% (8/19) within 9-22&#xa0;days of diagnosis; among survivors, 73% (8/11) exhibited neurological sequelae.<br><br>CONCLUSIONS: CNS infections in KTRs are rare but characterized by rapid progression and high fatality rate. While the risk of CNS infections persists throughout the post-transplant period, 1-6&#xa0;months after transplantation is a higher-incidence period of CNS infections. KTRs with neurological symptoms (particularly headache and elevated CSF pressure) should undergo CSF mNGS which is critical in diagnosing such infections.}, }
@article {pmid40312516, year = {2025}, author = {Kim, DD and Swarthout, JM and Worby, CJ and Chieng, B and Mboya, J and Earl, AM and Njenga, SM and Pickering, AJ}, title = {Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40312516}, issn = {2058-5276}, support = {n/a//Tufts University/ ; U19AI110818//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 5R21AI171890//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 5R21AI171890//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {Identifying bacterial transmission pathways is crucial to inform strategies that limit the spread of pathogenic and antibiotic-resistant bacteria. Here we assessed Escherichia coli strain-sharing and overlap of antibiotic resistance genes (ARGs) across humans, poultry, canines, soil, and drinking water within and between households in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households with half having access to chlorinated water. We performed Pooling Isolated Colonies-seq, which sequences pools of up to five E. coli colonies per sample to capture strain diversity. Pooling Isolated Colonies-seq captured 1,516 colonies and identified 154 strain-sharing events, overcoming limitations of single-isolate sequencing and metagenomics. Within households, strain-sharing rates and resistome similarities across sample types were strongly correlated, suggesting clonal transmission of ARGs. E. coli isolated from the environment carried clinically relevant ARGs. Strain-sharing was rare between animals and humans but frequent between humans and drinking water. E. coli-contaminated stored drinking water was associated with higher human-human strain-sharing within households. These results suggest that contaminated drinking water facilitates human to human strain-sharing, and water treatment can disrupt transmission.}, }
@article {pmid40312036, year = {2025}, author = {Patangia, DV and Grimaud, G and Lyons, K and Dempsey, E and Ryan, CA and O'Shea, CA and Ross, RP and Stanton, C}, title = {Influence of feeding habit and duration on infant gut microbiome - a 6 month pilot study.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-15}, doi = {10.1163/18762891-bja00075}, pmid = {40312036}, issn = {1876-2891}, abstract = {While the importance of breastfeeding on the developing infant gut microbiota has been established, few studies have compared the effect of breastfeeding duration on infant gut microbiota development. In this pilot study, we included 23 infants, divided into 4 groups to compare the effect of breastfeeding duration for first 4 (BreastFed_4) or 8 weeks (BreastFed_8) compared to exclusive breast (Exc Breast Fed) or formula feeding (Formula Fed) for 6 months. We used metagenomics shotgun sequencing of 88 infant stool samples and 64 corresponding maternal milk samples to examine the microbial composition. Breast milk samples showed the presence of previously defined core bacteria including spp. belonging to Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium, Rothia and Pseudomonas. We report that the Exc Breast Fed infant group had the lowest alpha diversity and a distinct microbial composition compared to the Formula Fed group. BreastFed_4 clustered distinctly from all other groups, indicating the impact of duration and time of feeding on infant microbiota. Certain Bifidobacterium spp. were more associated to certain groups, in particular, B. infantis was more associated to Exc Breast Fed while Bacteroides/Phocaeicola with BreastFed_8. Exc Breast Fed showed the highest frequency of persisters with B. infantis being the dominant persister, while B. bifidum was the dominant persister in Formula Fed group. Persisters showed significantly higher abundance of several glycoside hydrolases (GH) important in early life across all groups compared to non-persisters. This study highlights infant gut microbiota changes associated with breastfeeding duration, warranting more detailed studies on the impact of breastfeeding duration on long-term health outcomes.}, }
@article {pmid40311978, year = {2025}, author = {Wang, YX and Dong, BX and Liu, YJ and Tan, YQ and An, YT and Lin, LH and Li, G}, title = {Molecular cloning, characterization, and structural stability analysis of a rare acidic catechol 2,3-dioxygenase from the metagenome of coal-polluted soil.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {143652}, doi = {10.1016/j.ijbiomac.2025.143652}, pmid = {40311978}, issn = {1879-0003}, abstract = {Polycyclic Aromatic Hydrocarbons (PAHs) are ubiquitous environmental pollutants that pose substantial health hazards, especially in coal-mining areas. This study presented the metagenomic identification and comprehensive characterization of a novel acidic catechol 2,3-dioxygenase, C23O927, derived from a coal-contaminated soil metagenome. Optimal enzymatic activity for C23O927 was observed at pH 4.0 and 55 °C, with remarkable stability across a wide pH spectrum (2.0-10.0) and temperature range (30 °C-60 °C). The enzyme displayed robust tolerance to various organic solvents and salts, and its activity was notably activated by diverse metal ions. Distinct from other catechol 2,3-dioxygenases, C23O927 exhibited oxygen tolerance and maintained robust activity after purification at 4 °C for up to three days. The structural stability of C23O927 is attributed to its unique extended β-sheet structure and increased α-helices. These characteristics help enhance rigidity and reduce the exposure of the hydrophobic core, thereby conferring greater stability on C23O927. The unique properties of C23O927, which include an optimal pH for acidic environments, salt tolerance, resistance to metal ions and organic solvents, and thermal stability, render it a promising candidate for industrial waste management and soil bioremediation.}, }
@article {pmid40311618, year = {2025}, author = {Andreu-Sánchez, S and Blanco-Míguez, A and Wang, D and Golzato, D and Manghi, P and Heidrich, V and Fackelmann, G and Zhernakova, DV and Kurilshikov, A and Valles-Colomer, M and Weersma, RK and Zhernakova, A and Fu, J and Segata, N}, title = {Global genetic structure of human gut microbiome species is related to geographic location and host health.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.04.014}, pmid = {40311618}, issn = {1097-4172}, abstract = {The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have associated microbial relative abundances with human-health-related phenotypes, the substantial intraspecies genetic variability of gut microbes has not yet been comprehensively considered, limiting the potential of linking such genetic traits with host conditions. Here, we analyzed 32,152 metagenomes from 94 microbiome studies across the globe to investigate the human microbiome intraspecies genetic diversity. We reconstructed 583 species-specific phylogenies and linked them to geographic information and species' horizontal transmissibility. We identified 484 microbial-strain-level associations with 241 host phenotypes, encompassing human anthropometric factors, biochemical measurements, diseases, and lifestyle. We observed a higher prevalence of a Ruminococcus gnavus clade in nonagenarians correlated with distinct plasma bile acid profiles and a melanoma and prostate-cancer-associated Collinsella clade. Our large-scale intraspecies genetic analysis highlights the relevance of strain diversity as it relates to human health.}, }
@article {pmid40311598, year = {2025}, author = {Hong, Y and Cui, J and Xu, G and Li, N and Peng, G}, title = {Intestinal IL-17 family orchestrates microbiota-driven histone deacetylation and promotes Treg differentiation to mediate the alleviation of asthma by Ma-Xing-Shi-Gan decoction.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {142}, number = {}, pages = {156656}, doi = {10.1016/j.phymed.2025.156656}, pmid = {40311598}, issn = {1618-095X}, abstract = {BACKGROUND: Gut microbiota imbalance is well-known as one important trigger of allergic asthma. Ma-Xing-Shi-Gan decoction (MXSG) is a traditional Chinese medicine prescription with ideal clinical efficacy on asthma. However, whether and how MXSG exerts its efficacy on asthma through gut microbiota remains unclear.<br><br>PURPOSE: To investigate the underlying mechanism of MXSG against asthma using multi-omics technologies.<br><br>METHODS: An asthma model was established using 8-week-old C57BL/6 J mice, after which they were daily administrated with high-, medium- and low-dose MXSG for 7 days. Histopathological examinations and flow cytometry were performed to evaluate the effects of MXSG on lung immune injury. Key regulatory pathways were predicted via network pharmacology and verified using 16S rRNA sequencing, metagenomics, metabolomics, and in vivo experiments including the knockout of the targeting gene.<br><br>RESULTS: MXSG alleviated asthma symptoms, elevated intestinal microbial diversities, and enriched potential beneficial microbes such as Lactococcus, Lactobacillus, and Limosilactobacillus. Network pharmacology and experimental validation highlighted the IL-17/Treg signaling as crucial for asthma treatment. IL-17 knockout experiments revealed its necessity for Treg differentiation during asthma. Moreover, IL-17-deficient asthmatic mice exhibited lower levels of Lactobacillus and significant changes in microbial genes involving histone deacetylases (HDAC) and short-chain fatty acids (SCFAs). Finally, MXSG significantly boosted SCFA production and reduced HDAC9 expression, which were correlated with Treg cell ratios.<br><br>CONCLUSION: Our study delineates a novel mechanism where MXSG synergizes with the IL-17 family to enrich intestinal beneficial microbes (e.g. Lactobacillus) and SCFAs. This inhibits the expression of SCFA-downstream HDAC9 to promote Treg differentiation, and thus potentially alleviates asthma.}, }
@article {pmid40311430, year = {2025}, author = {Chen, Z and Hu, Y and Qiu, G and Liang, D and Cheng, J and Chen, Y and Wang, G and Zhu, X and Xie, J}, title = {Inoculation with Acinetobacter indicus CZH-5 in internal circulation airlift zeolite spheres sequencing batch reactor to augment simultaneous removal of nitrogen, phosphorus, and tetracycline.}, journal = {Journal of hazardous materials}, volume = {494}, number = {}, pages = {138384}, doi = {10.1016/j.jhazmat.2025.138384}, pmid = {40311430}, issn = {1873-3336}, abstract = {Inoculating functional bacterial strains is a cost-effective strategy for enhancing treatment of anaerobic digestion liquids in swine wastewater. This study systematically evaluated inoculation of heterotrophic nitrification aerobic denitrification strain Acinetobacter indicus CZH-5 in an internal circulation airlift zeolite sphere-based sequencing batch reactor (IR) for aerobic removal of nitrogen (N), phosphorus (P), and tetracycline (TEC). Inoculation with CZH-5 promoted secretion of quorum sensing signaling molecules, specifically N-acyl-homoserine lactones (C6-HSL and C10-HSL). These signaling molecules enhance quorum sensing and reinforce cooperation among functional bacteria. Under optimal conditions, average removal efficiencies of total nitrogen, total phosphate, and TEC were 92.8 %, 88.4 %, and 93.1 %, respectively. The removal performance in IR exceeded that of the control by 26 %-71 %. N removal involved complete nitrification-denitrification, while accumulated P was transformed into phosphate monoesters within biofilm. Metagenomic analysis identified Thauera and Acinetobacter as the dominant genera, and Acinetobacter indicus as predominant species. Inoculation enhanced microbial richness and diversity to improve system operational stability. The abundance of functional genes associated with N, P, and TEC transformations significantly increased compared to the control. This study aimed to investigate the characteristics and mechanisms of inoculating a heterotrophic nitrification aerobic denitrification strain into an aerated biofilm system for swine wastewater remediation.}, }
@article {pmid40311350, year = {2025}, author = {Monge-Olivares, L and Peñalva, G and Pulido, MR and Garrudo, L and Ángel Doval, M and Ballesta, S and Merchante, N and Rasero, P and Cuberos, L and Carpes, G and López-Cerero, L}, title = {Quantitative study of ESBL and carbapenemase producers in wastewater treatment plants in Seville, Spain: a culture-based detection analysis of raw and treated water.}, journal = {Water research}, volume = {281}, number = {}, pages = {123706}, doi = {10.1016/j.watres.2025.123706}, pmid = {40311350}, issn = {1879-2448}, abstract = {Antibiotics can modify populations of multidrug-resistant microorganism (MDRO) in urban wastewater. Our objectives were to quantify the differences in MDR Gram-negative bacteria between influents and effluents of WWTPs of a Spanish city and to evaluate the influence of human antibiotic prescriptions, as well as the persistence of these bacteria after treatment and their genetic relatedness to clinical isolates. The mean count of ESBL producers and carbapenemase producers were 3.77 and 2.74 log 10 CFU/ml, respectively. The reduction achieved by water treatment of ESBL-producing organisms was 1.4-log (96.11 %), whereas a 1.8-log reduction (98.36 %) was obtained regarding carbapenemase producing organisms. Aeromonas spp. predominated among MDROs and blaKPC-2 was the main carbapenemase detected in the influent wastewater samples. Among Escherichia coli and Klebsiella pneumoniae influent isolates, 44 % and 30 %, respectively, belonged to high-risk clones. Regarding Enterobacteriaceae, 10.6 % matched clinical isolates and one strain from an ongoing hospital outbreak was identified among raw samples. New MDROs and persistence of certain strains were detected in effluent samples. Quinolone and third-generation cephalosporin prescriptions, flow rate and population density were associated with higher OXA-48 producer counts. Despite reductions, additional technologies should be implemented in WWTPs receiving hospital discharges. Given the prevalence of environmental species, culture-based and metagenomic approaches should be combined to distinguish between human and sewage sources for antibiotic resistance monitoring. Overall, this study shows that WWTPs with secondary treatment are effective at removing MDRO, and antibiotic stewardship is a potential strategy to reduce the release of MDROs.}, }
@article {pmid40311348, year = {2025}, author = {Liu, C and Yan, S and Luo, X and Zheng, Y and Zhen, G}, title = {Iron-based materials maintain biofilm equilibrium and function as external capacitors to minimize electron loss under intermittent power supply in MEC-AD methane production.}, journal = {Water research}, volume = {281}, number = {}, pages = {123677}, doi = {10.1016/j.watres.2025.123677}, pmid = {40311348}, issn = {1879-2448}, abstract = {Microbial electrolysis cell-anaerobic digestion (MEC-AD) is a cost-effective approach for methane (CH4) recovery from food waste, but its CH4 conversion efficiency requires improvement. To address this, a MIL-100(Fe)-modified carbon cloth anode was developed to enhance anodic biofilm formation and CH4 bioconversion efficiency. At an applied voltage of 0.8 V, the highest daily CH4 yield reached 141.6 mL/g COD/d, a 61 % increase, and increased further to 227.5 mL/g COD/d under intermittent power supply. By facilitating extracellular electron transfer (EET) in electrogenic bacteria, MIL-100(Fe) regulated biofilm thickness and maintained dynamic biofilm equilibrium. Additionally, as an external capacitor, MIL-100(Fe) functioned as a "temporary storage site" for electrons under intermittent power supply, reducing bioelectron loss. Metagenomic analysis revealed that MIL-100(Fe) significantly enriched Bacteroidia and Methanosarcina, promoting carbohydrate metabolism and CH4 production. Under intermittent power supply, MIL-100(Fe) further enriched Geobacter, enhancing electron transfer efficiency. This study demonstrates that iron-based anode modification effectively enhances CH4 production from food waste by optimizing biofilm structure and metabolic pathways, providing a promising strategy for improving MEC-AD performance.}, }
@article {pmid40310938, year = {2025}, author = {Ma, WJ and Wang, C and Kothandapani, J and Luzentales-Simpson, M and Menzies, SC and Bescucci, DM and Lange, ME and Fraser, ASC and Gusse, JF and House, KE and Moote, PE and Xing, X and Grondin, JM and Hui, BW and Clarke, ST and Shelton, TG and Haskey, N and Gibson, DL and Martens, EC and Abbott, DW and Inglis, GD and Sly, LM and Brumer, H}, title = {Bespoke plant glycoconjugates for gut microbiota-mediated drug targeting.}, journal = {Science (New York, N.Y.)}, volume = {}, number = {}, pages = {eadk7633}, doi = {10.1126/science.adk7633}, pmid = {40310938}, issn = {1095-9203}, abstract = {The gut microbiota of mammals possess unique metabolic pathways with untapped therapeutic potential. Using molecular insights into dietary fiber metabolism by the human gut microbiota, we designed a targeted drug delivery system based on bespoke glycoconjugates of a complex plant oligosaccharide called GlycoCaging. GlycoCaging of exemplar anti-inflammatory drugs enabled release of active molecules triggered by unique glycosidases of autochthonous gut bacteria. GlycoCaging ensured drug efficacy was potentiated, and off-target effects were eliminated in murine models of inflammatory bowel disease. Biochemical and metagenomic analyses of gut microbiota of individual humans confirmed the broad applicability of this strategy.}, }
@article {pmid40309222, year = {2025}, author = {Slosser, T and Wenick, M and Markert, E and Trembath-Reichert, E and Ward, LM}, title = {Novel hot spring Thermoproteota support vertical inheritance of ammonia oxidation and carbon fixation in Nitrososphaeria.}, journal = {Access microbiology}, volume = {7}, number = {4}, pages = {}, pmid = {40309222}, issn = {2516-8290}, abstract = {Aerobic ammonia oxidation is crucial to the nitrogen cycle and is only known to be performed by a small number of bacterial lineages [ammonia-oxidizing bacteria (AOB)] and a single lineage of archaea belonging to the Nitrososphaeria class of Thermoproteota [ammonia-oxidizing Archaea (AOA)]. Most cultivated AOA originate from marine or soil environments, but this may capture only a limited subset of the full diversity of this clade. Here, we describe several genomes of AOA from metagenomic sequencing of a hot spring microbial mat, representing several poorly characterized basal lineages that may be important for understanding the early evolution of archaeal ammonia oxidation. These genomes include a novel genus most closely related to Nitrososphaera as well as novel species belonging to the genera Nitrosotenuis, Nitrososphaera and Nitrosotalea. Furthermore, the distributions and phylogenetic relationships of key metabolic genes support a history of vertical inheritance of ammonia oxidation and carbon fixation from the last common ancestor of crown group AOA.}, }
@article {pmid40309194, year = {2025}, author = {Tang, CT and Wu, Y and Tao, Q and Zeng, CY and Chen, YX}, title = {Thalidomide mitigates Crohn's disease colitis by modulating gut microbiota, metabolites, and regulatory T cell immunity.}, journal = {Journal of pharmaceutical analysis}, volume = {15}, number = {4}, pages = {101121}, pmid = {40309194}, issn = {2214-0883}, abstract = {Thalidomide (THA) is renowned for its potent anti-inflammatory properties. This study aimed to elucidate its underlying mechanisms in the context of Crohn's disease (CD) development. Mouse colitis models were established by dextran sulfate sodium (DSS) treatment. Fecal microbiota and metabolites were analyzed by metagenomic sequencing and mass spectrometry, respectively. Antibiotic-treated mice served as models for microbiota depletion and transplantation. The expression of forkhead box P3[+] (FOXP3[+]) regulatory T cells (Tregs) was measured by flow cytometry and immunohistochemical assay in colitis model and patient cohort. THA inhibited colitis in DSS-treated mice by altering the gut microbiota profile, with an increased abundance of probiotics Bacteroides fragilis, while pathogenic bacteria were depleted. In addition, THA increased beneficial metabolites bile acids and significantly restored gut barrier function. Transcriptomic profiling revealed that THA inhibited interleukin-17 (IL-17), IL-1β and cell cycle signaling. Fecal microbiota transplantation from THA-treated mice to microbiota-depleted mice partly recapitulated the effects of THA. Specifically, increased level of gut commensal B. fragilis was observed, correlated with elevated levels of the microbial metabolite 3alpha-hydroxy-7-oxo-5beta-cholanic acid (7-ketolithocholic acid, 7-KA) following THA treatment. This microbial metabolite may stable FOXP3 expression by targeting the receptor FMR1 autosomal homolog 1 (FXR1) to inhibit autophagy. An interaction between FOXP3 and FXR1 was identified, with binding regions localized to the FOXP3 domain (aa238-335) and the FXR1 domain (aa82-222), respectively. Conclusively, THA modulates the gut microbiota and metabolite profiles towards a more beneficial composition, enhances gut barrier function, promotes the differentiation of FOXP3[+] Tregs and curbs pro-inflammatory pathways.}, }
@article {pmid40309109, year = {2025}, author = {Zhang, Z and Sun, J and Wang, D and Lin, T and Yin, Y and Wang, W and Wang, Y and Wang, Z and Fan, L and Jiao, X}, title = {Effects of rotation corn on potato yield, quality, and soil microbial communities.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1493333}, pmid = {40309109}, issn = {1664-302X}, abstract = {INTRODUCTION: Potato is an important crop that can be used both as grain and vegetable in northern China. However, the continuous cropping system of potato has led to a sharp decline in its yield and quality. As one of the effective strategies to alleviate the continuous cropping obstacle, crop rotation has received extensive attention in agricultural practices. On this basis, we have conducted an in-depth exploration of the effects of the potato-maize rotation system on the structure and diversity of the soil microbial community, aiming to analyze the internal correlation mechanism between the structure of the soil microbial community and the yield and quality of crops.<br><br>METHODS: This study was based on fields that had been under potato monoculture for five years and established six experimental treatments: potato-potato-potato (IR-A), potato-maize-potato (IR-B), potato-maize-maize (IR-C), potato-potato-potato (RF-A), potato-maize-potato (RF-B), and potato-maize-maize (RF-C).<br><br>RESULTS: The results showed that under the IR planting model, IR-B significantly increased potato yield and vitamin C content while reducing reducing sugar content compared to IR-A (p < 0.05). In the RF planting model, RF-B significantly increased potato yield, starch content, and vitamin C content compared to RF-A (p < 0.05). Microbial community structure results indicated that crop rotation significantly enhanced the relative abundance of microorganisms such as Bradyrhizobium, Pseudomonas, Sphingomonas, Purpureocillium, Streptomyces, and Halovivax (p < 0.05). These microorganisms are involved in the cycling of carbon, phosphorus, and other nutrients in the soil, playing an important role in promoting root growth, organic matter decomposition, and alleviating soil salinization. The LEfSe and RDA indicated significant differences in microbial communities between monoculture and crop rotation (p < 0.05), with soil slow-growing rhizobia, Burkholderia, and actinomycetes positively correlated with potato yield and quality. Additionally, KEGG functional annotation of different treatments revealed that K00239, K00626, K01681, and K01915 were involved in three key metabolic pathways related to carbon and nitrogen. A total of 20 significantly enriched pathways were identified (p < 0.05), among which K01681 is involved in the tricarboxylic acid cycle and is a differential gene in the RF-B treatment, suggesting that the efficient expression of K01681 during crop rotation contributes to the material cycling of the soil ecosystem. LEfSe analysis of the bins revealed that under the RF-C treatment, the relative abundance of Hyphomicrobiales was significantly higher than in other treatments (p < 0.05). Hyphomicrobiales are involved in the nitrogen fixation process and play an important role in soil nutrient cycling and plant nutrition. In summary, the potato-maize rotation significantly altered the composition of soil microbial communities (p < 0.05), increasing the relative abundance of beneficial microorganisms. This change helps maintain the health of the soil ecosystem, promotes nutrient cycling, reduces the incidence of diseases, and effectively improves both the yield and quality of potatoes.<br><br>DISCUSSION: The potato-maize rotation significantly altered the composition of soil microbial communities (p < 0.05), increasing the relative abundance of beneficial microorganisms. This change helps maintain the health of the soil ecosystem, promotes nutrient cycling, reduces the incidence of diseases, and effectively improves both the yield and quality of potatoes.}, }
@article {pmid40309103, year = {2025}, author = {Cong, X and Liu, X and Zhou, D and Xu, Y and Liu, J and Tong, F}, title = {Characterization and comparison of the fecal bacterial microbiota in Red Back Pine Root Snake (Oligodon formosanus) and Chinese Slug-Eating Snake (Pareas chinensis).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1575405}, pmid = {40309103}, issn = {1664-302X}, abstract = {INTRODUCTION: The gastrointestinal tracts and oral cavities of animals harbor complex microbial communities that assist hosts in nutrient absorption and immune responses, thereby influencing behavior, development, reproduction, and overall health.<br><br>METHODS: We utilized metagenomic sequencing technology to conduct a detailed analysis of the fecal bacterial communities of six Red Back Pine Root Snakes (Oligodon formosanus, XT) and three Chinese Slug-Eating Snakes (Pareas chinensis, Z) individuals. The microbial composition was assessed through taxonomic profiling, alpha diversity analysis, and functional annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.<br><br>RESULTS: The results indicated that Proteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in XT samples, while Z samples additionally contained Patescibacteria. Alpha diversity analysis revealed significant differences in species abundance at the family level, with Z samples exhibiting higher microbial richness than XT. Furthermore, KEGG analysis showed that XT had higher functional gene abundance in pathways related to transcription, translation, environmental adaptation, membrane transport, cellular communities (prokaryotes), motility, and replication/repair compared to Z.<br><br>DISCUSSION: This study provides a comparative analysis of their gut microbiomes, offering valuable insights for future research on zoonotic diseases, host-microbe interactions, and ecological, evolutionary, behavioral, and seasonal influences on snake microbiota. These findings contribute to a broader understanding of microbial ecology in reptiles and its implications for conservation and disease dynamics.}, }
@article {pmid40308966, year = {2025}, author = {Li, W and Zhao, M and Wu, W and Chen, G and Hang, Y and Zheng, H and Gao, Z and Liu, J and Zhao, Y}, title = {The application prospect of metagenomic next-generation sequencing technology in diagnosing suspected lower respiratory tract infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1494638}, pmid = {40308966}, issn = {2235-2988}, mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology/virology ; Male ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Metagenomics/methods ; Retrospective Studies ; Aged ; Adult ; Bacteria/genetics/isolation &amp; purification/classification ; China ; Sensitivity and Specificity ; Aged, 80 and over ; Young Adult ; Viruses/genetics/isolation &amp; purification/classification ; Bacterial Infections/diagnosis/microbiology ; }, abstract = {OBJECTIVE: Lower respiratory tract infections present substantial diagnostic and therapeutic challenges, negatively impacting individual health. This study aims to utilize metagenomic next-generation sequencing (mNGS) technology to comprehensively explore the spectrum of pathogens, the detection of antibiotic resistance genes, and contributing factors associated with lung infections.<br><br>METHOD: The mNGS data of 217 patients with suspected lung infections attending the Respiratory Department of Nanjing Lishui People's Hospital and Gaochun People's Hospital from September 2022 to September 2023 were retrospectively analyzed. The study assessed the pathogenic spectrum of lung infections and compared the performance of patients with mNGS results from conventional microbiological techniques (CMT).<br><br>RESULTS: The overall positivity rate of mNGS was 95.20%, demonstrating superior sensitivity (97.01% vs. 41.79%) and accuracy (75.56% vs. 56.67%) compared to CMT. Bacterial infections were the most prevalent, accounting for 60.76% of cases. And the most prevalent bacteria, fungus and virus were Mycobacterium tuberculosis (14.41%), Candida albicans (15.72%), and EB virus (14.85%), respectively. The primary resistance genes detected were tetM (17, 8.29%), mel (6, 2.93%), and PC1 beta-lactamase (blaZ) (3, 1.46%). Notably, TEM-183, PDC-5 and PDC-3 were exclusively detected in the Chronic Obstructive Pulmonary Disease (COPD) group. The multivariate binary logistic regression analysis revealed that there was no significant association between gender, presence of hypertension, or COPD with the type of infection in patients (p=0.679, p=0.229, p=0.345). However, the immune status was found to be statistically significant (p=0.009).<br><br>CONCLUSION: With the guidance of mNGS, patients with suspected respiratory tract infections can rapidly and accurately establish a pathogenic basis for their conditions. mNGS effectively identify mixed infections, enrich the pathogen spectrum of lung infections, and provide a large and reliable information base for the clinical realization of targeted medication.}, }
@article {pmid40308204, year = {2025}, author = {Karalius, MC and Ramachandran, PS and Wapniarski, A and Wang, M and Zia, M and Hills, NK and Wintermark, M and Grose, C and Dowling, MM and Wilson, J and Lee, S and Chung, M and Barry, M and Xu, H and DeRisi, JL and Wilson, MR and Fullerton, HJ and , }, title = {Infection in Childhood Arterial Ischemic Stroke: Metagenomic Next-Generation Sequencing Results of the VIPS II Study.}, journal = {Stroke}, volume = {}, number = {}, pages = {}, doi = {10.1161/STROKEAHA.124.050548}, pmid = {40308204}, issn = {1524-4628}, abstract = {BACKGROUND: Acute respiratory infection transiently increases risk for childhood arterial ischemic stroke (AIS). We hypothesize that this paradox of a common exposure linked to a rare outcome could be explained by either (1) the infection hypothesis: unusual or multiple pathogens or (2) the host response hypothesis: heterogeneity in the inflammatory response to infection. We leverage metagenomic next-generation sequencing (mNGS), a comprehensive microbial detection tool, to test the first hypothesis.<br><br>METHODS: The VIPS II study (Vascular Effects of Infection in Pediatric Stroke II) prospectively enrolled children with AIS at 22 international sites over 5 years (December 2016 to January 2022). Sites measured prestroke clinical infection via standardized parental interviews and chart abstraction. To assess more broadly the background spectrum of pathogens, a central research laboratory performed mNGS on plasma and oropharyngeal swabs collected within 72 hours of stroke. mNGS was also performed on biological samples from stroke-free children (June 2017 to January 2022), both without (well) and with (ill) documentation of clinical infection.<br><br>RESULTS: VIPS II enrolled 205 patients with AIS, 95 stroke-free well children, and 47 stroke-free ill children. Clinical infection, most commonly upper respiratory tract infection, was detected in 81 of 205 (40%) of patients. Both plasma and oropharyngeal swab mNGS data were available for 190 of 205 patients with AIS, 91 of 95 stroke-free well children, and 27 of 47 stroke-free ill children. mNGS detected viruses in 27 of 190 (14%) patients with AIS, 9 of 91 stroke-free well children (10%), and 9 of 27 (33%) stroke-free ill children. Most were common upper respiratory viruses. Coinfections were rare. Similar viruses were found in patients with AIS and stroke-free children.<br><br>CONCLUSIONS: mNGS detected a variety of common childhood viruses in both patients with AIS and stroke-free children, suggesting that the type of infection does not explain AIS susceptibility. Rather, the alternative hypothesis regarding an unusual host immune response to common infections in the pathogenicity of AIS should be further explored.}, }
@article {pmid40307949, year = {2025}, author = {Lee, JY and Jo, S and Lee, J and Choi, M and Kim, K and Lee, S and Kim, HS and Bae, JW and Chung, SJ}, title = {Distinct gut microbiome characteristics and dynamics in patients with Parkinson's disease based on the presence of premotor rapid-eye movement sleep behavior disorders.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {108}, pmid = {40307949}, issn = {2049-2618}, support = {RS-2024-00353952//Ministry of Science and ICT, South Korea/ ; RS-2023-00265588//the Ministry of Health and Welfare, Republic of Korea/ ; }, mesh = {Humans ; *Parkinson Disease/microbiology/complications ; *Gastrointestinal Microbiome/genetics ; Male ; *REM Sleep Behavior Disorder/microbiology ; Female ; Aged ; Middle Aged ; Disease Progression ; *Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Alpha-synuclein aggregation, a hallmark of Parkinson's disease (PD), is hypothesized to often begin in the enteric or peripheral nervous system in "body-first" PD and progresses through the vagus nerve to the brain, therefore REM sleep behavior disorder (RBD) precedes the PD diagnosis. In contrast, "brain-first" PD begins in the central nervous system. Evidence that gut microbiome imbalances observed in PD and idiopathic RBD exhibit similar trends supports body-first and brain-first hypothesis and highlights the role of microbiota in PD pathogenesis. However, further investigation is needed to understand distinct microbiome changes in body-first versus brain-first PD over the disease progression.<br><br>RESULTS: Our investigation involved 104 patients with PD and 85 of their spouses as healthy controls (HC), with 57 patients (54.8%) categorized as PD-RBD(+) and 47 patients (45.2%) as PD-RBD(-) based on RBD presence before the PD diagnosis. We evaluated the microbiome differences between these groups over the disease progression through taxonomic and functional differential abundance analyses and carbohydrate-active enzyme (CAZyme) profiles based on metagenome-assembled genomes. The PD-RBD(+) gut microbiome showed a relatively stable microbiome composition irrespective of disease stage. In contrast, PD-RBD(-) microbiome exhibited a relatively dynamic microbiome change as the disease progressed. In early-stage PD-RBD(+), Escherichia and Akkermansia, associated with pathogenic biofilm formation and host mucin degradation, respectively, were enriched, which was supported by functional analysis. We discovered that genes of the UDP-GlcNAc synthesis/recycling pathway negatively correlated with biofilm formation; this finding was further validated in a separate cohort. Furthermore, fiber intake-associated taxa were decreased in early-stage PD-RBD(+) and the biased mucin-degrading capacity of CAZyme compared to fiber degradation.<br><br>CONCLUSION: We determined that the gut microbiome dynamics in patients with PD according to the disease progression depend on the presence of premotor RBD. Notably, early-stage PD-RBD(+) demonstrated distinct gut microbial characteristics, potentially contributing to exacerbation of PD pathophysiology. This outcome may contribute to the development of new therapeutic strategies targeting the gut microbiome in PD. Video Abstract.}, }
@article {pmid40307838, year = {2025}, author = {Huang, L and Li, K and Peng, C and Gu, S and Huang, X and Gao, C and Ren, X and Cheng, M and He, G and Xu, Y and Jiang, Y and Wang, H and Wang, M and Shen, P and Wang, Q and He, X and Zhong, L and Wang, S and Wang, N and Zhang, G and Cai, H and Jiang, C}, title = {Elevated antibiotic resistance gene abundance of ICU healthcare workers, a multicentre, cross-sectional study.}, journal = {Critical care (London, England)}, volume = {29}, number = {1}, pages = {170}, pmid = {40307838}, issn = {1466-609X}, support = {LTGY24H190001//Zhejiang Provincial Natural Science Fund/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; 2021YFA1301001//National Key Research and Development Program/ ; 2025C02090//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; WKJ-ZJ-2526//National Health Commission Scientific Research Fund - Zhejiang Provincial Health Major Science and Technology Plan Project/ ; }, mesh = {Humans ; Cross-Sectional Studies ; Male ; Female ; Intensive Care Units/organization &amp; administration/statistics &amp; numerical data ; Prospective Studies ; *Health Personnel/statistics &amp; numerical data ; China ; Adult ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/genetics ; Feces/microbiology ; }, abstract = {OBJECTIVE: Studies suggest that the colonization of multidrug-resistant organism in the gut of healthcare workers is similar to that of healthy individuals. However, due to exposure to medical environments, is the abundance of antibiotic resistance genes (ARG) in the gut of ICU healthcare workers higher than that of healthy individuals?<br><br>DESIGN: Prospective, multicentre, cross-sectional study.<br><br>SETTING: Eight medical centers in China, recruiting from January 2024 to February 2024.<br><br>PARTICIPANTS: 303 Healthy people (201 ICU healthcare workers and 103 healthy controls) were screened and 290 Healthy people (191 ICU healthcare workers and 99 healthy controls) were included in analysis.<br><br>MAIN OUTCOME MEASURES: Fecal samples were collected and subjected to metagenomic sequencing. We compared the total ARG abundance, ARG diversity, and gut microbiome composition between the two groups.<br><br>RESULTS: After adjusting for age, sex, and body mass index, ICU healthcare workers exhibited a significantly higher total ARG abundance compared to healthy controls (fold change&#x2009;=&#x2009;1.22, 95% CI: 1.12-1.34, p <&#x2009;0.001). The &#x3b2;-diversity of ARG between the two groups differed significantly (p =&#x2009;0.001). No significant linear or nonlinear relationship was observed between the duration of ICU occupational exposure and ARG abundance (p for overall&#x2009;=&#x2009;0.96, p for nonlinear&#x2009;=&#x2009;0.84).<br><br>CONCLUSION: In this prospective, multicenter study, we found that ICU healthcare workers exhibit significantly higher gut ARGs abundance compared to healthy controls. Meanwhile, ICU healthcare workers, including physicians, nurses, and nursing assistants, have a different composition of gut ARGs compared to healthy individuals.<br><br>TRIAL REGISTRATION: NCT06228248.}, }
@article {pmid40307822, year = {2025}, author = {Huo, Y and Wu, C and Ma, D}, title = {Application of metagenomic next-generation sequencing in the diagnosis and treatment of acute pneumonia caused by Tropheryma whipplei.}, journal = {BMC pulmonary medicine}, volume = {25}, number = {1}, pages = {207}, pmid = {40307822}, issn = {1471-2466}, mesh = {Humans ; Male ; Female ; Retrospective Studies ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/therapeutic use ; Aged ; *Tropheryma/genetics/isolation &amp; purification ; Bronchoalveolar Lavage Fluid/microbiology ; Metagenomics ; *Pneumonia, Bacterial/drug therapy/diagnosis/microbiology ; Adult ; Cilastatin, Imipenem Drug Combination/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Acute Disease ; Tomography, X-Ray Computed ; *Whipple Disease/drug therapy/diagnosis/microbiology ; Imipenem/therapeutic use ; }, abstract = {OBJECTIVE: The treatment plan and process for acute pneumonia caused by Tropheryma whipplei have not been clearly defined. The study aimed to conduct a retrospective analysis of the treatment for patients with acute pneumonia, caused by Tropheryma whipplei, diagnosed through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF).<br><br>METHODS: All patients underwent routine blood examinations and chest CT scans. Electronic fiberoptic bronchoscopy was performed to collect BALF samples from the lesion subsegments. The BALF samples were subjected to mNGS analysis. During hospitalization, all patients were treated with imipenem-cilastatin combined with compound sulfamethoxazole (SMZ-TMP) tablets for anti-infection, and they took SMZ-TMP orally for 3&#xa0;months after discharge and followed up.<br><br>RESULTS: We identified 7 cases where Tropheryma whipplei was the primary pathogen, with 3 of these cases having it as the sole detected pathogen. The clinical manifestations of acute Tropheryma whipplei pneumonia are atypical. Chest CT scans revealed that 3 cases had exudative lesions in both lungs, 4 cases had unilateral pulmonary exudative lesions, 3 cases had bilateral pulmonary nodules, 2 cases had interstitial changes, and 3 cases had pleural effusion. Following treatment, all follow-up cases showed no recurrence.<br><br>CONCLUSIONS: The mNGS examination of bronchoalveolar lavage fluid can significantly improve the early diagnosis of acute pneumonia caused by Tropheryma whipplei. The treatment involving imipenem-cilastatin combined with SMZ-TMP, followed by oral SMZ-TMP for three months, is effective.}, }
@article {pmid40307239, year = {2025}, author = {Langwig, MV and Koester, F and Martin, C and Zhou, Z and Joye, SB and Reysenbach, AL and Anantharaman, K}, title = {Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4076}, pmid = {40307239}, issn = {2041-1723}, support = {DBI-2047598//National Science Foundation (NSF)/ ; OCE-2049478//National Science Foundation (NSF)/ ; }, mesh = {*Hydrothermal Vents/virology/microbiology ; *Viruses/genetics/classification/isolation &amp; purification ; *Ecosystem ; Metagenome ; Genome, Viral ; Pacific Ocean ; Bacteriophages/genetics/classification ; Phylogeny ; Seawater/virology ; Gammaproteobacteria/virology ; Microbiota ; Virome ; }, abstract = {Viruses are ubiquitous in deep-sea hydrothermal vents, where they influence microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identify 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plume, 40 deposit, and 2 diffuse flow metagenomes), and reconstruct 5708 viral metagenome-assembled genomes, the majority of which were bacteriophages. Hydrothermal viruses were largely endemic, however, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses shared proteins related to core functions such as structural proteins, and rarely, proteins of auxiliary functions involved in processes such as fermentation and cobalamin biosynthesis. Common microbial hosts of viruses included members of Campylobacterota, Alpha-, and Gammaproteobacteria in deposits, and Gammaproteobacteria in plumes. Campylobacterota- and Gammaproteobacteria-infecting viruses reflected variations in hydrothermal chemistry and functional redundancy in their predicted microbial hosts, suggesting that hydrothermal geology is a driver of viral ecology and coevolution of viruses and hosts. Our results indicate that viral ecology and evolution in globally distributed hydrothermal vents is shaped by endemism and thus may have increased susceptibility to the negative impacts of deep-sea mining and anthropogenic change in ocean ecosystems.}, }
@article {pmid40307209, year = {2025}, author = {Song, X and Wang, Y and Wang, Y and Zhao, K and Tong, D and Gao, R and Lv, X and Kong, D and Ruan, Y and Wang, M and Tang, X and Li, F and Luo, Y and Zhu, Y and Xu, J and Ma, B}, title = {Rhizosphere-triggered viral lysogeny mediates microbial metabolic reprogramming to enhance arsenic oxidation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4048}, pmid = {40307209}, issn = {2041-1723}, support = {42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Rhizosphere ; *Arsenic/metabolism ; Oxidation-Reduction ; *Oryza/microbiology/virology/metabolism ; Soil Microbiology ; *Lysogeny/genetics ; Microbiota/genetics ; Gene Transfer, Horizontal ; Metagenome ; Plant Roots/microbiology/virology ; Oxidoreductases/genetics/metabolism ; Metabolic Reprogramming ; }, abstract = {The rhizosphere is a critical hotspot for metabolic activities involving arsenic (As). While recent studies indicate many functions for soil viruses, much remains overlooked regarding their quantitative impact on rhizosphere processes. Here, we analyze time-series metagenomes of rice (Oryza sativa L.)rhizosphere and bulk soil to explore how viruses mediate rhizosphere As biogeochemistry. We observe the rhizosphere favors lysogeny in viruses associated with As-oxidizing microbes, with a positive correlation between As oxidation and the prevalence of these microbial hosts. Moreover, results demonstrate these lysogenic viruses enrich both As oxidation and phosphorus co-metabolism genes and mediated horizontal gene transfers (HGTs) of As oxidases. In silico simulation with genome-scale metabolic models (GEMs) and in vitro validation with experiments estimate that rhizosphere lysogenic viruses contribute up to 25% of microbial As oxidation. These findings enhance our comprehension of the plant-microbiome-virome interplay and highlight the potential of rhizosphere viruses for improving soil health in sustainable agriculture.}, }
@article {pmid40287646, year = {2025}, author = {He, L and Zou, Q and Wang, Y}, title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {111}, pmid = {40287646}, issn = {1471-2105}, support = {62102269//National Natural Science Foundation of China/ ; }, mesh = {*Metagenomics/methods ; Computational Biology/methods ; *Software ; *Gene Expression Profiling/methods ; *Microbiota ; Data Collection ; Quality Control ; Workflow ; RNA, Untranslated ; Molecular Sequence Annotation ; Rhizosphere ; Automation ; }, abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.<br><br>RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.<br><br>CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .}, }
@article {pmid40306604, year = {2025}, author = {Lee, SH and Han, C and Shin, C}, title = {IUPHAR Review: Microbiota-Gut-Brain Axis and its role in Neuropsychiatric Disorders.}, journal = {Pharmacological research}, volume = {}, number = {}, pages = {107749}, doi = {10.1016/j.phrs.2025.107749}, pmid = {40306604}, issn = {1096-1186}, abstract = {The human gut microbiome, composed of a vast array of microorganisms that have co-evolved with humans, is crucial for the development and function of brain systems. Research has consistently shown bidirectional communication between the gut and the brain through neuronal, endocrine, and immunological, and chemical pathways. Recent neuroscience studies have linked changes in the microbiome and microbial metabolites to various neuropsychiatric disorders such as autism, depression, anxiety, schizophrenia, eating disorders, and neurocognitive disorders. Novel metagenome-wide association studies have confirmed these microbiome variations in large samples and expanded our understanding of the interactions between human genes and the gut microbiome. The causal relationship between gut microbiota and neuropsychiatric disorders is being elucidated through the establishment of large cohort studies incorporating microbiome data and advanced statistical techniques. Ongoing animal and human studies focused on the microbiota-gut-brain axis are promising for developing new prevention and treatment strategies for neuropsychiatric conditions. The scope of these studies has broadened from microbiome-modulating therapies including prebiotics, probiotics, synbiotics and postbiotics to more extensive approaches such as fecal microbiota transplantation. Recent systematic reviews and meta-analyses have strengthened the evidence base for these innovative treatments. Despite extensive research over the past decade, many intriguing aspects still need to be elucidated regarding the role and therapeutic interventions of the microbiota-gut-brain axis in neuropsychiatric disorders.}, }
@article {pmid40305950, year = {2025}, author = {An, S and Li, J and Du, J and Feng, L and Zhang, L and Zhang, X and Zhuang, Z and Zhao, Z and Yang, G}, title = {Coupled nitrogen and phosphorus cycles mediated by coordinated variations of functional microbes in industrial recirculating aquaculture system.}, journal = {Water research}, volume = {280}, number = {}, pages = {123726}, doi = {10.1016/j.watres.2025.123726}, pmid = {40305950}, issn = {1879-2448}, abstract = {Industrial Recirculating Aquaculture Systems (IRAS) represent a sustainable and efficient approach to aquaculture, offering significant benefits in water conservation and environmental management. A comprehensive understanding of nitrogen (N) and phosphorus (P) cycling is essential for optimizing system design and operational strategies, enabling the maintenance of a balanced ecosystem within IRAS. Here, water microbial communities in the shrimp aquaculture pond (AP) and nitrification tank (NT) of the IRAS were investigated using a metagenomics-based approach to explore the mechanisms of N and P coupling cycles. Results showed that (1) N and P cycling genes were more abundant in AP water than in NT, with higher potentials for degrading organic N and P compounds, nitrate reduction, denitrification, and phosphate uptake in AP; and their hosts (functional bacteria) were identified as Marivivens for nitrate reduction, Polaribacter and Erythobacter for organophosphorus hydrolysis, and Fluviibacter and Sediminibacterium for phosphate uptake; (2) the coupling of N and P cycles was observed through the abundance of functional genes, likely mediated by coordinated variations in host composition, with nitrite content as a key factor influencing this variation; several bacterial species possessing both N and P cycling genes were identified, primarily engaged in the degradation of organic N and P compounds, denitrification, and phosphate uptake. This study highlights the coupling of N and P cycling in IRAS and the important role of functional bacteria in maintaining water quality. The results also have important implications for the management and improvement of IRAS for more effective aquaculture activities.}, }
@article {pmid40305569, year = {2025}, author = {Hernandez-Valencia, JC and Gómez, GF and Correa, MM}, title = {Metagenomic analysis evidences a core virome in Anopheles darlingi from three contrasting Colombian ecoregions.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0320593}, doi = {10.1371/journal.pone.0320593}, pmid = {40305569}, issn = {1932-6203}, mesh = {Animals ; *Anopheles/virology ; Colombia ; *Virome/genetics ; *Metagenomics/methods ; *Mosquito Vectors/virology ; Phylogeny ; Malaria/transmission ; Metagenome ; }, abstract = {Anopheles darlingi is a main malaria vector in the neotropical region, but its viral component is not well studied, especially in the neotropics. This work aimed to analyze the virome in Anopheles darlingi from malaria endemic regions of Colombia. Specimens were collected from the Bajo Cauca, Chocoan Pacific and northwestern Amazonas regions and analyzed using an RNA-Seq approach. Results revealed a variety of RNA viral sequences with homology to those of Insect-Specific Viruses belonging to Rhabdoviridae, Partitiviridae, Metaviridae, Tymoviridae, Phasmaviridae, Totiviridae, Ortervirales and Riboviria. Despite geographical and ecological differences among regions, the An. darlingi viral composition remains consistent in different areas, with a core group of viral operational taxonomic units-vOTUs shared by the populations. Furthermore, diversity analysis uncovered greater dissimilarities in viral sequence among mosquitoes from geographically distant regions, particularly evident between populations located at both sides of the Andes Mountain range. This study provides the first characterization of the metavirome in An. darlingi from Colombia and lays the foundation for future research on the complex interactions among viruses, hosts, and microbiota; it also opens a new line of investigation on the viruses in Anopheles populations of Colombia.}, }
@article {pmid40305442, year = {2025}, author = {Cayrou, C and Silver, K and Owen, L and Dunlop, J and Laird, K}, title = {Domestic laundering of healthcare textiles: Disinfection efficacy and risks of antibiotic resistance transmission.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0321467}, doi = {10.1371/journal.pone.0321467}, pmid = {40305442}, issn = {1932-6203}, mesh = {*Disinfection/methods ; *Textiles/microbiology ; Humans ; *Laundering/methods ; Microbial Sensitivity Tests ; Detergents/pharmacology ; *Cross Infection/prevention &amp; control/microbiology ; *Drug Resistance, Microbial ; Staphylococcus aureus/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; United Kingdom ; Microbiota/drug effects ; Decontamination/methods ; Klebsiella pneumoniae/drug effects ; Pseudomonas aeruginosa/drug effects ; Enterococcus faecium/drug effects ; }, abstract = {Hospital-acquired infections (HAIs) and antimicrobial resistance (AMR) are a major public health concern, with the evidence base for the potential role of textiles as fomites in microbial transmission growing. In the UK, domestic laundering machines (DLMs) are commonly used to clean healthcare worker uniforms, raising concerns about their effectiveness in microbial decontamination and role in AMR development. This study aimed to evaluate DLMs' ability to decontaminate microorganisms and their potential impact on AMR. The performance of six DLMs was assessed using Enterococcus faecium bioindicators under various wash cycles and detergent conditions. Shotgun metagenomics was used to analyse the microbiome and resistome of DLMs. The minimum inhibitory concentrations of domestic detergents were determined for Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa, and detergent tolerance and antibiotic cross-resistance were assessed. Results showed only 50% (3/6) of DLMs achieved sufficient decontamination (≥5 log10 CFU reduction) at 60°C during full-length cycles, with rapid cycles performing inconsistently. Microbiome analysis revealed the presence of potentially pathogenic bacteria (e.g., Mycobacterium sp. Pseudomonas sp. and Acinetobacter sp.) and antibiotic resistance genes, including efflux pumps and target modification genes. Detergent tolerance assays showed increased bacterial tolerance to detergents, with cross-resistance to antibiotics observed in S. aureus and K. pneumoniae, including carbapenem and β-lactam groups. Whole genome sequencing identified mutations in genes encoding efflux pumps in S. aureus (MrgA) and K. pneumoniae (AcrB) after detergent exposure, which could impact efflux pump function. Findings suggest domestic laundering of healthcare uniforms may be insufficient for decontamination, posing risks for HAI transmission and AMR. Revising laundering guidelines to ensure effective DLM performance, detergent efficacy, and considering alternatives like onsite/industrial laundering are crucial to enhancing patient safety and controlling AMR in healthcare settings.}, }
@article {pmid40304791, year = {2025}, author = {Bu, Y and Zhang, X and Xiong, Z and Li, K and Zhang, S and Lin, M and Zhao, G and Zheng, N and Wang, J and Zhao, S}, title = {Effect of red clover isoflavones on ruminal microbial composition and fermentation in dairy cows.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {107}, pmid = {40304791}, issn = {1432-0614}, support = {2022YFD1301000//National Key R&amp;D Program of China/ ; CAAS-ZDRW202308//the Agricultural Science and Technology Innovation Program/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Fermentation/drug effects ; *Isoflavones/pharmacology/administration &amp; dosage/metabolism ; *Trifolium/chemistry ; Genistein/pharmacology/administration &amp; dosage ; *Bacteria/classification/genetics/drug effects/metabolism/isolation &amp; purification ; Female ; Ammonia/metabolism ; Urease/metabolism ; Urea/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Metagenomics ; }, abstract = {Red clover isoflavones, particularly biochanin A and formononetin, are known for their benefits in enhancing feed efficiency and nitrogen utilization in ruminants. However, their specific effects on rumen fermentation and microbial diversity remain insufficiently explored. This study investigated the impacts of red clover isoflavones on rumen function and bacterial diversity in dairy cows, utilizing both in vivo and in vitro methodologies. In the in vivo study, 40 Holstein dairy cows were allocated to four groups, each receiving red clover isoflavones at doses of 0, 0.4, 0.8, and 1.6 g/kg. Rumen fluid was collected for analysis of fermentation parameters, enzyme activity, and microbial composition through shotgun metagenomic sequencing. Concurrently, an in vitro rumen fermentation trial was conducted to evaluate the effects of biochanin A and formononetin on urea hydrolysis. Results from the in vivo experiments showed that red clover isoflavones significantly decreased ammonia nitrogen (NH3-N) concentrations and urease activity in the rumen (P < 0.05). Species level metagenomic analysis indicated a reduced abundance of proteolytic and ureolytic bacteria, such as Prevotella sp002317355 and Treponema_D bryantii_C, with a corresponding increase in cellulolytic bacteria, including Ruminococcus_D sp900319075 and Ruminococcus_C sp000433635 (P < 0.05). The in vitro trial further demonstrated that biochanin A and formononetin significantly reduced urea decomposition rates (P < 0.05), with biochanin A exerting a more pronounced effect. These findings align with the observed reduction in ureolytic and proteolytic bacteria, along with an increase in cellulolytic bacteria across both trials. In conclusion, biochanin A emerged as the primary active component of red clover isoflavones, modulating urea nitrogen hydrolysis and rumen fermentation. This study substantiates previous findings and highlights the potential of red clover isoflavones for enhancing rumen microbial fermentation, offering a promising strategy for future dairy industry applications. KEY POINTS: • Red clover isoflavones inhibit urease activity to decrease the abundance of urealytic bacteria. • Biochanin A reduces ammonia nitrogen and urease activity, promoting protein efficiency. • Red clover isoflavones may improve dairy cow rumen health and nitrogen utilization.}, }
@article {pmid40304704, year = {2025}, author = {Burnside, M and Tang, J and Baker, JL and Merritt, J and Kreth, J}, title = {Shining Light on Oral Biofilm Fluorescence In Situ Hybridization (FISH): Probing the Accuracy of In Situ Biogeography Studies.}, journal = {Molecular oral microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/omi.12494}, pmid = {40304704}, issn = {2041-1014}, support = {DE029612//NIH-NIDCR/ ; DE029492//NIH-NIDCR/ ; DE029228//NIH-NIDCR/ ; DE028252//NIH-NIDCR/ ; }, abstract = {The oral biofilm has been instrumental in advancing microbial research and enhancing our understanding of oral health and disease. Recent developments in next-generation sequencing have provided detailed insights into the microbial composition of the oral microbiome, enabling species-level analyses of biofilm interactions. Fluorescence in situ hybridization (FISH) has been especially valuable for studying the spatial organization of these microbes, revealing intricate arrangements such as "corncob" structures that highlight close bacterial interactions. As more genetic sequence data become available, the specificity and accuracy of existing FISH probes used in biogeographical studies require reevaluation. This study examines the performance of commonly used species-specific FISH probes, designed to differentiate oral microbes within in situ oral biofilms, when applied in vitro to an expanded set of bacterial strains. Our findings reveal that the specificity of several FISH probes is compromised, with cross-species hybridization being more common than previously assumed. Notably, we demonstrate that biogeographical associations within in situ oral biofilms, particularly involving Streptococcus and Corynebacterium, may need to be reassessed to align with the latest metagenomic data.}, }
@article {pmid40304525, year = {2025}, author = {Fernández-Quintela, A and Laveriano-Santos, EP and Portolés, T and Gual-Grau, A and Sancho, JV and Portillo, MP}, title = {Changes in Liver Metabolome Induced by Pterostilbene and Resveratrol in a Rat Model of Liver Steatosis.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70078}, doi = {10.1002/mnfr.70078}, pmid = {40304525}, issn = {1613-4133}, support = {AGL-2015-65719-R//Ministerio de Econom&#xed;a y Competitividad/ ; //Fondo Europeo de Desarrollo Regional (FEDER)/ ; CB12/03/30007//Instituto de Salud Carlos III (CIBERobn)/ ; IT1482-22//Government of the Basque Country/ ; }, abstract = {To gain more light on the effects of resveratrol and pterostilbene in the hepatic metabolic modifications in an in vivo model of diet-induced hepatic steatosis, and to explore their relationships with gut microbiota by untargeted metabolomics and metagenomics. Rats were divided into five groups receiving either a standard diet or a high-fat high-fructose (HFHF) diet supplemented or not with pterostilbene (15 or 30 mg/kg body weight/day; PT15 or PT30 groups, respectively) or resveratrol (30 mg/kg body weight/day; RSV30 group). Supplementation with the stilbenes reduced the hepatic steatosis induced by the HFHF diet. After the metabolomics study, 27 differentially expressed metabolites showed variable importance in projection scores > 1 and could be considered as potential biomarkers. Therefore, based on the pathway enrichment analysis, "riboflavin metabolism" and "nicotinate and nicotinamide metabolism" revealed significant enrichment. Further, riboflavin showed positive correlations to Eubacterium and Faecalibacterium, and negative correlations to Lactobacillus and Oscillospira genera. Nicotinamide mononucleotide was only positively correlated to the Ralstonia genus. The untargeted metabolomics approach showed that the actions of resveratrol or pterostilbene on the prevention of liver steatosis are mediated by specific mechanisms of action. Particularly, pterostilbene, but not resveratrol, is suggested to significantly enrich riboflavin or nicotinate and nicotinamide metabolic pathways.}, }
@article {pmid40304520, year = {2025}, author = {Flörl, L and Meyer, A and Bokulich, NA}, title = {Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0052425}, doi = {10.1128/aem.00524-25}, pmid = {40304520}, issn = {1098-5336}, abstract = {Within-species diversity of microorganisms in food systems significantly shapes community function. While next-generation sequencing (NGS) methods have advanced our understanding of microbiomes at the community level, it is essential to recognize the importance of within-species variation for understanding and predicting the functional activities of these communities. This review highlights the substantial variation observed among microbial species in food systems and its implications for their functionality. We discuss a selection of key species in fermented foods and food systems, highlighting examples of strain-level variation and its influence on quality and safety. We present a comprehensive roadmap of methodologies aimed at uncovering this often overlooked underlying diversity. Technologies like long-read marker-gene or shotgun metagenome sequencing offer enhanced resolution of microbial communities and insights into the functional potential of individual strains and should be integrated with techniques such as metabolomics, metatranscriptomics, and metaproteomics to link strain-level microbial community structure to functional activities. Furthermore, the interactions between viruses and microbes that contribute to strain diversity and community stability are also critical to consider. This article highlights existing research and emphasizes the importance of incorporating within-species diversity in microbial community studies to harness their full potential, advance fundamental science, and foster innovation.}, }
@article {pmid40303946, year = {2024}, author = {Dakal, TC and Xu, C and Kumar, A}, title = {Advanced computational tools, artificial intelligence and machine-learning approaches in gut microbiota and biomarker identification.}, journal = {Frontiers in medical technology}, volume = {6}, number = {}, pages = {1434799}, pmid = {40303946}, issn = {2673-3129}, abstract = {The microbiome of the gut is a complex ecosystem that contains a wide variety of microbial species and functional capabilities. The microbiome has a significant impact on health and disease by affecting endocrinology, physiology, and neurology. It can change the progression of certain diseases and enhance treatment responses and tolerance. The gut microbiota plays a pivotal role in human health, influencing a wide range of physiological processes. Recent advances in computational tools and artificial intelligence (AI) have revolutionized the study of gut microbiota, enabling the identification of biomarkers that are critical for diagnosing and treating various diseases. This review hunts through the cutting-edge computational methodologies that integrate multi-omics data-such as metagenomics, metaproteomics, and metabolomics-providing a comprehensive understanding of the gut microbiome's composition and function. Additionally, machine learning (ML) approaches, including deep learning and network-based methods, are explored for their ability to uncover complex patterns within microbiome data, offering unprecedented insights into microbial interactions and their link to host health. By highlighting the synergy between traditional bioinformatics tools and advanced AI techniques, this review underscores the potential of these approaches in enhancing biomarker discovery and developing personalized therapeutic strategies. The convergence of computational advancements and microbiome research marks a significant step forward in precision medicine, paving the way for novel diagnostics and treatments tailored to individual microbiome profiles. Investigators have the ability to discover connections between the composition of microorganisms, the expression of genes, and the profiles of metabolites. Individual reactions to medicines that target gut microbes can be predicted by models driven by artificial intelligence. It is possible to obtain personalized and precision medicine by first gaining an understanding of the impact that the gut microbiota has on the development of disease. The application of machine learning allows for the customization of treatments to the specific microbial environment of an individual.}, }
@article {pmid40303154, year = {2024}, author = {Albert, E and Kis, IE and Kiss, K and K-Jánosi, K and de Oliveira Costa, M and Tolnai, G and Biksi, I}, title = {Abortion and Lethal Septicaemia in Sows Caused by a Non-ST194 Streptococcus equi subsp. zooepidemicus.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {4008946}, pmid = {40303154}, issn = {1865-1682}, mesh = {Animals ; Swine ; *Streptococcal Infections/veterinary/microbiology/epidemiology/mortality ; Female ; *Abortion, Veterinary/microbiology/epidemiology ; *Swine Diseases/microbiology/epidemiology/mortality ; Pregnancy ; *Sepsis/veterinary/microbiology/epidemiology ; Disease Outbreaks/veterinary ; Hungary/epidemiology ; Streptococcus ; }, abstract = {Outbreaks of zoonotic Streptococcus equi subsp. zooepidemicus (SEZ) have caused severe epidemics in the pig sector since the 1970s in Southeastern Asia, China, and more recently North America. Cases of high mortality caused by peracute septicaemia were all attributed to strains of a highly virulent clonal lineage belonging to the sequence type (ST) 194. In Europe, only two outbreaks have been reported with similar features, caused by other sequence types. In August 2023, a febrile disease followed by abortion and subsequent death was observed among sows kept in a small-scale organic pig farm in West Hungary. Symptoms, pathological lesions, and microbiological findings were suggestive of septicaemia from bacterial origin caused by SEZ. According to the results of the routine laboratory testing, no other relevant infectious agents were involved. Whole-genome sequence analysis assigned the examined strains to ST138, unrelated to any of the European isolates. It also revealed a few common SEZ virulence genes, compared to the highly virulent ST194 strains. A sudden weather change and subsequent extremely high average daily temperature before the outbreak could be identified as the only predisposing factor. The immediate antibiotic treatment and applied biosecurity measures might have helped to restrict and terminate the outbreak. To our knowledge, this is the first report on abortion and lethal septicaemia in sows from Central and Eastern Europe. The results call attention to the potential of non-ST194 SEZ strains to cause outbreaks in pig farms.}, }
@article {pmid40303144, year = {2024}, author = {Meng, X and Sun, J and Yao, M and Sun, Y and Xu, H and Liu, C and Chen, H and Guo, J and Nie, X and He, L and Zhao, Z and Li, N and Wang, Z and Wang, J}, title = {Isolation and Identification of Severe Fever with Thrombocytopenia Syndrome Virus from Farmed Mink in Shandong, China.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {9604673}, pmid = {40303144}, issn = {1865-1682}, abstract = {Severe fever with thrombocytopenia syndrome (SFTS) virus, recently named Bandavirus dabieense, belongs to the genus Bandavirus of family Phenuiviridae, and it causes SFTS in humans with clinical symptoms including fever, thrombocytopenia, gastrointestinal symptoms, and leukocytopenia. However, there are few reports on the pathogenesis of SFTSV in animals. This study first isolated the SFTSV strain SD22-2 from sick-farmed mink. Viral metagenomics was used to detect SFTSV nucleotide in the clinical specimens obtained from symptomatic minks. Then, we isolated the virus using Vero and DH82 cells, and Real-Time Quantitative PCR (RT-qPCR), indirect immunofluorescence assay, transmission electron microscopy, and Western blotting identified it. Meanwhile, phylogenetic analysis based on partial L, M, and S segment sequences indicated that the mink-origin SFTSV strain SD22-2 belonged to genotype D and was genetically close to the HB2016-003 strain isolated from humans. Taken together, we isolated and identified an SFTSV from farmed mink that may be the reservoir hosts of SFTSV. We should pay more attention to farmed minks and biosecurity practices, and active surveillance at fur farms must be reviewed and enhanced.}, }
@article {pmid40303140, year = {2024}, author = {Song, Y and Zuo, O and Zhang, G and Hu, J and Tian, Z and Guan, G and Luo, J and Yin, H and Shang, Y and Du, J}, title = {Emergence of Lumpy Skin Disease Virus Infection in Yaks, Cattle-Yaks, and Cattle on the Qinghai-Xizang Plateau of China.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {2383886}, pmid = {40303140}, issn = {1865-1682}, mesh = {Animals ; Cattle ; *Lumpy Skin Disease/epidemiology/virology ; *Lumpy skin disease virus/genetics/isolation &amp; purification/classification ; China/epidemiology ; Phylogeny ; Tibet/epidemiology ; *Cattle Diseases/epidemiology/virology ; Genome, Viral ; }, abstract = {Lumpy skin disease (LSD) is a viral disease caused by lumpy skin disease virus (LSDV), which mainly infects cattle and can cause huge economic losses. In May 2023, yaks, cattle-yaks, and cattle in Tibet (Xizang), China, developed fever, skin nodules, and severe discharges and were suspected to be cases of LSD. Samples from these animals were analyzed using molecular biology and serological methods. The RPO30, P32, and GPCR genes were amplified by PCR and sequenced, and the whole genome of the virus was determined using viral metagenomics technology. Sequencing results showed that it was indeed an LSDV infection, and enzyme-linked immunosorbent assay results confirmed the presence of LSDV antibodies. The whole genome phylogenetic tree shows that LSDV/CHINA/Tibet/2023 is different from the previous epidemic strains in China, but clusters with India 2022 strain. This is the first report of LSD in yaks, cattle-yaks, and cattle on the highest altitude plateau in the world.}, }
@article {pmid40303134, year = {2024}, author = {Mulder, KP and Pasmans, F and van Nieuwerburgh, F and Terriere, N and Kelly, M and Bregman, S and Verbrugghe, E and Martel, A}, title = {High Prevalence of a Novel Circovirus in the European Hedgehog (Erinaceus europaeus), a Common Species in Decline.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {4670252}, pmid = {40303134}, issn = {1865-1682}, mesh = {Animals ; *Hedgehogs/virology ; *Circovirus/isolation &amp; purification/genetics/classification ; *Circoviridae Infections/veterinary/epidemiology/virology ; Phylogeny ; Europe/epidemiology ; Prevalence ; }, abstract = {Hedgehog (Erinaceus europaeus) declines in western Europe have been associated with the emergence of Hedgehog diphtheric disease (HDD), with a probable multifactorial, yet unidentified etiology. We used metagenomic sequencing of cell-free DNA (cfDNA) in hedgehog blood to identify possible causes of HDD. We detected a novel circovirus species in the European hedgehog, providing the first record of a circovirus within the mammalian order Eulipotyphla. The novel circovirus genome exhibits the characteristic circovirus structure, including a functional replicase (REP) and capsid (CAP) gene. Phylogenetic analysis placed all four detected genomes in a monophyletic clade, most closely related to sequences isolated from dogs. Subsequent PCR-based screening of 188 hedgehog liver samples demonstrated a high prevalence (61%) of this circovirus in hedgehogs brought to wildlife rescue centers, however, without any significant association with HDD. Since circoviruses are well known to interfere with host immunity across mammalian and avian taxa, the high level of circovirus detection in hedgehogs warrants further research into the role of this novel virus in hedgehog health.}, }
@article {pmid40303123, year = {2024}, author = {Wang, K and Liu, S and Liang, X and Hu, W and Wen, Z and Wang, J and Wang, X and An, F and Chen, Z and Yan, H and Yan, H and Wang, L and Zhang, X and Yu, J and Wei, WK and Hua, Y}, title = {Identification and Genetic Analysis of Species D Rotaviruses in Pangolin Samples.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {1773821}, pmid = {40303123}, issn = {1865-1682}, mesh = {Animals ; *Rotavirus/genetics/isolation &amp; purification/classification ; Phylogeny ; *Pangolins/virology ; *Rotavirus Infections/veterinary/virology ; Genome, Viral ; }, abstract = {Pangolins have been found to carry severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related coronaviruses. In light of this discovery, interest has been piqued in viromes of these heavily trafficked wild animals. In this study, we performed viral metagenomic sequencing to explore viromes of both confiscated dead pangolins and captive healthy pangolins. Sequence reads of vertebrate-associated viruses in Herpesviridae, Retroviridae, Iridoviridae, Reoviridae, Arenaviridae, and Flaviviridae were detected in confiscated dead pangolins. A novel rotavirus (RV) (Reoviridae), showing a high degree of genetic similarity to the RV species D (RVD) that was previously unreported in mammals, was further confirmed by using reverse transcription-polymerase chain reaction (RT-PCR) and Sanger sequencing. Three out of 18 samples from the confiscated dead pangolins were positive for genomic sequences of the novel RV. Importantly, sequence alignments and phylogenetic analyses demonstrated that these RV strains genetically belonged to the RVD. Nevertheless, these novel RVD strains were divergent from known RVD strains that have been found only in Avian. They formed a separate genetic cluster. Five serial passages were attempted to isolate the RV, but no live virus was obtained. In addition, fecal samples were collected from healthy pangolins (n = 41) in our institution and screened for RVs by viral metagenomic sequencing and RT-PCR. In these fecal samples, neither species D nor previously identified species A RVs were detected. This study reported RVDs in pangolin samples for the first time to our knowledge. Identifiability disagreements between wild and captive pangolins highlight the need for further exploration into pangolin viruses to better understand their emergence and transmission potential.}, }
@article {pmid40303119, year = {2024}, author = {Lovy, J and Iwanowicz, LR and Welch, TJ and Allam, B and Getchell, RG and Geraci-Yee, S and Good, C and Snyder, J and Raines, CD and Das, N}, title = {Seasonal Mortality of Wild Atlantic Menhaden (Brevoortia tyrannus) Is Caused by a Virulent Clone of Vibrio (Listonella) anguillarum; Implications for Biosecurity along the Atlantic Coastal United States.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {8816604}, pmid = {40303119}, issn = {1865-1682}, mesh = {Animals ; *Fish Diseases/microbiology/mortality/epidemiology ; *Vibrio/pathogenicity/genetics/isolation &amp; purification ; Seasons ; *Vibrio Infections/veterinary/mortality/microbiology/epidemiology ; Fishes ; New Jersey/epidemiology ; Atlantic Ocean/epidemiology ; New York/epidemiology ; Virulence ; }, abstract = {Atlantic menhaden are a highly migratory marine species in the Eastern United States that suffer from seasonal chronic mortality. Affected fish show neurologic signs referred to as spinning disease, including circling at the surface and erratic corkscrew swimming before death. We investigated three similar menhaden mortality events consistent with spinning disease in coastal New Jersey and New York between 2020 and 2021 to understand the cause. A unique strain of Vibrio (Listonella) anguillarum (serogroup O3) was detected regularly in high loads, particularly in the brains of moribund fish, by both metagenomics and bacterial isolation. The most common histopathological changes in moribund fish were hemorrhagic meningitis, encephalitis, pyknosis, and karyorrhexis of hematopoietic tissues in the kidney and spleen. Whole genome sequencing of isolates from moribund fish representing a wide spatial and temporal range showed that they were nearly identical clones, suggesting it to be a pathogenic strain circulating in the population. Though V. anguillarum is believed to be the main pathogen associated with spinning disease and mortality, Yersinia ruckeri (serotype O1) was isolated from smaller numbers of fish. Considering the highly migratory nature of Atlantic menhaden throughout the eastern United States and their use as bait for other fisheries, these findings identify potential biosecurity challenges that should be considered in Atlantic salmon aquaculture, fisheries, and emerging marine aquaculture in the region.}, }
@article {pmid40303091, year = {2024}, author = {Wang, YM and Deng, LS and Huang, BZ and Li, HY and Duan, JQ and Yan, YX and Lai, SY and Ai, YR and Zhou, YC and Qing, Y and Xu, ZW and Zhu, L}, title = {Whole Genome Characterization and Pathogenicity of a SC2020-1-Like PRRSV-1 Strain Emerging in Southwest China.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {5627927}, pmid = {40303091}, issn = {1865-1682}, mesh = {Animals ; *Porcine respiratory and reproductive syndrome virus/genetics/pathogenicity/classification ; Swine ; *Porcine Reproductive and Respiratory Syndrome/virology/epidemiology/pathology ; China/epidemiology ; *Genome, Viral ; Phylogeny ; Virulence ; }, abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV), encompassing PRRSV-1 and PRRSV-2, significantly impacts the global pig industry by causing reproductive disorders and respiratory difficulties. In this paper, we isolated a novel PRRSV-1 strain, named SCPJ2023, from weaned piglets in Sichuan. Utilizing primary macrophages, we isolated SCPJ2023 and performed complete genome sequencing through metagenomic analysis. Phylogenetic analysis classified SCPJ2023 as pan-European subtype 1. SCPJ2023 showed a 95.3% similarity to SC2020-1. Amino acid analysis identified differences in Nsp2, GP3, and GP4 between SCPJ2023 and other representative strains. In vivo challenge experiments demonstrated that SCPJ2023 induced clinical symptoms in piglets, including coughing, fever, reduced appetite, and depression. Pathological examinations revealed hemorrhage and congestion, increased inflammatory cells, thickening of the alveolar wall, and collapse of the alveolar cavity in SCPJ2023-infected piglets. Altogether, our study identified a novel pathogenic isolate of PRRSV-1, expanding the newly named SC2020-1-like subgroup by identifying additional strains beyond the initial SC2020-1 isolate.}, }
@article {pmid40303019, year = {2024}, author = {Stadler, J and Lillie-Jaschniski, K and Zwickl, S and Zoels, S and Theuns, S and Ritzmann, M and Vereecke, N}, title = {Cross-Correlation between Biosecurity Measures and the Detection of Viral and Bacterial Agents on German Farms with Respiratory Disease.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {6205899}, pmid = {40303019}, issn = {1865-1682}, mesh = {Animals ; Germany/epidemiology ; Swine ; *Swine Diseases/microbiology/epidemiology/virology/prevention &amp; control ; *Biosecurity ; Farms ; Animal Husbandry ; *Bacterial Infections/veterinary/epidemiology/microbiology ; Bacteria/isolation &amp; purification/classification ; Porcine respiratory and reproductive syndrome virus/isolation &amp; purification ; Porcine Reproductive and Respiratory Syndrome/epidemiology/virology/microbiology ; }, abstract = {Effective porcine health management relies majorly on diagnostic tests, vaccination, treatment strategies, and a proper biosecurity management plan. However, understanding the link between circulating microbes and biosecurity measures on a pig farm is not evident. Substantial progress has been made in recent years with the availability of new diagnostic tools (e.g., sequencing-based diagnostics) and extensive biosecurity management questionnaires. However, the interpretation and correlation of these results are hampered by the abundance of gained (meta)data. Therefore, we aimed to cross-correlate viral and bacterial pathogens with respiratory tropism detected by third-generation nanopore metagenomic sequencing with biosecurity measures assessed by Biocheck.UGent™. The study was conducted on 25 sow farms with attached nurseries in Germany with known respiratory distress. The biosecurity level of the study farms complied with the European averages. Interestingly, the farms with the highest biosecurity score showed the lowest overall prevalence of porcine reproductive and respiratory syndrome virus (PRRSV) and Actinobacillus sp.; the circulation of well-studied pathogenic viruses, such as PRRSV, was correlated with overall lower biosecurity scores, a higher number of stillborn piglets, and cocirculation of porcine parvovirus type 7. Moreover, potential risk factors for lesser-known agents (e.g., porcine hemagglutinating and encephalomyelitis virus, porcine respiratory coronavirus, and porcine polyomavirus) could also be addressed. For the bacterial pathogen Glaesserella sp., a correlation with increased clinical signs was observed, whereas Lactobacillus sp. and Moraxella sp. are putative biomarkers for pig farms with better biosecurity scores. In conclusion, in-depth cross-correlation of (meta)data from new diagnostic platforms with biosecurity measures on pig farms may contribute to a better understanding of new actions in adapting biosecurity measures. This will not only contribute to improved animal welfare and economic productivity but also helping to address (new) zoonotic disease threats and potential treatments.}, }
@article {pmid40302920, year = {2025}, author = {Gao, Z and Jiang, Y and Chen, M and Wang, W and Liu, Q and Ma, J}, title = {Enhancing fever of unknown origin diagnosis: machine learning approaches to predict metagenomic next-generation sequencing positivity.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1550933}, pmid = {40302920}, issn = {2235-2988}, mesh = {Humans ; *Machine Learning ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Fever of Unknown Origin/diagnosis/etiology ; Female ; Male ; Middle Aged ; Algorithms ; Adult ; Aged ; }, abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) can potentially detect various pathogenic microorganisms without bias to improve the diagnostic rate of fever of unknown origin (FUO), but there are no effective methods to predict mNGS-positive results. This study aimed to develop an interpretable machine learning algorithm for the effective prediction of mNGS results in patients with FUO.<br><br>METHODS: A clinical dataset from a large medical institution was used to develop and compare the performance of several predictive models, namely eXtreme Gradient Boosting (XGBoost), Light Gradient-Boosting Machine (LightGBM), and Random Forest, and the Shapley additive explanation (SHAP) method was employed to interpret and analyze the results.<br><br>RESULTS: The mNGS-positive rate among 284 patients with FUO reached 64.1%. Overall, the LightGBM-based model exhibited the best comprehensive predictive performance, with areas under the curve of 0.84 and 0.93 for the training and validation sets, respectively. Using the SHAP method, the five most important factors for predicting mNGS-positive results were albumin, procalcitonin, blood culture, disease type, and sample type.<br><br>CONCLUSION: The validated LightGBM-based predictive model could have practical clinical value in enhancing the application of mNGS in the etiological diagnosis of FUO, representing a powerful tool to optimize the timing of mNGS.}, }
@article {pmid40302838, year = {2025}, author = {Pallen, MJ and Ponsero, AJ and Telatin, A and Moss, CJ and Baker, D and Heavens, D and Davidson, GL}, title = {Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity.}, journal = {Access microbiology}, volume = {7}, number = {4}, pages = {}, pmid = {40302838}, issn = {2516-8290}, abstract = {Background. The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). Results. Short-read sequencing of five faecal samples generated a metagenomic dataset, revealing substantial variation in composition between samples. Reference-based profiling with Kraken2 identified key differences in the ratios of reads assigned to host, diet and microbes. Some samples showed high abundance of potential pathogens, including siadenoviruses, coccidian parasites and the antimicrobial-resistant bacterial species Serratia fonticola. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from Isospora spp., while metagenome-assembled genomes documented new prokaryotic species. Conclusions. Here, we have shown the utility of shotgun metagenomics in uncovering microbial diversity beyond what is possible with 16S rRNA gene sequencing. These findings provide a foundation for future hypothesis testing and microbiome manipulation to improve fitness in wild bird populations. The study also highlights the potential role of wild birds in the dissemination of antimicrobial resistance.}, }
@article {pmid40302016, year = {2025}, author = {Zhou, H and Tang, L and Fenton, KA and Song, X}, title = {Exploring and Evaluating Microbiome Resilience in the Gut.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf046}, pmid = {40302016}, issn = {1574-6941}, abstract = {The gut ecosystem is closely related to human gastrointestinal health and overall wellness. Microbiome resilience refers to the capability of a microbial community to resist or recover from perturbations to its original state of balance. So far, there is no consensus on the criteria for assessing microbiome resilience. This article provides new insights into the metrics and techniques for resilience assessment. We discussed several potential parameters, such as microbiome structure, keystone species, biomarkers, persistence degree, recovery rate, and various research techniques in microbiology, metagenomics, biochemistry and dynamic modeling. The article further explores the factors that influence the gut microbiome resilience. The microbiome structure (i.e. abundance and diversity), keystone species and microbe-microbe interplays determine microbiome resilience. Microorganisms employ a variety of mechanisms to achieve the microbiome resilience, including flexible metabolism, quorum sensing, functional redundancy, microbial cooperation and competition. Host-microbe interactions play a crucial role in maintaining microbiome stability and functionality. Unlike other articles, we focus on the regulation of host immune system on microbiome resilience. The immune system facilitates bacterial preservation and colonization, community construction, probiotic protection and pathogen elimination through the mechanisms of immunological tolerance, immune-driven microbial compartmentalization and immune inclusion and exclusion. Microbial immunomodulation indirectly modulates microbiome resilience.}, }
@article {pmid40301729, year = {2025}, author = {Hariprasath, K and Dhanvarsha, M and Mohankumar, S and Sudha, M and Saranya, N and Saminathan, VR and Subramanian, S}, title = {Characterization of gut microbiota in Apis cerana Across different altitudes in the Peninsular India.}, journal = {BMC ecology and evolution}, volume = {25}, number = {1}, pages = {39}, pmid = {40301729}, issn = {2730-7182}, mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome ; India ; RNA, Ribosomal, 16S/genetics/analysis ; *Altitude ; *Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Honey bees are vital to global ecosystems and agriculture due to their role as key pollinators. The gut microbiota of honey bees is essential for their health, providing nutrition and protection against pathogens. While extensive research has been conducted on Western honey bees, Less is understood about the gut microbiota of Apis cerana, an economically important species in South Asia. This study aimed to identify and describe the gut microbiota of Apis cerana across different elevations in the Indian peninsula to understand how these bacterial communities adapt to various ecological niches.<br><br>RESULTS: High-throughput metagenome sequencing of the 16S rRNA gene (V1-V9 region) showed that the core microbiota genera in Apis cerana guts across elevations were Gilliamella, Lactobacillus, Snodgrassella, and Frischella. Gilliamella apicola and Lactobacillus kunkeei were identified as the most abundant species. Alpha diversity analysis showed a trend of decreasing species diversity as altitude increased from 200 to 1200&#xa0;m, with a slight increase observed above 1400&#xa0;m. Culturable bacterial species identified through 16S rRNA amplification belonged to the Proteobacteria, Firmicutes, and Actinobacteria phyla. Different elevations harboured distinct bacterial communities, with some species being unique to certain altitudes.<br><br>CONCLUSIONS: This study provides valuable insights into the diversity and adaptations of Apis cerana gut microbiota across various ecological niches in the Indian peninsula. The observed variations in microbial communities at different elevations suggest that environmental factors play a significant role in shaping the gut microbiota of honey bees. Understanding these microbial dynamics could help in developing strategies to improve bee health and address critical questions in host-microbe symbiosis. Furthermore, this research lays the groundwork for future studies on the functional roles of these bacterial communities in Apis cerana and their potential applications in beekeeping practices.}, }
@article {pmid40301728, year = {2025}, author = {Munoz Briones, J and Brubaker, DK}, title = {A framework for predictive modeling of microbiome multi-omics data: latent interacting variable-effects (LIVE) modeling.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {115}, pmid = {40301728}, issn = {1471-2105}, support = {2120200//Directorate for Biological Sciences/ ; R01HD110367//National Institute of Child Health and Human Development/ ; }, mesh = {Humans ; *Microbiota ; *Metabolomics/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; *Computational Biology/methods ; Principal Component Analysis ; Crohn Disease/microbiology ; Multiomics ; }, abstract = {BACKGROUND: The number and size of multi-omics datasets with paired measurements of the host and microbiome is rapidly increasing with the advance of sequencing technologies. As it becomes routine to generate these datasets, computational methods to aid in their interpretation become increasingly important. Here, we present a framework for integration of microbiome multi-omics data: Latent Interacting Variable Effects (LIVE) modeling. LIVE integrates multi-omics data using single-omic latent variables (LV) organized in a structured meta-model to determine the combinations of features most predictive of a phenotype or condition.<br><br>RESULTS: We developed a supervised version of LIVE leveraging sparse Partial Least Squares Discriminant Analysis (sPLS-DA) LVs, and an unsupervised version leveraging sparse Principal Component Analysis (sPCA) principal components which both can incorporate covariate awarness. LIVE performance was tested on publicly available metagenomic and metabolomics data set from Crohn's Disease (CD) and Ulcerative Colitis (UC) status patients in the PRISM and LLDeep cohorts, and benchmarked against existing gut microbiome multi-omics approaches and vaginal microbiome datasests, achieving consistent and comparable performances. In addition to these benchmarking efforts, we present a detailed analysis and interpretation of both versions of LIVE using the PRISM and LLDeep cohorts. LIVE reduced the number of feature interactions from the original datasets for CD and UC from millions to less than 20,000 while conditioning the disease-predictive power of gut microbes, metabolites, enzymes, on clinical variables.<br><br>CONCLUSIONS: LIVE makes a distinct, complementary contribution to current methods to integrate microbiome data and offers key advantages to existing approaches in the interpretable integration of multi-omics data with clinical variables to predict to disease outcomes and identify microbiome mechanisms of disease.}, }
@article {pmid40301726, year = {2025}, author = {Yao, C and Zhang, Y and You, L and E, J and Wang, J}, title = {Comparative analysis of three experimental methods for revealing human fecal microbial diversity.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {258}, pmid = {40301726}, issn = {1471-2180}, support = {2024L154//the Fundamental Research Program of Shanxi Province/ ; 202403021212101//the Science and Technology Innovation Project of Shanxi Provincial Universities/ ; 2018ZD14//the Major Program of Natural Science Foundation of Inner Mongolia/ ; }, mesh = {Humans ; *Feces/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; Culture Media/chemistry ; *Biodiversity ; *Bacteriological Techniques/methods ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Due to the heterogeneity of the human gut environment, the gut microbiota is complex and diverse, and has been insufficiently explored. In this study, one fresh fecal sample was cultured using 12 commercial or modified media and incubation of culture plates anaerobically and aerobically, the conventional experienced colony picking (ECP) was first used to isolate the colonies and obtain pure culture strains. On this basis, all the colonies grown on the culture plates were collected for culture-enriched metagenomic sequencing (CEMS), and the original sample was also subjected to direct culture-independent metagenomic sequencing (CIMS), the study compared the effects of three methods for analyzing the microbiota contained in the sample. It was found that compared with CEMS, conventional ECP failed to detect a large proportion of strains grown in culture media, resulting in missed detection of culturable microorganisms in the gut. Microbes identified by CEMS and CIMS showed a low degree of overlap (18% of species), whereas species identified by CEMS and CIMS alone accounted for 36.5% and 45.5%, respectively. It suggests that both culture-dependent and culture-independent approaches are essential in revealing gut microbial diversity. Moreover, based on the CEMS results, growth rate index (GRiD) values for various strains on different media were calculated to predict the optimal medium for bacterial growth; this method can be used to design new media for intestinal microbial isolation, promote the recovery of specific microbiota, and obtain new insights into the human microbiome diversity. This is among the first studies on CEMS of the human gut microbiota.}, }
@article {pmid40300742, year = {2025}, author = {Wang, B and Huang, T and Zhu, L and Hu, J and Ma, S and Sun, Q and Chen, K}, title = {Effect of cyanobacterial bloom proliferation on antibiotic resistance genes in the sediments of a eutrophic lake.}, journal = {Environmental research}, volume = {278}, number = {}, pages = {121717}, doi = {10.1016/j.envres.2025.121717}, pmid = {40300742}, issn = {1096-0953}, abstract = {Antibiotic resistance genes (ARGs) represent an emerging pollutant of increasing concern. In this study, we analyzed the composition and spatiotemporal variation of ARGs in the sediments of eutrophic Chaohu Lake, China, using a metagenomic method. A total of 22 ARGs and 199 ARGs subtypes were detected, with the most prevalent subtypes being multidrug (57.720 %) and rifamycin (21.781 %). A higher abundance of ARGs in Chaohu Lake was observed (p < 0.05) during winter and spring owing to multiple factors, including variations in seasonal inputs and hydraulic conditions, occurrence of cyanobacterial blooms, and changes in ARGs host bacterial communities. Spatially, a higher abundance of multidrug was observed in sediments near the Nanfei River outlet, which flows through urban areas; whereas higher levels of bacitracin were observed in sediments near the Zhao River outlet, which flows through agricultural areas. Cyanobacterial blooms and declines change the sediment physicochemical properties, endogenous phosphorus contents, microbial communities, and seasonal ARGs distribution. Correlation and collinearity analyses indicated that ARGs were transferred horizontally via mobile genetic elements (MGEs). High-risk ARGs in Chaohu Lake were observed at a very low proportion, although certain ARGs presented health risks in the western lake during spring. In this study, we highlight the interactions between cyanobacterial blooms and variations in ARGs in Chaohu Lake and provide novel insights into ARGs dynamics in eutrophic freshwater ecosystems.}, }
@article {pmid39796227, year = {2025}, author = {Lu, Y and Li, M and Gao, Z and Ma, H and Chong, Y and Hong, J and Wu, J and Wu, D and Xi, D and Deng, W}, title = {Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics.}, journal = {International journal of molecular sciences}, volume = {26}, number = {1}, pages = {}, pmid = {39796227}, issn = {1422-0067}, support = {32160771//National Nature Science Foundation of China/ ; 32302707//National Nature Science Foundation of China/ ; 202101BD070001-006//Yunnan Provincial Agricultural Union Foundation/ ; 202202AE090005//Major Science and Technology Projects in Yunnan Province/ ; 202301AU070117//Yunnan Province Basic Research Program Project/ ; XDYC-CYCX-2022-0029//"Xingdian Talent" Industry Innovation Talent Program in Yunnan Province/ ; }, mesh = {Humans ; *Whole Genome Sequencing/methods ; *Genetics, Population/methods ; High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; Software ; *Genome, Human ; Genetic Variation ; *Metagenomics/methods ; Machine Learning ; }, abstract = {With the rapid advancement of high-throughput sequencing technologies, whole genome sequencing (WGS) has emerged as a crucial tool for studying genetic variation and population structure. Utilizing population genomics tools to analyze resequencing data allows for the effective integration of selection signals with population history, precise estimation of effective population size, historical population trends, and structural insights, along with the identification of specific genetic loci and variations. This paper reviews current whole genome sequencing technologies, detailing primary research methods, relevant software, and their advantages and limitations within population genomics. The goal is to examine the application and progress of resequencing technologies in this field and to consider future developments, including deep learning models and machine learning algorithms, which promise to enhance analytical methodologies and drive further advancements in population genomics.}, }
@article {pmid40303081, year = {2024}, author = {Yuan, Y and Li, L and Liu, Z and Yang, X and Wang, W and Xu, W and Liu, N and Sui, L and Zhao, Y and Liu, Q and Wang, Z}, title = {First Report and Genetic Characterization of Border Disease Virus in Sheep from Hulunbuir, Northeastern China.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {9924724}, pmid = {40303081}, issn = {1865-1682}, mesh = {Animals ; Sheep ; China/epidemiology ; Phylogeny ; *Border disease virus/genetics/isolation &amp; purification/classification ; *Border Disease/epidemiology/virology ; *Sheep Diseases/virology/epidemiology ; Genome, Viral ; }, abstract = {Border disease virus (BDV), a member of the Pestivirus genus within the Flaviviridae family, is known to inflict significant economic losses on livestock farms due to its association with reproductive disorders and persistent infections in sheep and goats. However, comprehensive epidemiological investigations of BDV in China are scarce. This study examined BDV infection in sheep from Hulunbuir, Inner Mongolia, northeastern China, utilizing metagenomic sequencing and polymerase chain reaction (PCR) assay. Among the 96 serum samples analyzed, only one tested positive for BDV nucleotide sequence, yielding a prevalence rate of 1.0%. A total of 11,985 nt long genome sequences was amplified, which showed nucleotide identities ranging from 76.6% to 87.2% and amino acid identities ranging from 85.2% to 93.2% with other BDV strains worldwide. Phylogenetic analysis unequivocally placed the viral strain within genotype BDV-3, showing a close genetic affinity with strain JSLS12-01 identified in Jiangsu province, China. Furthermore, selection pressure analyses suggested that purifying selection predominantly influenced the evolutionary dynamics of BDV genomes. This study marks the inaugural detection of BDV in sheep within Inner Mongolia, northeastern China, thereby enhancing our understanding of the extensive genetic diversity and geographical distribution of BDV strains across the country. These findings hold relevance for the livestock industry and disease surveillance efforts, offering valuable insights into the prevalence and genetic characteristics of BDV in this region.}, }
@article {pmid40303833, year = {2023}, author = {Wang, Y and Gu, C and Han, Q and Fu, S and Wang, J and Zhuang, J and Guo, G and Liu, J and Yu, X and Qu, G and Shen, Z}, title = {A Novel Pathogen of an Emerging Infectious Disease (Large Kidney Disease) in Farmed Blue Foxes.}, journal = {Transboundary and emerging diseases}, volume = {2023}, number = {}, pages = {6629054}, pmid = {40303833}, issn = {1865-1682}, mesh = {Animals ; *Foxes/virology ; *Communicable Diseases, Emerging/veterinary/virology/epidemiology ; *Retroviridae Infections/veterinary/virology/epidemiology ; *Kidney Diseases/veterinary/virology/epidemiology ; China/epidemiology ; Phylogeny ; }, abstract = {An emerging infectious disease (EID) in foxes called "large kidney disease", characterized by enlarged kidneys, has been breaking out in fox farms in China, although its pathogenesis has not yet been elucidated. Here, we performed viral metagenomics sequencing on diseased fox tissue samples that identified a virus with 82.6% homology to the xenotropic murine leukemia virus-related virus (XMRV) PreXMRV-1 provirus strain (GenBank accession number NC_007815.2) in sick fox tissue. It was named PreXMRV-20, and its genome was verified by reverse transcription-polymerase chain reaction (PCR) and PCR product sequencing. Nonenveloped and polygonal virus-like particles consistent with the shape and size of XMRV were observed by negative staining electron microscopy. Administered subcutaneously, PreXMRV-20 infected weaned foxes, leading to growth retardation. The discovery of the PreXMRV-20 strain (the first isolation of an XMRV homolog in blue foxes) identifies a potential public health issue in blue fox breeding since XMRV has been confirmed to be a zoonotic virus.}, }
@article {pmid40303754, year = {2023}, author = {Righi, C and Curini, V and Torresi, C and Cammà, C and Pirani, S and Di Lollo, V and Gobbi, P and Giammarioli, M and Viola, G and Pela, M and Feliziani, F and Petrini, S}, title = {Molecular Detection and Genetic Characterization of Bovine Kobuvirus (BKV) in Diarrhoeic Calves in a Central Italy Herd.}, journal = {Transboundary and emerging diseases}, volume = {2023}, number = {}, pages = {6637801}, pmid = {40303754}, issn = {1865-1682}, mesh = {Animals ; Cattle ; Italy/epidemiology ; *Cattle Diseases/virology/epidemiology ; *Diarrhea/veterinary/virology/epidemiology ; *Kobuvirus/genetics/isolation &amp; purification ; *Picornaviridae Infections/veterinary/virology/epidemiology ; Phylogeny ; *Polyomavirus Infections/veterinary/virology/epidemiology ; *Tumor Virus Infections/veterinary/virology/epidemiology ; }, abstract = {Bovine kobuvirus (BKV) is an infectious agent associated with neonatal calf diarrhoea (NCD), causing important economic losses to dairy and beef cattle herds worldwide. Here, we present the detection rate and characterize the genome of BKV isolated from diarrhoeic calves from a Central Italy herd. From January to December 2021, we collected blood samples and nasal and rectal swabs from 66 calves with severe NCD between 3 and 20 days of age. After virological (bovine coronavirus, bovine viral diarrhoea virus, and bovine rotavirus), bacteriological (Escherichia coli spp. and Salmonella spp.), and parasitological (Cryptosporidium spp., Eimeria spp., and Giardia duodenalis) investigations, we detected BKV using the metagenomic analysis. This result was confirmed using a specific polymerase chain reaction assay that revealed the number of BKV-positive nasal (24.2%) and rectal swabs (31.8%). The prevalence of BKV was higher than that of BCoV. Coinfection with BKV and BCoV was detected in 7.5% of the rectal swabs, highlighting the involvement of another infectious agent in NCD. Using next generation sequencing (NGS) approach, it was possible to obtain the complete sequence of the BKV genome from other two rectal swabs previously analysed by real-time PCR. This is the first report describing the whole genome sequence (WGS) of BKV from Italy. The Italian BKV genomes showed the highest nucleotide sequence identity with BKV KY407744.1, identified in Egypt in 2014. The sequence encoding VP1 best matched that of BKV KY024562, identified in Scotland in 2013. Considering the small number of BKV WGSs available in public databases, further studies are urgently required to assess the whole genome constellation of circulating BKV strains. Furthermore, pathogenicity studies should be conducted by inoculating calves with either only BKV or a combination with other enteric pathogens for understanding the probable role of BKV in NCD.}, }
@article {pmid40303817, year = {2023}, author = {Li, C and Qiu, M and Li, S and Sun, Z and Huang, Z and Qi, W and Qiu, Y and Li, J and Feng, B and Zhao, D and Lin, H and Zheng, W and Yu, X and Tian, K and Fan, K and Zhu, J and Chen, N}, title = {Metagenomic and Pathogenic Assessments Identify a Pathogenic Porcine Reproductive and Respiratory Syndrome Virus 1 with New Deletions from Adult Slaughter Pig in 2022.}, journal = {Transboundary and emerging diseases}, volume = {2023}, number = {}, pages = {1975039}, pmid = {40303817}, issn = {1865-1682}, mesh = {Animals ; *Porcine respiratory and reproductive syndrome virus/genetics/pathogenicity/isolation &amp; purification ; Swine ; *Porcine Reproductive and Respiratory Syndrome/virology/epidemiology ; China/epidemiology ; Phylogeny ; Metagenomics ; Genome, Viral ; Sequence Deletion ; }, abstract = {Since we first reported porcine reproductive and respiratory syndrome virus 1 (PRRSV1) wild type strains in mainland China in 2011, PRRSV1 infection has been detected in more than 20 provinces in China. During the routine investigation of PRRSV1 epidemiology in 2022, we isolated a novel PRRSV1 strain (SD1291) from an adult slaughter pig in Linyi, Shandong Province. The SD1291 could only be isolated with primary alveolar macrophages (PAMs), not with Marc-145 cells. In addition, the 2022 SD1291 isolate has higher in vitro replication efficacy than the 2014 PRRSV1 HLJB1 isolate in PAMs. Due to high genetic variation, the complete genome of SD1291 was determined by metagenomic sequencing, which showed that SD1291 shares the highest genome similarity (88.12%) with the PRRSV1 HeB47 isolate. Sequence alignment results identified a four-amino-acid deletion in nsp2 and a five-amino-acid deletion in the GP3 and GP4 overlap region of SD1291. A complete-genome-based phylogenetic tree showed that SD1291 is grouped with BJEU06-1-like PRRSV1 isolates. A piglets' challenge study showed that SD1291 can cause high fever (the highest is 41°C), reduced weight gain, mild lung consolidation, and interstitial pneumonia indicating that SD1291 is a pathogenic PRRSV1 isolate. Overall, this study first identified a novel pathogenic PRRSV1 isolate from an adult slaughter pig in China. Our findings also suggested that new PRRSV1 variants could escape the current PRRSV vaccination system and circulate in adult swine herds, which deserve more attention.}, }
@article {pmid40303779, year = {2023}, author = {Nelsen, A and Knudsen, D and Hause, BM}, title = {Identification of a Novel Astrovirus Associated with Bovine Respiratory Disease.}, journal = {Transboundary and emerging diseases}, volume = {2023}, number = {}, pages = {8512021}, pmid = {40303779}, issn = {1865-1682}, mesh = {Animals ; Cattle ; *Cattle Diseases/virology ; *Astroviridae Infections/veterinary/virology ; Phylogeny ; *Astroviridae/isolation &amp; purification/genetics/classification ; *Respiratory Tract Infections/veterinary/virology ; }, abstract = {Astroviruses (AstVs) cause gastrointestinal disease in mammals and avians. Emerging evidence suggests that some AstVs have extraintestinal tissue tropism, with AstVs detected in the liver, kidney, central nervous system, and the respiratory tract variably associated with disease. In cattle, AstV infection has been linked to gastroenteric or neurologic disease. Here, metagenomic sequencing of a lung from a bovine with respiratory disease identified a novel AstV with a predicted capsid-encoding ORF2 amino acid sequence with 66% identity to caprine astrovirus (CAstV G2.1). A quantitative reverse transcription PCR (qRT-PCR) targeting ORF2 found four out of 49 (8%) lungs and one out of 48 (2%) enteric samples obtained from bovine diagnostic submissions positive for the novel bovine astrovirus (BAstV). In two strongly qRT-PCR-positive lung samples, intense novel BAstV nucleic acid signals were mainly localized in the cytoplasm of alveolar macrophages and mononuclear cells using RNAscope® in situ hybridization (ISH). Genetic analysis of two novel BAstV genomes determined from qRT-PCR positive samples found high similarity for ORF1ab nucleotide sequence (92.1% and 93.9%) to BAstV strain BSRI-1, while ORF2 nucleotide sequence was most similar to CAstV G2.1 (74.6% and 77.6%). Phylogenetic analysis of the novel BAstV sequences found a close genetic relationship to the single BAstV (BSRI-1) previously identified from a bovine respiratory sample as well as bovine and caprine AstVs identified from various tissues. Further research is needed to determine the clinical significance of BAstV in respiratory diseases.}, }
@article {pmid40300608, year = {2025}, author = {Wirbel, J and Andermann, TM and Brooks, EF and Evans, L and Groth, A and Dvorak, M and Chakraborty, M and Palushaj, B and Reynolds, GZM and Porter, IE and Al Malki, M and Rezvani, A and Gooptu, M and Elmariah, H and Runaas, L and Fei, T and Martens, MJ and Bolaños-Meade, J and Hamadani, M and Holtan, S and Jenq, R and Peled, JU and Horowitz, MM and Poston, KL and Saber, W and Kean, LS and Perales, MA and Bhatt, AS}, title = {Accurate prediction of absolute prokaryotic abundance from DNA concentration.}, journal = {Cell reports methods}, volume = {}, number = {}, pages = {101030}, doi = {10.1016/j.crmeth.2025.101030}, pmid = {40300608}, issn = {2667-2375}, abstract = {Quantification of the absolute microbial abundance in a human stool sample is crucial for a comprehensive understanding of the microbial ecosystem, but this information is lost upon metagenomic sequencing. While several methods exist to measure absolute microbial abundance, they are technically challenging and costly, presenting an opportunity for machine learning. Here, we observe a strong correlation between DNA concentration and the absolute number of 16S ribosomal RNA copies as measured by digital droplet PCR in clinical stool samples from individuals undergoing hematopoietic cell transplantation (BMT CTN 1801). Based on this correlation and additional measurements, we trained an accurate yet simple machine learning model for the prediction of absolute prokaryotic load, which showed exceptional prediction accuracy on an external cohort that includes people living with Parkinson's disease and healthy controls. We propose that, with further validation, this model has the potential to enable accurate absolute abundance estimation based on readily available sample measurements.}, }
@article {pmid40300605, year = {2025}, author = {Lopez, JA and McKeithen-Mead, S and Shi, H and Nguyen, TH and Huang, KC and Good, BH}, title = {Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.03.073}, pmid = {40300605}, issn = {1879-0445}, abstract = {The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.}, }
@article {pmid40300566, year = {2025}, author = {Mahdi, ES and Komijani, M and Alaghmand, A}, title = {Metagenomics study suggests the role of vitamins and gut microbiome in autism spectrum disorder.}, journal = {Digestion}, volume = {}, number = {}, pages = {1-20}, doi = {10.1159/000545483}, pmid = {40300566}, issn = {1421-9867}, abstract = {INTRODUCTION: Autism is a neurological disability that often appears after the age of three in children, also known as an Autism Spectrum Disorder (ASD). Several studies have examined the influence of some environmental factors, and many parameters related to the behavior of autistic patients have been measured in order to find ways to reduce ASD. This study investigates the relationship between ASD and serum levels of vitamin D3, B12, folic acid, and the gut microbiome.<br><br>METHODS: The serum levels of vitamin D3, B12, and folic acid in ASD patients were measured by the ELISA method and compared to healthy groups. DNA was extracted from stool samples of ASD patients and the control group, and then the gut microbiome was investigated via a metagenomics approach. Metagenomics sequencing was performed to analyze the 16S rRNA gene sequencing for phylum and sub phylum level microbiome.<br><br>RESULT: The result showed no significant change in the VitD3 and folate levels of ASD patients compared to the control group (p=0.157 and p=0.0505, respectively). There was a significant difference in the VitB12 level between control healthy individuals and ASD patients, in which the serum VitB12 concentration was significantly lower than the control group (p=0.0001). Our results regarding gut metagenomics showed that the abundance of the Actinobacteria by the phylum level were significantly higher in the ASD patients compared to the control group (p=0.0013). The abundance of the Firmicutes by the phylum level were significantly lower in the ASD patients compared to the control group (p=0.0016).The abundance of Bifidobacteriaceae, and Ruminococcaceae by the family level were significantly higher in the ASD patients compared to the control group (p=0.0004. and p=0.0489, respectively).Our results indicated less species richness in the ASD patients compared to the control group.<br><br>CONCLUSION: Patients with ASD have lower serum levels of vitamin B12 and different gut microbiome compared to healthy controls. Low vitamin B12 levels and altered gut microbiome are significantly associated with ASD in this study. However, further research is needed to determine whether these factors could serve as predictors of severe outcomes in ASD.}, }
@article {pmid40300499, year = {2025}, author = {Hayes, A and Zhang, L and Feil, E and Kasprzyk-Hordern, B and Snape, J and Gaze, WH and Murray, AK}, title = {Antimicrobial effects, and selection for AMR by non-antibiotic drugs in a wastewater bacterial community.}, journal = {Environment international}, volume = {199}, number = {}, pages = {109490}, doi = {10.1016/j.envint.2025.109490}, pmid = {40300499}, issn = {1873-6750}, abstract = {Antimicrobial resistance (AMR) is a major threat to human, animal, and crop health. AMR can be directly selected for by antibiotics, and indirectly co-selected for by biocides and metals, at environmentally relevant concentrations. Some evidence suggests that non-antibiotic drugs (NADs) can co-select for AMR, but previous work focused on exposing single model bacterial species to predominately high concentrations of NADs. There is a significant knowledge gap in understanding a range of NAD concentrations, (including lower µg/L concentrations found in the environment) on mixed bacterial communities containing a diverse mobile resistome. Here, we determined the antimicrobial effect and selective potential of diclofenac, metformin, and 17-β-estradiol, NADs that are commonly found environmental pollutants, in a complex bacterial community using a combination of culture based, metagenome, and metratranscriptome approaches. We found that diclofenac, metformin, and 17-β-estradiol at 50 µg/L, 26 µg/L, and 24 µg/L respectively, significantly reduced growth of a bacterial community although only 17-β-estradiol selected for an AMR marker using qPCR (from 7 µg/L to 5400 µg/L). Whole metagenome sequencing indicated that there was no clear selection by NADs for antibiotic resistance genes, or effects on community composition. Additionally, increases in relative abundance of some specific metal resistance genes (such as arsB) were observed after exposure to diclofenac, metformin, and 17-β-estradiol. These results indicate that environmentally relevant concentrations of NADs are likely to affect community growth, function, and potentially selection for specific metal resistance genes.}, }
@article {pmid40300492, year = {2025}, author = {Huang, Y and Zong, S and Xu, D and He, J and Zhang, Y and Qian, M and Li, Y and Guo, B and Han, J and Qu, D}, title = {Metagenomic analysis reveals differences in antibiotic resistance and transmission risks across various poultry farming models.}, journal = {The Science of the total environment}, volume = {980}, number = {}, pages = {179519}, doi = {10.1016/j.scitotenv.2025.179519}, pmid = {40300492}, issn = {1879-1026}, abstract = {As living standards in rural areas continue to improve, farmers are increasingly seeking to diversify their farming models beyond monoculture farming. However, the differences in bacterial resistance and the associated transmission risks between monoculture poultry farming and integrated poultry farming remain poorly understood. This study utilizes metagenomic methods to examine the distribution and transmission of antibiotic resistance across three types of farms in Zhejiang Province, as well as to investigate the horizontal transmission mechanisms of plasmid-mediated blaNDM within these agricultural systems. An analysis of 26 environmental samples and 12 saliva samples from six poultry farms with different models has revealed that integrated poultry farms exhibit a more complex microbial composition and more severe resistance compared to monoculture farms. Furthermore, a blaNDM positive plasmid pndm-CD with complex conjugation transfer region was found in the integrated farms. The insertion sequence (IS) ISCR1 present in the upstream of blaNDM has the potential to promote its spread, while the downstream complex structure IS26-blaCTX-M-IS2-qnrB-TinR-ΔISKrA14 enhances the resistance of the host to β-lactam antibiotics, and improves the competition potential of the host bacteria in the anti-antibiotic environment. This research offers the first metagenomic analysis of the differences in bacterial resistance and transmission risks between various poultry farming models. These results offer a solid theoretical basis for managing the spread of antibiotic resistance in mixed chicken and duck farming operations. Additionally, they are significant for ensuring the health of agricultural workers and the hygiene safety of the poultry meat supply chain.}, }
@article {pmid40300291, year = {2025}, author = {Mei, J and Sheng, F and Zhang, C and Chen, X}, title = {Imaging monitoring of Balamuthia granulomatous amoebic encephalitis.}, journal = {Clinical neurology and neurosurgery}, volume = {254}, number = {}, pages = {108917}, doi = {10.1016/j.clineuro.2025.108917}, pmid = {40300291}, issn = {1872-6968}, abstract = {Balamuthia granulomatous amoebic encephalitis (GAE) is a rare and highly lethal infectious disease affecting the central nervous system, caused by the Balamuthia amoeba. This article reports the case of a child with normal immune function and no apparent epidemiological risk factors. In the initial stages, routine blood tests, cerebrospinal fluid cell tests, biochemical tests, and metagenomic next-generation sequencing (mNGS) were all normal. Surgical removal of the abscess and subsequent pathological diagnosis revealed a chronic granuloma. mNGS analysis of the brain abscess fluid identified Balamuthia mandrillaris (BM), leading to the diagnosis of Balamuthia GAE, after which antiparasitic treatment was initiated. This case underscores the importance of sustained imaging surveillance in suspected cases of Balamuthia GAE.}, }
@article {pmid40299688, year = {2025}, author = {Chen, Y and Nian, F and Chen, J and Jiang, Q and Yuan, T and Feng, H and Shen, X and Dong, L}, title = {Metagenomic Microbial Signatures for Noninvasive Detection of Pancreatic Cancer.}, journal = {Biomedicines}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/biomedicines13041000}, pmid = {40299688}, issn = {2227-9059}, support = {82173122, 81972234, 82273027//National Natural Science Foundation of China/ ; }, abstract = {Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with poor early detection rates owing to the limited sensitivity and specificity of the current biomarker CA19-9. Gut microbiota dysbiosis plays a key role in PDAC pathogenesis. This study aimed to evaluate the noninvasive approach we developed, combining metagenome-derived microbial signatures with CA19-9, to improve PDAC detection. Methods: This study included 50 treatment-naïve patients with PDAC and their matched controls. Fecal samples were analyzed using shotgun metagenomic sequencing. Machine learning algorithms were used to develop and validate a diagnostic panel integrating microbial signatures and CA19-9 levels. Subgroup analyses were used to confirm the robustness of the microbial markers. Results: The combined models at both species and genus levels effectively distinguished patients with PDAC from healthy individuals, and their strong diagnostic efficacy and accuracy were demonstrated through rigorous validation. Conclusions: In conclusion, the combination of gut microbiome profiling and CA19-9 improves PDAC detection accuracy compared to the use of CA19-9 alone, showing promise for early and noninvasive diagnosis.}, }
@article {pmid40299456, year = {2025}, author = {Meiirmanova, Z and Mukhanbetzhanov, N and Jarmukhanov, Z and Vinogradova, E and Kozhakhmetova, S and Morenko, M and Duisebayeva, A and Poddighe, D and Kushugulova, A and Kozhakhmetov, S}, title = {Alterations in Gut Microbiota of Infants Born to Mothers with Obesity.}, journal = {Biomedicines}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/biomedicines13040838}, pmid = {40299456}, issn = {2227-9059}, support = {Grant No. AP19575153 "Metagenomic predictors of childhood obesity, cross-talk with maternal mi-croflora", Grant No. AP23489538 and Grant No. BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; Grant No. 20122022CRP1602//Nazarbayev University under Collaborative Research Program/ ; }, abstract = {Background: The impact of maternal obesity on offspring health remains a major and pressing issue. We investigated its impact on the development of the infant gut microbiome during the first six months of life, examining the taxonomic composition, metabolic pathways, and antibiotic resistance genes. Methods: Twenty-four mother-infant pairs were divided into maternally obese (OB, BMI > 36) and normal weight (BM) groups. Shotgun metagenomic sequencing was performed on stool samples collected at birth and at 1, 3, and 6 months. A total of 12 maternal samples and 23 infant samples (n = 35) in the obese group and 12 maternal samples and 30 infant samples (n = 42) in the control group were sequenced. The analysis included taxonomic profiling (MetaPhlAn 4), metabolic pathway analysis (HUMAnN 3), and antibiotic resistance gene screening (CARD/ABRicate). Results: The OB group showed reduced alpha diversity in the first month (p ≤ 0.01) and an increased Firmicutes/Bacteroidetes ratio, peaking at 3 months (p ≤ 0.001). The metabolic profiling revealed enhanced carbohydrate breakdown (p ≤ 0.001) in the BM group and lipid biosynthesis (p ≤ 0.0001) in the OB group pathways. Strong correlations emerged between Lactobacillales and fatty acid biosynthesis (r = 0.7, p ≤ 0.0001) and between Firmicutes and lincosamide (r = 0.8, p ≤ 0.0001). Conclusions: The infants of obese mothers had significantly altered development of the infant gut microbiome, affecting both composition and metabolic potential. These changes may have long-term health consequences and suggest potential therapeutic targets for intervention.}, }
@article {pmid40299453, year = {2025}, author = {Qin, L and Chen, Y and Luan, S and Yin, X and Pan, J and Wang, L and Yao, Y and Zhou, C and Bao, R and Shen, J and Miao, Q and Hu, B}, title = {Lung Microenvironment Among Patients with Nontuberculous Mycobacterial Pulmonary Disease by Metagenomic Sequencing Technique.}, journal = {Biomedicines}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/biomedicines13040818}, pmid = {40299453}, issn = {2227-9059}, support = {NSFC82072325//National Natural Science Foundation of China/ ; }, abstract = {Background: Nontuberculous mycobacterial pulmonary disease (NTM-PD) is an increasingly prevalent chronic infection, where the host immune status plays a crucial role in disease susceptibility and progression. The complex pulmonary microenvironment, characterized by diverse microbial communities and host immune interactions, exhibits distinct features that may be fundamentally altered by the patient's underlying immune state. Methods: A total of 111 sputum specimens and 64 bronchoalveolar lavage fluid (BALF) specimens were collected from 143 patients diagnosed with NTM-PD under different immune states. Metagenomic sequencing was performed on these specimens to characterize and compare the pulmonary microenvironmental features among NTM-PD patients with a distinct immune status through comprehensive bioinformatic analyses. Results: The immunosuppressed group exhibited a lower α-diversity in sputum specimens (p < 0.05). Principal Coordinates Analysis (PCoA) of β-diversity for sputum and BALF specimens revealed significant differences between the groups (p < 0.05). Linear discriminant analysis Effect Size (LEfSe) analysis identified species enriched in the immunosuppressed group. A co-occurrence network analysis indicated that the immunosuppressed group had more structured and actively connected networks compared to the control group. The Mantel test confirmed that the abundance of these species enriched was associated with clinical immune-inflammation-related indicators in patients. Conclusions: Our study reveals the pulmonary microenvironment in immunosuppressed patients with NTM-PD. Further work is required to explore the two-way relationship between micro-organisms and immune and inflammatory responses, with the influence on patient outcomes.}, }
@article {pmid40298885, year = {2025}, author = {Liu, Y and Wu, R and Wu, J and Li, J and Zhang, Q and Wang, S and Sheng, G}, title = {Improving the shock resistance of anaerobic digestion under demand-oriented biogas production mode by using converter steel slag powder.}, journal = {Waste management &amp; research : the journal of the International Solid Wastes and Public Cleansing Association, ISWA}, volume = {}, number = {}, pages = {734242X251333692}, doi = {10.1177/0734242X251333692}, pmid = {40298885}, issn = {1096-3669}, abstract = {Introducing flexible biogas production (FB) can result in instantaneous high-shock loads for anaerobic digestion system, posing risks to the system's stable operation. Steel slag, a typical metallurgical solid waste, has been demonstrated to enhance the buffering capacity of digestion systems, thereby increasing methane production and achieving 'waste treatment using waste'. However, its efficacy under high-shock loads in FB is uncertain. Pulse feeding experiments simulating FB were conducted to analyse the system's impact resistance with steel slag addition and investigate its enhancement mechanisms. The addition of steel slag improved the methane production rate under various shock conditions, with a particularly notable enhancement under concentration shock. This scenario also saw a significant increase in the generation of soluble chemical oxygen demand and its utilization by microorganisms. This can be attributed to the enrichment of hydrolytic bacterial phyla (Firmicutes) and genera (Gelria), with functional gene analysis revealing an increase in genes associated with Fe(III) reduction and CO2-to-methane pathways. The study results indicate that the role of steel slag as an alkaline, iron-rich material enhances system alkalinity, reduces inhibition from H2 partial pressure and boosts hydrogenotrophic methanogen activity, making it suitable as an exogenous enhancer for demand-oriented anaerobic digestion.}, }
@article {pmid40298543, year = {2025}, author = {Bisaccia, M and Berini, F and Marinelli, F and Binda, E}, title = {Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/antibiotics14040394}, pmid = {40298543}, issn = {2079-6382}, support = {PNRA16_00105//Italian Ministry of Education, University and Research/ ; CMPT228810//Consorzio Interuniversitario per le Biotecnologie &amp; Italian Ministry of Education, University and Research/ ; IBFM NBFC CN00000033//National Biodiversity Future Center/ ; PNRA22_0000040//Italian Ministry of Education, University and Research/ ; }, abstract = {The global spread of antimicrobial resistance (AMR) threatens to plummet society back to the pre-antibiotic era through a resurgence of common everyday infections' morbidity. Thus, studies investigating antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in urban, agricultural, and clinical settings, as well as in extreme environments, have become increasingly relevant in the One Health perspective. Since the Antarctic and Arctic regions are considered amongst the few remaining pristine environments on Earth, the characterization of their native resistome appears to be of the utmost importance to understand whether and how it is evolving as a result of anthropogenic activities and climate change. In the present review, we report on the phenotypic (e.g., disk diffusion test) and genotypic (e.g., PCR, metagenomics) approaches used to study AMR in the aquatic environment of polar regions, as water represents one of AMR main dissemination routes in nature. Their advantages and limits are described, and the emerging trends resulting from the analysis of ARB and ARGs diffusion in polar waters discussed. The resistome detected in these extreme environments appears to be mostly comparable to those from more anthropized areas, with the predominance of tetracycline, β-lactam, and sulfonamide resistance (and related ARGs). Indeed, AMR is, in all cases, more consistently highlighted in sites impacted by human and wildlife activities with respect to more pristine ones. Surprisingly, aminoglycoside and fluroquinolone determinants seem to have an even higher incidence in the Antarctic and Arctic aquatic environment compared to that from other areas of the world, corroborating the need for a more thorough AMR surveillance in these regions.}, }
@article {pmid40298441, year = {2025}, author = {Peng, S-X and Gao, S-M and Lin, Z-L and Luo, Z-H and Zhang, S-Y and Shu, W-S and Meng, F and Huang, L-N}, title = {Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments.}, journal = {mBio}, volume = {}, number = {}, pages = {e0070525}, doi = {10.1128/mbio.00705-25}, pmid = {40298441}, issn = {2150-7511}, abstract = {Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.}, }
@article {pmid40298422, year = {2025}, author = {Koester, F and Myers, KS and Donohue, TJ and Noguera, DR}, title = {Metagenome-assembled genomes from microbial communities producing lactic acid from dairy residues.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0017925}, doi = {10.1128/mra.00179-25}, pmid = {40298422}, issn = {2576-098X}, abstract = {To advance the knowledge of microbial communities capable of fermenting agro-industrial residues into value-added products, we report metagenomes of microbial communities from four anaerobic bioreactors fed a mixture of ultra-filtered milk permeate and cottage cheese acid whey. This analysis produced 42 unique metagenome-assembled genomes (MAGs) that represent distinct taxa.}, }
@article {pmid40298412, year = {2025}, author = {Majernik, SN and Beaver, L and Bradley, PH}, title = {Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0085724}, doi = {10.1128/msphere.00857-24}, pmid = {40298412}, issn = {2379-5042}, abstract = {Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which, in turn, are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae and then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus, unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.IMPORTANCEMetagenome-assembled genomes, or MAGs, can be constructed without pure cultures of microbes. Large-scale efforts to build MAGs have yielded more complete pangenomes (i.e., sets of all genes found in one species). Pangenomes allow us to measure strain variation in gene content, which can strongly affect phenotype. However, because MAGs come from mixed communities, they can contaminate pangenomes with unrelated DNA; how much this impacts downstream analyses has not been studied. Using a metagenomic study of gut microbes in cirrhosis as our test case, we investigate how contamination affects analyses of microbial gene content. Surprisingly, even small, typical amounts of MAG contamination (<5%) result in disproportionately high levels of false positive associations (38%). Fortunately, we show that most contaminants can be automatically flagged and provide a simple method for doing so. Furthermore, applying this method reveals a new association between cirrhosis and gut microbial motility.}, }
@article {pmid40298386, year = {2025}, author = {Chen, Z and Zhang, Z and Nie, BN and Huang, W and Zhu, Y and Zhang, L and Xu, M and Wang, M and Yuan, C and Liu, N and Wang, X and Tian, J and Ba, Q and Wang, Z}, title = {Temporal network analysis of gut microbiota unveils aging trajectories associated with colon cancer.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0118824}, doi = {10.1128/msystems.01188-24}, pmid = {40298386}, issn = {2379-5077}, abstract = {UNLABELLED: The human gut microbiome's role in colorectal cancer (CRC) pathogenesis has gained increasing recognition. This study aimed to delineate the microbiome characteristics that distinguish CRC patients from healthy individuals, while also evaluating the influence of aging, through a comprehensive metagenomic approach. The study analyzed a cohort of 80 CRC patients and 80 matched healthy controls, dividing participants into a normal and a CRC group, further categorized by age into young, middle-aged, and old-aged subgroups. Extensive metagenomic sequencing of fecal samples allowed for the exploration of both the structural and functional profiles of the microbiome, with findings validated in an independent cohort to ensure robustness. Our results highlight notable differences in microbiome composition between CRC patients and healthy individuals, which exhibit age-dependent variations. Specifically, a higher prevalence of pathogenic bacteria, such as Bacteroides vulgatus, known to drive inflammation and carcinogenesis, was observed in CRC patients, alongside a reduction in beneficial microbes, including Lactobacillus. Functionally, the CRC-associated microbiome showed an increase in pathways related to DNA repair, cell cycle regulation, and metabolic activities, such as the Citrate cycle and Galactose metabolism, underscoring distinct microbial alterations in CRC patients that could influence disease onset and progression. These insights lay a foundation for future research into microbiome-based diagnostics and treatments for CRC.<br><br>IMPORTANCE: This study underscores the critical role of the gut microbiome in colorectal cancer (CRC) pathogenesis, particularly in the context of aging. By identifying age-specific microbial biomarkers and functional pathways associated with CRC, our findings provide novel insights into how microbiome composition and metabolic activities influence disease progression. These discoveries pave the way for developing personalized microbiome-based diagnostic tools and therapeutic strategies, potentially improving CRC prevention and treatment outcomes across different age groups. Understanding these microbial dynamics could also inform interventions targeting gut microbiota to mitigate CRC risk and progression.}, }
@article {pmid40298367, year = {2025}, author = {Zhou, Z and Ma, Y and Zhang, D and Ji, R and Wang, Y and Zhao, J and Ma, C and Zhu, H and Shen, H and Jiang, X and Niu, Y and Lu, J and Zhang, B and Tu, L and Zhang, H and Ma, X and Chen, P}, title = {Microbiome and fragmentation pattern of blood cell-free DNA and fecal metagenome enhance colorectal cancer micro-dysbiosis and diagnosis analysis: a proof-of-concept study.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0027625}, doi = {10.1128/msystems.00276-25}, pmid = {40298367}, issn = {2379-5077}, abstract = {Colorectal cancer (CRC) is the third most common cancer, and it can be prevented by performing early screening. As a hallmark of cancer, the human microbiome plays important roles in the occurrence and development of CRC. Recently, the blood microbiome has been proposed as an effective diagnostic tool for various diseases, yet its performance on CRC deserves further exploration. In this study, 133 human feces and 120 blood samples are collected, including healthy individuals, adenoma patients, and CRC patients. The blood cfDNA and fecal genome are subjected to shotgun metagenome sequencing. After removing human sequences, the microbial sequences in blood are analyzed. Based on the differential microbes and functions, random forest (RF) models are constructed for adenoma and CRC diagnosis. The results show that alterations of blood microbial signatures can be captured under low coverage (even at 3×). RF diagnostic models based on blood microbial markers achieve high area under the curve (AUC) values for adenoma patients (0.8849) and CRC patients (0.9824). When the fragmentation pattern is combined with microbial and KEGG markers, higher AUC values are obtained. Furthermore, compared to the blood microbiome, the fecal microbiome shows a different community composition, whereas their changes in KEGG pathways are similar. Pathogenic bacteria Fusobacterium nucleatum (F. nucleatum) in feces increased gradually from the healthy group to the adenoma and CRC groups. Additionally, F. nucleatum in feces and blood shows a positive correlation in CRC patients. Cumulatively, the integration of blood microbiome and fragmentation pattern is promising for CRC diagnosis.IMPORTANCEThe cell-free DNA of the human microbiome can enter the blood and can be used for cancer diagnosis, whereas its diagnostic potential in colorectal cancer and association with gut microbiome has not been explored. The microbial sequences in blood account for less than 1% of the total sequences. The blood microbial composition, KEGG functions, and fragmentation pattern are different among healthy individuals, adenoma patients, and CRC patients. Machine learning models based on these differential characteristics achieve high diagnostic accuracy, especially when they are integrated with fragmentation patterns. The great difference between fecal and blood microbiomes indicates that microbial sequences in blood may originate from various organs. Therefore, this study provides new insights into the community composition and functions of the blood microbiome of CRC and proposes an effective non-invasive diagnostic tool.}, }
@article {pmid40298267, year = {2025}, author = {Cheung, S and Zhou, NA and Ruhanya, V and J Jesser, K and Nezomba, I and Musvibe, J and Manyisa, B and Nyandoro, G and Chibukira, P and Mukaratirwa, A and Muserere, ST and Masunda, K and Ong, A and Meschke, JS}, title = {Characterization of enteric pathogens in Harare, Zimbabwe using environmental surveillance and metagenomics.}, journal = {Journal of water and health}, volume = {23}, number = {4}, pages = {477-492}, pmid = {40298267}, issn = {1477-8920}, mesh = {Zimbabwe ; *Metagenomics ; *Environmental Monitoring/methods ; *Wastewater/microbiology ; Humans ; *Bacteria/isolation &amp; purification/genetics/classification ; Drug Resistance, Bacterial ; Sewage/microbiology ; }, abstract = {High diarrheal disease burden remains an urgent concern in low- and middle-income countries, greatly affecting children under the age of 5 years and those living with HIV and AIDS. Treatment of infectious diseases has also become increasingly difficult with the rapid rise of antimicrobial resistance (AMR). Environmental surveillance of wastewater can supplement gaps in clinical surveillance as residents on a sewage system contribute to the wastewater, providing simple, composite samples that can improve understanding about both pathogens and AMR in the community. This study evaluated the effectiveness of environmental surveillance with shotgun metagenomics as a tool to characterize a broad range of enteric pathogens, antibiotic resistance genes, and virulence factor genes (VFGs) in wastewater from six neighborhoods in Harare, Zimbabwe. Alpha and beta diversity of the microbial community were similar between high-income and low-income suburbs. Enteric pathogens of high AMR and clinical concern, including Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella enterica, were detected in all samples. The top VFGs were encoded for delivery, adherence, and motility, functions important in toxin secretion, colonization, and immune modulation. The findings provide a foundation for future studies to explore environmental surveillance and shotgun metagenomics as a public health monitoring tool for enteric diseases.}, }
@article {pmid40297733, year = {2025}, author = {Nguyen, DS and Tran, DM}, title = {Endophytic bacteriome data of Litchi chinensis established by metagenomic 16S rRNA gene sequencing.}, journal = {Data in brief}, volume = {60}, number = {}, pages = {111544}, pmid = {40297733}, issn = {2352-3409}, abstract = {This work reported the diversity profiling and predicted metabolic function of the endophytic bacteriome of lychee (Litchi chinensis S.) cultivated in Dak Lak Province of Vietnam for the first time. Roots of lychee were collected from three different fields in Krong Ana District in Dak Lak. 16S rRNA primers were used to sequence the metagenomic library. Kraken 2 was used to analyze the taxonomic distribution, while the MetaCyc database was used to predict the metabolic function. We identified 10 phyla, 14 classes, 27 orders, 30 families, and 27 genera of the endophytic bacteria from the sample. Actinomycetota was the most predominant phylum (84.49%), and biosynthesis was the bacteriome's primary function (75.42%). Data provided insight into the taxonomic distribution and metabolic function of lychee endophytic bacteria and might be helpful for the next steps concerning sustainable lychee cultivation using endophytic bacteria.}, }
@article {pmid40297591, year = {2025}, author = {Pei, X and Liu, L and Han, Y}, title = {Advances in human microbiome and prostate cancer research.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1576679}, pmid = {40297591}, issn = {1664-3224}, mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology ; Male ; *Microbiota ; *Gastrointestinal Microbiome ; Tumor Microenvironment/immunology ; Animals ; }, abstract = {Prostate cancer (PCa) is the second most common malignant tumor in men worldwide, and its metastatic and heterogeneous nature makes it significantly more difficult to treat. Recent studies have revealed the critical role of microbiota in PCa occurrence, progression, and treatment. Accumulating evidence from 16S rRNA and metagenomic sequencing suggests the presence of specific microbiota in prostate tissues and macrogenomics techniques: cancerous tissues are enriched with pro-inflammatory genera (e.g., Fusobacterium, Propionibacterium acnes), whereas commensal bacteria (e.g., Pseudomonas) are more common in paracancerous tissues. The microbiota drive tumor progression through activation of the NF-κB/STAT3 pathway to induce chronic inflammation, modulation of the immune microenvironment (e.g., Treg/Th17 imbalance and M2-type macrophage polarization), and metabolite (e.g., LPS, short-chain fatty acids)-mediated hormonal and epigenetic regulation. In terms of clinical translation, urinary microbiota characterization combined with metabolomics analysis may enhance diagnostic specificity, while gut flora modulation (e.g., probiotic interventions or fecal transplants) may improve resistance to androgen deprivation therapy. Current challenges include sequencing accuracy of low-biomass samples, limitations of causal mechanism validation models, and large cohort heterogeneity. In the future, it will be necessary to integrate multi-omics technologies to explore the bidirectional regulation of the "gut-prostate axis" and develop personalized therapeutic strategies targeting microorganisms. In this paper, we systematically review the interactions between microbiota and PCa and their clinical potentials to provide a theoretical basis for precision diagnosis and treatment.}, }
@article {pmid40297587, year = {2025}, author = {Dora, D and Revisnyei, P and Pasic, A and Galffy, G and Dulka, E and Mihucz, A and Roskó, B and Szincsak, S and Iliuk, A and Weiss, GJ and Lohinai, Z}, title = {Host and bacterial urine proteomics might predict treatment outcomes for immunotherapy in advanced non-small cell lung cancer patients.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1543817}, pmid = {40297587}, issn = {1664-3224}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/urine/drug therapy/therapy/microbiology/immunology ; Male ; Female ; *Lung Neoplasms/urine/drug therapy/therapy/microbiology/immunology ; Middle Aged ; *Proteomics/methods ; Aged ; Immunotherapy/methods ; Treatment Outcome ; *Proteome ; Biomarkers, Tumor/urine ; Gastrointestinal Microbiome ; Immune Checkpoint Inhibitors/therapeutic use ; }, abstract = {INTRODUCTION: Urine samples are non-invasive approaches to study potential circulating biomarkers from the host organism. Specific proteins cross the bloodstream through the intestinal barrier and may also derive from gut microbiota. In this study, we aimed to evaluate the predictive role of the host and bacterial urine extracellular vesicle (EV) proteomes in patients with non-small cell lung cancer (NSCLC) treated with anti-PD1 immunotherapy.<br><br>METHODS: We analyzed the urine EV proteome of 33 advanced-stage NSCLC patients treated with anti-PD1 immunotherapy with LC-MS/MS, stratifying patients according to long (>6 months) and short (&#x2264;6 months) progression-free survival (PFS). Gut microbial communities on a subcohort of 23 patients were also analyzed with shotgun metagenomics. Internal validation was performed using the Random Forest (RF) machine learning (ML) algorithm. RF was validated with a non-linear Bayesian ML model. Gene enrichment, and pathway analysis of host urine proteins were analyzed using the Reactome and Gene Ontology databases.<br><br>RESULTS: We identified human (n=3513), bacterial (n=2647), fungal (n=19), and viral (n=4) proteins. 186 human proteins showed differential abundance (p<0.05) according to PFS groups, 101 being significantly more abundant in patients with short PFS and n=85 in patients with long PFS. We found several pathways that were significantly enriched in patients with short PFS (vs long PFS). Multivariate Cox regression showed that human urine proteins MPP5, IGKV6-21, NT5E, and KRT27 were strongly associated with long PFS, and LMAN2, NUTF2, NID1, TNC, IGF1, BCR, GPHN, and PPBP showed the strongest association with short PFS. We revealed that an increased bacterial/host protein ratio in the urine is more frequent in patients with long PFS. Increased abundance of E. coli and E. faecalis proteins in the urine positively correlates with their gut metagenomic abundance. RF ML model supported the reliability in predicting PFS for critical human urine proteins (AUC=0.89), accuracy (95%) and Bacterial proteins (AUC=0.74).<br><br>CONCLUSION: To our knowledge, this is the first study to depict the predictive role of the host and bacterial urine proteome in anti-PD1-treated advanced NSCLC.}, }
@article {pmid40297511, year = {2025}, author = {Valle, C and Parry, RH and Coutard, B and Colmant, AMG}, title = {Discovery of additional genomic segments reveals the fluidity of jingmenvirus genomic organization.}, journal = {Virus evolution}, volume = {11}, number = {1}, pages = {veaf023}, pmid = {40297511}, issn = {2057-1577}, abstract = {Jingmenviruses are a distinct group of flavi-like viruses characterized by a genome consisting of four to five segments. Here, we report the discovery of three novel putative jingmenviruses, identified by mining publicly available metagenomics data from mosquito and arachnid samples. Strikingly, these novel jingmenvirus sequences contain up to six genomic segments, with pairs of homologous segments coding for putative structural proteins. Following this discovery, we found an additional homologous segment for two other jingmenvirus genomes, which had gone unnoticed in the initial publications. The presence of a single version of the segments coding for non-structural proteins suggests that we have indeed identified jingmenviruses with infectious units that contain up to six segments. We compared these novel jingmenvirus sequences to published sequences, in particular the segments with multiple open reading frames (ORFs), and we propose that the putative translation initiation mechanisms involved for these segments are ribosomal frameshift resulting in the fusion of ORFs and leaky scanning for overlapping ORFs. These putative mechanisms, conserved for all jingmenvirus sequences analysed, including in homologous segments, require biological confirmation. We also generated structural models of two putative structural proteins in the duplicated segments, and the corresponding alignments enabled us to confirm or identify the homologous relationship between sequences that shared limited nucleotide or amino acid identity. Altogether, these results highlight the fluid nature of jingmenviruses, which is a hallmark of multipartite viruses. Different combinations of segments packaged in different virus particles could facilitate the acquisition or loss of genomic segments and a segment duplication following genomic drift. Our data therefore contribute to the evidence of the multipartite nature of jingmenviruses and the evolutionary role this organization may play.}, }
@article {pmid40297467, year = {2025}, author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D}, title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19120}, pmid = {40297467}, issn = {2167-8359}, mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.}, }
@article {pmid40297464, year = {2025}, author = {Zhang, Y and Ding, G and Gao, Y and Li, Y and Zhou, P and Wu, L and Zhou, M and Wang, J and Tang, J}, title = {Distribution status and influencing factors of antibiotic resistance genes in the Chaohu Lake, China.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19384}, pmid = {40297464}, issn = {2167-8359}, mesh = {*Lakes/microbiology/chemistry ; China ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Chaohu Lake (CL) is one of the most polluted areas in China due to its high content of antibiotics. However, the distribution and influencing factors of antibiotic resistance genes (ARGs) in this lake are still controversial.<br><br>METHODS: To solve this problem, we used metagenomic sequencing to investigate the distribution and in-fluencing factors of ARGs in CL.<br><br>RESULTS: Our findings revealed the existence of nine kinds of ARGs, including 45 specific genes. The most abundant types were multidrug, bacitracin, polymyxin, macrolide lincosamide streptogramin, and aminoglycoside. Multiple microorganisms were undeniable ARG reservoirs, although they were not dominant species in the microbiota. Our results also showed that both the microbiota and physiochemical factors played important roles in shaping the distributions of ARGs in CL. Specifically, the levels of PO4-P (0.5927) and total phosphorus (0.4971) had a greater impact than total nitrogen (0.0515), NO3-N (0.0352), NO2-N (-0.1975), and NH3-N (-0.0952).<br><br>CONCLUSIONS: These findings provide valuable insights into the distribution and influencing factors of ARGs in lakes.}, }
@article {pmid40296452, year = {2025}, author = {Wang, S and Kaur, S and Kunath, BJ and May, P and Richardson, L and Rogers, AB and Wilmes, P and Finn, RD and Vizcaíno, JA}, title = {An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e202500002}, doi = {10.1002/pmic.202500002}, pmid = {40296452}, issn = {1615-9861}, support = {C19/BM/13684739//National Research Fund Luxembourg (FNR)/ ; 223745/Z/21/Z//Wellcome/ ; //EMBL Core Funding/ ; }, abstract = {The availability of public metaproteomics, metagenomics and metatranscriptomics data in public resources such as MGnify (for metagenomics/metatranscriptomics) and the PRIDE database (for metaproteomics), continues to increase. When these omics techniques are applied to the same samples, their integration offers new opportunities to understand the structure (metagenome) and functional expression (metatranscriptome and metaproteome) of the microbiome. Here, we describe a pilot study aimed at integrating public multi-meta-omics datasets from studies based on human gut and marine hatchery samples. Reference search databases (search DBs) were built using assembled metagenomic (and metatranscriptomic, where available) sequence data followed by de novo gene calling, using both data from the same sampling event and from independent samples. The resulting protein sets were evaluated for their utility in metaproteomics analysis. In agreement with previous studies, the highest number of peptide identifications was generally obtained when using search DBs created from the same samples. Data integration of the multi-omics results was performed in MGnify. For that purpose, the MGnify website was extended to enable the visualisation of the resulting peptide/protein information from three reanalysed metaproteomics datasets. A workflow (https://github.com/PRIDE-reanalysis/MetaPUF) has been developed allowing researchers to perform equivalent data integration, using paired multi-omics datasets. This is the first time that a data integration approach for multi-omics datasets has been implemented from public data available in the world-leading MGnify and PRIDE resources.}, }
@article {pmid40296156, year = {2025}, author = {Fan, Y and Wang, D and Yang, JX and Ning, D and He, Z and Zhang, P and Rocha, AM and Xiao, N and Michael, JP and Walker, KF and Joyner, DC and Pan, C and Adams, MWW and Fields, MW and Alm, EJ and Stahl, DA and Hazen, TC and Adams, PD and Arkin, AP and Zhou, J}, title = {Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {106}, pmid = {40296156}, issn = {2049-2618}, support = {DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; DE-AC02-05CH11231//ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies; http://enigma.lbl.gov)/ ; }, mesh = {*Groundwater/microbiology/chemistry ; Phylogeny ; *Microbiota/genetics ; Tennessee ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Nitrates/analysis ; Water Pollutants, Chemical/analysis ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Metals, Heavy/analysis ; }, abstract = {BACKGROUND: Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3).<br><br>RESULTS: Both taxonomic and phylogenetic &#x3b1;-diversities were reduced in the most impacted wells, while the decline in functional &#x3b1;-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional &#x3b2;-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy.<br><br>CONCLUSIONS: Overall, we demonstrated that despite a reduced taxonomic &#x3b1;-diversity, microbial communities under stress maintained functionality underpinned by environmental selection. Video Abstract.}, }
@article {pmid40295870, year = {2024}, author = {Bell, MG and Parry, RH and Lee, TSE and Habarugira, G and McMahon, IE and Thompson, MA and Modhiran, N and Watterson, D and Batovska, J and Lynch, SE and Hall, RA and Harrison, JJ and Hobson-Peters, J}, title = {Synthetic recovery of Yada Yada virus expands insect-specific alphavirus knowledge and facilitates production of chimeric viruses.}, journal = {Npj viruses}, volume = {2}, number = {1}, pages = {45}, pmid = {40295870}, issn = {2948-1767}, support = {AQIRF067-2020-CV//Advance Queensland/ ; }, abstract = {Few insect-specific alphaviruses (ISA) have been discovered, with even fewer culturable to facilitate full characterisation. Here, we report the recovery of an infectious clone of Yada Yada virus (YYV)-a virus previously only detected by metagenomic sequencing of mosquito homogenates. Using the infectious clone, we confirmed the inability of YYV to replicate in vertebrate cells in vitro, with replication limited to only Aedes mosquito-derived cell lines. We further produced and characterised the first monoclonal antibodies (mAbs) to ISAs. Through successful replacement of the structural proteins of YYV with those of other ISAs, Eilat virus, Agua Salud (ASALV), Taï Forest (TALV) and Mwinilunga alphaviruses (MWAV), we established that a replication block for in vitro culture of TALV and MWAV in mosquito cells does not exist at virus entry. Unexpectedly, ASALV structural proteins were recognised by cross-reactive mAbs made to chikungunya (CHIKV) and Ross River viruses (RRV), suggesting a potential antigenic link between ASALV and pathogenic alphaviruses. The YYV genetic backbone was also investigated to generate chimeras displaying the structural proteins of various pathogenic vertebrate-infecting alphaviruses including CHIKV, RRV, Barmah Forest, Sindbis and Mayaro viruses. These chimeras retained the antigenic properties of the parental viruses and did not replicate in vertebrate cells, demonstrating the potential of the YYV platform for vaccine and diagnostic antigen production.}, }
@article {pmid40295861, year = {2025}, author = {Minch, B and Moniruzzaman, M}, title = {Expansion of the genomic and functional diversity of global ocean giant viruses.}, journal = {Npj viruses}, volume = {3}, number = {1}, pages = {32}, pmid = {40295861}, issn = {2948-1767}, abstract = {Giant viruses (GVs) play crucial roles in the global ocean microbial food web and biogeochemistry. Recent metagenomic advances have uncovered >1800 new GV genomes from the world's oceans. While this rapid increase in genomic information is impressive, it is nowhere close to the extensive genomic information available for other marine entities-e.g., prokaryotes and their "virome". We present 230 new high-quality GV genomes (genomes with 4 or more marker genes) and 398 partial genomes from nine global ocean datasets. Notably, we identified numerous GV genomes from the Baltic Sea, offering insights into their phylogenomics, metabolic potential, and environmental drivers in one of the largest brackish water ecosystems. We discovered new GV functions and identified a significant functional divide between the Imitervirales and Algavirales orders. Additionally, we evaluated factors affecting GV abundance through a case study on the Baltic Sea dataset. Our study significantly expands the marine GV genomic and functional diversity, broadening our understanding of their roles in the food web and biogeochemistry.}, }
@article {pmid40295121, year = {2025}, author = {Scheffer, G and Rattray, J and Evans, P and Shi, W and Bhatnagar, S and Hubert, CRJ}, title = {Nitrate-reducing microorganisms prevent souring of an oil field produced water storage pond.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf041}, pmid = {40295121}, issn = {1574-6941}, abstract = {Nitrate addition for mitigating sulfide production in oilfield systems has been studied in laboratory settings and in some subsurface oil reservoirs. To promote water recycling and re-use associated with oil reservoirs produced by hydraulic fracturing, high-salinity produced waters are temporarily stored in surface ponds prior to subsequent reinjection into the subsurface. In this study, nitrate was added directly to a storage pond to prevent sulfide accumulation. DNA sequencing of pond water over a 4-week period revealed a decrease in the proportion of sulfate-reducing microorganisms following nitrate application. Sulfate levels remained stable during this period, whereas nitrate and nitrite fluctuated in the days following the nitrate addition. Metagenome-assembled genomes (MAGs) reconstructed from the pond water microbiome highlighted different organisms with genes for organoheterotrophic and lithoheterotrophic nitrate reduction, whereas genes associated with sulfide production via sulfate or thiosulfate reduction were barely detected. Within those MAGs, genes for acetate metabolism were observed, consistent with acetate decreasing substantially in the pond water in the presence of nitrate. After nitrate was consumed an increase in relative abundance of putative autotrophic microorganisms was observed (e.g. Arhodomonas, Guyparkeria, Psychroflexus), corresponding to a drop in total inorganic carbon measurements in the storage pond. This trial offers an overview on microbial processes taking place in storage pond environments in response to nitrate addition.}, }
@article {pmid40295679, year = {2024}, author = {Ha, AD and Aylward, FO}, title = {Automated classification of giant virus genomes using a random forest model built on trademark protein families.}, journal = {Npj viruses}, volume = {2}, number = {1}, pages = {9}, pmid = {40295679}, issn = {2948-1767}, support = {1R35GM147290-01/NH/NIH HHS/United States ; CAREER-2141862//National Science Foundation/ ; }, abstract = {Viruses of the phylum Nucleocytoviricota, often referred to as "giant viruses," are prevalent in various environments around the globe and play significant roles in shaping eukaryotic diversity and activities in global ecosystems. Given the extensive phylogenetic diversity within this viral group and the highly complex composition of their genomes, taxonomic classification of giant viruses, particularly incomplete metagenome-assembled genomes (MAGs) can present a considerable challenge. Here we developed TIGTOG (Taxonomic Information of Giant viruses using Trademark Orthologous Groups), a machine learning-based approach to predict the taxonomic classification of novel giant virus MAGs based on profiles of protein family content. We applied a random forest algorithm to a training set of 1531 quality-checked, phylogenetically diverse Nucleocytoviricota genomes using pre-selected sets of giant virus orthologous groups (GVOGs). The classification models were predictive of viral taxonomic assignments with a cross-validation accuracy of 99.6% at the order level and 97.3% at the family level. We found that no individual GVOGs or genome features significantly influenced the algorithm's performance or the models' predictions, indicating that classification predictions were based on a comprehensive genomic signature, which reduced the necessity of a fixed set of marker genes for taxonomic assigning purposes. Our classification models were validated with an independent test set of 823 giant virus genomes with varied genomic completeness and taxonomy and demonstrated an accuracy of 98.6% and 95.9% at the order and family level, respectively. Our results indicate that protein family profiles can be used to accurately classify large DNA viruses at different taxonomic levels and provide a fast and accurate method for the classification of giant viruses. This approach could easily be adapted to other viral groups.}, }
@article {pmid40294792, year = {2025}, author = {Xiao, H and Zhou, J and Jia, H}, title = {Letter to the Editor Regarding "Clinical Application Value of Metagenomic Next-Generation Sequencing at Perioperative Period in Patients with Central Nervous System Infections in Neurosurgical Intensive Care Unit".}, journal = {World neurosurgery}, volume = {}, number = {}, pages = {124017}, doi = {10.1016/j.wneu.2025.124017}, pmid = {40294792}, issn = {1878-8769}, }
@article {pmid40294775, year = {2025}, author = {Liu, Z and Yang, S and Xie, S and Cao, D and Xi, W and Xiao, Y and Xu, X and Wang, Z and Li, L and Hu, J and Wang, X}, title = {Enhancing the detection sensitivity of mNGS in Bronchoalveolar Lavage fluid through cell Counting: An empirical study.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {}, number = {}, pages = {120311}, doi = {10.1016/j.cca.2025.120311}, pmid = {40294775}, issn = {1873-3492}, abstract = {OBJECTIVES: Lower respiratory tract infections pose significant clinical challenges due to their high morbidity and mortality rates. While metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool, its sensitivity is often compromised by host DNA contamination that overwhelms microbial signals. Selective host DNA depletion through cell lysis effectively reduces host DNA; however, it has an impact on microorganisms with relatively thin cell walls, and samples with low host content may introduce more environment or reagent-derived microbial contamination, interfering the detection results. Methods for determining host DNA depletion based on sample type, sample characteristics or using Spike-in controls to monitor sensitivity do not fully consider the potential limitations of host depletion technology on microbial detection, nor do they evaluate the possible significant impact on detection efficiency. This study aimed to develop a pre-analytical method for accurate host DNA content assessment.<br><br>METHODS: We established a cell-counting-based method for precise cellular content measurement in clinical BALF samples. The protocol involved: (1) evaluating the linearity and robustness of cell-counting dyes in BALF samples with varying characteristics, (2) assessing the correlation between cell counts and extracted nucleic acid mass, (3) investigating cellular counting thresholds for host depletion in clinical BALF analysis, and (4) implementing the optimized cell-counting method in clinical mNGS testing to guide selective-lysis treatment.<br><br>RESULTS: Acridine orange/propidium iodide (AO/PI) staining demonstrated superior performance compared to trypan blue and DAPI, particularly in turbid and bloody BALF samples. Implementing a host depletion threshold at 1&#x202f;&#xd7;&#x202f;10^6 cell counts significantly improves pathogen detection rates in high host background samples, while effectively preserving the detection sensitivity for pathogens in moderate and low host background samples.<br><br>CONCLUSIONS: Our findings demonstrate that cell counting serves as a reliable pre-analytical tool for determining optimal selective-lysis treatment in BALF mNGS testing, enhancing diagnostic accuracy while preserving pathogen integrity.}, }
@article {pmid40294758, year = {2025}, author = {Thangadural, T and Dobretsov, S and Aeby, G}, title = {Exploring Bacterial Diversity in Acropora pharaonis: Implications for Coral Health and Growth Anomalies.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107616}, doi = {10.1016/j.micpath.2025.107616}, pmid = {40294758}, issn = {1096-1208}, abstract = {Coral growth anomalies (GA) affect many coral genera across the world, yet the etiology of GAs remains unknown, with limited knowledge of associated bacteria. In this study, we investigated bacterial associations between the growth anomalies (GAs) and healthy (H) portions of coral colonies in Acropora faraonis for two seasons to understand microbial dynamics. Additionally, we examined bacteria in water (W), which could be affecting coral bacterial communities. We found that alpha diversity remained consistent between healthy and GA coral tissues, but their relative abundances differed significantly. Notably, differential analysis revealed the abundance of Endozoicomonas spp., differed significantly between GA and H tissue, although it remains the dominant genus in both GA and H tissue. The high relative abundance of Endozoicomonas spp. in both GA and healthy tissue underscores its potential role in maintaining coral health. Structural modifications in GAs, such as changes in polyp sizes or densities, could be responsible for these differences in bacterial abundance. Similarly, microbial community composition remained consistent between seasons but differed in abundance again. We found differences between microbial communities of GAs and water, but no significant differences were observed between GAs and H, and no previously established bacterial pathogens were detected in GA tissue. These findings describe bacterial community patterns in GAs, but their potential role in its pathogenesis remains unknown. Further metagenomic and meta-transcriptomic analyses are needed to understand potential bacterial involvement in GAs. Additionally, investigating viruses and fungi in GA tissue is recommended to gain deeper insights into GA pathogenesis.}, }
@article {pmid40294754, year = {2025}, author = {Devi, A and Singh, V and Raj, A and Saratale, GD and Ferreira, LFR and Mulla, SI and Bharagava, RN}, title = {Optimization of lipid production in Tetradesmus dimorphus using response surface methodology using tannery wastewater for biodiesel production.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132585}, doi = {10.1016/j.biortech.2025.132585}, pmid = {40294754}, issn = {1873-2976}, abstract = {The management of industrial wastewaters and generation of sustainable energy resources are the two major challenges concerned with the global population and depleting fossil fuels. Tannery wastewater (TWW) is a major source of environmental pollution and human health hazardous if released without adequate treatment. The microalgal treatment of TWW among other approaches seems to be beneficial and effective as microalgae use TWW as nutrient source offering wastewater treatment while producing large biomass for biofuel production. Biomass and lipid content are the adequate criteria for higher biodiesel yield. In present study, Tetradesmus dimorphus was grown in TWW with an objective to treat TWW along with the generation of large biomass for biodiesel production and Response Surface Methodology (RSM) was used to optimize the biodiesel production taking into count the parameters such as wastewater concentrations, pH and photoperiod. Results showed that highest biomass and lipid content produced were 1.63 ± 0.02 g/L and 487 ± 11 mg/L, respectively with 213.80 ± 7 mg/L of biodiesel production. Gas Chromatography-Flame Ionization Detection (GC-FID) analysis of biodiesel obtained from Tetradesmus dimorphus lipids showed that it was made up of more than 40 % Methyl decanoate (C11:0) and Methyl erucate (C22:1). The interrelationships between selected parameters like STTWW concentrations, pH and photoperiods reflected the positive impact on lipid productivity as 3D contour depicted the maximum yield at 80 % wastewater concentration, pH 8 and 14 h of photoperiod. Study showed that microalgal treatment of TWW among the other approaches seems beneficial and effective to harness wastewater nutrients while producing valuable biomass for biodiesel production.}, }
@article {pmid40294646, year = {2025}, author = {Wang, C and Zhang, H and Liu, J}, title = {The diagnostic efficacy of metagenomic next-generation sequencing in spontaneous bacterial peritonitis: System review and meta-analysis.}, journal = {Gastroenterologia y hepatologia}, volume = {}, number = {}, pages = {502456}, doi = {10.1016/j.gastrohep.2025.502456}, pmid = {40294646}, issn = {0210-5705}, abstract = {OBJECTIVE: The objective of this research is to assess the accuracy and reliability of metagenomic next-generation sequencing (mNGS) in identifying pathogens in spontaneous bacterial peritonitis (SBP) patients and its impact on antibiotic treatment decisions.<br><br>METHODS: Electronic databases were searched up to July 31, 2023. Studies reporting mNGS diagnostic sensitivity and specificity in SBP were included. Random or fixed-effects models were used. Heterogeneity was assessed using chi-squared test and I&#xb2; statistics.<br><br>RESULTS: Out of 75 identified studies, four studies with a total of 420 SBP patients were included. The pooled sensitivity for mNGS in ascites was 94% (95% CI: 86-97%), and specificity was 81% (95% CI: 71-89%). The AUC was calculated to be 0.95 (95% CI: 0.92-0.96), indicating high diagnostic accuracy. The most common pathogens identified by mNGS were Gram-positive bacteria (36%), followed by Gram-negative bacteria (29%), viruses (22%), and fungi (11%).<br><br>CONCLUSION: mNGS shows high diagnostic accuracy in detecting pathogens in SBP patients, offering significant value in optimizing antimicrobial therapy. Its ability to identify a broad spectrum of pathogens makes it a promising tool in clinical management of SBP.}, }
@article {pmid40294554, year = {2025}, author = {Zeng, H and Yang, H and Fu, Z and Ma, L and Lu, L and Zeng, T and Xiao, Y and Lyu, W}, title = {Integrated 16S rRNA and metagenomic sequencing reveals the distribution of key antibiotic resistance genes in duck gut microbiota.}, journal = {Poultry science}, volume = {104}, number = {7}, pages = {105206}, doi = {10.1016/j.psj.2025.105206}, pmid = {40294554}, issn = {1525-3171}, abstract = {The duck gut microbiota is essential for host health and is considered a potential reservoir for antibiotic resistance genes (ARGs). However, research on ARGs in the duck gut microbiota is limited. This study collected 120 intestinal content samples from five segments (duodenum, jejunum, ileum, cecum, and colorectum) of ducks raised under two rearing conditions (with or without an open-air swimming pool). We compiled a comprehensive inventory of microbial genes in the duck gut and conducted an analysis of microbial composition and function across all intestinal segments using 16S rRNA gene sequencing combined with metagenomics. The findings revealed that Firmicutes were the most prevalent microbes in all intestinal segments. In the foregut (duodenum, jejunum, and ileum), microbial functions were mainly related to genetic information processing such as transcription, translation, replication, and glycosynthesis/gluconeogenesis. Conversely, in the hindgut (cecum and colorectum), microbial functions were primarily associated with the biosynthesis of secondary metabolites and various metabolic pathways. The analysis of ARGs indicated a higher relative abundance of ARGs in the cecum and colorectum (P < 0.05) of ducks in the presence of an open-air swimming pool compared to the absence of one. Furthermore, through co-occurrence network analysis, we identified Bacteroides, Roseburia, Ruminococcus, and Blautia as potential hosts of ARGs such as tetQ, tet32, tet37, vanR, vanG, and acrB in the hindgut. This study provides new insights into the complex relationship between ARGs and the microbial community in duck intestines, laying a theoretical groundwork for understanding the transmission dynamics of ARGs in these ecosystems.}, }
@article {pmid40293591, year = {2025}, author = {Orlova, EA and Sinkov, VV and Ogarkov, OB and Suzdalnitsky, AE and Kondratov, IG and Zhdanova, SN and Rychkova, LV and Kolesnikova, LI}, title = {Metagenomic Analysis of Caseum of Tuberculosis Foci.}, journal = {Bulletin of experimental biology and medicine}, volume = {}, number = {}, pages = {}, pmid = {40293591}, issn = {1573-8221}, abstract = {The microbiota of the deep lung regions significantly differs from that of the upper respiratory tract by much lower biomass and dynamic diversity. In our previous studies we found that the biodiversity of the satellite microbiota of tuberculosis foci is sharply reduced in comparison with intact lung tissues. These findings allowed us to classify microbial communities in the caseous necrosis of tuberculomas into two types: (i) mycobacterial caseoma (tuberculoma), where 70% or more of the genomes correspond to Mycobacterium tuberculosis, and (ii) a polymicrobial community, where the concentration of M. tuberculosis varies from 0 to 10%. Using shotgun metagenomic sequencing, 14 tuberculomas from 13 patients were analyzed on a NextSeq 550 platform (Illumina). Taxonomic classification of short reads was performed using Kraken 2. The results show that, on average, 99.95% of the short reads belonged to human DNA or were unclassified. However, the classified reads related to bacterial genomes confirmed the concept that in many cases, tuberculomas contained polymicrobial communities that either replaced or supplemented the original mycobacterial microbiota of the caseous material.}, }
@article {pmid40293286, year = {2025}, author = {Elsakhawy, OK and Roozitalab, A and Abouelkhair, MA}, title = {Genome sequence of a bovine respiratory syncytial virus strain from a cow in Tennessee.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0007225}, doi = {10.1128/mra.00072-25}, pmid = {40293286}, issn = {2576-098X}, abstract = {We report the genome sequence of a bovine respiratory syncytial virus strain (hereafter referred to as BRSV_23), identified in a cow in Tennessee. This genome sequence updates the currently circulating BRSV field strains in the United States, providing insights into viral evolution and epidemiology to improve diagnostics and control strategies.}, }
@article {pmid40293266, year = {2025}, author = {Wilson, A and Gias, E and Little, A and Jauregui, R and Low, YS and Pulford, D and Steyn, A and Sylvester, K and Green, D and O'Keefe, J and McCulley, M}, title = {Genome sequence of a divergent strain of canine distemper virus detected in New Zealand fur seals.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0015125}, doi = {10.1128/mra.00151-25}, pmid = {40293266}, issn = {2576-098X}, abstract = {We report the draft genome sequence of a strain of canine distemper virus detected in New Zealand fur seals (Arctocephalus forsteri). A high-quality draft consensus genome was produced through a combination of long- and short-read metagenomic sequencing approaches. Phylogenetic analysis confirms that the virus is a divergent strain of canine distemper virus.}, }
@article {pmid40293263, year = {2025}, author = {Dias, D and Nascimento, B and Cruz, A and Silva, S and Reis, L and Silva, F and Silva, L and Silva, S and Vieira, D and Brandão, R and Junior, J and Santos, A and Reis, H and Neto, J}, title = {Coding-complete genome sequence of a divergent member of the genus Gordisvirus detected in Sabethes (Peytonulus) undosus Coquillet mosquitoes (Diptera: Culicidae) from Brazil.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0127524}, doi = {10.1128/mra.01275-24}, pmid = {40293263}, issn = {2576-098X}, abstract = {We report the complete genome sequence of a divergent member of the genus Gordisvirus (family Xinmoviridae, order Mononegavirales), obtained through metagenomic sequencing of Sabethes (Peytonulus) undosus Coquillett mosquitoes in the Brazilian Amazon. Phylogenetic analyses confirmed its classification. The genome comprises 12,150 nucleotides and encodes five open-reading frames.}, }
@article {pmid40291804, year = {2025}, author = {Wu, Y and Mo, J and Wang, Q and Li, J and Wei, J and Zhang, N and Dong, Y and Zhu, X and Lu, T and Huang, S}, title = {Microbiome and metabolome explain the high-fat diet-induced diabetes development and diabetes resistance in Guizhou mini-pigs.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1555069}, pmid = {40291804}, issn = {1664-302X}, abstract = {Type 2 diabetes mellitus (T2DM) is an obesity-related disease claiming substantial global mortality annually. Current animal models of T2DM remain limited, with low success rates in establishing porcine models of high-fat diet (HFD)-induced T2DM. Our experimental design employed 35 Guizhou mini-pigs to develop a T2DM model via HFD induction, aiming to identify microbial and metabolic signatures associated with disease pathogenesis and resistance. At month 10, five individuals from the control (CTR), T2DM (DM), and T2DM resistant (anti-DM) groups were slaughtered, samples were collected, and relevant indices were measured. Metagenomics, metabolomics, and 16S rRNA sequencing were performed to identify microbes and metabolites linked to T2DM progression and resistance. Key findings demonstrated anti-DM group parameters-including metabolic indices (fasting blood glucose, insulin levels, HbA1c, IVGTT), histopathology (HE-stained pancreatic/hepatic tissues), microbial profiles (structural, compositional, functional), and metabolomic signatures-occupied intermediate positions between CTR and DM groups. Network analyses revealed: (1) Lactobacillus, L. amylovorus, fingolimod, polyoxyethylene sorbitan monooleate, thiamine, and atrazine in HFD-associated networks; (2) Limosilactobacillus reuteri, N-oleoyl-L-serine, tolbutamide, tetradecanoyl carnitine, 3'-sulfogalactosylceramide, and guggulsterone in T2DM resistance networks; (3) Ruminococcaceae NK4A214 group, diethyl phthalate, zingerone, enalapril, 5-hydroxytryptophol, 2'-deoxyinosine, icariin, and emetine in T2DM progression networks. These results further clarify the role of the gut microbiota and serum metabolites in the development of T2DM in the Guizhou mini-pig model.}, }
@article {pmid40291803, year = {2025}, author = {Yang, M and Cai, Y and Bai, T and Han, X and Zeng, R and Liu, D and Liu, T and Liu, R and Ma, C and Yu, L}, title = {Changes in the community composition and function of the rhizosphere microbiome in tobacco plants with Fusarium root rot.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1512694}, pmid = {40291803}, issn = {1664-302X}, abstract = {INTRODUCTION: Tobacco root rot caused by Fusarium spp. is a soil-borne vascular disease that severely affects tobacco production worldwide. To date, the community composition and functional shifts of the rhizosphere microbiome in tobacco plants infected with Fusarium root rot remain poorly understood.<br><br>METHODS: In this study, we analyzed the differences in the compositions and functions of the bacterial and fungal communities in the rhizosphere and root endosphere of healthy tobacco plants and tobacco with Fusarium root rot using amplicon sequencing and metagenomic sequencing.<br><br>RESULTS AND DISCUSSION: Our results showed that Fusarium root rot disrupted the stability of bacteria-fungi interkingdom networks and reduced the network complexity. Compared to healthy tobacco plants, the Chao1 index of bacterial communities in the rhizosphere soil of diseased plants increased by 4.09% (P < 0.05), while the Shannon and Chao1 indices of fungal communities decreased by 13.87 and 8.17%, respectively (P < 0.05). In the root tissues of diseased plants, the Shannon index of bacterial and fungal communities decreased by 17.71-27.05% (P < 0.05). Additionally, we observed that the rhizosphere microbial community of diseased tobacco plants shifted toward a pathological combination, with a significant increase in the relative abundance of harmful microbes such as Alternaria, Fusarium, and Filobasidium (89.46-921.29%) and a notable decrease in the relative abundance of beneficial microbes such as Lysobacter, Streptomyces, Mortierella, and Penicillium (48.48-81.56%). Metagenomic analysis further revealed that the tobacco rhizosphere microbial communities of diseased plants played a significant role in basic biological metabolism, energy production and conversion, signal transduction, and N metabolism, but their functions involved in C metabolism were significantly weakened. Our findings provide new insights into the changes in and interactions within the rhizosphere and root endosphere microbiomes of tobacco plants under the stress of Fusarium soil-borne fungal pathogens, while laying the foundation for the exploration, development, and utilization of beneficial microbial resources in healthy tobacco plants in the future.}, }
@article {pmid40291800, year = {2025}, author = {Huang, YY and Zhu, D and Yang, LQ and Ortúzar, M and Yang, ZF and Lv, ZH and Xie, KQ and Jiang, HC and Li, WJ and Yin, YR}, title = {Characterization, thermostable mechanism, and molecular docking of a novel glucose-tolerant β-glucosidase/β-galactosidase from the GH1 family isolated from Rehai hot spring.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1559242}, pmid = {40291800}, issn = {1664-302X}, abstract = {INTRODUCTION: As a renewable alternative to fossil fuels, second-generation bioethanol production relies heavily on efficient lignocellulose conversion, with β-glucosidase playing a critical role.<br><br>METHODS: This study focused on the &#x3b2;-glucosidase gene y50bg4 discovered in the Tengchong Rehai metagenome. The recombinant enzyme Y50Bg4 was obtained through PCR amplification, cloning, and expression. It was subsequently separated and purified using a Ni-NTA affinity chromatography column, and its enzymatic properties were analyzed.<br><br>RESULTS: Enzymatic characterization revealed that Y50Bg4 efficiently hydrolyzes substrates like cellobiose, pNPGlc, and lactose. Y50Bg4 achieved optimal activity at 60&#xb0;C and pH 6.0, maintaining 100% stability after 2&#x202f;h of incubation at 60&#xb0;C. The residual activity remained above 60% after 24&#x202f;h of incubation across a pH range of 4.0 to 10.0. Kinetic constants analysis showed K m values of 4.69&#x202f;mg/mL for cellobiose and 0.53&#x202f;mM for pNPGlc, with V max values of 39.71&#x202f;&#x3bc;mol/min/mg and 20.39&#x202f;&#x3bc;mol/min/mg, respectively. Furthermore, the enzyme exhibits exceptional glucose tolerance, with Y50Bg4 retaining over 80% of its activity even at a glucose concentration of 3,000&#x202f;mM. In practical applications, Y50Bg4 can work synergistically to degrade corn straw when combined with commercial cellulase. When Y50Bg4 (0.05&#x202f;mg/mL) was added to the commercial cellulase reaction system, the glucose yield from corn straw increased by 11.6% after a reaction period of 24&#x202f;h at 50&#xb0;C. The results indicate that Y50Bg4 exhibits the activities of both &#x3b2;-glucosidase and &#x3b2;-galactosidase. Molecular docking and kinetic simulations revealed that Y50Bg4 has a higher affinity for cellobiose than for lactose and identified structural regions (residues 325-350 and 390-410) that contribute to its thermal stability.<br><br>DISCUSSION: These findings highlight the potential of Y50Bg4 for industrial applications in bioethanol production and cellulose hydrolysis. In summary, Y50Bg4, with its exceptional enzymatic properties, presents significant application value and market potential in industrial sectors such as bioethanol production and cellulose hydrolysis.}, }
@article {pmid40290900, year = {2025}, author = {Kodio, A and Coulibaly, D and Doumbo, S and Konaté, S and Koné, AK and Dama, S and Niangaly, A and Tall, ML and Konaté, AM and L'Ollivier, C and Levasseur, A and Bittar, F and Djimdé, A and Doumbo, OK and Raoult, D and Thera, MA and Ranque, S}, title = {Gut microbiota influences Plasmodium falciparum malaria susceptibility.}, journal = {New microbes and new infections}, volume = {65}, number = {}, pages = {101586}, pmid = {40290900}, issn = {2052-2975}, abstract = {BACKGROUND: The gut microbiota has recently been associated with malaria susceptibility/resistance in animal models and humans. This study aimed to assess its influence on malaria attack and Plasmodium parasitemia in children living in a malaria-endemic area of Mali.<br><br>METHODS: Healthy children were enrolled in a 16-month cohort study in Bandiagara. Their gut bacteria and fungi community structures were characterized via 16S and ITS metabarcoding at enrolment. Clinicians monitored malaria attacks. Asymptomatic Plasmodium carriage was assessed by real-time polymerase chain reaction.<br><br>RESULTS: Of the 300 children, 107 (36&#xa0;%) had at least one malaria attack, and 82 (27&#xa0;%) had at least one episode of asymptomatic Plasmodium parasitemia. The gut bacterial community structure, but not the fungal community, was associated with susceptibility/resistance to both malaria attacks and asymptomatic P. falciparum parasitemia. Higher gut bacteria richness was independently associated with susceptibility to both asymptomatic parasitemia episodes and malaria attacks. 17 bacteria, and 7 fungi were associated with susceptibility to malaria attacks, and 8 bacteria, and 3 fungi were associated with resistance. 15 bacteria and 13 fungi were associated with susceptibility to asymptomatic Plasmodium parasitemia episodes, and 19 bacteria and 3 fungi were associated with resistance.<br><br>CONCLUSION: Further studies are needed to confirm these findings, which point the way to strategies aimed at reducing the risk of malaria by modulating gut microbiota components in at-risk populations.}, }
@article {pmid40290560, year = {2025}, author = {Hosszu-Fellous, K and Cordey, S and Masouridi-Levrat, S and Simonetta, F and Laubscher, F and Combescure, C and Mamez, AC and Giannotti, F and Morin, S and Docquier, M and Pradier, A and Royston, L and Chalandon, Y and Neofytos, D and Kaiser, L}, title = {Blood Virome After Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {Open forum infectious diseases}, volume = {12}, number = {4}, pages = {ofaf213}, pmid = {40290560}, issn = {2328-8957}, abstract = {BACKGROUND: Haploidentical allogeneic hematopoietic cell transplant recipients (allo-HCTr) receiving posttransplant cyclophosphamide (haplo-PTCy) are at higher risk for infectious complications, including viral infections.<br><br>METHODS: We performed a retrospective, single-center, propensity-score matched-pair study including adult haplo-PTCy and allo-HCTr from human leukocyte antigen (HLA)-matched donors, undergoing transplantation in our institution between 2016 and 2022. For each patient, 4 blood samples (day [D] 0, D30, D90, and D180 posttransplantation) were extracted from the biobank and tested with metagenomic next-generation sequencing (mNGS) to describe the blood virome and identify viral RNA/DNA signatures potentially unrecognized by routinely available tests. Routine and symptom-driven polymerase chain reaction (PCR) test results performed during the study period were reviewed.<br><br>RESULTS: Twenty-five matched pairs of haplo-PTCy and HLA-matched allo-HCTr were included in the analysis. Plasma mNGS detected a total of 155 and 190 different viral RNA/DNA signatures in haplo-PTCy and HLA-matched allo-HCTr, respectively between D0 and D180. The number of viral signatures was significantly lower in the haplo-PTCy group compared to HLA-matched allo-HCTr at D90 (-1.0 [95% confidence interval {CI}, -1.7 to -.3]; P = .01) and during the period between D30 and D180 (-1.9 [95% CI, -3.3 to -.5]; P = .01). Certain viral species (Anelloviridae, Epstein-Barr virus) were more prevalent in HLA-matched patients. Symptom-driven PCR tests showed higher infection rates of usual viral pathogens in haplo-PTCy versus HLA-matched allo-HCTr (P = .02).<br><br>CONCLUSIONS: Frequently deployed, targeted PCR tests showed increased viral infection prevalence in haplo-PTCy patients. Conversely, mNGS testing applied at specific timepoints revealed a lower number of commensal viruses in this patient group. More studies on routine use of mNGS are needed to further assess its clinical relevance and value.}, }
@article {pmid40290406, year = {2025}, author = {Zhu, H and Guo, Y and Chen, H and Ni, L and Zhu, B and Qu, T}, title = {A Case of Pulmonary Infection Caused by Rhodococcus equi in an AIDS Patient and Literature Review.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {2021-2027}, pmid = {40290406}, issn = {1178-6973}, abstract = {Rhodococcus equi is a rare opportunistic Gram-positive bacterium that primarily affects immunocompromised individuals, particularly those with human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS). The infection often presents as a multisystem, disseminated disease with rapid progression and high mortality if not promptly diagnosed and treated. We report the case of a 34-year-old male AIDS patient who developed pulmonary infection due to Rhodococcus equi. Cultures from bronchoalveolar lavage fluid, metagenomic next-generation sequencing (mNGS), and bronchoscopic brushing all indicated infection with Rhodococcus equi. Following combined anti-infective treatment, the pulmonary infection was controlled, and his condition improved. Clinicians should be alert to the possibility of Rhodococcus equi infection in AIDS patients, emphasizing early diagnosis and targeted therapy to improve patient outcomes.}, }
@article {pmid40290137, year = {2025}, author = {Kong, F and Wang, S and Zhang, Y and Li, C and Dai, D and Wang, Y and Cao, Z and Yang, H and Shengli Li,  and Wei Wang, }, title = {Alanine Derived from Ruminococcus_E bovis Alleviates Energy Metabolic Disorders during the Peripartum Period by Providing Glucogenic Precursors.}, journal = {Research (Washington, D.C.)}, volume = {8}, number = {}, pages = {0682}, pmid = {40290137}, issn = {2639-5274}, abstract = {Peripartum dairy cows commonly experience energy metabolism disorders, which lead to passive culling of postpartum cows and a decrease in milk quality. By using ketosis peripartum dairy cows as a model, this study aims to elucidate the metabolic mechanism of peripartum cows and provide a novel way for managing energy metabolic disorders. From a cohort of 211 cows, we integrated multi-omics data (metagenomics, metabolomics, and transcriptomics) to identify key microbes and then utilized an in vitro rumen fermentation simulation system and ketogenic hepatic cells to validate the potential mechanisms and the effects of postbiotics derived from key microbes. Postpartum cows with metabolic disorders compensate for glucose deficiency through mobilizing muscle proteins, which leads to marked decreases in milk protein content. Concurrently, these cows experience rumen microbiota disturbance, with marked decreases in the concentrations of volatile fatty acids and microbial protein, and the deficiency of alanine (Ala) in microbial protein is correlated with the metabolic disorder phenotype. Metagenomic binning and in vitro fermentation assays reveal that Ruminococcus_E bovis (MAG 189) is enriched in amino acid biosynthesis functions and responsible for Ala synthesis. Furthermore, transcriptomic and metabolomic analyses of the liver in metabolic disorder cows also show impaired amino acid metabolism. Supplementation with Ala can alleviate ketogenesis in liver cell models by activating the gluconeogenesis pathway. This study reveals that Ruminococcus_E bovis is associated with host energy metabolism homeostasis by supplying glucogenic precursors to the liver and suggests the use of Ala as a method for the treatment of energy metabolism disorders in peripartum cows.}, }
@article {pmid40289407, year = {2025}, author = {Aho, VTE and Clerbaux, LA and Kupczok, A and Tillett, B and Garg, N and Henderickx, JGE}, title = {A Non-Metaproteomics Researchers' View on Metaproteomics in Microbiome Research.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e202500019}, doi = {10.1002/pmic.202500019}, pmid = {40289407}, issn = {1615-9861}, abstract = {Metaproteomics, an emerging field among the omic techniques, holds great promise for unraveling the function of microbiomes in host health and our environment. Metaproteomics can also be a valuable addition to multiomics studies of the microbiome, complementing genome-resolved metagenomics, metatranscriptomics, and metabolomics. The potential advancements from metaproteomics and multiomics research touch a breadth of disciplines, including ecology, biochemistry, immunology, medical microbiology, cell physiology, and medicine, and could lead to both fundamental and applied discoveries. However, there are significant roadblocks to widespread adoption of metaproteomics among microbiome researchers. In this Viewpoint article, we highlight the pivotal role of metaproteomics in microbiome research by showcasing its advantages, exploring opportunities to overcome challenges, and paving the way for its broader adoption as a mainstream technique. We hope that the recommendations provided in this Viewpoint article will inspire new, beneficial collaborations between proteomics experts, algorithm and infrastructure developers, biochemists, cell biologists, and microbiologists, enabling the construction of a knowledge base of microbiome function that can have an immediate and direct impact on host health and the environment.}, }
@article {pmid40289251, year = {2025}, author = {Slager, J and Simpson, HL and Gacesa, R and Chen, L and Tan, IL and Gelderloos, J and Maatman, A and Wijmenga, C and Zhernakova, A and Fu, J and Weersma, RK and Gonera, G and Jonkers, IH and Withoff, S}, title = {High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2489071}, doi = {10.1080/19490976.2025.2489071}, pmid = {40289251}, issn = {1949-0984}, mesh = {Humans ; *Celiac Disease/microbiology/diet therapy ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Feces/microbiology ; Middle Aged ; Adult ; Netherlands ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Aged ; }, abstract = {BACKGROUND: Coeliac disease (CeD) is an immune-mediated disorder primarily affecting the small intestine, characterized by an inflammatory immune reaction to dietary gluten. CeD onset results from a multifaceted interplay of genetic and environmental factors. While recent data show that alterations in gut microbiome composition could play an important role, many current studies are constrained by small sample sizes and limited resolution.<br><br>METHODS: To address these limitations, we analyzed fecal gut microbiota from two Dutch cohorts, CeDNN (128 treated CeD patients (tCeD), 106 controls) and the Lifelines Dutch Microbiome Project (24 self-reported tCeD, 654 controls), using shotgun metagenomic sequencing. Self-reported IBS (570 cases, 1710 controls) and IBD (93 cases, 465 controls) were used as comparative conditions of the gastrointestinal tract. Interindividual variation within the case and control groups was calculated at whole microbiome and strain level. Finally, species-specific gene repertoires were analyzed in tCeD patients and controls.<br><br>RESULTS: Within-individual microbiome diversity was decreased in patients with self-reported IBS and IBD but not in tCeD patients. Each condition displayed a unique microbial pattern and, in addition to confirming previously reported microbiome associations, we identify an increase in the levels of Clostridium sp. CAG:253, Roseburia hominis, and Eggerthella lenta, amongst others. We further show that the observed changes can partially be explained by gluten-free diet adherence. We also observe increased interindividual variation of gut microbiome composition among tCeD patients and a higher bacterial mutation frequency in tCeD that contributes to higher interindividual variation at strain level. In addition, the immotile European subspecies of Eubacterium rectale, which has a distinct carbohydrate metabolism potential, was nearly absent in tCeD patients.<br><br>CONCLUSION: Our study sheds light on the complex interplay between the gut microbiome and CeD, revealing increased interindividual variation and strain-level variation in tCeD patients. These findings expand our understanding of the microbiome's role in intestinal health and disease.}, }
@article {pmid40289223, year = {2025}, author = {Salma Santhosh, S and Meena, S and Baskar, M and Karthikeyan, S and Vanniarajan, C and Ramesh, T}, title = {Transformative strategies for saline soil restoration: Harnessing halotolerant microorganisms and advanced technologies.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {5}, pages = {140}, pmid = {40289223}, issn = {1573-0972}, support = {UGCES-22-OB-TAM-F-SJSGC-16232//University Grants Commission (UGC) - Savitribai Jyotirao Phule Fellowship for Single Girl Child (SJSGC)/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; Salinity ; Biodegradation, Environmental ; Salt Tolerance ; *Bacteria/metabolism/genetics ; Gene Editing ; }, abstract = {Soil salinity is a critical global challenge that severely impairs crop productivity and soil health by disrupting water uptake, nutrient acquisition, and ionic balance in plants, thereby posing a significant threat to food security. This review underscores innovative strategies to mitigate salinity stress, focusing on the pivotal role of halotolerant microorganisms and their synergistic interactions with plants. Halotolerant microorganisms enhance plant resilience through diverse mechanisms under salinity, including exopolysaccharide production, sodium sequestration, and phytohormone regulation. It improves ionic balance, nutrient uptake, and root development, facilitated by osmoregulatory and genetic adaptations. In this discussion, we explored emerging technologies, including genome editing (e.g., CRISPR-Cas9), synthetic biology, and advanced omics-based tools such as metagenomics and metatranscriptomics. These cutting-edge approaches offer profound insights into microbial diversity and their functional adaptations to saline environments. By leveraging these technologies, it is possible to design targeted bioremediation strategies through the customization of microbial functionalities to address specific environmental challenges effectively. Advanced methodologies, such as microbial volatile organic compounds (mVOCs), nanotechnology, and stress-tolerant microbial consortia, significantly enhance plant stress tolerance and facilitate soil restoration. Moreover, integrating digital technologies, including machine learning and artificial intelligence (AI), optimizes bioremediation processes by providing precise, scalable, and adaptable solutions tailored to diverse agricultural ecosystems. The synergistic application of halotolerant microbe-mediated approaches with advanced biotechnological and digital innovations presents a transformative strategy for saline soil restoration. Future research should focus on harmonizing these technologies and methodologies to maximize plant-microbe interactions and establish resilient, sustainable agricultural systems.}, }
@article {pmid40289152, year = {2025}, author = {Jarrige, D and Tardy, V and Loux, V and Rué, O and Chabbi, A and Terrat, S and Maron, PA}, title = {Metagenomics reveals contrasted responses of microbial communities to wheat straw amendment in cropland and grassland soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {14723}, pmid = {40289152}, issn = {2045-2322}, support = {ANR-20-PAMR-0004//Agence Nationale de la Recherche/ ; }, mesh = {*Soil Microbiology ; *Triticum ; *Metagenomics/methods ; *Microbiota/genetics ; *Grassland ; Bacteria/genetics/classification ; Soil/chemistry ; Crops, Agricultural ; High-Throughput Nucleotide Sequencing ; }, abstract = {Soil microbial communities respond quickly to natural and/or anthropic-induced changes in environmental conditions. Metagenomics allows studying taxa that are often overlooked in microbiota studies, such as protists or viruses. Here, we employed metagenomics to characterise microbial successions after wheat straw input in a 4-month in-situ field study. We compared microbial successions patterns with those obtained by high throughput amplicon sequencing on the same soil samples to validate metagenomics as a tool for the fine analysis of microbial population dynamics in situ. Taxonomic patterns were concordant between the two methodologies but metagenomics allowed studying all the microbial groups simultaneously. Notably, our results evidenced that each domain displayed a specific dynamic pattern after wheat straw amendment. For instance, viral sequences multiplied in the early phase of straw decomposition, in parallel to copiotrophic bacteria, suggesting a "kill-the-winner" pattern that, to our knowledge, had not been observed before in soil. Altogether, our results highlighted that both inter and intra-domain trophic interactions were impacted by wheat amendment and these patterns depended on the land use history. Our study highlights that top-down regulation by microbial predators or viruses might play a key role in soil microbiota dynamics and structure.}, }
@article {pmid40289138, year = {2025}, author = {Weathers, SP and Li, X and Zhu, H and Damania, AV and Knafl, M and McKinley, B and Lin, H and Harrison, RA and Majd, NK and O'Brien, BJ and Penas-Prado, M and Loghin, M and Kamiya-Matsuoka, C and Yung, WKA and Solis Soto, LM and Maru, DM and Wistuba, I and Parra Cuentas, ER and Hernandez, S and Futreal, A and Wargo, JA and Schulze, K and Darbonne, WC and Ajami, NJ and Woodman, SE and de Groot, JF}, title = {Improved overall survival in an anti-PD-L1 treated cohort of newly diagnosed glioblastoma patients is associated with distinct immune, mutation, and gut microbiome features: a single arm prospective phase I/II trial.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3950}, pmid = {40289138}, issn = {2041-1723}, mesh = {Humans ; *Glioblastoma/genetics/immunology/mortality/therapy/drug therapy ; *Gastrointestinal Microbiome/genetics/drug effects ; Male ; Female ; Middle Aged ; *Brain Neoplasms/genetics/immunology/mortality/therapy/drug therapy ; Temozolomide/therapeutic use/administration &amp; dosage ; Antibodies, Monoclonal, Humanized/therapeutic use/administration &amp; dosage ; Mutation ; Aged ; Adult ; *B7-H1 Antigen/antagonists &amp; inhibitors ; Tumor Microenvironment ; Prospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use ; Treatment Outcome ; }, abstract = {This phase I/II trial aims to evaluate the efficacy of concurrent atezolizumab with radiation therapy and temozolomide (TMZ) followed by adjuvant atezolizumab and TMZ in newly diagnosed glioblastoma (GBM) patients and to identify pre-treatment correlates with outcome (N = 60). Trial number: NCT03174197. The primary outcome was overall survival (OS) whereas secondary outcomes were retrospective global-omics analyses to identify pre-treatment immune and genetic tumor features that correlated with survival. Concurrent use of atezolizumab with radiation and TMZ demonstrated OS in line with published trials for newly diagnosed GBM. Tumor genomic (WES and/or targeted NGS panel), transcriptomic (RNAseq) and tissue microenvironment imaging, as well as fecal metagenomic sequencing were conducted. Gene set enrichment analysis of tumors identified multiple immune-based transcriptomic programs to distinguish patients with longer versus shorter survival (p ≤ 0.01). GBM immune enrichment was highly associated with the pre-treatment tumor mesenchymal subtype and patient gastrointestinal bacterial taxa profile.}, }
@article {pmid40289100, year = {2025}, author = {Mok, K and Tomtong, P and Ogawa, T and Nagai, K and Torrungruang, P and Charoensiddhi, S and Nakayama, J and Wanikorn, B and Nitisinprasert, S and Vongsangnak, W and Nakphaichit, M}, title = {Synbiotic-driven modulation of the gut microbiota and metabolic functions related to obesity: insights from a human gastrointestinal model.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {250}, pmid = {40289100}, issn = {1471-2180}, support = {FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; FF(KU)51.67//Kasetsart University Research and Development Institute (KURDI) under the research topic "Center for Microbiota Innovation: Empowering Health via Probiotics, Prebiotics, Postbiotics, and Functional Products"/ ; }, mesh = {Humans ; *Synbiotics/administration &amp; dosage ; *Obesity/microbiology/metabolism ; *Gastrointestinal Tract/microbiology/metabolism ; Feces/microbiology ; Limosilactobacillus reuteri/growth &amp; development ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Microbial Viability ; Adult ; Male ; *Gastrointestinal Microbiome ; Female ; }, abstract = {Synbiotic interventions have gained increasing attention for modulating gut microbiota and metabolic functions in obesity-related disorders. This study evaluated the effects of Limosilactobacillus reuteri KUB-AC5 (10[8] CFU) and Wolffia globosa powder (6 g/day) using an in vitro continuous human gastrointestinal model. Fecal samples from obese donors were used to simulate the ascending and descending colon, with microbial viability, diversity, and metabolite production assessed over 14 days via culture-dependent and culture-independent methods. Synbiotic supplementation increased anaerobic bacterial counts by 2.6 log CFU/mL in the ascending colon and 2.2 log CFU/mL in the descending colon, with notable increases in lactic acid bacteria and reductions in Enterobacteriaceae. Metagenomic analysis revealed an increasing trend in microbial diversity and evenness after 7 days of treatment, though the changes were not statistically significant. PERMANOVA analysis confirmed significant shift in microbial community composition between stabilization, treatment, and washout periods (p < 0.05). Additionally, butyrate levels significantly increased (p < 0.05), while p-cresol, a deleterious metabolite, significantly decreased (p < 0.05). Bile acid composition was modulated, with increased tertiary bile acid 3-oxo-LCA and enhanced bile acid deconjugation, suggesting improved lipid metabolism and potential weight management benefits. These findings highlight the potential of synbiotic supplementation to enhance beneficial bacterial populations, improve microbial diversity, and support metabolic health in obesity management.}, }
@article {pmid40289092, year = {2025}, author = {Qiu, J and Hu, P and Li, F and Huang, Y and Yang, Y and Sun, F and Wu, P and Lai, Y and Wang, Y and He, X and Dong, Y and Zhang, P and Zhang, S and Wu, N and Wang, T and Yang, S and Li, S and Yuan, J and Liu, X and Liu, G and Hu, Y and Wu, JHY and Chen, D and Pan, A and Pan, XF}, title = {Circulating linoleic acid and its interplay with gut microbiota during pregnancy for gestational diabetes mellitus.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {245}, pmid = {40289092}, issn = {1741-7015}, support = {2022YFC2702905//National Key R&amp;D Program of China/ ; 82325043//the National Science Fund for Distinguished Young Scholars/ ; 82473646//Natural Science Foundation of China/ ; 2024NSFSC0578//Sichuan Provincial Natural Science Foundation/ ; YJ202346//Fundamental Research Funds for the Central Universities/ ; }, abstract = {BACKGROUND: Circulating linoleic acid (LA) levels have been reported to be associated with various metabolic outcomes. However, the role of LA and its interplay with gut microbiota in gestational diabetes mellitus (GDM) remains unclear. This study aimed to investigate the longitudinal association between circulating LA levels during pregnancy and the risk of GDM, and the potential role of gut microbiota.<br><br>METHODS: A nested case-control study was conducted within the ongoing Tongji-Huaxi-Shuangliu Birth Cohort in Chengdu, China. Blood and fecal samples were collected during early and middle pregnancy from 807 participants. GDM was diagnosed in middle pregnancy using the International Association of Diabetes and Pregnancy Study Groups criteria. Plasma LA levels were measured using gas chromatography-mass spectrometry, and gut microbiota was analyzed through 16S rRNA gene sequencing and shotgun metagenomic sequencing. A two-sample Mendelian randomization study was conducted using data from the IEU OpenGWAS database and the FinnGen consortium.<br><br>RESULTS: Elevated plasma LA levels were associated with a lower risk of GDM in both early (P for trend&#x2009;=&#x2009;0.002) and middle pregnancy (P for trend&#x2009;=&#x2009;0.02). Consistently, Mendelian randomization analysis revealed that each unit increase in LA was associated with a 16% reduction in GDM risk (odds ratio: 0.84, 95% confidence interval: 0.72, 0.95). In early pregnancy, higher plasma LA levels were correlated with higher adiponectin&#xa0;levels (P&#x2009;<&#x2009;0.001) and lower levels of triglycerides (P&#x2009;<&#x2009;0.001), HbA1c (P&#x2009;=&#x2009;0.04), and C-peptide (P&#x2009;=&#x2009;0.04). The LA-accociated microbiota mediated the relationship between LA and C-peptide (P&#x2009;=&#x2009;0.01). Additionally, the inverse association between LA and GDM was modified by Bilophila&#xa0;(P for interaction&#x2009;=&#x2009;0.03), with a stronger association observed in participants with lower Bilophila levels in early pregnancy. Metagenomic analyses further showed that&#xa0;the LA-associated pathway (D-galacturonate degradation I) and its key enzyme (EC 4.2.1.7) were associated with metabolic traits.<br><br>CONCLUSIONS: Our study provides evidence for an inverse causal association between plasma LA levels during pregnancy and GDM risk, which is both mediated and modified by gut microbiota.}, }
@article {pmid40289075, year = {2025}, author = {Wu, J and Xiang, Y and Li, F and Liu, X and Dang, N and Guo, J}, title = {Phialophora americana infection in a patient with a compound heterozygous CARD9 mutation.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {613}, pmid = {40289075}, issn = {1471-2334}, support = {2022M710852//China Postdoctoral Science Foundation/ ; 82102420//National Natural Science Foundation of China/ ; ZR2024QH034//Natural Science Foundation of Shandong Province/ ; }, abstract = {Phaeohyphomycosis caused by Phialophora americana is relatively rare in clinical practice. Deficiency in the human caspase recruitment domain-containing protein 9 (CARD9) is associated with infections caused by Phialophora americana. In this case, the patient has had a decade-long history of recurrent tinea corporis and recently presented with an invasive, deep subcutaneous infection in the right axilla caused by Phialophora americana. Metagenomic next-generation sequencing (mNGS) confirmed that the pathogen infecting the patient was Phialophora americana. Whole exome sequencing (WES) revealed that the patient had compound heterozygous CARD9 gene mutations, with a c.952-1G > A mutation in intron 6 and a c.184 + 5G > T mutation in intron 2. The expression of the CARD9 protein and the levels of cytokines, including IL-17 and IFN-γ, were observed to be decreased in the patient. After an ineffective treatment with amphotericin B, voriconazole was administered for antifungal therapy and yielded satisfactory results. Following discharge, the patient continued oral voriconazole for ongoing antifungal treatment. One month after discharge, the patient returned to the hospital for a follow-up examination, during which it was observed that the symptoms had been successfully resolved. The novel compound heterozygous mutations may lead to CARD9 deficiency, which in turn results in susceptibility to Phialophora americana infection.}, }
@article {pmid40288855, year = {2025}, author = {Prisacar, M and Leichert, LI}, title = {Functional metaproteomics for enzyme discovery.}, journal = {Methods in enzymology}, volume = {714}, number = {}, pages = {61-82}, doi = {10.1016/bs.mie.2025.01.029}, pmid = {40288855}, issn = {1557-7988}, abstract = {Discovery of microbial biocatalysts traditionally relied on activity screening of isolated bacterial strains. However, since most microorganisms cannot be cultivated in the lab, such an approach leaves the majority of the microbial enzyme diversity untapped. Metagenomic approaches, in which the DNA from a microbial community is directly isolated and then used either for the creation of an expression library or for sequencing and metagenome annotation have alleviated this shortcoming to an extent, but have their own limitations: the generation of large expression libraries is time-consuming and their screening is costly, while metagenome annotation can infer biocatalytic function only from prior knowledge. We have thus developed a functional metaproteomic approach, which combines the immediacy of traditional activity screening with the comprehensiveness of a meta-omics approach. Briefly, the whole metaproteome of an environmental sample is separated on a 2-D gel, biocatalytically active proteins are visualized in-gel through zymography, and those candidate biocatalysts are then identified through mass spectrometry, searching against a metagenome-derived database obtained from the very same environmental sample. Here we explain the process in detail, with a focus on esterases, and give guidelines on how to develop a functional metaproteomic workflow for enzyme discovery.}, }
@article {pmid40288854, year = {2025}, author = {Lorente-Arévalo, &#xc1; and Gimeno-Pérez, M and Ortega, C and Finnigan, J and Charnock, S and Hidalgo, A}, title = {Ultrahigh-throughput screening assay for PET-degrading enzymes.}, journal = {Methods in enzymology}, volume = {714}, number = {}, pages = {489-503}, doi = {10.1016/bs.mie.2025.01.021}, pmid = {40288854}, issn = {1557-7988}, abstract = {In recent years, several PET-degrading enzymes have been identified from both known microorganisms and metagenomic sources in response to the growing environmental issue of polyethylene terephthalate (PET) accumulation. Despite this progress, there is a limited number of (ultra)high-throughput screening methods for assessing PET-hydrolyzing activity without relying on surrogate substrates. This method utilizes the coupled activity of ketoreductases (KREDs) and diaphorase to produce a fluorescent compound (resorufin) in the presence of PET degradation products, offering a more direct and efficient screening approach. A metagenomic KRED was coupled with the diaphorase from Clostridium kluyveri to enable the detection of the hydrolysis of PET degradation products catalyzed by the Bacillus subtilis BS2 esterase. The coupled reaction was established in water-in-oil microdroplets, encapsulating a single E. coli cell per droplet, demonstrating its potential for use in the ultrahigh-throughput screening of metagenomic libraries or randomized libraries for directed evolution campaigns.}, }
@article {pmid40288852, year = {2025}, author = {Ashcroft, E and Poma, M and Tischler, D and Munoz-Munoz, J}, title = {Mining metagenomes from extremophiles as a resource for novel glycoside hydrolases for industrial applications.}, journal = {Methods in enzymology}, volume = {714}, number = {}, pages = {45-60}, doi = {10.1016/bs.mie.2025.02.008}, pmid = {40288852}, issn = {1557-7988}, abstract = {The exploration of metagenomes from extremophiles has emerged as a promising approach for discovering novel glycoside hydrolases (GHs) with potential industrial applications. Extremophiles, which thrive in harsh conditions such as high salinity, extreme temperatures, and acidic or alkaline environments, produce enzymes naturally adapted to function under these conditions. This unique adaptability makes them highly desirable for industrial processes requiring robust and efficient biocatalysts. These biocatalysts reduce reliance on harsh chemicals and energy-intensive processes, contributing to greener industrial operations. This review underscores the power of metagenomics in bypassing the need to culture large libraries of extremophiles in the lab. High-throughput sequencing and bioinformatics enable the identification of novel GH-encoding genes directly from environmental DNA. While metagenomic mining has yielded promising results, challenges such as the expression of extremophile-derived genes in mesophilic hosts, low activity yields, and scalability remain. Advances in synthetic biology and protein engineering could address these bottlenecks, enabling more efficient utilization of GHs. Additionally, integrating machine learning for predictive functional annotation may accelerate the identification of high-value candidates.}, }
@article {pmid40288735, year = {2025}, author = {Wang, M and Masoudi, A and Wang, C and Feng, J and Yu, Z and Liu, J}, title = {Urban afforestation converges soil resistome and mitigates the abundance of human pathogenic bacteria.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121693}, doi = {10.1016/j.envres.2025.121693}, pmid = {40288735}, issn = {1096-0953}, abstract = {Afforestation has emerged as a nature-based strategy for climate mitigation and urban sustainability, yet its effects on antibiotic resistance genes (ARGs) in soils remain underexplored. This study investigates how the conversion of croplands into plantation forests affects the soil resistome, bacterial communities, and physicochemical properties in an urban environment. Using high-throughput metagenomic and 16S rRNA amplicon sequencing, we analyzed soil samples from croplands and afforested plots with Chinese pine (Pinus tabulaeformis) and Chinese scholar (Sophora japonica) trees, across two-time points post-afforestation. Our results show that afforestation promotes the convergence of both bacterial and ARG communities over time, accompanied by a significant reduction in the relative abundance of human pathogenic bacteria. Afforested soils exhibited a lower prevalence of high-risk ARGs (e.g., qnrA, qnrB from the quinolone class) and reduced co-occurrence between ARGs and mobile genetic elements (MGEs), particularly transposases and recombinases, suggesting diminished horizontal gene transfer. Additionally, afforestation-induced changes in soil pH and nutrient dynamics emerged as key ecological factors shaping ARG profiles. Differences between afforestation types were also observed, with Pinus plantations presenting lower ARG-derived risks than Sophora forests. This study supports afforestation as a nature-based solution for enhancing urban sustainability, reducing public health risks, and achieving resilient ecosystems under anthropogenic influence.}, }
@article {pmid40288632, year = {2025}, author = {Gao, Y and Cheng, Z and Huang, B and Mao, Y and Hu, J and Wang, S and Wang, Z and Wang, M and Huang, S and Han, M}, title = {Deciphering the profiles and hosts of antibiotic resistance genes and evaluating the risk assessment of general and non-general hospital wastewater by metagenomic sequencing.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126313}, doi = {10.1016/j.envpol.2025.126313}, pmid = {40288632}, issn = {1873-6424}, abstract = {Hospital wastewater (HWW) is a substantial environmental reservoir of antibiotic resistance genes (ARGs) and poses risks to public health and aquatic ecosystems. However, research on the diversity, transmission mechanisms, pathogenic hosts, and risks of ARGs in different HWW types is limited. This study involved the collection of HWW samples from 15 hospitals in Hefei, China, which were subsequently categorized as general hospitals (GHs) and non-general hospitals (NGHs). A 280.28-Gbp sequencing dataset was generated using a metagenomic sequencing strategy and analyzed using metagenomic assembly and binning approaches to highlight these issues in GHs and NGHs. Results showed significant differences between GHs and NGHs in ARG distribution, microbial community composition, and hosts of ARGs. Potential pathogens such as Rhodocyclaceae bacterium ICHIAU1 and Acidovorax caeni were more abundant in GHs. Furthermore, plasmid-mediated ARGs (45.21%) were more prevalent than chromosome-mediated ARGs (25.74%) in HWW, with a significantly higher proportion of plasmid-mediated ARGs in GHs compared to NGHs. The co-occurrence of ARGs and mobile genetic elements was more frequent in GHs. Additionally, the antibiotic resistome risk index was higher in GHs (38.73 ± 12.84) than NGHs (22.53 ± 11.80), indicating a greater risk of ARG transmission in GHs. This pioneering study provides valuable insights into the transmission mechanisms and hosts of ARGs in hospital settings, emphasizing the increased risk of ARG transmission in GHs.}, }
@article {pmid40288628, year = {2025}, author = {Zhou, S and Li, Y and Yang, S and Lin, L and Deng, T and Gan, C and An, W and Xu, M}, title = {The role of electroactive biofilms in enhanced para-chlorophenol transformation collaborated with biosynthetic palladium nanoparticles.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126312}, doi = {10.1016/j.envpol.2025.126312}, pmid = {40288628}, issn = {1873-6424}, abstract = {Bioremediation is a cost-effective strategy for decomposition of chlorinated organic contaminants, but its application is often hindered by the generation of toxic chlorinated byproducts. Though the design of functional biofilms, incorporating microbially-inspired catalytic materials, has emerged as a promising solution for tackling the byproducts issues, the microbial mechanisms driving these processes remain inadequately understood. This study demonstrates a hybrid electroactive biofilm (EAB)-palladium nanoparticles (Pd NPs) system that effectively separates the dechlorination and mineralization of para-chlorophenol (4-CP), and most importantly, it provides new insights into the microbial and genetic roles of EABs in this process. Under an applied potential of -0.6 V, Pd NPs via palladate reduction were biogenically synthesized and deposited on the cytomembranes within the biofilm, achieving an 82% decrease in 4-CP concentration within 48 hours. The ultra-performance liquid chromatogram and mass spectrum confirmed that 4-CP was initially dechlorinated to phenol by the biogenic Pd NPs before undergoing further degradation by the biofilm, effectively preventing toxic chlorinated byproducts. The Dechloromonas, Pseudomonas, and Geobacter were identified as predominant genera in the system and the metagenomics analysis noted increased relative abundance of ring-cleavage genes like pcaG, dmpB/xylE, and catA. Importantly, the abundance of dmpB/xylE was primarily associated with Dechloromonas and Pseudomonas, further highlighted that the dmpB/xylE-pathway was important for rapid 4-CP decomposition in the system. This study advances the understanding of EAB-Pd NPs synergy, showcasing an innovative and sustainable approach for the efficient removal of halogenated pollutants.}, }
@article {pmid40288249, year = {2025}, author = {Wang, K and Ding, W and Yang, X and Lü, W and Ren, H and Jiang, X}, title = {The components and aromaticity of dissolved organic matter derived from aquatic plants determine the CO2 and CH4 emission potential.}, journal = {Water research}, volume = {281}, number = {}, pages = {123685}, doi = {10.1016/j.watres.2025.123685}, pmid = {40288249}, issn = {1879-2448}, abstract = {Lakes are integral to the carbon cycle through the processing of dissolved organic matter (DOM). However, the specific contributions of various aquatic plants to carbon emissions during their decomposition remain inadequately understood. In this study, decomposition experiments were performed on three aquatic plants-algae, Phragmites australis (PA), and Potamogeton crispus L. (PC)-using advanced techniques, including FT-ICR-MS and metagenomics, to investigate the mechanisms of carbon dioxide (CO2) and methane (CH4) emissions. The results indicate that algae exhibit a substantial potential for CO2 emissions, with emissions reaching up to 2193 μmol·g[-1]. Conversely, PA contributes the highest CH4 emissions, reaching up to 2397 μmol·g[-1]. Factors such as the protein-like content and aromaticity of DOM molecules significantly influence emission levels. DOM with lower aromaticity undergoes easier decomposition in the first 6 days, leading to increased CO2 production. Elevated C/N and C/P ratios in plants enhance the abundance of methanogenic bacteria and genes. Surplus carbon will be mineralized under anaerobic conditions, giving rise to mineralization of organics to CH4. These findings elucidate the mechanisms underlying CO2 and CH4 emissions during the decomposition of different aquatic plants and provide valuable insights for lake water environment management.}, }
@article {pmid40288073, year = {2025}, author = {Song, Y and Baniakina, LFT and Jiang, L and Chai, L}, title = {Metagenomic insights into the alterations of gut microbial community in Bufo gargarizans tadpoles following lead exposure.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {55}, number = {}, pages = {101522}, doi = {10.1016/j.cbd.2025.101522}, pmid = {40288073}, issn = {1878-0407}, abstract = {Lead (Pb), a prevalent heavy metal contaminant in aquatic environments, has complex effects on the gut microbiome function of aquatic animals. In this study, metagenomic analysis of Bufo gargarizans tadpoles was carried out following Pb exposure. Moreover, histological analysis was performed on the intestines. The results showed that Pb exposure induced histological damage to the intestinal epithelium. Significant differences in microbial abundance and function were detected in the 200 μg/L Pb group compared to the control group. Specifically, an increase in Bosea and Klebsiella was noted at 200 μg/L Pb, which potentially could induce inflammation in tadpoles. Notably, the decrease in the abundance of glycoside hydrolases subsequent to exposure to 200 μg/L Pb is likely to attenuate carbohydrate metabolism. Furthermore, increased fluoroquinolone-related antibiotic resistance genes (ARGs), phenolic-related ARGs, and iron uptake systems following 200 μg/L Pb exposure might heighten the disease risk for tadpoles. These discoveries augment our comprehension of the influences of Pb on the intestinal well-being of amphibians and offer valuable insights for further assessment of the ecological risks that Pb poses to amphibians.}, }
@article {pmid40287860, year = {2025}, author = {Li, Y and Liu, C and Wang, Y and Li, M and Zou, S and Hu, X and Chen, Z and Li, M and Ma, C and Obi, CJ and Zhou, X and Zou, Y and Tang, M}, title = {Urban wild bee well-being revealed by gut metagenome data: A mason bee model.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70051}, pmid = {40287860}, issn = {1744-7917}, support = {//Research Development Fund, Xi'an Jiaotong-Liverpool University/ ; //Summer Undergraduate Research Fellowship (SURF) Programme, Xi'an Jiaotong-Liverpool University/ ; }, abstract = {Wild bees are ecologically vital but increasingly threatened by anthropogenic activities, leading to uncertain survival and health outcomes in urban environments. The gut microbiome contains features indicating host health and reflecting long-term evolutionary adaptation and acute reactions to real-time stressors. Moving beyond bacteria, we propose a comprehensive analysis integrating diet, bacteriome, virome, resistome, and their association to understand the survival status of urban lives better. We conducted a study on mason bees (Osmia excavata) across 10 urban agricultural sites in Suzhou, China, using shotgun gut metagenome sequencing for data derived from total gut DNA. Our findings revealed that most ingested pollen originated from Brassica crops and the unexpected garden tree Plantanus, indicating that floral resources at the 10 sites supported Osmia but with limited plant diversity. Varied city landscapes revealed site-specific flowers that all contributed to Osmia sustenance. The gut bacterial community, dominated by Gammaproteobacteria, showed remarkable structural stability across 8 sites but suggested perturbations at 2 sites. Antibiotic resistance gene profiles highly varied across 10 sites with prevalent unclassified drug classes, highlighting environmental threats to both bees and humans. The virome analysis identified honeybee pathogens, suggesting potential virus spillover. Many unknown bacteriophages were detected, some of which targeted the core gut bacteria, underscoring their role in maintaining gut homeostasis. These multifaceted metagenomic insights hold the potential to predict bee health and identify environmental threats, thereby guiding probiotic development and city management for effective bee conservation.}, }
@article {pmid40287822, year = {2025}, author = {Sun, C and Qin, Z and Liu, R and Guo, Y and Ge, Y and Du, Y}, title = {MetaHiCNet: a web server for normalizing and visualizing microbial Hi-C interaction networks.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkaf340}, pmid = {40287822}, issn = {1362-4962}, support = {//University of Texas Systems STAR Program/ ; }, abstract = {Metagenomic Hi-C (metaHi-C) enables the reconstruction of microbial genome organization and interspecies interactions by capturing physical contacts between genomic fragments. However, raw metaHi-C data are often confounded by systematic biases and spurious contacts, which can obscure meaningful biological signals. Existing metaHi-C pipelines typically lack user-friendly normalization workflows and intuitive visualization tools, limiting the ability to explore microbial interaction networks. Here, we introduce MetaHiCNet, a web-based platform that supports widely used normalization methods with customizable parameters. MetaHiCNet provides a stepwise workflow for bias correction, spurious contact removal, and interactive visualization of microbial interactions. The platform supports multiple visualization modes, including taxonomic treemaps, cross-taxa networks, and cross-bin networks, enabling seamless transitions from community-wide overviews to detailed analyses of specific taxa or bins. This functionality facilitates the investigation of host-microbe interactions and the relationships between mobile genetic elements and their microbial hosts, offering deeper insights into microbial community structures and dynamics. MetaHiCNet is freely accessible at www.metahicnet.com without login.}, }
@article {pmid40287775, year = {2025}, author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W}, title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {105}, pmid = {40287775}, issn = {2049-2618}, mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Glycine max/microbiology/growth &amp; development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation &amp; purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.<br><br>RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r&#x2009;= 0.5, p&#x2009;= 0.039) between microbial diversity and seed yield.<br><br>CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.}, }
@article {pmid40287690, year = {2025}, author = {Mohamed, FS and Jalal, D and Fadel, YM and El-Mashtoly, SF and Khaled, WZ and Sayed, AA and Ghazy, MA}, title = {Characterization and comparative profiling of piRNAs in serum biopsies of pediatric Wilms tumor patients.}, journal = {Cancer cell international}, volume = {25}, number = {1}, pages = {163}, pmid = {40287690}, issn = {1475-2867}, abstract = {Piwi-interacting RNAs (piRNAs) are small non-coding RNAs involved in transposon silencing and linked to cancer progression. However, their role in Wilms tumors (WT) remains unexplored. We conducted a thorough analysis and characterization of piRNAs in serum liquid biopsies of WT patients. Our study examined their expression patterns and functional annotations related to WT pathogenesis, as well as their clinical potential for diagnosis and monitoring. We identified 307 piRNAs expressed in WT serum samples, with 4% classified as repeat-related and 96% as non-repeat-related. The most abundant repeat-related piRNAs originated from LINEs retrotransposon, while tRNA-derived piRNAs were the most prevalent among non-repeat-related piRNAs. Furthermore, a distinct profile of 34 piRNAs showed significant differential expression in WT patients compared to healthy controls-22 downregulated and 12 upregulated. The target genes of differentially expressed piRNAs exhibited significant enrichment in biological pathways related to cytokine activity, inflammatory responses, TGF-beta signaling, p38 MAPK, and ErbB signaling. These genes are also involved in DNA damage response, DNA methylation, cell cycle regulation, as well as kidney development and function. Low expression levels of several piRNAs, especially piR-hsa-1,913,711, piR-hsa-28,190, piR-hsa-28,849, piR-hsa-28,848, and piR-hsa-28,318, showed significant diagnostic potential as non-invasive biomarkers for WT (AUC > 0.8, p < 0.05). Their expression levels also significantly correlated with adverse pathological features, including metastasis, anaplasia, and bilateral WT development. In conclusion, non-transposon-related piRNAs may serve as reliable biomarkers for WT and possess potential non-germline functions, particularly in regulating DNA methylation, cell growth, immune responses, and immune responses. Further studies are warranted to elucidate their functional significance.}, }
@article {pmid40287117, year = {2025}, author = {Lu, W and Liu, Z and Song, Z and Wang, C and Yu, Z and Peng, S and Tian, Z and Lyu, A and Ning, Z}, title = {Vinegar-processed frankincense ameliorates ulcerative colitis by targeting BSH-active bacteria preference-mediated GDCA hydrolysis.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {119845}, doi = {10.1016/j.jep.2025.119845}, pmid = {40287117}, issn = {1872-7573}, abstract = {Frankincense, is extensively used in both traditional Chinese medicine (TCM) and Indian practices for the treatment of ulcerative colitis (UC). In TCM, it is typically subjected to process with vinegar, which is believed to enhance its therapeutic efficacy. However, the underlying mechanism has yet to be elucidated.<br><br>AIM OF THE STUDY: To elucidate the underlying mechanism of frankincense vinegar processing from the perspective of bile salt hydrolase (BSH)-active bacteria preference and glycodeoxycholic acid (GDCA) hydrolysis.<br><br>MATERIALS AND METHODS: Dextran sodium sulfate (DSS)-induced UC model was used to elucidate the superior improving effects of vinegar-processed frankincense (PF). 16S rRNA and metagenomic sequencing along with ultra-high performance liquid chromatography-triple quadrupole mass spectroscopy (UHPLC-TQ-MS) were employed to reveal the differential bacteria and its related disturbance of GDCA. The effects of PF and GDCA on BSH-active bacteria were confirmed using real-time quantitative polymerase chain reaction (RT-qPCR) and in vitro experiments. Finally, the pro-inflammatory effects of GDCA and the mechanisms by which PF ameliorates UC were verified by establishing a UC pseudo-sterile mice model with GDCA intervention.<br><br>RESULTS: PF exhibited remarkable mitigating effects on UC (P<0.05 or P<0.01). Specifically, PF enhanced the BSH activity of Bifidobacterium longum and Lactobacillus acidophilus (P<0.01), thereby promoting their dissociation efficiency toward glycine-conjugated bile acids (G-CBAs), particularly GDCA (P<0.01). Furthermore, PF reduced GDCA levels by regulating the dissociation efficiency of Bifidobacterium longum and Lactobacillus acidophilus toward GDCA, thereby alleviating GDCA-induced exacerbation of UC.<br><br>CONCLUSION: PF exhibits its superior amelioration effects on UC by enhancing the dissociation efficiency of Bifidobacteruum longum and Lactobacillus acidophilus towards G-CBAs, particularly GDCA.}, }
@article {pmid40286758, year = {2025}, author = {Gan, Y and Cui, J and Nie, A and Yang, Y and Zhao, X}, title = {Revealing the influence of Lacticaseibacillus paracasei C5 on the flavor formation of bread dough by metagenomics and flavouromics.}, journal = {International journal of food microbiology}, volume = {437}, number = {}, pages = {111220}, doi = {10.1016/j.ijfoodmicro.2025.111220}, pmid = {40286758}, issn = {1879-3460}, abstract = {This study investigated the impact of L. paracasei C5 on the generation of flavor compounds in bread through metagenomics and flavouromics. Metagenomic profiling revealed that L. paracasei C5 facilitated carbohydrate, amino acid, and lipid metabolism in the dough. Correlative analyses between specific microbial species and flavor compounds demonstrated a positive association between L. paracasei and key flavor compounds in bread, such as 2-nonenal,(E)-, 2-octenal,(E)-, benzeneacetaldehyde, and hexanoic acid, ethyl ester. A predictive network outlining the metabolic pathways responsible for L. paracasei C5 sourdough bread flavor compounds was established, elucidating the microbial annotation of pertinent genes and enzymes. The findings underscored the synergistic role of L. paracasei and S. cerevisiae in enhancing the activity of encoded enzymes involved in carbohydrate degradation, acetyl-CoA synthesis, succinate conversion, acyl-CoA production, transaminases, alcohol dehydrogenase, and carboxylesterases. These results offer novel insights into the mechanisms by which L. paracasei C5 augments bread flavor.}, }
@article {pmid40286682, year = {2025}, author = {Xin, Y and Gao, Q and Zhang, S and Zhang, Z and Wang, J and Xia, X}, title = {Microbial regulatory mechanisms underlying methane emission in rivers with different land covers.}, journal = {Water research}, volume = {281}, number = {}, pages = {123680}, doi = {10.1016/j.watres.2025.123680}, pmid = {40286682}, issn = {1879-2448}, abstract = {Inland rivers play a crucial role in regulating the methane (CH4) budget via microbial carbon cycling. CH4 emissions vary significantly among rivers with different land covers, yet the regulatory mechanisms of CH4-cycling microorganisms across different land covers remain less understood. This study intergrates in-situ CH4 measurements with amplicon and metagenomic sequencing to investigate CH4-cycling microbial community composition and metabolic functions in regulating CH4 emissions across rivers with different land covers. Our results show that agricultural and urban rivers significantly increase riverine CH4 emission fluxes by 14 and 34 times than forest rivers, respectively. Urban and agricultural river sediments exhibited higher methanogenic abundance, but lower methanotrophic abundance than forest river sediments. Acetoclastic methanogens dominate the methanogenic communities of agricultural rivers, enhanced by high NO3[-] and DOC concentrations. Furthermore, methanogenic metagenome-assembled genomes (MAGs) recovered from agricultural rivers, which affiliated to Methanosarcina, carried the complete set of genes encoding for the enzymes in acetoclastic methanogenesis. In contrast, hydrogenotrophic methanogens drive CH4 production in urban rivers, favored by low DOC: NH4[+] ratios that enable methanogenesis independent of organic carbon. Lower CH4 emissions in agricultural rivers compared to urban rivers might be partly due to the greater sulfate-dependent anaerobic methane-oxidation. In forest rivers, type I methanotrophs outcompetes methanogens, aided by suitable sediment pH and larger sediment particle sizes, fostering oxic conditions that suppress CH4 emissions. This study reveals versatile microbial mechanisms underlying riverine CH4 emissions across land covers, enhancing understanding of microbial-mediated riverine CH4 cycling.}, }
@article {pmid40286059, year = {2025}, author = {Men, C and Pan, Z and Liu, J and Miao, S and Yuan, X and Zhang, Y and Yang, N and Cheng, S and Li, Z and Zuo, J}, title = {Single and Combined Effects of Aged Polyethylene Microplastics and Cadmium on Nitrogen Species in Stormwater Filtration Systems: Perspectives from Treatment Efficiency, Key Microbial Communities, and Nitrogen Cycling Functional Genes.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {7}, pages = {}, doi = {10.3390/molecules30071464}, pmid = {40286059}, issn = {1420-3049}, support = {52400245//National Natural Science Foundation of China/ ; 2017ZX07103-007//National Key Research and Development Program of China/ ; 5221101156//National Natural Science Foundation of China/ ; }, mesh = {*Cadmium/chemistry ; *Microplastics/chemistry ; *Nitrogen Cycle/genetics/drug effects ; *Water Pollutants, Chemical ; *Nitrogen ; Filtration ; *Polyethylene/chemistry ; *Microbiota/drug effects ; Denitrification ; Water Purification/methods ; }, abstract = {Microplastics and heavy metal contamination frequently co-occur in stormwater filtration systems, where their interactions may potentially compromise nitrogen removal. Current research on microplastics and Cd contamination predominantly focuses on soils and constructed wetlands, with limited attention given to stormwater filtration systems. In this study, the single and synergistic effects of aged polyethylene microplastics (PE) and cadmium (Cd) contamination in stormwater infiltration systems were investigated from perspectives of nitrogen removal, microbial community structures, and predicted functional genes in nitrogen cycling. Results showed that PE single contamination demonstrated stronger inhibition on NO3[-]-N removal than Cd. Low-level PE contamination (PE content: 0.1% w/w) in Cd-contaminated systems showed stronger inhibitory effect than high-level PE contamination (PE content: 5% w/w). The mean NO3[-]-N removal efficiency under combined Cd50 (Cd concentration: 50 μg/L) and PE5 contamination during the sixth rainstorm event was 1.04 to 34.68 times that under other contamination scenarios. Metagenomic analysis identified keystone genera (Saccharimonadales, Enterobacter, Aeromonas, etc.), and critical nitrogen transformation pathways (nitrate reduction to ammonium, denitrification, nitrogen fixation, and nitrification) govern system performance. PE and Cd contamination effects were most pronounced on nitrification/denitrification enzymes beyond nitrite oxidase and nitrate reductase. These mechanistic findings advance our understanding of co-contaminant interactions in stormwater filtration systems.}, }
@article {pmid40285962, year = {2025}, author = {Liao, J and Wei, JH and Liu, J and Ren, L and Zang, N and Liu, E}, title = {Respiratory virome in hospitalized children and analysis of its correlation with disease severity.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40285962}, issn = {1435-4373}, support = {Grant No. 82341111//The National Natural Science Foundation of China Special Project/ ; }, abstract = {PURPOSE: To investigate the composition of respiratory viromes and their association with disease severity among hospitalized pediatric patients.<br><br>METHODS: Clinical data and metagenomic next-generation sequencing (mNGS) results were collected from pediatric patients hospitalized at the Children's Hospital of Chongqing Medical University between January 2022 and September 2023. The analyzed specimens included sputum and bronchoalveolar lavage fluid (BALF).<br><br>RESULTS: The study included 229 patients (65.07% male, median age 3 years) with 25 sputum and 204 BALF samples, of whom 40.17% met the WHO criteria for severe acute respiratory infection (SARI). Herpesviruses were detected in 166 cases (72.49%), including 85 cases of cytomegalovirus (CMV), 64 cases of Epstein-Barr virus (EBV), 34 cases of human herpesvirus-7 (HHV-7), 12 cases of human herpesvirus-6 (HHV-6), and 6 cases of herpes simplex virus type 1 (HSV-1). Additionally, 53 cases of torque teno virus (TTV) and 7 cases of torque teno mini virus (TLMV) were detected. CMV prevalence was highest in neonates, while EBV peaked in the 3-6 year group (37.78%). HSV-1 and HHV-6 were predominantly identified in severe infections.<br><br>CONCLUSION: Herpesviruses, particularly CMV and EBV, were the most frequently detected viruses, followed by anelloviruses. The age-specific viral distribution patterns provide novel epidemiological perspectives for understanding pediatric respiratory pathogenesis, though their clinical significance requires validation through mechanistic studies.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40285778, year = {2025}, author = {Alotaib, AS and Anwar, W and Albalawi, HQ and Albalawi, HS and Alshehri, MA and Al-Atawi, FM and Al Joundi, IT and Y Al Samini, A and Alqarni, RZ and Alzahrani, NE and Huraysi, MA}, title = {Metagenomic analysis microbial biodiversity of Trojena' the Mountains of Neom.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {71}, number = {4}, pages = {100-110}, doi = {10.14715/cmb/2025.71.4.13}, pmid = {40285778}, issn = {1165-158X}, mesh = {*Metagenomics/methods ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Saudi Arabia ; Soil Microbiology ; *Metagenome/genetics ; Phylogeny ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; }, abstract = {About 80% of the biosphere is constantly exposed to temperatures below 5 °C in cold environments. Microorganisms in cold environments can grow and decompose various organic compounds at sub-zero temperatures despite exposure to conditions that are harmful to their survival, such as sub-zero temperatures and low nutrient and water availability. The present study was designed to investigate metagenomic insights into the microbial diversity in (Al-Lawz Mountains / Trojena Mountains) Saudi Arabia. Metagenomic data sets are obtained by high-throughput sequencing of environmental soil samples and provide an aggregation of all the conceptually genetic materials of the intended area of this project. This study easily overcomes the bottlenecks associated with conventional molecular methods of retrieving genetic information and the unscientific shortage of microbial biodiversity research at Tabuk. High throughput bioinformatic analysis has been highlighted as the accurate exploration of the abundance and diversity of bacterial communities. Environmental DNA can be sequenced to identify the recent presence, relative abundance &amp; distribution of a prokaryotic species or whole communities of bacteria. A total of 333 bacterial metagenomes were sequenced over two seasons, fall and winter. The 16S rRNA genes were quantified during this period. The most significant species regarding the relative abundance and diversity were in the location of sample1 by, Klebsiella michiganensis (251), stenotrophomonass maltophilia (110), Escherichia coli USML2 (88), Zhongshania aliphaticivorans (40), Acidibrevibacterium fodinaquatile (12) Calothrix spp. &amp; Nibribacter ruber (10) Bacillus spp (10) respectively. On the other hand, the lowest abundances were in sample 4 location with Pseudomonas fluorescens (5) and Corynebacterium glutamicum (3) with (NA) species. This means these were unidentified yet. All these species have a growing demand for microbial biodiversity evaluations, given the pronounced impact of climate change in this region (Al-Lawz Mountains/Trojena Mountain). Benthic microbial communities are to be considered, given they have a potential role in CO2 and nitrogen fixation, which is related to plant growth-promoting properties. They can resist salinity, radiation, low-temperature adaptation, and biocontrol properties. Thus, eDNA cold-mountain biodiversity is a fraction of the time it costs to conduct conventional ecological monitoring.}, }
@article {pmid40285533, year = {2025}, author = {Liao, X and Wang, H and Wu, D and Grossart, HP and Yang, X and Li, L and Wang, Y and Li, S and Li, J and Cao, M and Chen, N and Hu, A}, title = {Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers.}, journal = {Global change biology}, volume = {31}, number = {4}, pages = {e70211}, doi = {10.1111/gcb.70211}, pmid = {40285533}, issn = {1365-2486}, support = {//the Ocean Negative Carbon Emissions (ONCE) Program/ ; 2021QZKK0103//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2023YFC3804904//National Key Research and Development Program/ ; }, mesh = {*Microbiota ; *Plankton ; China ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Urbanization ; }, abstract = {Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.}, }
@article {pmid40285445, year = {2025}, author = {Pérez Díaz, M and de Azevedo Gomes, AM and Quiroga Berdeal, MI and Bermúdez Pose, R}, title = {How to Dissect Zebrafish: A Standardized Sampling Protocol for Histological and Molecular Studies in Adult Zebrafish.}, journal = {Zebrafish}, volume = {}, number = {}, pages = {}, doi = {10.1089/zeb.2024.0184}, pmid = {40285445}, issn = {1557-8542}, abstract = {The zebrafish (Danio rerio) has become an essential model in fields such as developmental biology, toxicology, genetics, and regenerative medicine due to its low cost, small size, transparent embryos, and genetic similarity to humans. Nowadays, this model is increasingly recognized as a valuable tool in other fields, including veterinary medicine and animal production research, particularly aquaculture, due to its unique characteristics that make it suitable for studying economically significant diseases affecting production species. However, unlike established models such as mice, zebrafish lack standardized protocols for housing, feeding, anesthesia, and sample collection, which affects study reproducibility. In addition, it is a common practice to use whole zebrafish larvae or juveniles for metagenomic studies rather than analyzing individual organs, despite the fact that gene expression can vary between organs. This approach complicates the attribution of findings to specific biological processes. To address this, various authors proposed protocols for sample collection in larvae, juveniles, and adult zebrafish; however, comprehensive studies encompassing nearly all fish organs are scarce. Understanding zebrafish anatomy and the technical requirements of the study is essential for accurate sample collection. Some challenges present during zebrafish dissection include the small size of the fish, the fragility of their organs, and the faster onset of autolysis and heterolysis after the death of the animal. Using magnifying lenses, microdissection tools, and conducting dissections on cold surfaces can help mitigate these issues. This article aims to improve sample collection for histopathological and genetic studies in adult zebrafish by establishing a comprehensive, organized, and systematic dissection protocol that accounts for the anatomical specifics of this experimental model.}, }
@article {pmid40285000, year = {2025}, author = {VanAcker, MC and Ergunay, K and Webala, PW and Kamau, M and Mutura, J and Lebunge, R and Ochola, GO and Bourke, BP and McDermott, EG and Achee, NL and Jiang, L and Grieco, JP and Keter, E and Musanga, A and Murray, S and Stabach, JA and Craft, ME and Fèvre, EM and Linton, YM and Hassell, J}, title = {A Novel Nobecovirus in an Epomophorus wahlbergi Bat from Nairobi, Kenya.}, journal = {Viruses}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/v17040557}, pmid = {40285000}, issn = {1999-4915}, support = {W81XWH-21-C-0001, W81XWH-22-C-0093 and HT9425-23-C-0059//United States Army Medical Research and Development Command/ ; George E. Burch Fellowship//Smithsonian Institution/ ; G1100783/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; CGIAR Trust Fund//CGIAR/ ; }, mesh = {Kenya ; *Chiroptera/virology ; Animals ; Phylogeny ; Genome, Viral ; Feces/virology ; *Coronaviridae/genetics/classification/isolation &amp; purification ; }, abstract = {Most human emerging infectious diseases are zoonotic, originating in animal hosts prior to spillover to humans. Prioritizing the surveillance of wildlife that overlaps with humans and human activities can increase the likelihood of detecting viruses with a high potential for human infection. Here, we obtained fecal swabs from two fruit bat species-Eidolon helvum (n = 6) and Epomophorus wahlbergi (n = 43) (family Pteropodidae)-in peridomestic habitats in Nairobi, Kenya, and used metagenome sequencing to detect microorganisms. A near-complete genome of a novel virus assigned taxonomically to the Coronaviridae family Betacoronavirus genus and Nobecovirus subclade was characterized from E. wahlbergi. Phylogenetic analysis indicates this unique Nobecovirus clade shares a common ancestor with Eidolon/Rousettus Nobecovirus subclades isolated from Madagascar, Kenya, and Cameroon. Recombination was detected across open reading frames, except the spike protein, in all BOOTSCAN analyses, indicating intra-host coinfection and genetic exchange between genome regions. Although Nobecoviruses are currently bat-specific and are not known to be zoonotic, the propensity of coronaviruses to undergo frequent recombination events and the location of the virus alongside high human and livestock densities in one of East Africa's most rapidly developing cities justifies continued surveillance of animal viruses in high-risk urban landscapes.}, }
@article {pmid40284976, year = {2025}, author = {Ibañez, JM and Zambrana, R and Carreras, P and Obregón, V and Irazoqui, JM and Vera, PA and Lattar, TE and Blanco Fernández, MD and Puebla, AF and Amadio, AF and Torres, C and López Lambertini, PM}, title = {Phylodynamic of Tomato Brown Rugose Fruit Virus and Tomato Chlorosis Virus, Two Emergent Viruses in Mixed Infections in Argentina.}, journal = {Viruses}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/v17040533}, pmid = {40284976}, issn = {1999-4915}, support = {INTA 2023-PEM-L01-I704//National Agricultural Technology Institute/ ; }, mesh = {Argentina ; *Solanum lycopersicum/virology ; *Plant Diseases/virology ; Genome, Viral ; Phylogeny ; *Crinivirus/genetics/classification/isolation &amp; purification ; Genetic Variation ; *Tobamovirus/genetics/classification/isolation &amp; purification ; Metagenomics ; Coinfection/virology ; Sewage/virology ; Evolution, Molecular ; }, abstract = {Tobamovirus fructirugosum (ToBRFV) and Crinivirus tomatichlorosis (ToCV) are emerging viral threats to tomato production worldwide, with expanding global distribution. Both viruses exhibit distinct biological characteristics and transmission mechanisms that influence their spread. This study aimed to reconstruct the complete genomes of ToBRFV and ToCV from infected tomato plants and wastewater samples in Argentina to explore their global evolutionary dynamics. Additionally, it compared the genetic diversity of ToBRFV in plant tissue and sewage samples. Using metagenomic analysis, the complete genome sequences of two ToBRFV isolates and two ToCV isolates from co-infected tomatoes, along with four ToBRFV isolates from sewage, were obtained. The analysis showed that ToBRFV exhibited higher genetic diversity in environmental samples than in plant samples. Phylodynamic analysis indicated that both viruses had a recent, single introduction in Argentina but predicted different times for ancestral diversification. The evolutionary analysis estimated that ToBRFV began its global diversification in June 2013 in Israel, with rapid diversification and exponential growth until 2020, after which the effective population size declined. Moreover, ToCV's global expansion was characterized by exponential growth from 1979 to 2010, with Turkey identified as the most probable location with the current data available. This study highlights how sequencing and monitoring plant viruses can enhance our understanding of their global spread and impact on agriculture.}, }
@article {pmid40284912, year = {2025}, author = {Guo, M and Li, M and Liu, T and Sun, W and Du, K and Yang, S and Fu, Z and Kou, Z}, title = {Epidemiological and Genetic Characteristics of Sapovirus in Shandong, China, 2022-2023.}, journal = {Viruses}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/v17040469}, pmid = {40284912}, issn = {1999-4915}, support = {2021YFC2302003//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Sapovirus/genetics/classification/isolation &amp; purification ; China/epidemiology ; *Caliciviridae Infections/epidemiology/virology ; Child, Preschool ; Child ; Infant ; *Gastroenteritis/epidemiology/virology ; Male ; Female ; Adolescent ; Adult ; Phylogeny ; Middle Aged ; Young Adult ; Diarrhea/virology/epidemiology ; Genotype ; Prevalence ; Aged ; Genome, Viral ; Infant, Newborn ; Incidence ; Whole Genome Sequencing ; Feces/virology ; }, abstract = {Sapovirus (SaV) is a major pathogen responsible for acute gastroenteritis (AGE), and its incidence has been increasing in recent years. This study investigates the prevalence and the genetic characteristics of SaV in Shandong Province during 2022-2023, based on a surveillance network covering all age groups. Samples were obtained from a viral diarrhea surveillance network in Shandong Province during 2022-2023. SaVs were identified through quantitative reverse-transcription polymerase chain reaction (RT-qPCR). PCR amplification and Sanger sequencing were performed on positive samples, and whole-genome sequencing was conducted using metagenomic sequencing technology. Sequence analysis was conducted using BioEdit 7.0.9.0 and MEGA X, while statistical analysis was performed with SPSS 26.0. A total of 157 SaV-positive cases were identified, resulting in a positivity rate of 1.12%. The positivity rate for SaV was 0.75% in 2022 and it increased significantly to 1.42% in 2023. The highest positivity rates for both 2022 and 2023 were observed in November. The highest positivity rate was observed in the 3-5-year-old age group. In 2022, Dongying City had the highest positivity rate, while Zaozhuang City exhibited the highest rate in 2023. The incidence of vomiting in SaV-positive patients was significantly higher compared to SaV-negative patients (P = 0.002). Eight genotypes were identified in both the VP1 and RdRp regions. The complete genome sequence analysis of a GI.3 strain showed that NS1 (5.88%, 4/68) was the region most prone to amino acid variation, followed by VP2 (5.45%, 9/165) within the same genotype. SaV infections are more prevalent in cold weather, with young children being particularly susceptible. The SaV positivity rate in 2023 increased significantly accompanied by an increased diversity of genotypes, compared to that of 2022. The NS1 region exhibits the biggest variation within the same genotype, indicating that more attention should be paid to other regions besides VP1 in the future study. Ongoing surveillance of SaV is recommended for effective prevention and control.}, }
@article {pmid40284799, year = {2025}, author = {Wang, Y and Cui, Q and Hou, Y and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Wang, W}, title = {Metagenomic Insights into the Diverse Antibiotic Resistome of Non-Migratory Corvidae Species on the Qinghai-Tibetan Plateau.}, journal = {Veterinary sciences}, volume = {12}, number = {4}, pages = {}, doi = {10.3390/vetsci12040297}, pmid = {40284799}, issn = {2306-7381}, support = {2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; }, abstract = {Antibiotic resistance represents a global health crisis with far-reaching implications, impacting multiple domains concurrently, including human health, animal health, and the natural environment. Wild birds were identified as carriers and disseminators of antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs). A majority of studies in this area have concentrated on migratory birds as carriers for the spread of antibiotic resistance over long distances. However, there has been scant research on the resistome of non-migratory Corvidae species that heavily overlap with human activities, which limits our understanding of antibiotic resistance in these birds and hinders the development of effective management strategies. This study employed a metagenomics approach to examine the characteristics of ARGs and mobile genetic elements (MGEs) in five common Corvidae species inhabiting the Qinghai-Tibetan Plateau. The ARGs were classified into 20 major types and 567 subtypes. Notably, ARGs associated with multidrug resistance, including to macrolide-lincosamide-streptogramins, tetracyclines, beta-lactam, and bacitracin, were particularly abundant, with the subtypes acrB, bacA, macB, class C beta-lactamase, and tetA being especially prevalent. A total of 5 types of MGEs (166 subtypes) were identified across five groups of crows, and transposase genes, which indicated the presence of transposons, were identified as the most abundant type of MGEs. Moreover, some common opportunistic pathogens were identified as potential hosts for these ARGs and MGEs. Procrustes analysis and co-occurrence network analysis showed that the composition of the gut microbiota shaped the ARGs and MGEs, indicating a substantial association between these factors. The primary resistance mechanisms of ARGs in crows were identified as multidrug efflux pumps, alteration of antibiotic targets, and enzymatic inactivation. High-risk ARGs which were found to potentially pose significant risks to public health were also analyzed and resulted in the identification of 81 Rank I and 47 Rank II ARGs. Overall, our study offers a comprehensive characterization of the resistome in wild Corvidae species, enhancing our understanding of the potential public health risks associated with these birds.}, }
@article {pmid40284724, year = {2025}, author = {Brinkerhoff, RJ and Pandian, J and Leber, M and Hauser, ID and Gaff, HD}, title = {Impacts of Tick Parasitism on the Rodent Gut Microbiome.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040888}, pmid = {40284724}, issn = {2076-2607}, support = {5R01AI136035/GF/NIH HHS/United States ; }, abstract = {Host microbiota may impact disease vector behavior and pathogen transmission, but little is known about associations between ectoparasites and microbial communities in wildlife reservoir species. We used Illumina metagenomic sequencing to explore the impacts of tick parasitism on the rodent fecal microbiome in both a field and laboratory setting. We found that tick parasitism on wild hosts was associated with variation in the fecal microbiota of both the white-footed deermouse, Peromyscus leucopus, and the southern cotton rat, Sigmodon hispidus. In a lab experiment, we detected significant changes to the fecal microbiome after experimental exposure to immature ticks in treated versus control BALB/c mice. Whereas there is variation in the fecal microbiome associated with each of the host species we tested, some of the same microbial taxa, notably members of the family Muribaculaceae, occurred at higher relative abundance in tick-parasitized hosts in both the field and laboratory studies, suggesting that there are consistent impacts of tick parasitism on the host gut microbiome. We recommend future studies to test the hypothesis that epithelial cell secretions, generated as part of the host's immune response to tick parasitism, could provide resources that allow particular microbial lineages in the mammalian gut to flourish.}, }
@article {pmid40284718, year = {2025}, author = {Wu, X and Liao, H and Zhang, X and Ma, Z and Fu, Z}, title = {Unraveling the Impact of Microplastic-Tetracycline Composite Pollution on the Moon Jellyfish Aurelia aurita: Insights from Its Microbiome.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040882}, pmid = {40284718}, issn = {2076-2607}, support = {2022GXNSFBA035473//Natural Science Foundation of Guangxi Province China/ ; 2023A1515011859//Guangdong Natural Science Foundation of China/ ; 2021KJQD18//Guangxi&#xa0;Minzu&#xa0;University&#xa0;Research&#xa0;Fund/ ; }, abstract = {Microplastics have emerged as a pervasive marine contaminant, with extreme concentrations reported in deep-sea sediments (e.g., 1.9 million particles/m[2]) and localized accumulations near Antarctic research stations. Particular concern has been raised regarding their synergistic effects with co-occurring antibiotics, which may potentiate toxicity and facilitate antibiotic resistance gene dissemination through microbial colonization of plastic surfaces. To investigate these interactions, a 185-day controlled exposure experiment was conducted using Aurelia aurita polyps. Factorial combinations of microplastics (0, 0.1, 1 mg/L) and tetracycline (0, 0.5, 5 mg/L) were employed to simulate environmentally relevant pollution scenarios. Microbiome alterations were characterized using metagenomic approaches. Analysis revealed that while alpha and beta diversity measures remained unaffected at environmental concentrations, significant shifts occurred in the relative abundance of dominant bacterial taxa, including Pseudomonadota, Actinomycetota, and Mycoplasmatota. Metabolic pathway analysis demonstrated perturbations in key functional categories including cellular processes and environmental signal transduction. Furthermore, microplastic exposure was associated with modifications in polyp life-stage characteristics, suggesting potential implications for benthic-pelagic population dynamics. These findings provide evidence for the impacts of microplastic-antibiotic interactions on cnidarian holobionts, with ramifications for predicting jellyfish population responses in contaminated ecosystems.}, }
@article {pmid40284693, year = {2025}, author = {Olivos-Caicedo, KY and Fernandez-Materan, FV and Daniel, SL and Anantharaman, K and Ridlon, JM and Alves, JMP}, title = {Pangenome Analysis of Clostridium scindens: A Collection of Diverse Bile Acid- and Steroid-Metabolizing Commensal Gut Bacterial Strains.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040857}, pmid = {40284693}, issn = {2076-2607}, support = {1R03AI147127-20A1/NH/NIH HHS/United States ; }, abstract = {Clostridium scindens is a commensal gut bacterium capable of forming the secondary bile acids as well as converting glucocorticoids to androgens. Historically, only two strains, C. scindens ATCC 35704 and C. scindens VPI 12708, have been characterized to any significant extent. The formation of secondary bile acids is important in the etiology of cancers of the GI tract and in the prevention of Clostridioides difficile infection. We determined the presence and absence of bile acid inducible (bai) and steroid-17,20-desmolase (des) genes among C. scindens strains and the features of the pangenome of 34 cultured strains of C. scindens and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the C. scindens cultivars have an open pangenome with 12,720 orthologous gene groups and a core genome with 1630 gene families, in addition to 7051 and 4039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The pangenome profile including the MAGs also proved to be open. Our analyses reveal that C. scindens strains are distributed into two clades, indicating the possible onset of C. scindens separation into two species, as suggested by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the C. scindens pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.}, }
@article {pmid40284690, year = {2025}, author = {Galanova, OO and Mitkin, NA and Danilova, AA and Pavshintsev, VV and Tsybizov, DA and Zakharenko, AM and Golokhvast, KS and Grigoryeva, TV and Markelova, MI and Vatlin, AA}, title = {Assessment of Soil Health Through Metagenomic Analysis of Bacterial Diversity in Russian Black Soil.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040854}, pmid = {40284690}, issn = {2076-2607}, support = {202760-2-000//RUDN University Scientific Projects Grant System/ ; }, abstract = {Soil health is a critical determinant of agricultural productivity and environmental sustainability. Traditional assessment methods often fail to provide a comprehensive understanding of soil microbial communities and their functions. This study addresses this challenge by employing metagenomic techniques to assess the functionality of soil microbiomes in Russian black soil, renowned for its high fertility. We utilized shotgun metagenomic sequencing to analyze soil samples from Western Siberia subjected to different degrees of agro-soil disturbance. We identified functional genes involved in carbon (accA, argG, acsA, mphE, miaB), phosphorus (phoB, ppa, pstB, pnp, phnJ), and nitrogen (queC, amiF, pyrG, guaA, guaB, napA) metabolic pathways and associated with changes in microbial diversity, in general, and higher representation of certain bacterial species-Bradyrhizobium spp. The results demonstrated significant differences in microbial composition and functional potential between tillage treatments. No-Till technology and conventional tillage practices promoted beneficial microbial communities and enhanced soil health compared to long-term fallow soil. This work underscores the potential of metagenomic analysis in providing a comprehensive understanding of soil health, marking a significant advancement in the field.}, }
@article {pmid40284681, year = {2025}, author = {Wang, X and Li, Y and Zuo, L and Li, P and Lou, H and Zhao, R}, title = {Revealing the Characteristics and Correlations Among Microbial Communities, Functional Genes, and Vital Metabolites Through Metagenomics in Henan Mung Bean Sour.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040845}, pmid = {40284681}, issn = {2076-2607}, support = {231100110300//the Major Science and Technology Project of Henan, China/ ; 221100110700//Major Science and Technology Project of Henan, China/ ; }, abstract = {Henan mung bean sour (HMBS) is the raw material for mung bean sour noodles (MBSNs), a traditional fermented food. To investigate the characteristic flavor compounds, we have detected the content of free amino acids (FAAs) and key metabolites including organic acids, sugars, and alcohols. The results revealed that the content associated with umami, sweetness, and bitterness (TVA > 1) showed significant differences. Metagenomic analysis indicated that Lactobacillus delbrueckii was the dominant and characteristic species in WJ and LY15, whereas Bifidobacterium mongoliense, Lactiplantibacillus plantarum, and Acetobacter indonesiensis were the dominant species in GY. The abundance of functional genes related to carbohydrate and amino acid metabolism was higher in WJ and LY15. There was a strong correlation between dominant genera and vital metabolites (r |>| 0.7). This study provides a theoretical foundation for the development of HMBS.}, }
@article {pmid40284671, year = {2025}, author = {de Obeso Fernández Del Valle, A and Membrillo-Hernández, J}, title = {Metagenomics Analysis of the Microbial Consortium in Samples from Lake Xochimilco, a World Cultural Heritage Site.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040835}, pmid = {40284671}, issn = {2076-2607}, support = {1/CX/CSRD VA/United States ; }, abstract = {Since ancient times, the community of Xochimilco in the south of Mexico City has provided vegetables for the entire city. Today, Lake Xochimilco is listed as a UNESCO World Heritage Site because it is the last remaining bastion of Aztec culture and preserves the extraordinary ecological landscape of chinampas, a system of arable islands that has endured for over 1000 years. Here, we report on the microbiological communities currently existing in the lake. This is relevant since the water irrigates crops on the islands, known as chinampas. To achieve this, samples from the lake were collected at two different sites, and metagenomics analysis of the 16S gene was conducted. The results indicate the presence of five dominant bacterial phyla: Actinobacteria (44.5%), Proteobacteria (22.5%), Firmicutes (13%), Bacteroidota (6%), and Chloroflexi (4.6%). The most abundant families were Micrococcaceae, Intrasporangiaceae, and Rhodobacteraceae. The results correlate with current anthropogenic activity, indicating a moderate problem associated with contamination. Our findings suggest that immediate actions and increased awareness are necessary to preserve this cultural and natural heritage site and to take steps to comply with Sustainable Development Goal 11 (Sustainable Cities and Communities). Furthermore, this is the first report to characterize microbial communities in the water of Lake Xochimilco using 16S rRNA gene sequencing.}, }
@article {pmid40284644, year = {2025}, author = {Xin, ZZ and Ma, K and Che, YZ and Dong, JL and Xu, YL and Zhang, XT and Li, XY and Zhang, JY}, title = {Differences in Microbial Community Structure Determine the Functional Specialization of Gut Segments of Ligia exotica.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040808}, pmid = {40284644}, issn = {2076-2607}, support = {CARS-47//the earmarked fund for the China Agriculture Research System/ ; ZR2022QC250//the Natural Science Foundation of Shandong Province/ ; 32173019//National Natural Science Foundation of China/ ; }, abstract = {Ligia feed on seashore algae and remove organic debris from the coastal zone, thereby playing an important role in the intertidal ecosystem. Nevertheless, the specific roles of distinct gut segments in the gut transit remain unclear. We collected and identified Ligia exotica specimens in the coast of Aoshanwei, Qingdao, Shandong Province, and analyzed their foreguts and hindguts for 16S rRNA, metagenomics, metabolomics, and proteomics. The concentrations of common metabolites, NO3[-]-N and NH4[+]-N, and the contents of C and N were measured. The gut transit decreased the abundances of the dominant phyla Cyanobacteria but increased Proteobacteria, Firmicutes, and Actinobacteria, and Planctomycetes and Bacteroidetes remained relatively constant. The foregut gut microbiota is involved in the carbohydrates and amino acids metabolism, as well as the decomposition of polysaccharides. The hindgut gut microbiota performs a variety of functions, including carbohydrate and amino acid metabolism, fermentation, cell motility, intracellular transport, secretion, and vesicular translocation, and the decomposition of polysaccharides, disaccharides, and oligosaccharides. The results of omics analyses and molecular experiments demonstrated that the metabolic processes involving amino acids and carbohydrates are more active in the foregut, whereas the fermentation, absorption, and assimilation processes are more active in the hindgut. Taken together, the differences in microbial community structure determine the functional specialization of different gut segments, i.e., the foregut appears to be the primary site for digesting food, while the hindgut further processes and absorbs nutrients and then excretes them.}, }
@article {pmid40284617, year = {2025}, author = {Mohapatra, A and Trivedi, S and Tejpal, CS and Aware, MJ and Vaswani, S and Prajapati, VJ and Kolte, AP and Malik, PK and Sahoo, A and Ravishankar, CN and Bhatta, R}, title = {Effect of Two Selected Levels of Padina gymnospora Biowaste and Enteric Methane Emission, Nutrient Digestibility, and Rumen Metagenome in Growing Sheep.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040780}, pmid = {40284617}, issn = {2076-2607}, support = {Outreach Methane//Indian Council of Agricultural Research/ ; }, abstract = {A study was conducted on growing sheep to investigate the effect of two selected levels of biowaste of Padina gymnospora on feed intake, digestibility, daily enteric methane (CH4) emission, growth performance, and rumen metagenome. We randomly divided the 18 growing male sheep into three groups of six animals each. The animals were fed on a basal diet comprising finger millet straw (Eleusine coracana) and a concentrate mixture in a 35:65 ratio. The sheep in the control group (C) were offered a concentrate mixture without waste, whereas the wheat bran in the concentrate mixture in test group I (A2) and test group II (A5) was replaced (w/w) with the biowaste of Padina gymnospora at a level of 3.07 and 7.69%, respectively. The biowaste of Padina gymnospora at the above levels in concentrate constituted 2 and 5% of the diet. A significant decrease of 28.4% in daily enteric CH4 emission (g/d) was reported in the A5 group, whereas the difference in daily enteric CH4 emission between the C and A2 &amp; A2 and A5 groups did not prove significant. The inclusion of Padina gymnospora biowaste did not affect the nutrient intake and digestibility among the groups. The inclusion of Padina gymnospora biowaste in the A5 group resulted in a significant reduction (p = 0.0012) in daily CH4 emissions compared with group C; however, no significant differences were observed in daily CH4 emissions between groups C-A2 (p = 0.0793) and A2-A5 (p = 0.3269). Likewise, the adjustment of data to CH4 emissions per 100 g of organic matter intake indicated a substantial decrease in the A5 group relative to C. The energy loss in CH4 as a percentage of GE relative to group C decreased significantly (-23.4%) in the A5 group; however, this reduction was not associated with an increase in productivity, as almost similar average daily gain (p = 0.827) was observed in the groups. The replacement of wheat bran with the biowaste of Padina gymnospora significantly decreased the numbers of total protozoa and holotrichs in the A5 group. Irrespective of the group, the Bacteroidota was the single largest phylum in the rumen metagenome, representing >60% of the microbiota. However, the abundance of Bacteroidota was similar among the groups. The methanogenic phyla Euryarchaeota was the 5th most abundant; however, it constituted only 3.14% of the metagenome. The abundance of Desulfovibrio was significantly higher in the A5 group as compared with the control. In conclusion, the significant increase in the abundance of sulfate-reducing bacteria and reduction in protozoal numbers led to a significant reduction in CH4 emissions with the incorporation of biowaste of Padina gymnospora at a 5% level of the diet.}, }
@article {pmid40284605, year = {2025}, author = {Xiao, C and Wan, K and Chen, Y and Jin, Y and Zhou, F and Yu, J and Chi, R}, title = {Metagenomic Analysis Revealed the Changes in Antibiotic Resistance Genes and Heavy Metal Resistance Genes in Phosphate Tailings Compost.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040768}, pmid = {40284605}, issn = {2076-2607}, abstract = {Phosphate tailings are usually rich in phosphorus and some other mineral nutrients, which is very suitable for composting. In this study, 60 days of composting using phosphate tailings, chicken manure, and straw resulted in a significant decrease in total nitrogen (TN) content from 1.75 ± 0.12 g/kg to 0.98 ± 0.23 g/kg (p < 0.01), with a nitrogen retention of 56%, an increase in water-soluble phosphorus (Ws-P) from 3.24 ± 0.14 mg/kg to 7.21 ± 0.09 mg/kg, and an increase in immediate potassium (AK) from 0.56 ± 0.21 mg/kg to 1.90 ± 0.11 mg/kg (p < 0.05). Metagenomic sequencing showed little changes in the diversity and abundance of microbial communities before and after composting, but changes in species composition and the abundance of archaea, bacteria, and fungi resulted in differences in community structure before and after composting. Composting contributed to a lower gene abundance of ARGs and MRGs. The addition of phosphate tailings combined the functions of chemical regulation and nutrient enrichment, and its synergistic effect significantly optimized the nutrient cycling in the composting system.}, }
@article {pmid40284601, year = {2025}, author = {Song, Z and Zhang, T and Liang, Y and Mcminn, A and Wang, M and Jiao, N and Luo, T}, title = {Seasonal Variations of Community Structure and Functional Genes of Synechococcus in the Subtropical Coastal Waters: Insights from FACS and High-Throughput Sequencing.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040764}, pmid = {40284601}, issn = {2076-2607}, abstract = {Synechococcus plays a pivotal role in the marine biogeochemical cycle. Advances in isolation techniques and high-throughput sequencing have expanded our understanding of the diversity of the Synechococcus community. However, their genomic diversity, functional dynamics and seasonal variations in the coastal waters are still not well known. Here, seawater samples were collected seasonally (March, June, August, December) from three stations in the coastal waters of Xiamen. Using fluorescence-activated cell sorting (FACS), we isolated 1000 Synechococcus cells per sample and performed ITS amplicon sequencing and metagenomic sequencing to analyze the seasonal variations in community structure and functional genes of Synechococcus. Firstly, we conducted a comparative analysis of in situ data and FACS data from three sampling sites in August. FACS samples revealed low-abundance Synechococcus strains underdetected by in situ samples. In addition, 24 clades representing Synechococcus subclusters S5.1, S5.2, and S5.3 were detected from three in situ samples and twelve FACS samples, suggesting the high diversity of Synechococcus in the coastal waters of Xiamen. Furthermore, the Synechococcus community displayed pronounced seasonal variations, and temperature significantly influenced the variations in Synechococcus community composition. Additionally, Synechococcus populations exhibit seasonal functional dynamics, with enhanced metabolic activity in summer characterized by higher numbers of functional genes associated with metabolic pathways compared to winter samples. Altogether, this study underscored the significance of FACS and high-throughput sequencing to reveal the diversity and functional dynamics of Synechococcus.}, }
@article {pmid40284573, year = {2025}, author = {Russell, G and Alegoz, R and Hester, K and Sierzega, KL and Szul, MJ and Hubert, N and Rylander, T and Jensen, S and Ciancio, MJ and Martinez-Guryn, K and Evans, CC}, title = {The Microbiome of an Outpatient Sports Medicine Clinic During a Global Pandemic: Effects of Implementation of a Microbiome-Specific Cleaning Program.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040737}, pmid = {40284573}, issn = {2076-2607}, support = {2018//Illinois Physical Therapy Association/ ; 2020//Illinois Physical Therapy Association/ ; }, abstract = {Outpatient healthcare facilities represent potential sources of healthcare-associated infections (HAIs). The purpose of this study was to survey high-contact surfaces in an outpatient physical therapy clinic, characterize the microbiome of those surfaces, and investigate the effects of a microbiome-specific cleaning and hygiene plan. Hand sanitizer containing a fluorescent probe used by patients and staff identified surface contact. High-contact surfaces were analyzed for bacterial DNA and SARS-CoV-2. A microbiome-specific cleaning and hygiene plan was developed based on initial analysis. After the implementation of the revised cleaning regimen, microbial community diversity and predicted metagenome content (PICRUSt) were employed for differential analysis. Patients had greater surface contact than staff. Ralstonia pickettii was the dominant species pre-cleaning, comprising 49.76% of the total, and observed on 79.5% of surfaces. The cleaning and hygiene plan significantly increased Shannon diversity, and R. pickettii decreased to 4.05% of total bacteria. SARS-CoV-2 was not observed on any surfaces. This study found ecological dominance by a single species in this outpatient clinic, suggesting a potential source of HAIs. However, a microbiome-specific cleaning strategy was successful in diversifying the microbiome and reducing ecological dominance. Additional research is needed to confirm these findings.}, }
@article {pmid40284568, year = {2025}, author = {Ma, W and Han, Z and Liu, X and Cui, W and Zhen, D and Zhou, X and Song, Y and Jiang, S}, title = {Distinct Effects of Lactiplantibacillus plantarum HNU082 on Microbial Single-Nucleotide Variants in Large Intestine and Small Intestine.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040731}, pmid = {40284568}, issn = {2076-2607}, abstract = {The intestinal tract extends several times the length of bodies, with varying environmental conditions across different segments (small intestinal and large intestinal), thereby harboring distinct gut microbiota. Most studies focused on the quantitative responses of gut microbiota upon probiotics entering the gut, without an in-depth analysis of how the genetic change in local gut microbiota. Therefore, in this experiment, C57BL/6J male mice were once administered Lactiplantibacillus plantarum HNU082 (Lp082). Then, the mice were euthanized on the 1st, 3rd, and 7th days after gavage, and the contents of the small and large intestines of the mice were scraped for metagenomic analysis. Based on the characterization of large intestine and small intestine bacteria, changes in the diversity and abundance of single-nucleotide variants (SNVs) of microbiota were analyzed. There were observable distinct responses at the genetic level. A significant number of SNVs were identified in Ligilactobacillus murinus in the large intestine. These SNVs may impact the utilization of carbohydrates in L. murinus. Ingested probiotics traversed the entire gut and interacted with the indigenous microbiota, driving the evolution of the indigenous gut microbiota in the different intestinal segments, thereby influencing microbial growth and metabolism. This study investigates the role of probiotics in the evolution of gut microbiota. It offers new probiotic insights and a basis for targeted interventions.}, }
@article {pmid40284547, year = {2025}, author = {Alzahrani, AJ and Al-Hebshi, BM and Yahia, ZA and Al-Judaibi, EA and Alsaadi, KH and Al-Judaibi, AA}, title = {Impact of Microbiota Diversity on Inflammatory Bowel Disease.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/microorganisms13040710}, pmid = {40284547}, issn = {2076-2607}, abstract = {Inflammatory bowel disease (IBD) is a chronic condition that includes two main types, Crohn's disease (CD) and ulcerative colitis (UC), involving inflammation of the gastrointestinal (GI) tract. The exact cause of IBD is unknown but could be a combination of genetic, environmental, and immune system factors. This study investigated the impact of IBD on microbiota diversity by evaluating the differences in microbial composition and the microbiota of a control group (A) of healthy individuals and a group (B) of IBD patients. Sixty biopsies were collected from participants recruited from hospitals in Makkah, Saudi Arabia. Biopsy specimens were taken during colonoscopy examination, and bacterial identification was performed by extracting ribosomal DNA from sigmoid colon biopsies using a DNeasy Blood &amp; Tissue Kit. Metagenomics and bioinformatics analyses were then conducted to analyze and compare the microbiota in the two groups. The results showed that the varieties of core microbiome species were 3.81% greater in the IBD patients than in the members of the control group. Furthermore, the differences between the groups were significantly greater than the variations within each group. Differences between the two groups were detected in the relative abundance of Clostridium nexile, Ruminococcus gnavus, Ruminococcus faecis, and Escherichia coli. These results indicate that microbiota could play a role in the pathogenesis of IBD and suggest that microbial diversity can serve as a biomarker for diagnosing the disease and monitoring its progression.}, }
@article {pmid40284188, year = {2025}, author = {Bonomo, MG and D'Angelo, S and Picerno, V and Carriero, A and Salzano, G}, title = {Recent Advances in Gut Microbiota in Psoriatic Arthritis.}, journal = {Nutrients}, volume = {17}, number = {8}, pages = {}, doi = {10.3390/nu17081323}, pmid = {40284188}, issn = {2072-6643}, mesh = {Humans ; *Arthritis, Psoriatic/microbiology/therapy/immunology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; }, abstract = {Psoriatic arthritis (PsA) is a chronic inflammatory disease characterized by joint inflammation and skin lesions. Recent research has underscored the critical role of gut microbiota-comprising bacteria, fungi, viruses, and archaea-in the pathogenesis and progression of PsA. This narrative review synthesizes the latest findings on the influence of gut microbiota on PsA, focusing on mechanisms such as immune modulation, microbial dysbiosis, the gut-joint axis, and its impact on treatment. Advances in high-throughput sequencing and metagenomics have revealed distinct microbial profiles associated with PsA. Studies show that individuals with PsA have a unique gut microbiota composition, differing significantly from healthy controls. Alterations in the abundance of specific bacterial taxa, including a decrease in beneficial bacteria and an increase in potentially pathogenic microbes, contribute to systemic inflammation by affecting the intestinal barrier and promoting immune responses. This review explores the impact of various factors on gut microbiota composition, including age, hygiene, comorbidities, and medication use. Additionally, it highlights the role of diet, probiotics, and fecal microbiota transplantation as promising strategies to modulate gut microbiota and alleviate PsA symptoms. The gut-skin-joint axis concept illustrates how gut microbiota influences not only gastrointestinal health but also skin and joint inflammation. Understanding the complex interplay between gut microbiota and PsA could lead to novel, microbiome-based therapeutic approaches. These insights offer hope for improved patient outcomes through targeted manipulation of the gut microbiota, enhancing both diagnosis and treatment strategies for PsA.}, }
@article {pmid40284057, year = {2025}, author = {Lan, W and Ding, H and Zhang, Z and Li, F and Feng, H and Guo, Q and Qin, F and Zhang, G and Xu, M and Xu, Y}, title = {Diversified Soil Types Differentially Regulated the Peanut (Arachis hydropoaea L.) Growth and Rhizosphere Bacterial Community Structure.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/plants14081169}, pmid = {40284057}, issn = {2223-7747}, support = {24-4-4-zrjj-132-jch//Natural Science Foundation of Qingdao/ ; CXGC2025D19//2025 Innovation Project of Shandong Academy of Agricultural Sciences/ ; ZR2024QC012//Natural Science Foundation of Shandong Province/ ; 110202201029(LS-13)//Major Science and Technology Project/ ; }, abstract = {Peanut (Arachis hydropoaea L.) demonstrates a prominent adaptability to diverse soil types. However, the specific effects of soil types on peanut growth and bacterial communities remain elusive. This study conducted a thorough examination of the agronomic traits, the corresponding physicochemical properties, and bacterial structure of rhizosphere soil in acidic (AT), neutral (NT), and saline-alkali (ST) soils, elucidating the internal relationship between soil type and peanut yield. Our results showed that different soil types exhibited significant differences in peanut yield, with ST demonstrating the lowest yield per plant, showing an 85.05% reduction compared to NT. Furthermore, available phosphorus content, urease, and invertase activities were substantially reduced in both ST and AT, particularly in ST by 95.35%, 38.57%, and 62.54%, respectively. Meanwhile, metagenomic sequencing unveiled a notable decline in Bradyrhizobium and Streptomyces in these soils, which is crucial for soil improvement. Further metabolic pathway analysis revealed that the reduction in pathways related to soil remediation, fertility improvement, and stress response in AT and ST may lead to slower peanut growth. In conclusion, peanuts cultivated in acidic and saline-alkali soils can increase yield via implementing soil management practices such as improving soil quality and refining micro-environments. Our study provides practical applications for enhancing peanut yield in low- to medium-yield fields.}, }
@article {pmid40283102, year = {2025}, author = {Zhao, Y and Wang, Y and Lu, J and Zhu, B and Li, AD}, title = {Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/life15040547}, pmid = {40283102}, issn = {2075-1729}, support = {BK20230742//the Natural Science Foundation of Jiangsu Province/ ; GWJJ2024100202//2024 Annual Project of the National Health Commission (NHC) Capacity Building and Continuing Education Center/ ; M2022083//Scientific Research Project of Jiangsu Health Committee/ ; ZDXK202249//Jiangsu Provincial Medical Key Discipline/ ; 2024ZB315//Jiangsu Funding Program for Excellent Postdoctor/ ; }, abstract = {The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.}, }
@article {pmid40282815, year = {2025}, author = {Lee, JH and Moon, H and Park, HR and Noh, JI and Kim, SS}, title = {Metagenomic Analysis of Raw Milk and the Inactivation of Foodborne Pathogens Using Ultraviolet-C.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/foods14081414}, pmid = {40282815}, issn = {2304-8158}, support = {WISET-2024-056//Ministry of Science and ICT/ ; }, abstract = {The purpose of this study was to identify the microbial community of raw milk samples before and after UV-C irradiation and to establish fundamental data on UV-C treatment to improve the safety and shelf life of raw milk. Metagenomic analysis revealed that Lactococcus spp., Lactobacillus spp., and Staphylococcus spp. were the dominant genera in raw milk, while Pseudomonas spp. became more prevalent after 14 days of refrigerated storage. The microorganisms in raw milk were isolated using selective media and identified as Serratia quinivorans 4364 and Latilactobacillus curvatus DSM 20019. To compare the UV resistance of these microorganisms, Pseudomonas aeruginosa, Staphylococcus aureus, Lactococcus lactis, and Latilactobacillus curvatus were inoculated into sterilized milk and subjected to UV-C treatment. The reduction rates of P. aeruginosa were significantly lower than those of the other strains (S. aureus, L. lactis, and L. curvatus). These findings provide insights into the microbial distribution in raw milk and the degree of resistance to UV treatment, which can serve as fundamental data for the pasteurization of raw milk.}, }
@article {pmid40282811, year = {2025}, author = {Dong, K and Song, D and Li, S and Wang, X and Dai, L and Pei, X and Yang, X and Jiang, Y}, title = {Significance of Whole-Genome Sequencing for the Traceability of Foodborne Pathogens: During the Processing of Meat and Dairy Products.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/foods14081410}, pmid = {40282811}, issn = {2304-8158}, support = {No. 2023-JSGG-29//National Center of Technology Innovation for Dairy/ ; }, abstract = {The complexity of tracing foodborne pathogens in the food chain has increased significantly due to the long and complicated chain, the involvement of numerous links, and the presence of various types of pathogens at different stages and environments. Traditional typing techniques are not sufficient to meet the requirements of tracing pathogens in the food chain. Whole-Genome Sequencing (WGS) has gradually become an important technological tool for characterizing and tracing pathogens in the food chain due to comprehensive information, speed, and superior discriminatory power. This paper provides an overview of the advantages of WGS and its application in foodborne pathogen traceability. This paper focused on foodborne pathogen contamination pathways during the processing of animal foods in commercial restaurant kitchens and the potential contamination of milk, milk powder, and other dairy products by pathogens during processing in the dairy industry chain and environments. Improper handling practices during meat processing (i.e., using cloths, washing hands without soap, and cleaning boards with knives) were a critical point of foodborne pathogen cross-contamination in commercial kitchen premises. However, in dairy products, contamination of pathogens in raw milk was the main cause of foodborne disease outbreaks. Therefore, preventing the contamination of pathogens in food should not only be focused on hygiene measures during processing and in environments but also on the quality and hygiene of raw materials to prevent the spread of foodborne pathogens throughout the entire production chain. Further, Whole-Metagenome Sequencing and DNA sequence markers are considered to be the future direction of WGS. The purpose of this work is to promote the wider application of WGS during the processing of meat and dairy products and provide theoretical support for the rapid investigation and accurate traceability of foodborne pathogen outbreaks in food.}, }
@article {pmid40282779, year = {2025}, author = {Nie, X and Chen, X and Lu, X and Yang, S and Wang, X and Liu, F and Yang, J and Guo, Y and Shi, H and Xu, H and Zhang, X and Fang, M and Tao, Y and Liu, C}, title = {Metagenomics Insights into the Role of Microbial Communities in Mycotoxin Accumulation During Maize Ripening and Storage.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/foods14081378}, pmid = {40282779}, issn = {2304-8158}, support = {No. 32060710//the National Natural Science Foundation of China/ ; }, abstract = {Mycotoxins are among the primary factors compromising food quality and safety. To investigate mycotoxin contamination, microbial diversity, and functional profiles in maize across distinct geographic regions, this study analyzed samples from Xuanwei, Fuyuan, and Zhanyi. Mycotoxin concentrations were quantified through standardized assays, while microbial community structures were characterized using metagenomics sequencing. Metabolic pathways, functional genes, and enzymatic activities were systematically annotated with the KEGG, eggNOG, and CAZy databases. The results demonstrated an absence of detectable aflatoxin (AF) levels. Deoxynivalenol (DON) concentrations varied significantly among experimental cohorts, although all values remained within regulatory thresholds. Zearalenone (ZEN) contamination exceeded permissible limits by 40%. The metagenomic profiling identified 85 phyla, 1219 classes, 277 orders, 590 families, 1171 genera, and 2130 species of microorganisms, including six mycotoxigenic fungal species. The abundance and diversity of microorganisms were similar among different treatment groups. Among 32,333 annotated KEGG pathways, primary metabolic processes predominated (43.99%), while glycoside hydrolases (GH) and glycosyltransferases (GT) constituted 76.67% of the 40,202 carbohydrate-active enzymes. These empirical findings establish a scientific framework for optimizing agronomic practices, harvest scheduling, and post-harvest management in maize cultivation.}, }
@article {pmid40282295, year = {2025}, author = {Laguerre, H and Noël, C and Jégou, C and Fleury, Y and Le Chevalier, P}, title = {The Cœlomic Microbiota Among Three Echinoderms: The Black Sea Cucumber Holothuria forskali, the Sea Star Marthasterias glacialis, and the Sea Urchin Sphaerechinus granularis.}, journal = {Biology}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/biology14040430}, pmid = {40282295}, issn = {2079-7737}, abstract = {In this study, the bacterial communities of the cœlomic microbiota were characterized in three Echinoderms: the deposit feeder sea Cucumber Holothuria forskali, the herbivorous sea Urchin Sphaerechinus granularis, and the carnivorous sea Star Marthasterias glacialis. Samples were collected from the same habitat in the Glénan Archipelago (Brittany, France) at different times for 2 years. The cœlomic microbiota were analyzed by targeted metagenomic with V4-16S metabarcoding and by a culturable approach with the isolation of strains and antimicrobial activity assays. Most of the OTUs of the cœlomic microbiota were affiliated with the phylum Proteobacteria and, notably, five orders: Burkholderiales, Flavobacteriales, Alteromonadales, Vibrionales and Pseudomonadales. Significant differences were observed regarding richness, biodiversity and composition between species and sampling dates. They could be explained by sub-abundant taxa that represented the global diversity. Cœlomic microbiota also revealed shared and unshared bacterial communities, validating a potential "specific" microbiota among the three Echinoderm species. Moreover, significant variations of the microbiota occurred among the sampling dates, suggesting a plasticity and, thus, a potential selection of these microbiota. Finally, out of the 831 bacterial strains isolated from culturable microbiota, 20 strains exhibited antibacterial activities, most of them assigned to the genera Shewanella, Pseudoalteromonas and Vibrio.}, }
@article {pmid40281970, year = {2025}, author = {Khalid, N and Bukhari, SM and Ali, W and Sheikh, AA and Abdullah, HM and Nazmi, A}, title = {Probiotic Lactocaseibacillus casei NK1 Enhances Growth and Gut Microbiota in Avian Pathogenic Escherichia coli Challenged Broilers.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/ani15081136}, pmid = {40281970}, issn = {2076-2615}, abstract = {The present study was conducted to assess the efficacy of Laboratory-Isolated Lactocaseibacillus casei NK1 (Lc. NK1) in broilers hypothesizing that, Lc. NK1 supplementation will enhance growth performance, modulate the gut microbiome, and reduce fecal pathogenic Escherichia coli in broilers. The experiment spanned 35 days where 60 one-day-old broiler chicks were randomly assigned to four treatment groups (n = 15); control-group with no treatment (NC), APEC (challenged with E. coli only), CProb (received commercial probiotics), and LNK1 (treated with Lc. NK1). The APEC, CProb, and LNK1 groups were infected with E. coli O78 strain at 11 days of age. Growth performance analysis revealed that the LNK1 group by day 35 gained body weight similar to the CProb group, with both groups significantly outperforming the APEC group (p < 0.001). Both the LNK1 and CProp groups exhibited similar reduction in E. coli while increasing Lactobacillus colorizations in the cloacal swabs from day 21 to 35 of age (p > 0.05). Metagenomic analysis using 16S rRNA sequencing showed that the LNK1 group maintained a diverse and balanced gut microbiota, characterized by increased Firmicutes and reduced Proteobacteria. In contrast, the APEC group exhibited reduced diversity and dominance of Escherichia-Shigella (p < 0.001). These findings suggest Lc. NK1 could be a promising probiotic for enhancing gut health and growth performance in broilers, even under pathogenic challenges, offering a potential alternative to antibiotics in poultry production.}, }
@article {pmid40281939, year = {2025}, author = {Hu, J and An, X and Yang, P and Tan, R and Chen, T and Chen, J and Tao, Y and Li, X and Sun, R and Zhang, S and Liu, S and Yang, L}, title = {Analysis of the Primary Pathogenic Bacteria in Abscess Disease of Musk Deer Using Metagenomic Approaches.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/ani15081105}, pmid = {40281939}, issn = {2076-2615}, support = {Grant No. 5242015//Beijing Municipal Natural Science Foundation/ ; 2024HXFWBH-LSQ-03//Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd/ ; 2024HXFWBH-LSQ-01//Huailai Zhiyangtianbao Technical development Co., Ltd/ ; }, abstract = {Abscesses are among the diseases affecting the survival of captive musk deer and are difficult to identify in their early stages. In this study, metagenomic sequencing, 16S rRNA sequencing, and paraffin sectioning were used to analyze the microbiota in the abscess musk deer pus group (AMP), abscess musk deer oral group (AMO), and healthy musk deer oral group (HMO) to compare the differences in microbiota in musk deer. By detecting differences in the oral microbiota through throat swabs, we aimed to monitor the early onset of abscess disease to facilitate timely intervention and treatment. The results showed that the alpha diversity of HMO microbiota was significantly higher than that of the AMP and AMO samples. Beta diversity results indicated that there were significant differences in the bacterial communities of HMO and AMO samples, and no significant difference was found between AMO and AMP samples. A taxonomic analysis of the bacterial species indicated that differences between HMO and AMP groups were found in the Fusobacterium and Trueperella species. Fusobacterium and Trueperella were the main pathogenic bacteria responsible for the occurrence of abscess diseases in forest musk deer in this study. Furthermore, the appearance of Fusobacterium and Trueperella in the oral cavity can serve as biomarkers for the early diagnosis of abscess disease in musk deer.}, }
@article {pmid40280794, year = {2025}, author = {Ruppé, E and Lazarevic, V and Schrenzel, J}, title = {9th International Conference on Clinical Metagenomics (ICCMg9): meeting report.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.03.012}, pmid = {40280794}, issn = {1878-4380}, }
@article {pmid40280386, year = {2025}, author = {An, X and Zhao, R and Wang, L and Xiao, X and Xu, Z and Zhang, S and Xie, D and Xiao, Y and Zhang, Q}, title = {Thiocyanate degradation by mixed bacterial consortia: Adaptive mechanism in response to thiocyanate stress and metabolic pathway.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121688}, doi = {10.1016/j.envres.2025.121688}, pmid = {40280386}, issn = {1096-0953}, abstract = {Thiocyanate, frequently detected in various industrial wastewater, poses significant risks to organisms. The activated sludge isolate thiocyanate-degrading bacterial consortia (TDBC) efficiently metabolizes thiocyanate. However, the adaptive mechanism in response to thiocyanate stress and metabolic pathway by TDBC have not been elucidated. Metagenomic analysis showed that Thiobacillus (77.73 %) were the primary degraders for the efficient degradation of thiocyanate. A total of 27 genes related to thiocyanate biodegradation were identified, including SCNase, COSase, sulfur oxidation, denitrification and carbon fixation. Metaproteomic revealed the high expression of chemotaxis protein and thioredoxin enhances cellular oxidative stress and maintains normal physiological metabolism. Additionally, the differentially expressed proteins were primarily involved in metabolic pathways including sphingolipid metabolism, energy metabolism, oxidative phosphorylation, two-component system and amino acid metabolism. Then the lipid, organic acid and amino acid metabolism were up-regulated by metabolomic analysis, thereby achieving the degradation of thiocyanate. Using a combination of qRT-PCR and parallel reaction monitoring (PRM), 27 key genes involved in thiocyanate biodegradation have been identified, providing a theoretical basis for developing microbial strategies to mitigate thiocyanate pollution. Molecular docking deepens the understanding of the interaction between degrading enzyme and thiocyanate. This study provides a theoretical basis for the microbial remediation of thiocyanate-containing wastewater.}, }
@article {pmid40280272, year = {2025}, author = {Bačnik, K and Kranjc, L and Botella, L and Maguire, I and Pavić, D and Patoka, J and Dragičević, P and Bláha, M and Bielen, A and Kouba, A and Kutnjak, D and Hudina, S}, title = {Crayfish pet trade as a pathway for the introduction of known and novel viruses.}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108345}, doi = {10.1016/j.jip.2025.108345}, pmid = {40280272}, issn = {1096-0805}, abstract = {Expanding international pet trade has emerged as one of the main introduction pathways of aquatic invasive species, with ornamental crayfish species commonly available on the EU and global markets. Besides most frequently studied crayfish pathogens, such as Aphanomyces astaci and white spot syndrome virus (WSSV), ornamental crayfish carry associated microbial communities, which may potentially lead to the emergence of known or even novel diseases following intentional or unintentional release of animals into the wild. This is especially problematic in the case of viruses, which represent an important, yet considerably understudied, group of crayfish pathogens. Here we analyzed viromes of hepatopancreas tissue of four crayfish species acquired in the international pet trade in Europe (Procambarus clarkii, Procambarus alleni, Cherax holthuisi, and Cherax quadricarinatus) using a high throughput sequencing based metagenomic approach. Seven different known viruses were identified, which were previously either directly associated with crayfish (WSSV, Cherax quadricarinatus reovirus, chequa iflavirus, athtab bunya-like virus) or with hosts from subphylum Crustacea or invertebrates associated with freshwater environment (Shahe ispoda virus 5, Dicistroviridae sp.). Additional sequences represented 8 potential novel and divergent RNA viruses, most similar to sequences belonging to members of Picornavirales, Elliovirales, Reovirales, Hepelivirales, Tolivirales and Ghabrivirales orders. We discuss our findings in relation to their phylogenetic relationships, geographical origins, and putative pathogenicity implications. The results highlight the need for further research into the risks related to disease emergence associated with the pet trade.}, }
@article {pmid40280009, year = {2025}, author = {Gao, FZ and Hu, LX and Liu, YS and Yang, HY and He, LY and Bai, H and Liu, F and Jin, XW and Ying, GG}, title = {Unveiling the prevalence of metal resistance genes and their associations with antibiotic resistance genes in heavy metal-contaminated rivers.}, journal = {Water research}, volume = {281}, number = {}, pages = {123699}, doi = {10.1016/j.watres.2025.123699}, pmid = {40280009}, issn = {1879-2448}, abstract = {Heavy metals can drive antibiotic resistance through co-selection mechanisms. Current knowledge predominantly focuses on relationships between metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) at the river reach scale. It remains unclear the links between MRGs and ARGs at the large river basin scale, as does the role of MRG-ARG colocalization in resistance dissemination. This study employed metagenomics to investigate the prevalence of MRGs in the Xiangjiang River, a historically heavy metal-contaminated river, and their connections with ARGs by combining resistome profiling with colocalization analyses. Results revealed the significant prevalence of MRGs in the river compared to nationwide rivers, but it showed weak correlations with metal concentrations in either water or sediment. The prevalence of MRGs in water was weakly driven by abiotic parameters, but was strongly influenced by microbial composition. The proportion of water MRGs attributable to sewage sources was tightly positively correlated with MRG abundances, suggesting the significant contribution of external waste input. Plasmid-originated MRGs were more abundant in water, while chromosomal MRGs dominated in sediment, indicating medium-specific transfer dynamics. The profile of MRGs were strongly correlated with that of ARGs in both media, encompassing several clinically high-risk ARGs. However, MRG-ARG colocalization events were rarely detected (eight instances in total), consistent with low frequencies in nationwide rivers (3.5 % in sediment; 2.0 % in water), implying their limited roles in resistance dissemination. Overall, the findings enhance our understanding of riverine metal resistome and its associations with antibiotic resistome, while emphasize the rare presence of MRG-ARG colocalization in riverine environments.}, }
@article {pmid40280002, year = {2025}, author = {Liu, X and Yang, Y and Graham, NJD and Takizawa, S and Ng, HY}, title = {Deciphering membrane biofouling induced by micro-/nano-plastics in nanofiltration: Metagenomic insights and spacer-driven mitigations.}, journal = {Water research}, volume = {281}, number = {}, pages = {123682}, doi = {10.1016/j.watres.2025.123682}, pmid = {40280002}, issn = {1879-2448}, abstract = {Nanofiltration (NF) is an effective process for micro-/nano-plastics (MNPs) interception, but the impact of accumulated MNPs on the microbial community structure and metabolic pathways of biofilms on NF membranes remains unclear. This provides uncertainty with respect to membrane biofouling behavior and the risks to efficient NF operations. In this study, the size-dependent (20 nm-25 μm) and concentration-dependent (0.1-50 mg·L[-1]) effects of MNPs on the biofouling of a NF membrane treating secondary wastewater effluent were studied. Three MNPs-tolerant, hypermetabolic and polystyrene-degradable genera (i.e., Acinetobacter, Novosphingobium and Asticcacaulis) were detected in biofilms as dominant taxonomic compositions. MNPs led to an increase of 19.3 %-76.7 % in biomass contents and a more rapid decrease in permeate flux, with 0.1 mg·L[-1] of 80 nm NPs causing the most severe membrane biofouling. Metagenomic analysis revealed that MNPs upregulated enzymes involved in exopolysaccharide (ExoA/L/M/P/Q/X/Y/Z) and tyrosine (COMT, FeaB and AOC3) biosynthesis and quorum sensing (PhzF and CiaH/R), and suppressed cell motility pathways including flagellar assembly and bacterial chemotaxis. Novel types of perforated column spacer (PCS) enhanced the hydrodynamics of the membrane feed with a lower pressure drop and higher fluid velocity, introduced micro-jets and greater mass transfer inside feed channels, thus eliminating the deposition of MNPs and mitigating membrane biofouling. Overall, a greater understanding of the interaction mechanisms between MNPs and membrane biofouling in secondary effluent filtration will help develop more effective MNPs management strategies and achieve more sustainable NF operations.}, }
@article {pmid40279015, year = {2025}, author = {Han, X and Ma, P and Liu, C and Yao, C and Yi, Y and Du, Z and Liu, P and Zhang, M and Xu, J and Meng, X and Liu, Z and Wang, W and Ren, R and Xie, L and Han, X and Xiao, K}, title = {Pathogenic profiles and lower respiratory tract microbiota in severe pneumonia patients using metagenomic next-generation sequencing.}, journal = {Advanced biotechnology}, volume = {3}, number = {2}, pages = {13}, pmid = {40279015}, issn = {2948-2801}, support = {82100096//National Science Foundation/ ; }, abstract = {INTRODUCTION: The homeostatic balance of the lung microbiota is important for the maintenance of normal physiological function of the lung, but its role in pathological processes such as severe pneumonia is poorly understood.<br><br>METHODS: We screened 34 patients with community-acquired pneumonia (CAP) and 12 patients with hospital-acquired pneumonia (HAP), all of whom were admitted to the respiratory intensive care unit. Clinical samples, including bronchoalveolar lavage fluid (BALF), sputum, peripheral blood, and tissue specimens, were collected along with traditional microbiological test results, routine clinical test data, and clinical treatment information. The pathogenic spectrum of lower respiratory tract pathogens in critically ill respiratory patients was characterized through metagenomic next-generation sequencing (mNGS). Additionally, we analyzed the composition of the commensal microbiota and its correlation with clinical characteristics.<br><br>RESULTS: The sensitivity of the mNGS test for pathogens was 92.2% and the specificity 71.4% compared with the clinical diagnosis of the patients. Using mNGS, we detected more fungi and viruses in the lower respiratory tract of CAP-onset severe pneumonia patients, whereas bacterial species were predominant in HAP-onset patients. On the other hand, using mNGS data, commensal microorganisms such as Fusobacterium yohimbe were observed in the lower respiratory tract of patients with HAP rather than those with CAP, and most of these commensal microorganisms were associated with hospitalization or the staying time in ICU, and were significantly and positively correlated with the total length of stay.<br><br>CONCLUSION: mNGS can be used to effectively identify pathogenic pathogens or lower respiratory microbiome associated with pulmonary infectious diseases, playing a crucial role in the early and accurate diagnosis of these conditions. Based on the findings of this study, it is possible that a novel set of biomarkers and predictive models could be developed in the future to efficiently identify the cause and prognosis of patients with severe pneumonia.}, }
@article {pmid40278577, year = {2025}, author = {Yang, Z and Zhang, Y and Ran, S and Zhang, J and Tian, F and Shi, H and Wei, S and Li, X and Li, X and Gao, Y and Jia, G and Lin, H and Chen, Z and Zhang, Z}, title = {A Multi-Omics Study of Neurodamage Induced by Growth-Stage Real-Time Air Pollution Exposure in Mice via the Microbiome-Gut-Brain Axis.}, journal = {Toxics}, volume = {13}, number = {4}, pages = {}, pmid = {40278577}, issn = {2305-6304}, support = {82203988//National Natural Science Foundation of China/ ; 2022A1515010695//Guangdong Basic and Applied Basic Research Foundation/ ; 2024A1515010465//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A04J2071//Science and Technology Program of Guangzhou/ ; 23qnpy107//the Fundamental Research Funds for the Central Universities of Sun Yat-sen University/ ; }, abstract = {Air pollution has been widely recognized as a risk factor for neurological disorders, and the gut microbiome may play a mediating role. However, current evidence remains limited. In this study, a mouse model was employed with continuous exposure to real-time air pollution from conception to late adolescence. Effects of growth-stage air pollution exposure on the gut microbiome, host metabolites, and brain tissue were assessed. Pathological damage in the hippocampus and cortex was observed. Fecal metagenomic sequencing revealed alterations in both compositions and functions of the gut microbiome. Metabolic disturbances in unsaturated fatty acids and glycerophospholipids were identified in the intestine, serum, and brain tissues, with significant changes in metabolites (e.g., gamma-linolenic acid, alpha-linolenic acid, docosahexaenoic acid (DHA), phosphatidylethanolamine (PE), phosphatidylcholine (PC) and phosphatidylserine (PS). Serum levels of the pro-inflammatory mediator leukotriene C4 were also elevated. Correlation analysis identified a group of different gut microbiome species that were associated with host metabolites. Furthermore, mediation analysis showed that intestinal and serum metabolites mediated the associations between the key gut microbiome and brain microbiome. These findings indicate that the metabolic crosstalk in the gut-brain axis mediates the neuronal damage in mice induced by growth-stage air pollution exposure, potentially through pathways involving lipid metabolism and inflammation.}, }
@article {pmid40278377, year = {2025}, author = {Xiong, S}, title = {Gut-Microbiota-Driven Lipid Metabolism: Mechanisms and Applications in Swine Production.}, journal = {Metabolites}, volume = {15}, number = {4}, pages = {}, pmid = {40278377}, issn = {2218-1989}, support = {32272831//National Natural Science Foundation of China/ ; }, abstract = {Background/Objectives: The gut microbiota plays a pivotal role in host physiology through metabolite production, with lipids serving as essential biomolecules for cellular structure, metabolism, and signaling. This review aims to elucidate the interactions between gut microbiota and lipid metabolism and their implications for enhancing swine production. Methods: We systematically analyzed current literature on microbial lipid metabolism, focusing on mechanistic studies on microbiota-lipid interactions, key regulatory pathways in microbial lipid metabolism, and multi-omics evidence (metagenomic/metabolomic) from swine models. Results: This review outlines the structural and functional roles of lipids in bacterial membranes and examines the influence of gut microbiota on the metabolism of key lipid classes, including cholesterol, bile acids, choline, sphingolipids, and fatty acids. Additionally, we explore the potential applications of microbial lipid metabolism in enhancing swine production performance. Conclusions: Our analysis establishes a scientific framework for microbiota-based strategies to optimize lipid metabolism. The findings highlight potential interventions to improve livestock productivity through targeted manipulation of gut microbial communities.}, }
@article {pmid40278299, year = {2025}, author = {Wu, K and Xu, G and Tian, Y and Li, G and Yi, Z and Tang, X}, title = {Synthesis and Evaluation of Aquatic Antimicrobial Peptides Derived from Marine Metagenomes Using a High-Throughput Screening Approach.}, journal = {Marine drugs}, volume = {23}, number = {4}, pages = {}, pmid = {40278299}, issn = {1660-3397}, support = {2021J02015//Fujian Provincial Natural Science Foundation of China/ ; 23CZB005HJ08//Xiamen Southern Oceanographic Center/ ; K240301(1)//Xiamen Ocean Research and Development Institute/ ; }, mesh = {Animals ; High-Throughput Screening Assays/methods ; *Antimicrobial Peptides/pharmacology/chemical synthesis/chemistry ; *Metagenome ; Penaeidae ; *Anti-Bacterial Agents/pharmacology/chemistry ; Aquaculture ; Aquatic Organisms ; Microbial Sensitivity Tests ; *Antimicrobial Cationic Peptides/pharmacology ; Machine Learning ; }, abstract = {Bacterial diseases cause high mortality and considerable losses in aquaculture. The rapid expansion of intensive aquaculture has further increased the risk of large-scale outbreaks. However, the emergence of drug-resistant bacteria, food safety concerns, and environmental regulations have severely limited the availability of antimicrobial. Compared to traditional antibiotics, antimicrobial peptides (AMPs) offer broad spectrum activity, physicochemical stability, and lower resistance development. However, their low natural yield and high extraction costs along with the time-consuming and expensive nature of traditional drug discovery, pose a challenge. In this study, we applied a machine-learning macro-model to predict AMPs from three macrogenomes in the water column of South American white shrimp aquaculture ponds. The AMP content per megabase in the traditional earthen pond (TC1) was 1.8 times higher than in the biofloc pond (ZA1) and 63% higher than in the elevated pond (ZP11). A total of 1033 potential AMPs were predicted, including 6 anionic linear peptides, 616 cationic linear peptides, and 411 cationic cysteine-containing peptides. After screening based on structural, and physio-chemical properties, we selected 10 candidate peptides. Using a rapid high-throughput cell-free protein expression system, we identified nine peptides with antimicrobial activity against aquatic pathogens. Three were further validated through chemical synthesis. The three antimicrobial peptides (K-5, K-58, K-61) showed some inhibitory effects on all four pathogenic bacteria. The MIC of K-5 against Vibrio alginolyticus was 25 μM, the cell viability of the three peptides was higher than 70% at low concentrations (≤12.5 μM), and the hemolysis rate of K-5 and K-58 was lower than 5% at 200 μM. This study highlights the benefits of machine learning in AMP discovery, demonstrates the potential of cell-free protein synthesis systems for peptide screening, and provides an efficient method for high-throughput AMP identification for aquatic applications.}, }
@article {pmid40278100, year = {2025}, author = {El Jaddaoui, I and Sehli, S and Al Idrissi, N and Bakri, Y and Belyamani, L and Ghazal, H}, title = {The Gut Mycobiome for Precision Medicine.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {4}, pages = {}, pmid = {40278100}, issn = {2309-608X}, abstract = {The human gastrointestinal tract harbors a vast array of microorganisms, which play essential roles in maintaining metabolic balance and immune function. While bacteria dominate the gut microbiome, fungi represent a much smaller, often overlooked fraction. Despite their relatively low abundance, fungi may significantly influence both health and disease. Advances in next-generation sequencing, metagenomics, metatranscriptomics, metaproteomics, metabolomics, and computational biology have provided novel opportunities to study the gut mycobiome, shedding light on its composition, functional genes, and metabolite interactions. Emerging evidence links fungal dysbiosis to various diseases, including inflammatory bowel disease, colorectal cancer, metabolic disorders, and neurological conditions. The gut mycobiome also presents a promising avenue for precision medicine, particularly in biomarker discovery, disease diagnostics, and targeted therapeutics. Nonetheless, significant challenges remain in effectively integrating gut mycobiome knowledge into clinical practice. This review examines gut fungal microbiota, highlighting analytical methods, associations with human diseases, and its potential role in precision medicine. It also discusses pathways for clinical translation, particularly in diagnosis and treatment, while addressing key barriers to implementation.}, }
@article {pmid40278085, year = {2025}, author = {Guo, MC and Wu, BC and Luo, CY and Sa, W and Wang, L and Li, ZH and Shang, QH}, title = {The Effects of Fungal Pathogen Infestation on Soil Microbial Communities for Morchella sextelata Cultivation on the Qinghai-Xizang Plateau.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/jof11040264}, pmid = {40278085}, issn = {2309-608X}, support = {2023-NK-134//Key R &amp; D and Transformation Projects of Science and Technology Department of Qinghai Province/ ; }, abstract = {Fungi infestation as a disease has serious impacts on the cultivation of Morchella species. To investigate the effects of fungi infestation on the microbial diversity and community structure of soil when cultivating Morchella sextelata, we sampled soil samples of Morchella cultivars in the Qinghai-Xizang Platea and used metagenome sequencing technology to identify the disease fungi and analyze the differences in microbial diversity and structure between disease-infested and healthy soils. The disease fungi identified were Tricharina gilva and Peziza lohjaoensis, and the microbial diversity of T. gilva-infected soil was higher than that of healthy soil, while the diversity of P. lohjaoensis-infected soil was lower. Interestingly, whether infected with T. gilva or P. lohjaoensis, the soil microbial community was changed, and the dominant phyla and genera were different in different soil samples. When infected with P. lohjaoensis, the dominant phyla with relatively high abundances included Proteobacteria, Bacteroidetes, and Ascomycota, with average relative abundances of 44%, 18%, and 15%, respectively, and the dominant genera with high relative abundances encompassed Pseudomonadaceae, Terfezia, and Pedobacter, with average relative abundances of 8%, 9%, and 5%, respectively. Following infection with T. gilva, the dominant phyla with higher relative abundances were Proteobacteria, Acidobacteria, and Bacteroidetes, with average relative abundances of 46%, 15%, and 12%, respectively, and the dominant genera with high relative abundances included Hydrogenophaga, Sphingomonas, and Polaromonas, with average relative abundances of 9%, 3%, and 2%, respectively. Additionally, we found that lipid-metabolism-related genes were less abundant in the soil infected with P. lohjaoensis than in the other soil samples, and glycoside hydrolase diversity was lower in the soil infected with T. gilva than in other healthy soils. The results showed that the effects of different disease fungi on soil microbial communities and functional genes were different, which provided a theoretical basis for the sustainable cultivation of Morchella.}, }
@article {pmid40278081, year = {2025}, author = {Wicaksono, S and Ngokwe, ZB and McCullough, M and Yap, T}, title = {The Role of Oral Yeasts in the Development and Progression of Oral Squamous Cell Carcinoma: A Scoping Review.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/jof11040260}, pmid = {40278081}, issn = {2309-608X}, support = {202403220801271//Lembaga Pengelola Dana Pendidikan/ ; }, abstract = {The role of oral yeasts in oral squamous cell carcinoma (OSCC) has gained attention due to evidence linking fungal dysbiosis to carcinogenesis. While Candida albicans has been the primary focus, emerging studies highlight the importance of non-Candida species yeast genera. This scoping review synthesises the evidence on the role of oral yeasts, including Candida spp. and non-Candida species, in the development and progression of OSCC. A PRISMA-ScR-guided search was conducted in Medline, Embase, EBM Reviews, and CINAHL. Observational and experimental studies involving humans with OSCC, oral potentially malignant disorders (OPMDs), or oral epithelial dysplasia (OED) were included. This review analysed 75 studies. Research on oral yeast in OSCC has progressed since the 1970s, with advancements in identification techniques-from conventional culture methods to metagenomic sequencing and multi-omics approaches-alongside improved animal and cellular models of OSCC. These methodological advancements have identified notable distinctions in the oral mycobiome between carcinomatous and healthy states. Clinical findings reinforce the hypothesis that oral yeasts, particularly Candida spp., actively contribute to the dysplasia-carcinoma sequence. Emerging evidence suggests that oral yeasts may significantly modulate events contributing to OSCC progression. However, further mechanistic studies and robust clinical evidence are essential to establish causality and clarify their role in OSCC.}, }
@article {pmid40278065, year = {2025}, author = {Li, XZ and Li, YL and Zhu, JS}, title = {Three-Dimensional Structural Heteromorphs of Mating-Type Proteins in Hirsutella sinensis and the Natural Cordyceps sinensis Insect-Fungal Complex.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {4}, pages = {}, doi = {10.3390/jof11040244}, pmid = {40278065}, issn = {2309-608X}, support = {2021-SF-A4//the Major Science and Technology Projects of Qinghai Province, China/ ; LHZX-2022-01//the Joint Science Project of the Chinese Academy of Sciences, Qinghai Provincial Government, and Sanjiangyuan National Park/ ; QHCY-2023-057//Qinghai Province of China/ ; 2024-NK-P67//Qinghai Province Science and Technology Commissioner Special Project/ ; }, abstract = {The MAT1-1-1 and MAT1-2-1 proteins are essential for the sexual reproduction of Ophiocordyceps sinensis. Although Hirsutella sinensis has been postulated to be the sole anamorph of O. sinensis and to undergo self-fertilization under homothallism or pseudohomothallism, little is known about the three-dimensional (3D) structures of the mating proteins in the natural Cordyceps sinensis insect-fungal complex, which is a valuable therapeutic agent in traditional Chinese medicine. However, the alternative splicing and differential occurrence and translation of the MAT1-1-1 and MAT1-2-1 genes have been revealed in H. sinensis, negating the self-fertilization hypothesis but rather suggesting the occurrence of self-sterility under heterothallic or hybrid outcrossing. In this study, the MAT1-1-1 and MAT1-2-1 proteins in 173 H. sinensis strains and wild-type C. sinensis isolates were clustered into six and five clades in the Bayesian clustering trees and belonged to 24 and 21 diverse AlphaFold-predicted 3D structural morphs, respectively. Over three-quarters of the strains/isolates contained either MAT1-1-1 or MAT1-2-1 proteins but not both. The diversity of the heteromorphic 3D structures of the mating proteins suggested functional alterations of the proteins and provided additional evidence supporting the self-sterility hypothesis under heterothallism and hybridization for H. sinensis, Genotype #1 of the 17 genome-independent O. sinensis genotypes. The heteromorphic stereostructures and mutations of the MAT1-1-1 and MAT1-2-1 proteins in the wild-type C. sinensis isolates and natural C. sinensis insect-fungi complex suggest that there are various sources of the mating proteins produced by two or more cooccurring heterospecific fungal species in natural C. sinensis that have been discovered in mycobiotic, molecular, metagenomic, and metatranscriptomic studies, which may inspire future studies on the biochemistry of mating and pheromone receptor proteins and the reproductive physiology of O. sinensis.}, }
@article {pmid40277368, year = {2025}, author = {Martins, DT and Alegria, OVC and Dantas, CWD and De Los Santos, EFF and Pontes, PRM and Cavalcante, RBL and Ramos, RTJ}, title = {CrAssphage distribution analysis in an Amazonian river based on metagenomic sequencing data and georeferencing.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0147024}, doi = {10.1128/aem.01470-24}, pmid = {40277368}, issn = {1098-5336}, abstract = {UNLABELLED: Viruses are the most abundant biological entities in all ecosystems of the world. Their ubiquity makes them suitable candidates for indicating fecal contamination in rivers. Recently, a group of Bacteroidetes bacteriophages named CrAssphages, which are highly abundant, sensitive, and specific to human feces, were studied as potential viral biomarkers for human fecal pollution in water bodies. In this study, we evaluated the presence, diversity, and abundance of viruses with a focus on crAssphages via metagenomic analysis in an Amazonian river and conducted correlation analyses on the basis of physicochemical and georeferencing data. Several significant differences in viral alpha diversity indexes were observed among the sample points, suggesting an accumulation of viral organisms in the river mouth, whereas beta diversity analysis revealed a significant divergence between replicates of the most downstream point (IT4) when compared to the rest of the samples, possibly due to increased human impact at this point. In terms of the presence of crAssphage, the analysis identified 61 crAssphage contigs distributed along the Itacaiúnas River. Moreover, our analysis revealed significant correlations between 19 crAssphage contigs and human population density, substantiating the use of these viruses as possible markers for human fecal pollution in the Itacaiúnas River. This study is the first to assess the presence of crAssphages in an Amazonian river, with results suggesting the potential use of these viruses as markers for human fecal pollution in the Amazon.<br><br>IMPORTANCE: The Amazon biome is one of the most diverse ecosystems in the world and contains the most vast river network; however, the continuous advance of urban centers toward aquatic bodies exacerbates the discharge of pollutants into these water bodies. Fecal contamination contributes significantly to water pollution, and the application of an improved fecal indicator is essential for evaluating water quality. In this study, we evaluated the presence, diversity, and abundance of crAssphages in an Amazonian river and performed correlation analysis on the basis of physicochemical and georeferencing data to test whether crAssphages are viable fecal pollution markers. Our analysis revealed both the presence of crAssphages and their correlation with physicochemical data and showed significant correlations between the relative abundance of crAssphages and human density. These results suggest the potential use of these viruses as markers for water quality assessment in Amazonian rivers.}, }
@article {pmid40276513, year = {2025}, author = {Xu, X and Li, Y and Huang, X}, title = {Case Report: A rare case of community-acquired Roseomonas mucosa sepsis that presented with persistently normal host-response biomarkers.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1521161}, pmid = {40276513}, issn = {1664-3224}, mesh = {Humans ; Female ; Middle Aged ; Biomarkers/blood ; *Gram-Negative Bacterial Infections/diagnosis/microbiology/drug therapy ; *Community-Acquired Infections/microbiology/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Methylobacteriaceae ; *Sepsis/microbiology/diagnosis/drug therapy ; Meropenem/therapeutic use ; }, abstract = {Community-acquired Roseomonas mucosa sepsis can lead to significant morbidity and mortality if not diagnosed promptly. We report a case of a 59-year-old woman with community-acquired Roseomonas mucosa sepsis who presented with persistent fever progressing to septic shock, despite repeatedly negative host-response biomarker results. Initial metagenomic analysis of peripheral blood suggested Pseudomonas aeruginosa infection. However, a peripheral blood culture identified Roseomonas mucosa as the causative pathogen. She was cured after switching to meropenem according to blood cultures and antimicrobial susceptibility testing.}, }
@article {pmid40276369, year = {2025}, author = {Boshuizen, B and De Maré, L and Oosterlinck, M and Van Immerseel, F and Eeckhaut, V and De Meeus, C and Devisscher, L and Vidal Moreno de Vega, C and Willems, M and De Oliveira, JE and Hosotani, G and Gansemans, Y and Meese, T and Van Nieuwerburgh, F and Deforce, D and Vanderperren, K and Verdegaal, EL and Delesalle, C}, title = {Aleurone supplementation enhances the metabolic benefits of training in Standardbred mares: impacts on glucose-insulin dynamics and gut microbiome composition.}, journal = {Frontiers in physiology}, volume = {16}, number = {}, pages = {1565005}, pmid = {40276369}, issn = {1664-042X}, abstract = {INTRODUCTION: Aleurone, derived from the bran layer of grains like wheat and barley, has demonstrated positive effects on energy metabolism in pigs, mice, and untrained horses, influencing glucose-insulin dynamics and gut microbiome composition. Training itself enhances insulin sensitivity in horses, similar to the improvements in performance capacity observed in human athletes. This study aimed to investigate whether aleurone supplementation provides additional benefits to training by modulating insulin metabolism and gut microbiota in Standardbred mares.<br><br>METHODS: Sixteen Standardbred mares (aged 3-5 years) participated in a cross-over study with two 8-week training periods separated by 8 weeks of detraining. Each horse received either 200 g/day aleurone supplementation or a control diet. Insulin metabolism was evaluated using oral (OGTT) and intravenous (FSIGTT) glucose tolerance tests, measuring parameters such as Maximumglucose, AUCglucose, Maximuminsulin, AUCinsulin, Time to peakinsulin (OGTT), Acute Insulin Response to Glucose (AIRg), glucose effectiveness (Sg), and disposition index (DI) (FSIGTT). Fecal samples underwent metagenomic analysis to assess alpha and beta diversity and microbial composition.<br><br>RESULTS: Training alone: Training significantly improved OGTT parameters by decreasing Maximuminsulin (P = 0.005) and AUCinsulin (P = 0.001), while increasing Time to peakinsulin (P = 0.03), indicating enhanced insulin sensitivity. FSIGTT results also showed a decrease in logAIRg (P = 0.044). Training with Aleurone: Aleurone supplementation further reduced FSIGTT AIRg (P = 0.030), logAIRg (P = 0.021) while increasing glucose effectiveness (Sg; P = 0.031). These findings suggest aleurone improves insulin sensitivity, glucose disposal, and fasting glucose regulation beyond training. Microbiome analysis revealed training decreased Pseudomonas, associated with dysbiosis, while aleurone reduced inflammation-associated Desulfovibrio. Beta diversity metrics showed no significant changes.<br><br>CONCLUSION: Aleurone supplementation enhances training-induced improvements in glucose metabolism and fecal microbiota composition, which could offer potential benefits for equine athletes by optimizing metabolic flexibility. It also supports improvements in glucose and insulin dynamics, particularly by further enhancing insulin sensitivity and glucose-mediated disposal. Future studies should investigate the mechanisms of aleurone at the muscle and gut level and explore its potential applications for metabolic disorders such as Equine Metabolic Syndrome.}, }
@article {pmid40275546, year = {2025}, author = {Jungpraditphol, I and Sutthiboonyapan, P and Khamwachirapitak, C and Krasaesin, A and Srithanyarat, S and Porntaveetus, T and Wiriyakijja, P}, title = {Shotgun Metagenomics of Biofilm Microbiome in Oral Lichen Planus With Desquamative Gingivitis.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.15349}, pmid = {40275546}, issn = {1601-0825}, support = {68-032,68-059//Health Systems Research Institute/ ; HEA_FF_68_008_3200_001,HEA_FF_68_223_3200_015//Thailand Science Research and Innovation Chulalongkorn University/ ; DRF68_007//Faculty of Dentistry, Chulalongkorn University/ ; }, abstract = {INTRODUCTION: Oral lichen planus (OLP) is a chronic inflammatory condition often associated with desquamative gingivitis (DG). The oral microbiome's role in OLP and DG (OLP-DG) is gaining recognition, but prior 16S rRNA studies lacked taxonomic resolution. This study introduced shotgun metagenomic sequencing to thoroughly compare the supragingival and subgingival plaque microbiomes of individuals with and without OLP-DG.<br><br>METHODS: Twenty-seven participants (9 OLP-DG, 18 non-OLP) were recruited. Supra- and subgingival plaque samples were collected separately. Genomic DNA was analyzed using shotgun metagenomic sequencing. Microbial abundance and diversity were assessed through bioinformatic and statistical analyses.<br><br>RESULTS: We observed significant changes in the supragingival and subgingival microbiomes in OLP-DG. Supragingival plaque showed reduced Corynebacteriaceae and Porphyromonadaceae, with enrichment of an unnamed Synergistaceae genus and three unnamed species (Candidatus Saccharibacteria bacterium oral taxon 955 and 488 and GGB10852_SGB17523). Subgingival plaque revealed increased Flavobacteriaceae and Rhodocyclaceae, and reduced Actinomycetaceae. Although alpha or beta diversity was not significantly different, common commensals like Corynebacterium matruchotii and Streptococcus mitis were less abundant in OLP-DG patients.<br><br>CONCLUSION: This first-time application of metagenomic sequencing revealed a distinct microbiome in OLP-DG, characterized by novel bacterial species and reduced commensals, suggesting a potential role in OLP-DG pathogenesis, and warranting further study.}, }
@article {pmid40275408, year = {2025}, author = {Pérez-Carrascal, OM and Pratama, AA and Sullivan, MB and Küsel, K}, title = {Unveiling plasmid diversity and functionality in pristine groundwater.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {42}, pmid = {40275408}, issn = {2524-6372}, abstract = {BACKGROUND: Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).<br><br>RESULTS: Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater.<br><br>CONCLUSIONS: Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.}, }
@article {pmid40275402, year = {2025}, author = {Maaskant, A and Lee, D and Ngo, H and Montijn, RC and Bakker, J and Langermans, JAM and Levin, E}, title = {AI for rapid identification of major butyrate-producing bacteria in rhesus macaques (Macaca mulatta).}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {39}, pmid = {40275402}, issn = {2524-4671}, abstract = {BACKGROUND: The gut microbiome plays a crucial role in health and disease, influencing digestion, metabolism, and immune function. Traditional microbiome analysis methods are often expensive, time-consuming, and require specialized expertise, limiting their practical application in clinical settings. Evolving artificial intelligence (AI) technologies present opportunities for developing alternative methods. However, the lack of transparency in these technologies limits the ability of clinicians to incorporate AI-driven diagnostic tools into their healthcare systems. The aim of this study was to investigate an AI approach that rapidly predicts different bacterial genera and bacterial groups, specifically butyrate producers, from digital images of fecal smears of rhesus macaques (Macaca mulatta). In addition, to improve transparency, we employed explainability analysis to uncover the image features influencing the model's predictions.<br><br>RESULTS: By integrating fecal image data with corresponding metagenomic sequencing information, the deep learning (DL) and machine learning (ML) algorithms successfully predicted 16 individual bacterial genera (area under the curve (AUC)&#x2009;>&#x2009;0.7) among the 50 most abundant genera in rhesus macaques (Macaca mulatta). The model was successful in predicting functional groups, major butyrate producers (AUC 0.75) and a mixed group including fermenters and short-chain fatty acid (SCFA) producers (AUC 0.81). For both models of butyrate producers and mixed fermenters, the explainability experiments revealed no decline in the AUC when random noise was added to the images. Increased blurring led to a gradual decline in the AUC. The model's performance was robust against the impact of fecal shape from smearing, with a stable AUC maintained until patch 4 for all groups, as assessed through scrambling. No significant correlation was detected between the prediction probabilities and the total fecal weight used in the smear; r&#x2009;=&#x2009;0.30&#x2009;&#xb1;&#x2009;0.3 (p&#x2009;>&#x2009;0.1) and r&#x2009;=&#x2009;0.04&#x2009;&#xb1;&#x2009;0.36 (p&#x2009;>&#x2009;0.8) for the butyrate producers and mixed fermenters, respectively.<br><br>CONCLUSION: Our approach demonstrated the ability to predict a wide range of clinically relevant microbial genera and microbial groups in the gut microbiome based on digital images from a fecal smear. The models proved to be robust to the smearing method, random noise and the amount of fecal matter. This study introduces a rapid, non-invasive, and cost-effective method for microbiome profiling, with potential applications in veterinary diagnostics.}, }
@article {pmid40275259, year = {2025}, author = {He, H and Cai, L and Xue, X and Zhang, K and Huang, Q and Qiu, A and Fan, H and Lin, Y and Xu, B and Pan, W}, title = {Disseminated talaromycosis in HIV-negative patients with lung cancer: a rare case report and literature review.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {601}, pmid = {40275259}, issn = {1471-2334}, support = {2024SSY06041//Jiangxi Key Laboratory of oncology/ ; JDLCZDZK-PWH//the National Natural Science Foundation of China/ ; SHDC22022302//the Clinical Research Plan of SHDC/ ; 2023YJBF-FH03, 2020YCGPZ-102//the Clinical Research Project of Second Affiliated Hospital of Naval Medical University/ ; 2023ZD005//2023 Key Project for Science and Technology Innovation of Jiangxi Provincial Health Commission/ ; 2024DZXYYXK-104//the National Key Research and Development Program of China/ ; }, mesh = {Humans ; Male ; *Lung Neoplasms/complications/microbiology ; Talaromyces/isolation &amp; purification ; Fatal Outcome ; *Mycoses/complications/microbiology/diagnosis/drug therapy ; Middle Aged ; Antifungal Agents/therapeutic use ; *Carcinoma, Squamous Cell/complications ; Tomography, X-Ray Computed ; }, abstract = {BACKGROUND: Talaromycosis has long been considered to be exclusively associated with human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS). In recent years, with effective control measures for HIV, the number of talaromycosis patients without HIV infection has been increasing annually. All of these patients have various immunosuppressive factors, including tumors. However, we find that talaromycosis among HIV-negative lung cancer patients remains a rarity and is without comprehensive reviews, contributing to significant gaps in clinical knowledge.<br><br>CASE PRESENTATION: We report a case of lung squamous cell carcinoma combined with Talaromyces marneffei (T.marneffei) infection in an HIV-negative patient. The patient, a male with a history of long-term smoking, presented with recurrent fever and cough. Chest computed tomography (CT) scans revealed pleural effusion and nodules. The patient was diagnosed with lung squamous cell carcinoma and talaromycosis through sputum cytology and blood/cerebrospinal fluid metagenomics next-generation sequencing (mNGS). The patient underwent only antifungal therapy and succumbed to respiratory failure, liver and kidney failure, and sepsis in January 2024, before receiving any anti-tumor therapy.<br><br>CONCLUSION: The mortality rate of talaromycosis combined with lung cancer is extremely high. Therefore, regardless of whether patients have a history of travel to endemic areas of T. marneffei infection, it is crucial to test for HIV and anti-IFN-&#x3b3; autoantibodies (AIGA) in patients suspected of having a pulmonary fungal infection, as well as conducting multiple cultures of specimens from different sites and utilizing mNGS to enhance diagnostic accuracy. Additionally, it is essential to perform biopsies in various methods from multiple sites to ascertain the presence of lung cancer. With effective control of T. marneffei infection and timely diagnosis and treatment of lung cancer, there can be a significant improvement in patient survival rates.}, }
@article {pmid40274091, year = {2025}, author = {Huo, X and He, M and Qiao, J and Zhao, J and Yang, B}, title = {Regulatory effects of nano-carbon on poplar growth and rhizosphere soil organic carbon accumulation.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121628}, doi = {10.1016/j.envres.2025.121628}, pmid = {40274091}, issn = {1096-0953}, abstract = {The positive effects of nano-carbon on plant growth and soil C sequestration within the rhizosphere have been widely recognized. Nevertheless, information is seriously deficient in understanding the underlying mechanisms based on microbial communities and carbon cycle functional genes. Here, metagenomic sequencing was employed to explore different responses of poplar seedling growth and organic carbon fractions to nano-carbon fertilizers at concentrations of 0 ml/kg (CK), 5 ml/kg (NC-5), 10 ml/kg (NC-10) and 20 ml/kg (NC-20). We observed that, after 120 days of nano-carbon fertilizers treatments, the growth indexes (height and biomass) of poplar were significantly increased by 53-173 %, and C fractions in the rhizosphere soil were significantly increased by 1.6-8.2 % with the NC-5 treatment having a greater impact on organic carbon components than the NC-10 and NC-20 treatments. Compared to CK, the additions of nano-carbon fertilizers significantly increased the content of total nitrogen (TN), nitrate nitrogen (NN), and available potassium (AK) in the rhizosphere soil and decreased the pH, and improved stochastic processes in microbial communities, which elevates the abundance of microbes involved in carbon fixation (e.g., Proteobacteria, Actinobacteria) and carbon-cycling genes. In addition, network complexity and stability of microbes were significantly enhanced by nano-carbon treatments. Structural equation model indicated that microbial community assembly processes directly alter rhizosphere SOC accumulation. Carbon functional genes influenced by microbial structure have positive effects on biomass of poplar and SOC contents. Our observations provide key evidence for evaluating how nano-carbon fertilizers may influence functional changes in C cycle that are mediated by microbial synergy.}, }
@article {pmid40273857, year = {2025}, author = {Yu, H and Zhang, D and Xiong, R and Liu, S and Hu, R and Chen, P and Wu, X and Zou, H and Hu, N and Ding, D and Yan, Q and He, Z}, title = {Soil-dependent responses of bacterial communities, phosphorus and carbon turnover to uranium stress in different soil ecosystems.}, journal = {Journal of hazardous materials}, volume = {493}, number = {}, pages = {138383}, doi = {10.1016/j.jhazmat.2025.138383}, pmid = {40273857}, issn = {1873-3336}, abstract = {Uranium (U) can impact microbially driven soil phosphorus (P) and carbon (C) cycling. However, the response of microbial P and C turnover to U in different soils is not well understood. Through the quantitative assay of P pools and soil organic C (SOC) quantitative assay and sequencing of 16S rRNA gene amplicons and metagenomes, we investigated the effect of U on P and C biotransformation in grassland (GL), paddy soil (PY), forest soil (FT). U (60 mg kg[-1]) impacted the diversity, interaction and stability of soil bacterial communities, leading to a decrease in available P (AP). Under U stress, organophosphate mineralization substantially contributed to the AP in GL and FT, whereas intracellular P metabolism dominated the AP in PY. Also, the reductive citrate cycle (rTCA cycle) promoted the content of SOC in GL, while the rTCA cycle and complex organic C degradation pathways enhanced the SOC in PY and FT, respectively. Notably, functional bacteria carrying organic C degradation genes could decompose SOC to enhance soil AP. Bacteria developed various resistance strategies to cope with U stress. This study reveals soil-dependent response of microbial P and C cycling and its ecological functions under the influence of radioactive contaminants in different soil systems.}, }
@article {pmid40273693, year = {2025}, author = {Yan, X and Xin, Y and Zhu, L and Tang, Q and Chen, M and Wei, Y and Zhang, J and Richnow, HH}, title = {Neglected role of virus-host interactions driving antibiotic resistance genes reduction in an urban river receiving treated wastewater.}, journal = {Water research}, volume = {282}, number = {}, pages = {123627}, doi = {10.1016/j.watres.2025.123627}, pmid = {40273693}, issn = {1879-2448}, abstract = {Treated wastewater from wastewater treatment plants (WWTPs) is a major contributor to the transfer of antibiotic resistance genes (ARGs) into urban rivers. However, the role of viral communities in this process remains poorly understood. This study focused on North Canal in Beijing, China, which receives over 80 % of its water from treated wastewater, to investigate the impact of viral communities on ARGs transfer. Results showed significant seasonal variation in the abundance and composition of ARGs, with 30 high-risk ARGs detected, accounting for 1.50 % ± 1.28 % of total ARGs. The assembly of ARGs in North Canal followed a stochastic process of homogenizing dispersal, with conjugative mobility playing a key role in horizontal gene transfer with Pseudomonas as primary host for HGT. The potential conjugative mobility of ARGs is significantly higher in wet season (69.4 % ± 17.3 %) compared to dry season (42.9 % ± 17.1 %), with conjugation frequencies ranging from 1.18 × 10[-6] to 2.26 × 10[-4]. Viral species accumulation curves approaching saturation indicated the well captured viral diversity, and no phages carrying ARGs were found among 27,523 non-redundant viral operational taxonomic units. Most of the phages (89.2 % ± 3.8 %) were lytic in North Canal, which were observed to contribute to ARGs reduction by lysing their host bacteria, reflected by higher virus-host ratio and demonstrated by the phage lysis assays in treated wastewater and receiving river. We provided compelling evidence that phage-host interactions can reduce ARGs through host lysis, highlighting their potential role in mitigating ARG transmission in urban rivers receiving treated wastewater.}, }
@article {pmid40273602, year = {2025}, author = {Hu, C and Lu, JN and Chen, Z and Tian, L and Yin, Y and Jiang, G and Fei, YH and Tang, YT and Wang, S and Jin, C and Qiu, R and Chao, Y}, title = {Viral diversity and auxiliary metabolic genes in rare earth element mine drainage in South China.}, journal = {Water research}, volume = {281}, number = {}, pages = {123666}, doi = {10.1016/j.watres.2025.123666}, pmid = {40273602}, issn = {1879-2448}, abstract = {In extreme environments, viruses play a crucial role in regulating the structure and metabolic activities of microbial communities, thereby impacting the overall biogeochemical cycles. Previous research found that rare earth element acid mine drainage (REE-AMD) harbors a wide array of microbial species. However, our understanding of the viruses that infect these microorganisms remains limited. In this study, we utilized metagenomic analysis to explore the viral diversity, interactions between viruses and their hosts, as well as the viruses encoded auxiliary metabolic genes (AMGs) within REE-AMD. The results demonstrated that viral communities showed increased diversity with REEs pollution. Furthermore, AMGs exhibited habitat and host specificity. Viruses in water samples contaminated with REEs tended to encode AMGs related to cellular metabolic processes and stress responses to protect their hosts. In contrast, viruses in sediment samples were more likely to encode AMGs associated with nutrient competition, thereby expanding the ecological niches of hosts and viruses. Viruses would carry more AMGs from the dominant prokaryotes. Additionally, under REEs stress, viruses encode a greater number of carbon- and sulfur-related AMGs, influencing the carbon and sulfur cycles of microorganisms in REE-AMD. Overall, our study provides a first systematic characterization of the viral community in REE-AMD, which is crucial for understanding the intricate interactions among viruses, their hosts, and the surrounding environment.}, }
@article {pmid40273394, year = {2025}, author = {Chen, CC and Chiu, JY and Tan, AH and Toh, TS and Lim, SY and Tan, EK and Pettersson, S and Hsu, CC and Liou, JM and Wu, MS and Hsu, CL and Lin, CH}, title = {Investigating Plasma Metabolomics and Gut Microbiota Changes Associated With Parkinson Disease: A Focus on Caffeine Metabolism.}, journal = {Neurology}, volume = {104}, number = {10}, pages = {e213592}, doi = {10.1212/WNL.0000000000213592}, pmid = {40273394}, issn = {1526-632X}, abstract = {BACKGROUND AND OBJECTIVES: Coffee intake is linked to a reduced risk of Parkinson disease (PD), but whether this effect is mediated by gut microbiota and metabolomic changes remains unclear. This study examines PD-associated metabolomic shifts, caffeine metabolism, and their connection to gut microbiome alterations in a multicenter study.<br><br>METHODS: We conducted an untargeted serum metabolomic assay using liquid chromatography with high-resolution mass spectrometry on an exploratory cohort recruited from National Taiwan University Hospital (NTUH). A targeted metabolomic assay focusing on caffeine and its 12 downstream metabolites was conducted and validated in an independent cohort from University Malaya Medical Centre (UMMC). In the exploratory cohort, the association of each caffeine metabolite with gut microbiota changes was investigated by metagenomic shotgun sequencing. A clustering-based approach was used to correlate microbiome changes with plasma caffeine metabolite level and clinical severity. Body mass index, antiparkinsonism medication use, and dietary habits (including coffee and tea intake) were recorded.<br><br>RESULTS: Sixty-three patients with PD and 54 controls from NTUH formed the exploratory cohort while 36 patients with PD and 20 controls from UMMC served as an validation cohort to replicate the plasma caffeine findings. A total of 5,158 metabolites were detected from untargeted metabolomic analysis, with 3,131 having high confidence for analysis. Compared with controls, the abundance of 56 metabolites was significantly higher and that of 7 metabolites was significantly lower (adjusted p < 0.05 and log2 fold change >1) in patients with PD. Caffeine metabolism was significantly lower in patients with PD (p = 0.0013), and serum levels of caffeine and its metabolites negatively correlated with motor severity (p < 0.01). Targeted metabolomic analysis confirmed reduced levels of caffeine and its metabolites, including theophylline, paraxanthine, 1,7-dimethyluric acid, and 5-acetylamino-6-amino-3-methyluracil, in patients with PD; these findings were replicated in the validation cohort (p < 0.05). A clustering approach found that 56 microbiome species enriched in patients with PD negatively correlated with caffeine and its metabolites paraxanthine and theophylline (both p < 0.05), notably Clostridium sp000435655, Acetatifactor sp900066565, Oliverpabstia intestinalis, and Ruminiclostridium siraeum.<br><br>DISCUSSION: This study identifies PD-related changes in microbial-caffeine metabolism compared with controls. Our findings offer insights for future functional research on caffeine-microbiome interactions in PD.}, }
@article {pmid40272442, year = {2025}, author = {Diao, Z and Zhao, Z and Han, Y and Chen, Y and Huang, T and Feng, L and Ma, Y and Li, J and Zhang, R}, title = {A Comprehensive Assessment of Metagenomic cfDNA Sequencing for Microbe Detection.}, journal = {Clinical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/clinchem/hvaf044}, pmid = {40272442}, issn = {1530-8561}, support = {2024-2-40510//Capital's Funds for Health Improvement and Research/ ; 2022YFC2603800//National Key R&amp;D Program of China/ ; }, abstract = {BACKGROUND: Metagenomic cell-free DNA (cfDNA) sequencing provides a new avenue for diagnosing infectious diseases. Owing to the low concentration and highly fragmented nature of microbial cfDNA in plasma, coupled with methodological complexity, ensuring accurate and comparable metagenomic cfDNA sequencing results has proved challenging. This study aims to evaluate the performance of metagenomic cfDNA sequencing for detecting microorganisms in plasma across various laboratories and to examine factors affecting accuracy.<br><br>METHODS: A reference panel consisting of 18 microbial cfDNA communities was designed and used to investigate the performance of metagenomic cfDNA sequencing across 130 laboratories. We comprehensively assessed the accuracy, repeatability, anti-interference, limit of detection (LoD), and linear correlation.<br><br>RESULTS: The results showed that the performance of most laboratories was excellent, with an average F1 score of 0.98. Most contamination in metagenomic cfDNA sequencing originated from "wet labs," as 68.25% (475/696) of the false-positive sequences matched reported microorganisms. The chief cause (74.24%, 49/66) of false-negative errors in metagenomic cfDNA sequencing was from "dry labs." Laboratories showed favorable reproducibility, LoD, and linearity. Interference from elevated human cfDNA concentrations was minimal, whereas interference from genetically similar microorganisms was more pronounced. Overall, viral cfDNA detection showed weaker performance compared to bacterial and fungal detection.<br><br>CONCLUSIONS: This study presented the performance of metagenomic cfDNA sequencing in real-world settings, identifying key factors critical for its development and optimization. These findings provide valuable guidance for accurate pathogen detection in infectious diseases and promote the adoption of metagenomic cfDNA sequencing in diagnostics.}, }
@article {pmid40272326, year = {2025}, author = {Adi, A and Lebrun, S and Kondo, M and Alvarez Villela, M and Fontes, JD}, title = {Culture-Negative Subacute Lactobacillus Endocarditis Diagnosed by Microbial Cell-Free DNA Sequencing.}, journal = {JACC. Case reports}, volume = {}, number = {}, pages = {103505}, doi = {10.1016/j.jaccas.2025.103505}, pmid = {40272326}, issn = {2666-0849}, abstract = {BACKGROUND: Lactobacillus endocarditis is a rare infection generally occurring in patients with heart disease and immunosuppression. Although Lactobacillus is typically a benign part of the gastrointestinal and genitourinary flora, it can cause invasive infections.<br><br>CASE SUMMARY: We present a case of a 74-year-old patient with low-grade fever and a nonproductive cough following recent cardiac surgery. Transesophageal echocardiography revealed vegetations, suggestive of endocarditis, despite negative blood cultures. Due to high suspicion for endocarditis, advanced genetic testing identified Lactobacillus fermentum as the causative pathogen. The patient disclosed daily probiotic use, likely the infection source. Treatment with intravenous ampicillin resulted in significant symptom improvement.<br><br>DISCUSSION: This case underscores the importance of considering probiotics as a potential source of bacteremia in patients with negative cultures after surgery and highlights how metagenomic sequencing can identify pathogens and guide effective therapy in challenging cases.}, }
@article {pmid40272234, year = {2025}, author = {Wang, X and Zhang, J and Yang, B and Mao, H and Yu, Q and Zhang, Y}, title = {Intermittent Microaeration Enhanced Anaerobic Digestion: The Key Role of Fe(III)/Fe(II) Cycle and Reactive Oxygen Species.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c04187}, pmid = {40272234}, issn = {1520-5851}, abstract = {Microaeration has been reported to improve anaerobic digestion, which is generally attributed to increased microbial diversity, but a thorough explanation is lacking. In this study, it was found that intermittent microaeration (IMA) supplied to an anaerobic digester could oxidize Fe(II) produced by dissimilatory iron reduction (DIR) to form a Fe(III)/Fe(II) cycle and generate extracellular reactive oxygen species (ROS) to improve anaerobic treatment of phenol-containing wastewater. The results showed that compared to the control group without IMA, the removal rates of COD and phenol increased by 29.54 and 49.68 percentage points, respectively, and daily average methane production increased by 85.44%. The Fe(III)/Fe(II) cycle slowed down the loss of iron (13.97%) released from sludge due to the lower solubility of Fe(III) and facilitated [•]OH generation (1.22 ± 0.04 μM) via Fenton-like reactions. The DIR and the generation of [•]OH accelerated phenol degradation. Metagenomic analysis revealed that the abundance of methanogens and antioxidant enzymes-encoding genes in response to oxidative stress significantly increased in the IMA group compared to the control, enabling methanogenesis to proceed smoothly under microaeration. This study investigated the extracellular ROS generation induced by microaeration during anaerobic digestion and their roles in promoting anaerobic performance, thereby providing a new perspective for optimizing anaerobic systems with microaeration.}, }
@article {pmid40272147, year = {2025}, author = {Dai, X and Cao, Y and Li, L and Gao, Y-X and Wang, J-X and Liu, Y-J and Ma, T-T and Zheng, J-M and Zhan, P-P and Shen, Z-Y}, title = {Gut microbiome and metabolome profiles in renal allograft rejection from multiomics integration.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0162624}, doi = {10.1128/msystems.01626-24}, pmid = {40272147}, issn = {2379-5077}, abstract = {UNLABELLED: The gut microbiome and metabolome play crucial roles in renal allograft rejection progression. Integrated multiomics analyses may provide a comprehensive understanding of specific underlying mechanisms, which remain elusive. This study aimed to identify new approaches for clinical renal allograft rejection diagnosis and treatment. Thirty-five patients were divided into three groups: the rejection (n = 16), dysfunction (n = 7), and control (n = 12) groups. Metagenomic sequencing and nontargeted metabolomics were used to analyze stool and plasma samples. Significant microbiota, metabolites, and signaling pathways were identified. LASSO regression was used to construct a diagnostic model, and its diagnostic value was assessed via receiver operating characteristic curves. The microbiota composition and the related genes in the rejection group significantly differed from that in the dysfunction and control groups at the phylum, genus, and species levels (P < 0.001). The core species in the rejection group networks were Escherichia coli and Ruminococcus gnavus, while core species in the dysfunction group networks were Faecalibacterium prausnitzii and Bacteroides ovatus. The balance of specific microbial species was associated with kidney function in rejection patients. Spearman analysis revealed that specific differential species like Agathobaculum butyriciproducens and Gemmiger qucibialis were closely linked to the levels of serum 4-pyridoxic acid, 4-acetamidobutanoate, and fecal tryptamine from specific differential pathways. Finally, we constructed four clinical models to distinguish the rejection and dysfunction groups, and the model had excellent diagnostic performance. Altered gut microbiota may contribute to changes in metabolic pathway activity and metabolite abundance in rejection and dysfunction patients, which are strongly correlated with host immunological rejection. The diagnostic model, developed based on the gut microbiota and metabolites, has high clinical value for diagnosing renal rejection.<br><br>IMPORTANCE: This study aimed to screen new markers for non-invasive diagnosis by the gut microbiome and metabolome analysis, providing new insights into rejection mechanisms and identifying new approaches for clinical renal allograft rejection diagnosis.}, }
@article {pmid40271228, year = {2025}, author = {Liu, J and Wu, X}, title = {Rare Bloodstream Infection of Rhodococcus rhodochrous as the Prodromal Signal for Malignancy.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1951-1959}, doi = {10.2147/IDR.S512213}, pmid = {40271228}, issn = {1178-6973}, abstract = {Rhodococcus-associated infections are extremely rare, and previous publications have indicated that such infections are primarily observed among individuals with HIV. Limited information is available regarding therapy, and no clear consensus has been reached to guide treatment. Here, we report the first case of bloodstream infection with Rhodococcus rhodochrous in a non-HIV patient with a viral intracranial infection. During follow-up, lymph node biopsy and bone marrow aspiration were performed because superficial lymphadenectasis had failed to regress as expected within 3 months. The patient was newly diagnosed with nodal T-follicular helper cell lymphoma, angioimmunoblastic-type. For cases of rare infection or co-infection, screening for pathogenic microorganisms is the priority, and several methods should be employed, such as microorganism culture, antigen and antibody detection, and metagenomic next-generation sequencing. In retrospect to integrated case management, our case indicated that early malignancy screening is significant for early diagnosis and treatment of occult cancer during patients with rare opportunistic infections.}, }
@article {pmid40270817, year = {2025}, author = {Onohuean, H and Olot, H and Onohuean, FE and Bukke, SPN and Akinsuyi, OS and Kade, A}, title = {A scoping review of the prevalence of antimicrobial-resistant pathogens and signatures in ready-to-eat street foods in Africa: implications for public health.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1525564}, doi = {10.3389/fmicb.2025.1525564}, pmid = {40270817}, issn = {1664-302X}, abstract = {BACKGROUND AND OBJECTIVE: Despite its critical role in individual and societal health, food hygiene remains underexplored. Antibiotic-resistant pathogenic bacteria in ready-to-eat (RTE) food threaten public health. This scoping review collected data on the epidemiological prevalence of RTE food-contaminated pathogens resistant to antimicrobial drugs and resistance genes in Africa.<br><br>METHOD: Using electronic databases, such as PubMed, Scopus, and Web of Science (WoS), handpicked from references, pre-reviewed published articles were retrieved and analyzed according to the PRISMA-ScR guidelines.<br><br>RESULTS: The findings indicate 40 previewed published articles qualified for meta-synthesis in the scoping review with a population/case ratio of 11,653/5,338 (45.80%). The most frequently reported RTE foods were meat or beef/beef-soup, chicken or poultry products, salads, vegetable salads, and sandwiches, which harboured pathogens such as E. coli, Salmonella, and Staphylococcus. Antibiotic susceptibility tests revealed the use of 48 antibiotics to manage infections, following CLSI (Clinical and Laboratory Standards Institute) protocols. Moreover, 10 authors reported 54 resistance genes associated with pathogenic resistant bacteria. In addition, only 15 studies received funding or financial support.<br><br>CONCLUSION: These findings from several researchers indicate that RTE street foods in African and resource-limited nations harbour enteric pathogens and are a significant concern to the public health system and reservoir of the spread of antibiotic resistance. This underscores the necessity of implementing effective control strategies to address challenges and limit the spread of resistant bacteria in RTE foods. The antimicrobial resistance surveillance system in the region is a significant concern. Notably, Africa needs to strengthen the national and international regulatory bodies and a health surveillance system on antimicrobial resistance, particularly among developing nations.}, }
@article {pmid40270812, year = {2025}, author = {Fagerlund, A and Møretrø, T and Jensen, MR and Langsrud, S and Moen, B}, title = {Early detection and population dynamics of Listeria monocytogenes in naturally contaminated drains from a meat processing plant.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1541481}, doi = {10.3389/fmicb.2025.1541481}, pmid = {40270812}, issn = {1664-302X}, abstract = {Listeria monocytogenes, a significant foodborne pathogen, often contaminates ready-to-eat foods through cross-contamination in food processing environments, and floor drains represent one of the most common sites of persistence. Subtyping of L. monocytogenes from food processing plants for the purpose of source tracking is usually performed on a single colony obtained after selective enrichment. This study investigates the temporal variation and population dynamics of L. monocytogenes in drains, focusing on the diversity of L. monocytogenes and the impact of the resident microbiota. Six different drains in a meat processing plant were each sampled four times over a period of 8 weeks and subjected to two-step selective enrichment in Half Fraser and Full Fraser broths. The clonal complexes (CCs) of at least 20 individual L. monocytogenes isolates from each positive sample (460 isolates in total) were determined using either the GenoListeria Multiplex qPCR assay or whole genome sequencing (WGS). The microbiota in drains and enrichment cultures was analyzed by 16S rRNA gene amplicon sequencing and metagenomic or quasimetagenomic sequencing. L. monocytogenes was detected in the majority of samples and four different CCs were identified - CC9, CC11 (ST451), CC121 and CC8 - with up to three CCs in the same sample and with different CCs dominating in different drains. The same clones of CC9, CC11, and CC121 had persisted in the facility for 3-5 years. The composition of the drain microbiota remained relatively stable over time, with Pseudomonas, Acinetobacter, Janthinobacterium, Chryseobacterium, Staphylococcus, and Sphingomonas as the most commonly identified genera. There were no apparent differences in the microbial genera present in L. monocytogenes positive and negative drains or samples. The study highlights the use of techniques such as qPCR and quasimetagenomics for monitoring and controlling the risk of L. monocytogenes contamination in processing environments.}, }
@article {pmid40270585, year = {2025}, author = {Zheng, Z and Gong, Z and Zhang, R and Lin, X and Hong, W and Song, L}, title = {Potential pathogens drive ARGs enrichment during biofilms formation on environmental surfaces.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf057}, doi = {10.1093/ismeco/ycaf057}, pmid = {40270585}, issn = {2730-6151}, abstract = {The enrichment of antibiotic resistance genes (ARGs) on environmental surfaces is a fundamental question in microbial ecology. Understanding the processes driving ARG variations can provide clues into their transfer mechanisms between phases and offer insights for public health management. In this study, we examined microbiota, potential pathogen, and ARG dynamics on two common environment surfaces-polyvinyl chloride (PVC) and carbon steel (CS)-under environmental stress (induced by landfill leachate flow) in a Center for Disease Control and Prevention Biofilm Reactor using metagenomics and quantitative polymerase chain reaction-Chip techniques. Contrary to the expected changes in biofilms morphology and physiochemical properties, microbiota, potential pathogens, and ARGs exhibited a divergence-convergence pattern, primarily shaped by attachment surface properties and, subsequently, biofilm maturity during biofilms formation. During this process, ARG levels in biofilms gradually increased to and exceeded the levels in the surrounding environment, but with a distinct structure (P < .05). Furthermore, 1.93- and 3.05-fold increases in the concentrations of mobile genetic elements intI-1 in PVC and CS biofilms, respectively, suggested their important role in the transfer and spread of ARGs within the biofilm matrix. Although potential pathogens were less abundant (3.48%-5.63%) in the biofilms microbiota, they accounted for 18.28%-45.16% of the ARG hosts and harbored multiple ARGs. Pathogens significantly impacted ARG enrichment (Procrustes analysis: P = .0136, M[2] = 0.34) although microbiota development also influenced this process (P = .0385, M[2] = 0.67). These results suggest that pathogens are key in shaping ARG enrichment in biofilms. Our findings provide dynamic insights into resistome enrichment on environmental surfaces.}, }
@article {pmid40270483, year = {2025}, author = {McElwee-Adame, A and Esplin-Stout, R and Mugoya, T and Vourlitis, G and Welch, N and Henning, J and Afram, K and Jeshvaghane, MA and Bingham, N and Dockter, A and Eslava, J and Gil, G and Mergens, J and Mohamed, A and Nguyen, T and Noor, F and Salcedo, N and Sethuraman, A}, title = {Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops (Humulus lupulus L.).}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17769}, doi = {10.1111/mec.17769}, pmid = {40270483}, issn = {1365-294X}, support = {2017-06423//USDA; National Institute of Food and Agriculture/ ; 2022-77040-38529//USDA; National Institute of Food and Agriculture/ ; 1564659//NSF; Division of Biological Infrastructure/ ; 2147812//NSF; Division of Biological Infrastructure/ ; }, abstract = {Humulus lupulus L., commonly known as hop, is a perennial crop grown worldwide and is well known for its pharmacological, commercial, and most importantly brewing applications. For hundreds of years, hop has undergone intense artificial selection, with over 250 cultivated varieties being developed worldwide, all displaying differences in key characteristics such as bitter acid concentrations, flavour and aroma profiles, changes in photoperiod, growth, and pathogen/pest resistances. Previous studies have individually explored differences between cultivars, aiming to identify markers that can quickly and cost-effectively differentiate between cultivars. However, little is known about their evolutionary history and the variability in their associated rhizospheric microbial communities. Coupling phenotypic, genomic, and soil metagenomic data, our study explores the global population structure and domestication history of 98 hop cultivars. We assessed differences in growth rates, rates of viral infection, usage of dissolvable nitrogen, and soil microbial community compositions between US and non-US based cultivars. Our study revealed that worldwide hop cultivars cluster into four subpopulations: Central European, English, and American ancestry as previously reported, and one new group, the Nobles, revealing further substructure amongst Central European cultivars. Modelling the evolutionary history of domesticated hop reveals divergence of the common ancestors of modern US cultivars around 2800 years before present (ybp), and more recent divergences with gene flow across English, Central European, and Noble cultivars, reconciled with key events in human history and migrations. Furthermore, cultivars of US origin were shown to overall outperform non-US cultivars in both growth rates and usage of dissolvable nitrogen and display novel microbial composition under common-garden settings in the United States.}, }
@article {pmid40270118, year = {2025}, author = {Murtaza, N and Collins, L and Yao, CK and Thwaites, PA and Veitch, P and Varney, JE and Gill, PA and Gibson, PR and Morrison, M and Muir, JG}, title = {Effects of dietary FODMAP content on the faecal microbiome and gastrointestinal physiology in healthy adults: a randomised, controlled cross-over feeding study.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-39}, doi = {10.1017/S0007114525000868}, pmid = {40270118}, issn = {1475-2662}, abstract = {The effect dietary FODMAPs (fermentable oligo-, di- and mono-saccharides and polyols) in healthy adults is poorly documented. This study compared specific effects of low and moderate FODMAP intake (relative to typical intake) on the faecal microbiome, participant-reported outcomes and gastrointestinal physiology. In a single-blind cross-over study, 25 healthy participants were randomised to one of two provided diets, 'low' (LFD) <4 g/d or 'moderate' (MFD) 14-18 g/d, for 3 weeks each, with ≥2-week washout between. Endpoints were assessed in the last week of each diet. The faecal bacterial/archaeal and fungal communities were characterised in 18 participants in whom high quality DNA was extracted by 16S rRNA and ITS2 profiling, and by metagenomic sequencing. There were no differences in gastrointestinal or behavioural symptoms (fatigue, depression, anxiety), or in faecal characteristics and biochemistry (including short-chain fatty acids). Mean colonic transit time (telemetry) was 23 (95% confidence interval: 15, 30) h with the MFD compared with 34 (24, 44) h with LFD (n=12; p=0.009). Fungal diversity (richness) increased in response to MFD, but bacterial richness was reduced, coincident with expansion of the relative abundances of Bifidobacterium, Anaerostipes, and Eubacterium. Metagenomic analysis showed expansion of polyol-utilising Bifidobacteria, and Anaerostipes with MFD. In conclusion, short-term alterations of FODMAP intake are not associated with symptomatic, stool or behavioural manifestations in healthy adults, but remarkable shifts within the bacterial and mycobiome populations were observed. These findings emphasise the need to quantitatively assess all microbial Domains and their interrelationships to improve understanding of consequences of diet on gut function.}, }
@article {pmid40270064, year = {2025}, author = {Basu, A and Chalasani, D and Sarma, PVSRN and Uikey, S and Chenna, VR and Choudhari, PL and Podile, AR}, title = {Influence of genotype, nodule position, and edaphic factors on microbial diversity and assembly of pigeonpea (Cajanus cajan) root nodules in Indian soils.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {41}, pmid = {40270064}, issn = {2524-6372}, abstract = {BACKGROUND: Pigeonpea (Cajanus cajan) is an important legume crop in semi-arid regions with multiple uses. The microbial diversity within its root nodules in Indian soils remains poorly explored. We investigated the bacterial diversity of pigeonpea root nodules across different genotypes and soil types to identify the factors driving their assembly. Using a metagenomic approach and high-throughput sequencing of the 16S rRNA gene, we analyzed the nodule microbiomes of three pigeonpea genotypes (Asha, Durga, and Mannem Konda Kandi) grown in three different soil types (Alfisol, Vertisol, and Inceptisol) and wild pigeonpea (C. scarabaeoides) in its native soil.<br><br>RESULTS: Our results indicated that pigeonpea nodules harbor diverse rhizobial and non-rhizobial endophytes and that host genotype, nodule position, soil type, and other edaphic factors influence significant variation in the microbial community structure. The core nodule microbiome was dominated by Proteobacteria and Bacteroidetes. Bradyrhizobium and Ensifer were predominant among the rhizobial taxa, and non-rhizobial genera such as Pseudomonas, Chitinophaga, and Limnobacter were also abundant. Edaphic factors, particularly soil type, pH, and nutrient availability, had a stronger influence on the nodule bacterial community composition than the host genotype. Although bulk soil exhibited higher bacterial diversity, nodule microbiomes were less diverse but more specialized, indicating host-mediated selection. A comparison of the nodule microbiomes of wild and cultivated pigeonpea revealed distinct differences, with the core nodule microbiome of wild pigeonpea dominated by Bradyrhizobium, while that of cultivated pigeonpea exhibited a diverse bacterial community.<br><br>CONCLUSIONS: These findings demonstrate that soil properties play a more critical role than host genetics in shaping the pigeonpea nodule microbiome, emphasizing the importance of environmental conditions in symbiotic interactions. The differences between wild and cultivated genotypes suggest that domestication has altered microbial recruitment strategies. This study provides foundational insights into the factors driving microbial assembly in pigeonpea nodules, with implications for improving crop productivity through targeted microbial management. Future research should explore the functional roles of these microbial communities to optimize their use in sustainable agriculture.}, }
@article {pmid40269715, year = {2025}, author = {Poopedi, E and Pierneef, R and Singh, T and Gomba, A}, title = {Antibiotic resistance profiles and mutations that might affect drug susceptibility in metagenome-assembled genomes of Legionella pneumophila and Aeromonas species from municipal wastewater.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {237}, pmid = {40269715}, issn = {1471-2180}, support = {121333//National Research Foundation/ ; K5/2885//3//Water Research Commission/ ; }, mesh = {*Wastewater/microbiology ; *Aeromonas/genetics/drug effects/isolation &amp; purification ; *Anti-Bacterial Agents/pharmacology ; *Legionella pneumophila/genetics/drug effects/isolation &amp; purification ; Genome, Bacterial ; Mutation ; *Metagenome ; *Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; }, abstract = {Antibiotic resistance (AR) has emerged as a significant global health issue. Wastewater treatment plants (WWTPs) contain diverse bacterial communities, including pathogens, and have been identified as crucial reservoirs for the emergence and dissemination of AR. The present study aimed to identify antibiotic resistance genes (ARGs) and screen for the presence of mutations associated with AR in Legionella pneumophila and Aeromonas spp. from municipal wastewater. Metagenome-assembled genomes (MAGs) of L. pneumophila and Aeromonas spp. were reconstructed to investigate the molecular mechanisms of AR in these organisms. A total of 138 nonsynonymous single nucleotide variants (SNVs) in seven genes associated with AR and one deletion mutation in the lpeB gene were identified in L. pneumophila. In Aeromonas spp., two (aph(6)-Id and aph(3'')-Ib) and five (blaMOX-4, blaOXA-1143, blaOXA-724, cepH, and imiH) ARGs conferring resistance to aminoglycosides and β-lactams were identified, respectively. Moreover, this study presents β-lactam resistance genes, blaOXA-1143 and blaOXA-724, for the first time in Aeromonas spp. from a municipal WWTP. In conclusion, these findings shed light on the molecular mechanisms through which clinically relevant pathogenic bacteria such as L. pneumophila and Aeromonas spp. found in natural environments like municipal wastewater acquire AR.}, }
@article {pmid40269516, year = {2025}, author = {Cumbo, F and Truglia, S and Weitschek, E and Blankenberg, D}, title = {Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf177}, pmid = {40269516}, issn = {1477-4054}, support = {U24HG006620/NH/NIH HHS/United States ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Metagenomics/methods ; *Metagenome ; *Microbiota ; *Gastrointestinal Microbiome ; Computational Biology/methods ; Algorithms ; }, abstract = {UNLABELLED: The continuously decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal of identifying microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here, we propose a novel backward variable selection method based on the hyperdimensional computing (HDC) paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.<br><br>AUTHOR SUMMARY: Characterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the HDC paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.}, }
@article {pmid40269515, year = {2025}, author = {Sirasani, JP and Gardner, C and Jung, G and Lee, H and Ahn, TH}, title = {Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf176}, pmid = {40269515}, issn = {1477-4054}, support = {2430236//National Science Foundation/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Machine Learning ; Biomarkers/blood ; }, abstract = {Advances in next-generation sequencing have resulted in a growing understanding of the microbiome and its role in human health. Unlike traditional microbiome analysis, blood and tissue microbiome analyses focus on the detection and characterization of microbial DNA in blood and tissue, previously considered a sterile environment. In this review, we discuss the challenges and methodologies associated with analyzing these samples, particularly emphasizing blood and tissue microbiome research. Key preprocessing steps-including the removal of ribosomal RNA, host DNA, and other contaminants-are critical to reducing noise and accurately capturing microbial evidence. We also explore how taxonomic profiling tools, machine learning, and advanced normalization techniques address contamination and low microbial biomass, thereby improving reliability. While it offers the potential for identifying microbial involvement in systemic diseases previously undetectable by traditional methods, this methodology also carries risks and lacks universal acceptance due to concerns over reliability and interpretation errors. This paper critically reviews these factors, highlighting both the promise and pitfalls of using blood and tissue microbiome analyses as a tool for biomarker discovery.}, }
@article {pmid40269473, year = {2025}, author = {Khan, MAW and Bohannan, BJM and Meyer, KM and Womack, AM and Nüsslein, K and Grover, JP and Mazza Rodrigues, JL}, title = {Community-Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70088}, doi = {10.1111/1758-2229.70088}, pmid = {40269473}, issn = {1758-2229}, support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; DEB 14422214//National Science Foundation/ ; }, mesh = {*Rainforest ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Microbiota ; Metagenomics/methods ; Metagenome ; *Archaea/genetics/metabolism/classification/isolation &amp; purification ; Soil/chemistry ; Viruses/genetics/classification/metabolism/isolation &amp; purification ; Machine Learning ; Brazil ; }, abstract = {The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long-term established pastures in the Amazon. Machine learning-derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein-coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein-coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long-term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long-term established pastures with implications for the C and N cycles.}, }
@article {pmid40269059, year = {2025}, author = {Aljutaily, T and Aladhadh, M and Alsaleem, KA and Alharbi, HF and Barakat, H and Aljumayi, H and Moustafa, MMA and Rehan, M}, title = {Gut microbiota diversity in obese rats treated with intermittent fasting, probiotic-fermented camel milk with or without dates and their combinations.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {14204}, pmid = {40269059}, issn = {2045-2322}, support = {QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Camelus ; Rats ; *Obesity/microbiology/diet therapy ; *Probiotics/administration &amp; dosage ; *Fasting ; *Milk ; Male ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Biodiversity ; Cultured Milk Products ; Intermittent Fasting ; }, abstract = {Dietary alternatives help effectively in obesity management. The present study examines the gut microbiota diversity in obesity-induced rats treated with intermittent fasting, fermented camel milk (FCM), and FCM-incorporated Sukkari date or their combinations. The metagenomic analysis of the gut microbiome through 16 S rRNA revealed 226 families, 499 genera, and 879 bacterial species. In the taxonomy distributions and heatmap analysis, Bacteroidota (i.e., Prevotella) had the uppermost relative abundance in groups before treatments (Before_Groups, most samples clustered in one sub-cluster) reached 80.50% in sample S11 (Before_G2), whereas Firmicutes (i.e., Lactobacillus) presented the dominant in groups after treatments (After_Groups, generality samples grouped in another sub-cluster) and counted 70.86% in sample S88 (After_G6), reflecting potential short-chain fatty acids production. The alpha and beta diversity explored by Shannon and PCoA indices presented high diversity in most groups after treatment. Deferribacterota and Fusobacteriota, in addition to Stenotrophomonas and Listeria, were the key phylotypes in the treated groups at the Phylum and genus levels, respectively. The proposed functional pathways involving mannan, rhamnose I, glucose, and xylose degradation were the most supported pathways in After_Groups with potential carbohydrate degradation. Eventually, intermittent fasting and probiotic fermented camel milk increased microbiome diversity and accelerated weight loss, preventing health issues.}, }
@article {pmid40268958, year = {2025}, author = {Luo, Q and Gao, H and Xiang, Y and Li, J and Dong, L and Wang, X and Liu, F and Guo, Y and Shen, C and Ding, Q and Qin, C and Liang, G and Wen, L}, title = {The dynamics of microbiome and virome in migratory birds of southwest China.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {64}, pmid = {40268958}, issn = {2055-5008}, mesh = {Animals ; China ; *Virome ; Feces/microbiology/virology ; *Gastrointestinal Microbiome ; *Charadriiformes/microbiology/virology ; Animal Migration ; *Bacteria/classification/genetics/isolation &amp; purification ; *Viruses/classification/genetics/isolation &amp; purification ; *Birds/microbiology/virology ; Metagenomics ; Phylogeny ; }, abstract = {Migratory birds carry pathogens, posing a significant threat to environmental and human health. We documented the metatranscriptome and RNA virome of 896 stool samples from migratory birds and environmental samples over four consecutive years in southwest China. Our analysis identified Catellicoccus marimammalium as the predominant bacterium in the gut of black-headed gulls, with an average relative abundance of 79.3%. Strain-level analysis of C. marimammalium revealed a dominant population with some longitudinal diversity over the four years. Additionally, the gut of black-headed gulls was found to harbor numerous viruses, including a novel hepatovirus. Lysates of cells of C. marimammalium but not other bacteria derived from black-headed gulls could inhibit the replication of human hepatovirus, suggesting a potential regulatory role for gut commensal bacteria in modulating viral carriage. These findings enhance our understanding of the microbiome and RNA virome diversity in migratory birds and provide insights into the modulation of asymptomatic infections.}, }
@article {pmid40268922, year = {2025}, author = {Patsis, AC and Schuler, CJ and Toner, BM and Santelli, CM and Sheik, CS}, title = {The potential for coupled organic and inorganic sulfur cycles across the terrestrial deep subsurface biosphere.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3827}, pmid = {40268922}, issn = {2041-1723}, support = {EAR-1813526//National Science Foundation (NSF)/ ; EAR-1813526//National Science Foundation (NSF)/ ; }, mesh = {*Sulfur/metabolism ; Ecosystem ; *Sulfur Compounds/metabolism ; *Bacteria/metabolism/genetics/classification ; Metagenome ; Sulfides/metabolism ; Metagenomics ; Sulfites/metabolism ; Soil Microbiology ; Sulfonium Compounds ; }, abstract = {Organosulfur compounds (OrgS) are fundamental components of life's biomass, yet the cycling of these compounds in the terrestrial deep subsurface, one of Earth's largest ecosystems, has gone relatively unexplored. Here, we show that all subsurface microbial genomes reconstructed from Soudan Underground Mine State Park have the capacity to cycle organic sulfur species. Our findings suggest that OrgS degradation may be an integral link between the organic and inorganic sulfur cycle via the production of sulfite and sulfide. Furthermore, despite isolation from surface ecosystems, most Soudan microorganisms retained genes for dimethylsulfoniopropionate and taurine biosynthesis. Metagenomic analyses of an additional 54 deep subsurface sites spanning diverse lithologies revealed the capacity for OrgS cycling to be widespread, occurring in 89% of assembled metagenomes. Our results indicate that consideration of OrgS cycling may be necessary to accurately constrain sulfur fluxes, discern the energetic limits of deep life, and determine the impact of deep subsurface biogeochemical sulfur cycling on greater Earth system processes.}, }
@article {pmid40268850, year = {2025}, author = {Zhao, J and Zhuge, R and Hu, B and Wang, Y and Wang, X and Zhang, Y and Yuan, L and Qiu, C and Yan, Y and Zhang, X and Hua, Z and Tang, J and Guo, K and Sun, Y and Wang, K and Qiu, L and Luo, J and Zhang, W and Zhuge, J and Fang, H}, title = {Clinical impact of bronchoalveolar lavage fluid metagenomic next-generation sequencing in immunocompromised patients with severe community-acquired pneumonia in ICU: a multicenter retrospective study.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {40268850}, issn = {1439-0973}, support = {2023KY1296//The Project of Zhejiang Provincial Department of Health/ ; 2022K71//Quzhou Bureau of Science and Technology/ ; }, abstract = {BACKGROUND: An increasing number of critically ill patients are immunocompromised. These patients are at high risk of intensive care unit (ICU) admission because of numerous complications. Acute respiratory failure due to severe community-acquired pneumonia (SCAP) is one of the leading causes of admission. Early targeted antibiotic therapy is crucial for improving the prognosis of these patients. Metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) has shown significant value in pathogen detection in recent years. However, there are few studies on summarizing pathogen profiles of SCAP in immunocompromised patients.<br><br>METHODS: We performed a multicenter retrospective analysis of patients with SCAP in the ICU diagnosed between May 2021 to October 2024. Bronchoalveolar lavage fluid (BALF), blood, and sputum samples were collected and subjected to mNGS and conventional microbiological tests (CMTs). The pathogen profiles detected by the two methods were compared.<br><br>RESULTS: In our study, compared to CMTs, mNGS increased the detection rates of mixed infections in the immunocompromised group (58.82% vs 17.96%, P&#x2009;<&#x2009;0.05) and immunocompetent group (44.58% vs 18.72%, P&#x2009;<&#x2009;0.05), while also reducing the rate of no pathogen detected (4.90% vs 38.73%, P&#x2009;<&#x2009;0.05; 8.37% vs 32.76%, P&#x2009;<&#x2009;0.05). In both groups, the proportion of positive clinical impacts (diagnosis) resulting from mNGS results exceeded 90% (96.57% vs 93.84%), and the treatment effectiveness rate in the immunocompromised group was higher than in the immunocompetent group (65.69% vs 56.40%, P&#x2009;<&#x2009;0.05). Further analysis showed that when mNGS-guided treatment was effective, the 28-day mortality rate significantly improved in both the immunocompromised group (31.34% vs 74.29%, P&#x2009;<&#x2009;0.05) and the immunocompetent group (42.36% vs 40.68%, P&#x2009;<&#x2009;0.05) compared to when the treatment was ineffective.<br><br>CONCLUSION: This study indicates that ICU patients with SCAP, particularly those who are immunocompromised, are more likely to have polymicrobial infections. mNGS in BALF provides rapid and comprehensive pathogen profiling of pulmonary infections, thereby having a positive impact on both the diagnosis, treatment and prognosis of immunocompromised patients with SCAP.}, }
@article {pmid40268777, year = {2025}, author = {Claverie, JM and Legendre, M and Rigou, S and Abergel, C}, title = {Refining the taxonomy of pithovirus-related giant DNA viruses within the order Pimascovirales.}, journal = {Archives of virology}, volume = {170}, number = {5}, pages = {111}, pmid = {40268777}, issn = {1432-8798}, mesh = {Genome, Viral ; Phylogeny ; *DNA Viruses/classification/genetics/ultrastructure ; *Giant Viruses/classification/genetics/ultrastructure ; DNA, Viral/genetics ; }, abstract = {The first member of the family Pithoviridae (Pithovirus sibericum) was isolated from ancient Siberian permafrost and characterized in 2014. Since then, many relatives have been isolated, characterized, and classified as members of the genera Alphapithovirus, Alphacedratvirus, and Alphaorpheovirus. In addition, one complete circular genome sequence was assembled from metagenomic data (hydrivirus). All of these viruses form distinctive giant elongated ovoid particles, up to 2 µm in length, but they differ significantly in the size of their genome, their nucleotide composition, and their gene content. Based on their shared ovoid virion shape, common replication strategy, and core gene similarity, we recently proposed to update their taxonomic status by classifying them in three distinct families (Pithoviridae, Orpheoviridae, and Hydriviridae) within a new suborder, the Ocovirineae, to separate them clearly from the other more distant families (Marseilleviridae, Ascoviridae, Iridoviridae) of the order Pimascovirales. This new taxonomy, validated by the last ICTV Ratification vote held in March 2025, extends the previous partition from three clades to four (to include hydrivirus) while keeping the genera Alphacedratvirus and Alphapithovirus in the same family, Pithoviridae (but split into two subfamilies), due to their much greater similarity to each other than to orpheovirus and hydrivirus.}, }
@article {pmid40268631, year = {2025}, author = {Pemán, J and Ruiz-Gaitán, A}, title = {Diagnosing invasive fungal infections in the laboratory today: It's all good news?.}, journal = {Revista iberoamericana de micologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.riam.2025.01.004}, pmid = {40268631}, issn = {2173-9188}, abstract = {Despite the advances in medical science, invasive fungal infections (IFI) remain a diagnostic challenge. The increasing prevalence of IFI, driven by immunosuppressive therapies, advances in intensive care and emerging pathogens, underscores the need for early and accurate diagnosis. This review evaluates current laboratory methods for the diagnosis of IFI, highlighting their strengths and limitations. Conventional techniques, including fungal culture, direct microscopy, and histopathology, remain the gold standard for the diagnosis of proven IFIs. These methods allow pathogen isolation, species identification and antifungal susceptibility testing. However, these techniques have limitations in terms of sensitivity and turnaround times. Although microscopy is a rapid technique, its sensitivity and species discrimination profile are limited. Modern serological assays, such as β-d-glucan and galactomannan detection, have improved the diagnostic accuracy of probable IFI cases. Integration of these assays with clinical and radiological findings, enables earlier intervention, although this is accompanied by an increased risk of false positives and necessitates careful clinical correlation. Molecular diagnostics, particularly polymerase chain reaction (PCR), allow rapid, species-specific identification directly from clinical samples. The advent of MALDI-TOF mass spectrometry has further improved diagnostic efficiency, particularly for yeast identification, although challenges remain for filamentous fungi. Innovative techniques, such as metagenomic sequencing, lateral-flow assays, and loop-mediated isothermal amplification, offer the potential for rapid and precise detection, even in resource-limited settings. The combination of conventional and innovative methods provides a comprehensive diagnostic framework. The continuous refinement of these tools, in conjunction with multidisciplinary collaboration, is imperative to improve the early diagnostic and targeted treatment of patients with IFI.}, }
@article {pmid40268236, year = {2025}, author = {Emon, MI and Cheung, YF and Stoll, J and Rumi, MA and Brown, C and Choi, JM and Moumi, NA and Ahmed, S and Song, H and Sein, J and Yao, S and Khan, A and Gupta, S and Kulkarni, R and Butt, A and Vikesland, P and Pruden, A and Zhang, L}, title = {CIWARS: a web server for antibiotic resistance surveillance using longitudinal metagenomic data.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {169159}, doi = {10.1016/j.jmb.2025.169159}, pmid = {40268236}, issn = {1089-8638}, abstract = {The rise of antibiotic resistance (AR) poses a substantial threat to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate analysis of longitudinal metagenomic data are lacking. To address this, we introduce CyberInfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive profiling of ARGs and taxonomic profiling of pathogen-associated bacterial taxonomic groups, identifies potential associations of ARGs with mobile genetic elements (MGEs) and pathogen-containing taxa, and assesses resistome risk based on the co-occurrence of ARGs, MGEs, and pathogen-like sequences. Additionally, it detects anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and can serve as a tool to inform effective and timely interventions to mitigate the spread and transmission of AR. Here, CIWARS is demonstrated using longitudinal metagenomic data from a wastewater treatment plant (WWTP) influent and effluent, but it can be extended to any environment. CIWARS provides a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use. The web server is freely available at https://ciwars.cs.vt.edu/.}, }
@article {pmid40271438, year = {2017}, author = {Lu, J and Breitwieser, FP and Thielen, P and Salzberg, SL}, title = {Bracken: estimating species abundance in metagenomics data.}, journal = {PeerJ. Computer science}, volume = {3}, number = {}, pages = {}, doi = {10.7717/peerj-cs.104}, pmid = {40271438}, issn = {2376-5992}, abstract = {Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.}, }
@article {pmid40268215, year = {2025}, author = {Sun, X and Hu, P and Xiao, M and Zhang, S and Shi, J and Cai, D and Wang, D and Xu, L and Liu, L and Liu, Y}, title = {Synergy of Multi-Enzyme Pretreatment and Paraclostridium benzoelyticum Bioaugmentation: A Dual Strategy for Enhancing Methane Production in Dry Anaerobic Digestion of Kitchen Waste.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121671}, doi = {10.1016/j.envres.2025.121671}, pmid = {40268215}, issn = {1096-0953}, abstract = {Dry anaerobic digestion (DAD) of kitchen waste (KW) has low methane production due to the poor mass transfer and the low abundance of functional microorganisms. This study employed multi-enzyme pretreatment (PRE), bioaugmentation with Paraclostridium benzoelyticum (BIO), and their combination (COM) to enhance methane production. Interestingly, the COM group had the highest methane production, which was increased by 18.51%, 9.91% and 12.39% compared with the control, PRE and BIO groups, respectively, which indicated that there was a synergy between multi-enzyme pretreatment and bioaugmentation. Further analysis of microbial community and metagenome was conducted to reveal the synergistic mechanism. The results showed that in COM group, the enrichment of the Rikenellaceae, Methanobacteriaceae and Methanosaetaceae was the directly reason for enhancing methane production. Additionally, key metabolic functions including biosynthesis of cofactors, methane metabolism and oxidative phosphorylation also played a pivotal role in boosting methane production. Furthermore, the enhancement of the hydrogenotrophic methanogenesis pathway has been demonstrated to be a critical factor in the synergistic effects. It provided a reliable theoretical basis for the practical application of the multi-enzyme pretreatment combined with Paraclostridium benzoelyticum bioaugmentation for DAD.}, }
@article {pmid40268122, year = {2025}, author = {Highmore, C and Cooper, K and Parker, J and Robinson, J and Castangia, R and Webb, JS}, title = {Real-time detection of Foodborne Pathogens and Biofilm in the food processing environment with Bactiscan, a macro-scale fluorescence device.}, journal = {Journal of food protection}, volume = {}, number = {}, pages = {100511}, doi = {10.1016/j.jfp.2025.100511}, pmid = {40268122}, issn = {1944-9097}, abstract = {Food safety relies on rapid detection methods and rigorous sampling of the food processing environment, and is challenged by recurrent biofilm contamination and by sub-lethally injured bacteria that can evade detection. Bactiscan is investigated as an alternative detection approach, a macro-scale and reagentless device that detects microbial contamination through activating green fluorescence of glycoproteins in the bacterial cell wall. The detection capability of Bactiscan was tested on foodborne pathogens Escherichia coli, Listeria monocytogenes, Salmonella enterica, and Staphylococcus aureus. Detection by Bactiscan was assessed using 3 independent observers viewing bacterial samples dried on stainless steel, using 3 biological repeats and 5 technical repeats. Detection by Bactiscan was possible to 1.20*10[6] colony forming units (CFU), compared to 1.36*10[4] CFU by ATP swab testing, where Bactiscan detection limits were defined by the concentration at which 50% of the samples were observed under illumination of the device. Heat-killed and chlorine stressed E. coli and S. enterica caused a 2-log reduction in detection by ATP swab tests (p≤0.05), while detection by Bactiscan was unaffected (p≥0.05). Pathogen biofilms were detectable via Bactiscan with >80% accuracy at 4 days of growth; E. coli and L. monocytogenes biofilms were visible at 2 days of growth. In situ contamination studies determined that Bactiscan can detect microbial contamination on chicken, salmon, and yoghurt samples with stronger fluorescence than a competitor UV torch. The presence of one of the pathogens on the food samples was confirmed by metagenome sequencing, determining that S. aureus was present in 7 samples out of 9 with a relative abundance of >0.5%. These data demonstrate that Bactiscan can effectively detect bacteria present in the food processing environment and can complement existing technologies to improve food industry cleaning practices and infection prevention.}, }
@article {pmid40267797, year = {2025}, author = {Sun, X and Sun, Y and Li, P and Gao, Y and Han, M and Zhang, P}, title = {Intensive oyster farming alters the microbial-regulated blue carbon storage in sediment.}, journal = {Marine pollution bulletin}, volume = {216}, number = {}, pages = {118016}, doi = {10.1016/j.marpolbul.2025.118016}, pmid = {40267797}, issn = {1879-3363}, abstract = {Intensive oyster farming enhances the organic matter coupling from water to sediment through biodeposition, potentially contributing to carbon storage. Microbes play a key role in regulating biogeochemical cycling in the coastal sediment. However, their specific contributions to carbon storage under oyster farming remain poorly understood. This study investigates microbial necromass and associated biogeochemical processes in sediments from an intensive oyster farm in Sanggou Bay, China, and compares these indicators with adjacent seagrass beds and bare zones. Additionally, carbon use efficiency (CUE) was employed to indicate microbial-regulated carbon cycling and storage in sediment. The results demonstrate that oyster farming promotes organic carbon accumulation in surface sediments but reduces its stability. Microbial necromass was identified as a critical driver of sedimentary organic carbon in oyster farm sediments, supported by enhanced nitrogen and sulfur cycling pathways. Notably, contrasting relationships between CUE and organic carbon were observed between the seagrass bed and the oyster farm. Functional metagenomic analysis further revealed distinct microbial metabolic pathways across habitats, highlighting the role of biodeposition in shaping microbial functions. These findings enhance our understanding of microbial contributions to blue carbon storage in aquaculture systems and provide new insights into coastal carbon storage beyond vegetated ecosystems.}, }
@article {pmid40267563, year = {2025}, author = {Jian, Z and Wu, H and Yan, S and Li, T and Zhao, R and Zhao, J and Zi, X and Wang, K and Huang, Y and Gu, D and Zhao, S and Ge, C and Jia, J and Liu, L and Xu, Z and Dou, T}, title = {Species and functional composition of cecal microbiota and resistance gene diversity in different Yunnan native chicken breeds: A metagenomic analysis.}, journal = {Poultry science}, volume = {104}, number = {7}, pages = {105138}, doi = {10.1016/j.psj.2025.105138}, pmid = {40267563}, issn = {1525-3171}, abstract = {The gut microbiota of chickens not only modulates host immune function and production performance through nutrient metabolism but also serves as a reservoir for antibiotic resistance genes (ARGs), whose accumulation exacerbates bacterial resistance. This study integrated 108 cecal microbiome samples from six Yunnan native chicken breeds under free-range and caged farming systems, constructing a comprehensive catalog comprising 12,715 microbial genomes. We systematically revealed the dual mechanisms by which the gut microbiota regulates host phenotypes and ARG dissemination. Metagenomic analysis demonstrated that Alistipes, Prevotella, and Spirochaeta synergistically regulate body weight and immune indices through metabolic networks, which are linked to the significant enrichment of carbohydrate-active enzymes. GH23 and GT2 presented the greatest abundance, highlighting their pivotal role in dietary fiber metabolism. A total of 1327 ARGs were identified, spanning seven resistance mechanisms dominated by antibiotic efflux and target alteration. Alistipes_sp._CAG:831 presented the highest ARG abundance and diversity, with ARG levels strongly correlated with host bacterial abundance. Metagenomic-phenotype association networks further revealed that environmental stress drives disparities in ARG enrichment by altering the microbial community structure. This study elucidates the gut microbiota-host interaction network in Yunnan native chickens and provides critical insights into ARG transmission dynamics, offering a theoretical foundation for antibiotic resistance risk assessment and sustainable poultry farming strategies.}, }
@article {pmid40266944, year = {2025}, author = {Herzog, F and Crissman, KR and Beckers, KF and Zhou, G and Liu, CC and Sones, JL}, title = {Lactobacillus Genus Complex Probiotic-Induced Changes on the Equine Clitoral Microbiome.}, journal = {Veterinary sciences}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/vetsci12030232}, pmid = {40266944}, issn = {2306-7381}, support = {2022//Louisiana State University Charles V. Cusimano/ ; }, abstract = {Dysbiosis of the lower reproductive tract (LRT) in mares may play a role in clinical diseases, including endometritis and placentitis. Metagenomic/metagenetic analysis of bacterial DNA can identify organisms that are not readily cultured and, thus, may go undetected. In this study, we tested the following hypotheses: (1) the clitoris of estrual mares harbors a unique resident microbiome, (2) topical Lactobacillus genus complex (LGC)-containing probiotic will alter the equine clitoral microbiome, and (3) early pregnancy rates following clitoral LGC application will not differ significantly from industry standards. Mares (n = 12) in estrus had sterile clitoral swabs collected (0) prior to daily topical LGC for 4 days. Second (12 h) and third clitoral swabs (48 h) were collected following final LGC application. During the next estrus, the mares were bred by artificial insemination. Genomic DNA was extracted and used for 16S rRNA sequencing via the Illumina Miseq platform. Abundance was evaluated via Friedman test with pairwise Dunn's post hoc comparisons. Statistical significance was set at p < 0.05. Compared to time 0, Desulfobacterota decreased and Corynebacterium spp. increased at 12 h and 48 h compared to 0, while Actinobacillus and Fusobacterium spp. increased in a time-dependent manner. Furthermore, Mobiluncus spp. and Christensenellacea_R-7_group decreased at 12 h and 48 h compared to 0. LGC changed the beta but not alpha diversity at both 12 h and 48 h. Mares with LGC application achieved an 85% pregnancy rate in the subsequent estrus. Future investigations are needed to understand the role of the LRT microbiome and probiotics in equine breeding.}, }
@article {pmid40266232, year = {2025}, author = {Zhang, M and Shi, S and Feng, Y and Zhang, F and Xiao, Y and Li, X and Pan, X and Feng, Y and Liu, D and Guo, Y and Hu, Y}, title = {Synthetic microbial community improves chicken intestinal homeostasis and provokes anti-Salmonella immunity mediated by segmented filamentous bacteria.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf076}, pmid = {40266232}, issn = {1751-7370}, support = {2024TZXD026//Shandong Provincial Key Research and Development Program of China/ ; 2022YFA1304201//National Key Research and Development Program of China/ ; }, abstract = {Applying synthetic microbial communities to manipulate the gut microbiota is a promising manner for reshaping the chicken gut microbial community. However, it remains elusive the role of a designed microbial community in chicken physiological metabolism and immune responses. In this study, we constructed a ten-member synthetic microbial community (SynComBac10) that recapitulated the phylogenetic diversity and functional capability of adult chicken intestinal microbiota. We found that early life SynComBac10 exposure significantly enhanced chicken growth performance and facilitated the maturation of both the intestinal epithelial barrier function and the gut microbiota. Additionally, SynComBac10 promoted the pre-colonization and growth of segmented filamentous bacteria, which in turn induced Th17 cell-mediated immune responses, thereby conferring resistance to Salmonella infection. Through metagenomic sequencing, we assembled the genomes of two distinct species of segmented filamentous bacteria from the chicken gut microbiota, which displayed common metabolic deficiency with segmented filamentous bacteria of other host origins. In silico analyses indicated that the SynComBac10-stimulated early establishment of segmented filamentous bacteria in the chicken intestine was likely through SynComBac10-derived metabolite cross-feeding. Our study demonstrated the pivotal role of a designed microbial consortium in promoting chicken gut homeostasis and anti-infection immunity, providing a new avenue for engineering chicken gut microbiota.}, }
@article {pmid40265464, year = {2025}, author = {Yan, X and Xie, F and Yang, S and Sun, Y and Lei, Y and Ren, Q and Si, H and Li, Z and Qiu, Q}, title = {Metagenomic Insights into the Rumen Microbiome in Solid and Liquid Fractions of Yaks and their Differences Compared to Other Ruminants.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12984}, pmid = {40265464}, issn = {1749-4877}, support = {32225009//National Natural Science Foundation of China/ ; 32122083//National Natural Science Foundation of China/ ; 32402780//National Natural Science Foundation of China/ ; XDA26040301//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, abstract = {The rumen microbiome plays a critical role in nutrient metabolism and adaptation of the yak (Bos grunniens), an import livestock animal of the Qinghai-Tibet Plateau renowned for their superior plant fiber degradation capacity. However, the microbiome among the different ecological niches within yak's rumen remains unelucidated. Through shotgun sequencing of rumen solid and liquid fractions from five yaks, we identified significant differences in the microbial communities and their genetic functions between the solid and liquid fractions. Solid fractions exhibited dominance by Ruminococcus, Succiniclasticum, and Aspergillus, while Prevotella, Paludibacter, Parabacteroides, and Bacteroides prevailed in liquid fractions. Comparative CAZyme profiling revealed solid fractions were significantly enriched in cellulose/hemicellulose-targeting enzymes (GH5, GH11, and CBM63), implicating their specialization in breaking down the fibrous grasses. In contrast, liquid fractions showed higher abundances of starch-degrading enzymes (GH13, CBM48) and host-glycan utilizers (GH92), suggesting roles in soluble nutrient extraction and host-microbe interactions. Comparative analysis of 574 metagenome-assembled genomes suggested that Methanomethylophilaceae_UBA71 and nitrate-respiring Ruminococcaceae_Firm-04 preferentially colonized in the solids, whereas propionate-producing Quinella and animal glycan-degrading Bacteroides were more prevalent in the liquids. Moreover, compared to Hu sheep, yak's rumen microbiome showed significantly enhanced utilization of plant polysaccharide capacity. Comparative analysis across 10 ruminant species further highlighted host phylogeny as a key driver of rumen microbiome variation. These findings advance our understanding of niche differentiation and functional specialization within the unique yak rumen ecosystem.}, }
@article {pmid40265338, year = {2025}, author = {Venkatraman, K and Lipp, NF and Budin, I}, title = {Origin and evolution of mitochondrial inner membrane composition.}, journal = {Journal of cell science}, volume = {138}, number = {9}, pages = {}, doi = {10.1242/jcs.263780}, pmid = {40265338}, issn = {1477-9137}, support = {GM142960/NH/NIH HHS/United States ; GBMF9734//Gordon and Betty Moore Foundation/ ; //University of California/ ; }, mesh = {*Mitochondrial Membranes/metabolism/chemistry ; *Mitochondria/metabolism/genetics ; Humans ; Animals ; Mitochondrial Proteins/metabolism ; *Evolution, Molecular ; }, abstract = {Unique membrane architectures and lipid building blocks underlie the metabolic and non-metabolic functions of mitochondria. During eukaryogenesis, mitochondria likely arose from an alphaproteobacterial symbiont of an Asgard archaea-related host cell. Subsequently, mitochondria evolved inner membrane folds known as cristae alongside a specialized lipid composition supported by metabolic and transport machinery. Advancements in phylogenetic methods and genomic and metagenomic data have suggested potential origins for cristae-shaping protein complexes, such as the mitochondrial contact site and cristae-organizing system (MICOS). MICOS protein homologs function in the formation of cristae-like intracytoplasmic membranes (ICMs) in diverse extant alphaproteobacteria. The machinery responsible for synthesizing key mitochondrial phospholipids - which cooperate with cristae-shaping proteins to establish inner membrane architecture - could have also evolved from a bacterial ancestor, but its origins have been less explored. In this Review, we examine the current understanding of mitochondrial membrane evolution, highlighting distinctions between prokaryotic and eukaryotic mitochondrial-specific proteins and lipids and their differing roles in shaping cristae and ICM architecture, and propose a model explaining the concurrent specialization of the mitochondrial lipidome and inner membrane structure in eukaryogenesis. We discuss how advancements across a range of disciplines are shedding light on how multiple membrane components co-evolved to support the central functions of eukaryotic mitochondria.}, }
@article {pmid40265160, year = {2025}, author = {Fässler, D and Heinken, A and Hertel, J}, title = {Characterising functional redundancy in microbiome communities via relative entropy.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {1482-1497}, pmid = {40265160}, issn = {2001-0370}, abstract = {Functional redundancy has been hypothesised to be at the core of the well-evidenced relation between high ecological microbiome diversity and human health. Here, we conceptualise and operationalise functional redundancy on a single-trait level for functionally annotated microbial communities, utilising an information-theoretic approach based on relative entropy that also allows for the quantification of functional interdependency across species. Via constraint-based microbiome community modelling of a public faecal metagenomic dataset, we demonstrate that the strength of the relation between species diversity and functional redundancy is dependent on specific attributes of the function under consideration such as the rarity and the occurring functional interdependencies. Moreover, by integrating faecal metabolome data, we highlight that measures of functional redundancy have correlates in the host's metabolome. We further demonstrate that microbiomes sampled from colorectal cancer patients display higher levels of species-species functional interdependencies than those of healthy controls. By analysing microbiome community models from an inflammatory bowel disease (IBD) study, we show that although species diversity decreased in IBD subjects, functional redundancy increased for certain metabolites, notably hydrogen sulphide. This finding highlights their potential to provide valuable insights beyond species diversity. Here, we formalise the concept of functional redundancy in microbial communities and demonstrate its usefulness in real microbiome data, providing a foundation for a deeper understanding of how microbiome diversity shapes the functional capacities of a microbiome.}, }
@article {pmid40264979, year = {2025}, author = {Zhong, Y and Chi, H and Wu, T and Fan, W and Su, H and Li, R and Jiang, W and Du, X and Ma, Z}, title = {Diversity of rhizosphere microbial communities in different rice varieties and their diverse adaptive responses to saline and alkaline stress.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1537846}, pmid = {40264979}, issn = {1664-302X}, abstract = {Rice rhizosphere microbiota plays a crucial role in crop yield and abiotic stress tolerance. However, little is known about how the composition and function of rhizosphere soil microbial communities respond to soil salinity, alkalinity, and rice variety in rice paddy ecosystems. In this study, we analyzed the composition and function of rhizosphere soil microbial communities associated with two rice varieties (Jida177 and Tongxi933) cultivated in soils with different levels of salinity-alkalinity in Northeast China using a metagenomics approach. Our results indicate that the rhizospheres of Jida177 and Tongxi933 rice varieties harbor distinct microbial communities, and these microbial communities are differentiated based on both soil salinity-alkalinity and rice varieties. Furthermore, the observed differences in rice yield and grain quality between the Jida177 and Tongxi933 rice varieties suggest that these changes may be attributed to alterations in the rhizosphere microbiome under varying salinity conditions. These findings may pave the way for more efficient soil management and deeper understanding of the potential effects of soil salinization on the rice rhizosphere system.}, }
@article {pmid40264936, year = {2025}, author = {Hou, F and Qiao, Y and Qiao, Y and Shi, Y and Chen, M and Kong, M and Hu, X and Jiang, L and Liu, X}, title = {A retrospective analysis comparing metagenomic next-generation sequencing with conventional microbiology testing for the identification of pathogens in patients with severe infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1530486}, pmid = {40264936}, issn = {2235-2988}, abstract = {INTRODUCTION: The application value of metagenomic next-generation sequencing (mNGS) in detecting pathogenic bacteria was evaluated to promote the rational and accurate use of antibiotics. A total of 180 patients with severe infections were included in this study.<br><br>METHODS: Based on their different symptoms, bronchoalveolar lavage fluid (BALF) or blood samples were collected for conventional microbiological testing (CMT) and mNGS.<br><br>RESULTS: The results indicated that the etiological diagnosis rate of mNGS (78.89%) was significantly higher than that of CMT (20%) (p<0.001). Notably, mNGS exhibited greater sensitivity towards rare pathogens such as Chlamydia pneumoniae, Mycobacterium tuberculosis complex, and Legionella pneumophila, which were undetectable by CMT. Additionally, 64 cases underwent blood culture, BALF culture, and mNGS testing. Analysis revealed that the positive rate of blood culture (3.1%) was lower than that of BALF (25%), and the positive rate of CMT from both types was significantly lower than that of mNGS (89.1%) (p<0.001). In this study, 168 mNGS results were accepted, and 116 patients had their antibiotic therapy adjustment based on mNGS. Paired analysis indicated that white blood cell count (WBC), procalcitonin (PCT), C-reactive protein (CRP), and neutrophil (NEU) percentage provided valuable therapeutic guidance. The survival rate of patients was 55.36%, influenced by patient physical condition and age.<br><br>DISCUSSION: Our data indicated that mNGS had significant auxiliary value in the clinical diagnosis and treatment for critically ill patients, especially for those with negative CMT results and clinically undefined infections. mNGS could broaden the detection scope, especially for special pathogens, and improve the detection rate, providing powerful assistance for early clinical diagnosis and treatment.}, }
@article {pmid40263874, year = {2025}, author = {Huang, X and Li, R and Xu, J and Kang, J and Chen, X and Han, B and Xue, Y}, title = {Integrated multi-omics uncover viruses, active fermenting microbes and their metabolic profiles in the Daqu microbiome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {208}, number = {}, pages = {116061}, doi = {10.1016/j.foodres.2025.116061}, pmid = {40263874}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; Fungi/metabolism/genetics ; *Bacteria/metabolism/genetics ; *Viruses/genetics/classification ; Metagenomics ; Food Microbiology ; *Fermented Foods/microbiology/virology ; Bacteriophages/genetics ; *Metabolome ; Multiomics ; }, abstract = {The coexistence and coevolution of viruses and fermenting microbes have a significant impact on the structure and function of microbial communities. Although the presence of viruses in Daqu, the fermentation starter for Chinese Baijiu, has been documented, their specific effects on the community composition and metabolic functions of low, medium, and high-temperature Daqu remain unclear. In this study, we employed multi-omics technology to explore the distribution of viruses and active bacteria and fungi in various Daqu and their potential metabolic roles. Viral metagenomic sequencing showed a predominance of Parvoviridae in High-Temperature Daqu (HTQ), while Genomoviridae were dominant in Medium-Temperature Daqu (MTQ) and Low- Temperature Daqu (LTQ). Phages belonging to the Siphoviridae, Podoviridae, Herelleviridae, and Myoviridae families showed significantly different abundances across three Daqu groups. Metatranscriptomic analysis showed that fungal communities were most active in LTQ, whereas bacterial communities were dominant in MTQ and HTQ. By employing the CRISPR-Cas spacer, a higher predicted number of phage-host linkages was identified in LTQ, particularly with hosts including Lactobacillus, Staphylococcus, Acinetobacter, Enterobacter, and Bacillus. Correlation analysis showed that bacteria like Acinetobacter, Lactobacillus, and Streptococcus exhibited the strongest associations with metabolites, particularly amino acids and organic acids. The potential phage-induced metabolic differences in the three Daqu groups were mainly linked to pathways involved in the metabolism of amino acids, sugars, and organic acids. Overall, our study elucidates the impact of viruses on shaping microbial composition and influencing metabolic functions in Daqu. These results improve our comprehension of viruses and microbes in Daqu microbial communities and provide valuable insights for enhancing quality control in Daqu production.}, }
@article {pmid40263747, year = {2025}, author = {Liu, CG and Lin, MX and Xin, Y and Sun, M and Cui, J and Liu, D and Zang, D and Chen, J}, title = {Metagenomics and Non-Targeted Metabolomics Reveal the Role of Gut Microbiota and Its Metabolites in Brain Metastasis of Non-Small Cell Lung Cancer.}, journal = {Thoracic cancer}, volume = {16}, number = {8}, pages = {e70068}, doi = {10.1111/1759-7714.70068}, pmid = {40263747}, issn = {1759-7714}, support = {2022RQ091//Science and Technology Talent Innovation Support Plan of Dalian/ ; 82203056//National Natural Science Foundation of China/ ; 2022LCYJYB01//The "1+X" program for Clinical Competency enhancement-Clinical Research Incubation Project of the Second Hospital of Dalian Medical University/ ; 2023-BS-167//Natural Science Foundation of Liaoning Province/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/pathology/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Brain Neoplasms/secondary/metabolism ; *Lung Neoplasms/pathology/metabolism/microbiology ; *Metabolomics/methods ; Female ; Male ; *Metagenomics/methods ; Middle Aged ; Aged ; Prognosis ; }, abstract = {BACKGROUND: Brain metastasis is a common and severe complication in non-small cell lung cancer (NSCLC) patients, significantly affecting prognosis. However, the role of gut microbiota and its metabolites in NSCLC brain metastasis remains poorly understood. This study aims to explore the relationship between gut microbiota, metabolites, and the development of brain metastasis in NSCLC.<br><br>METHODS: We conducted an integrative analysis combining metagenomics and non-targeted metabolomics on baseline fecal samples from NSCLC patients with brain metastasis (n&#x2009;=&#x2009;18) and those without distant metastasis (n&#x2009;=&#x2009;12). Gut microbiota composition and metabolite profiles were detected and analyzed, and statistical methods, including machine learning models, were applied to identify differences and potential biomarkers.<br><br>RESULTS: Significant differences in gut microbiota composition were found between the two groups, with higher microbial diversity observed in patients with brain metastasis. Specific genera, such as Paenibacillus, Fournierella, and Adlercreutzia, were enriched in the brain metastasis group. Metabolomic analysis revealed altered levels of short-chain fatty acids and other metabolites associated with immune modulation and vascular permeability, including angiotensin (1-7). These changes were linked to the metastatic process and may influence brain metastasis development. Furthermore, machine learning models identified key biomarkers, such as Raoultibacter, Mobilibacterium, and N-acetyl-L-glutamic acid, which could serve as valuable indicators for brain metastasis.<br><br>CONCLUSIONS: Our findings suggest that gut microbiota dysbiosis and its metabolic products may contribute to the development of brain metastasis in NSCLC. The identification of microbiota-derived biomarkers holds potential for early detection and therapeutic intervention in NSCLC brain metastasis.}, }
@article {pmid40263712, year = {2025}, author = {Hör, J}, title = {Advancing RNA phage biology through meta-omics.}, journal = {Nucleic acids research}, volume = {53}, number = {8}, pages = {}, doi = {10.1093/nar/gkaf314}, pmid = {40263712}, issn = {1362-4962}, mesh = {*Bacteria/virology/genetics ; *RNA Phages/genetics/physiology/classification ; Genome, Viral ; *Metagenomics/methods ; *Genomics/methods ; Transcriptome ; Bacteriophages/genetics ; }, abstract = {Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as important models to understand the principal processes of life, including translation and the genetic code. While RNA phages were generally thought of as rare oddities in nature, meta-omics methods are rapidly changing this simplistic view by studying diverse biomes with unprecedented resolution. Metatranscriptomics dramatically expanded the number of known RNA phages from tens to tens of thousands, revealed their widespread abundance, and discovered several new families of potential RNA phages with largely unknown hosts, biology, and environmental impact. At the same time, (meta)genomic analyses of bacterial hosts are discovering an arsenal of defense systems bacteria employ to protect themselves from predation, whose functions in immunity against RNA phages we are only beginning to understand. Here, I review how meta-omics approaches are advancing the field of RNA phage biology with a focus on the discovery of new RNA phages and how bacteria might fight them.}, }
@article {pmid40263502, year = {2025}, author = {Canderan, J and Ye, Y}, title = {Identification of microbial species and proteins associated with colorectal cancer by reanalyzing CPTAC proteomic datasets.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13926}, pmid = {40263502}, issn = {2045-2322}, support = {R01AI143254//U.S. Department of Health &amp; Human Services | NIH | Center for Information Technology (Center for Information Technology, National Institutes of Health)/ ; EF-202545//National Science Foundation (NSF)/ ; }, mesh = {*Colorectal Neoplasms/microbiology/metabolism ; Humans ; *Proteomics/methods ; *Bacterial Proteins/metabolism ; Aspergillus/metabolism ; }, abstract = {Microbiome research has revealed associations between microbial species and colorectal cancer (CRC). Most of the existing research relied on metagenomic data. We leveraged a tool that we recently developed for detecting human and microbial peptides from (meta)proteomics data to reanalyze Clinical Proteomic Tumor Analysis Consortium CRC proteomics datasets. Our analyses revealed potential microbial species and proteins that are associated with CRC, especially when analyzing multiplexed proteomics data consisting of cancerous and healthy tissue taken from the same individuals. Many of the identified proteins are associated with species with known links to CRC, such as the fungi Aspergillus kawachii, but many are unstudied or their specific roles unknown. Proteins from other microbial species, such as Paenibacillus cellulosilyticus, were also identified in the samples. We showed that Aspergillus kawachii and others are depleted overall in cancer samples, which is consistent with a previous genomic-based multi-cohort study. Our analysis also revealed that some proteins belonging to this species are more abundantly detected, while others in this and other species are not. Further, we showed that microbial identifications could be used to build predictive models for tumor detection, but caution needs to be taken when applying such models trained on one dataset to another due to the substantial impacts of different experimental techniques on peptide detection profiles.}, }
@article {pmid40263397, year = {2025}, author = {Li, C and Zhu, J and Wang, Y and Jiang, W and Lin, Y}, title = {Metagenomic NGS reveals determinants of polymicrobial spinal infection pathogenesis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13959}, pmid = {40263397}, issn = {2045-2322}, support = {20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; }, mesh = {Humans ; Male ; Female ; Middle Aged ; Retrospective Studies ; Aged ; Risk Factors ; *Coinfection/microbiology ; *Metagenomics/methods ; ROC Curve ; Adult ; *Spinal Diseases/microbiology ; }, abstract = {To explore the influencing factors of spinal mixed infection under mNGS-assisted detection. A retrospective analysis was conducted on the general clinical data of patients diagnosed with spinal infections at Guilin People's Hospital, covering the period from October 2022 to October 2024, to evaluate the effectiveness of different treatment modalities including conservative, pharmacological, and surgical interventions. In the end, a total of 45 cases were included, including 18 cases of mixed infection and 27 cases of single infection. The receiver operating characteristic (ROC) curve was utilized to evaluate the predictive efficacy of various indices for the occurrence of mixed infection in patients with spinal infections, with the curve's proximity to the top left corner indicating higher diagnostic accuracy. Multivariate Logistic regression was used to analyze the independent risk factors affecting the development of mixed infection in patients with spinal infection. No significant differences were found between the two groups regarding gender, smoking, alcohol consumption, hypertension, albumin levels, liver function, malignancy, or rheumatic immune disease history (P > 0.05). However, the mixed infection group had significantly higher proportions of patients aged > 60 years (78% (14/18) vs. 48% (13/27)), diabetes mellitus (44% (8/18) vs. 15% (4/27)), chronic kidney disease (17% (3/18) vs. 0.00 (0/27)), and previous spinal surgery (39% (7/18) vs. 11% (3/27)), along with lower BMI (20.70 ± 2.15 vs. 24.04 ± 3.76) and hemoglobin levels (105.17 ± 14.05 g/L vs. 117.48 ± 18.08 g/L). The results of the ROC curve analysis showed that the area under the curve for BMI and hemoglobin in predicting the occurrence of mixed infection in patients was 0.787 and 0.704, respectively, with optimal cutoff values of 21.12 kg/m[2] and 119 g/L. Multivariate logistic regression identified BMI < 21.12 kg/m[2], hemoglobin < 119 g/L, and diabetes as independent risk factors. Lower BMI, diabetes and hemoglobin are independent risk factors for spinal mixed infection. Increasing BMI, effectively controlling blood glucose and improving anemia are helpful to reduce the occurrence of spinal mixed infection.}, }
@article {pmid40263287, year = {2025}, author = {Gao, D and Zhuang, Y and Liu, S and Ma, B and Xu, Y and Zhang, H and Nuermaimaiti, Y and Chen, T and Hou, G and Guo, W and You, J and Huang, Z and Xiao, J and Wang, W and Li, M and Li, S and Cao, Z}, title = {Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {61}, pmid = {40263287}, issn = {2055-5008}, support = {2024BBF01006//Key Research and Development Program of Ningxia/ ; 2023YFD1300904//National Key Research and Development Program of China/ ; 2024-KFKT-026//National Center of Technology Innovation for Dairy/ ; PC2023B02002//Pinduoduo-China Agricultural University Research Fund/ ; }, mesh = {Animals ; Cattle ; *Oxidative Stress ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Female ; Mice ; Fatty Acids, Volatile/metabolism ; Metabolomics ; Metagenomics ; *Clostridiales/genetics/metabolism/isolation &amp; purification ; Multiomics ; }, abstract = {An imbalance between oxidative and antioxidant processes in the host can lead to excessive oxidation, a condition known as oxidative stress (OS). Although changes in the hindgut microbiota have been frequently linked to OS, the specific microbial and metabolic underpinnings of this association remain unclear. In this study, we enrolled 81 postpartum Holstein cows and stratified them into high oxidative stress (HOS, n = 9) and low oxidative stress (LOS, n = 9) groups based on the oxidative stress index (OSi). Using a multi-omics approach, we performed 16S rRNA gene sequencing to evaluate microbial diversity, conducted metagenomic analysis to identify functional bacteria, and utilized untargeted metabolomics to profile serum metabolites. Our analyses revealed elevated levels of kynurenine, formyl-5-hydroxykynurenamine, and 5-hydroxyindole-3-acetic acid in LOS dairy cows. Additionally, the LOS cows had a higher abundance of short-chain fatty acids (SCFAs)-producing bacteria, including Bacteroidetes bacterium, Paludibacter propionicigenes, and Phascolarctobacterium succinatutens (P. succinatutens), which were negatively correlated with OSi. To explore the potential role of these bacteria in mitigating OS, we administered P. succinatutens (10[8] cfu/day for 14 days) to C57BL/6 J mice (n = 10). Oral administration of P. succinatutens significantly increased serum total antioxidant capacity, decreased total oxidants, and reduced OSi in mice. Moreover, this treatment promoted activation of the Nrf2-Keap1 antioxidant pathway, significantly enhancing the enzymatic activities of GSH-Px and SOD, as well as the concentrations of acetate and propionate in the colon. In conclusion, our findings suggest that systemic tryptophan metabolism and disordered SCFAs production are concurrent factors influenced by hindgut microbiota and associated with OS development. Modulating the hindgut microbiota, particularly by introducing specific SCFAs-producing bacteria, could be a promising strategy for combating OS.}, }
@article {pmid40263159, year = {2025}, author = {Pandey, A and Israr, J and Pandey, J and Misra, S}, title = {Current Approaches and Implications in Discovery of Novel Bioactive Products from Microbial Sources.}, journal = {Current microbiology}, volume = {82}, number = {6}, pages = {258}, pmid = {40263159}, issn = {1432-0991}, mesh = {*Biological Products/metabolism/pharmacology/isolation &amp; purification/chemistry ; *Drug Discovery/methods ; *Bacteria/metabolism/genetics ; Multigene Family ; Biosynthetic Pathways/genetics ; Microbiota ; }, abstract = {Bioactive Natural Products (BNPs) are in high demand due to their disease-preventive capabilities and resistance to pathogens. However, our understanding of BNP-producing microbes is limited, because many microbial populations remain uncultivated. Various approaches have been employed to explore the potential of these hidden microbes for new bioactive therapeutic compounds. Nevertheless, the possibility of discovering BNPs from microbial communities is largely cryptic due to their unculturable nature and the absence of triggers to activate the dormant Biosynthetic Gene Clusters (BGCs). Metagenome sequencing, followed by mining and characterization, is an effective approach for discovering new therapeutic BNPs. The inactive state of BGCs can be activated through the combinatorial interaction of different microbial communities within a common niche, overcoming programmable co-evolutionary stress and producing new BNPs. The present review discusses and explores the potential of hidden, uncultivated microbes for discovering novel Bioactive Natural Products (BNPs). Moreover, it provides insights into optimizing microbial production systems and fostering sustainable drug discovery and development practices by integrating multidisciplinary strategies. This review also emphasizes the critical role of microbial sources in the ongoing search for new bioactive products that can meet the demands of modern healthcare and environmental sustainability.}, }
@article {pmid40262434, year = {2025}, author = {Lima, RAT and Garay, AV and Frederico, TD and de Oliveira, GM and Quirino, BF and Barbosa, JARG and Freitas, SM and Krüger, RH}, title = {Biochemical and structural characterization of a family-9 glycoside hydrolase bioprospected from the termite Syntermes wheeleri gut bacteria metagenome.}, journal = {Enzyme and microbial technology}, volume = {189}, number = {}, pages = {110654}, doi = {10.1016/j.enzmictec.2025.110654}, pmid = {40262434}, issn = {1879-0909}, abstract = {Glycosyl hydrolases (GH) are enzymes involved in the degradation of plant biomass. They are important for biorefineries that aim at the sustainable utilization of lignocellulosic residues to generate value-added products. The termite Syntermes wheeleri gut microbiota showed an abundance of bacteria from the phylum Firmicutes, a phylum with enzymes capable of breaking down cellulose and degrading lignin, facilitating the use of plant materials as a food source for termites. Using bioinformatics techniques, cellobiohydrolases were searched for in the gut metagenome of the termite Syntermes wheeleri, endemic to the Cerrado. After selecting sequences of the target enzymes, termite gut microbiome metatranscriptome data were used as the criteria to choose the GH9 enzyme sequence Exo8574. Here we present the biochemical and structural characterization of Exo8574, a GH9 enzyme that showed activity with the substrate p-nitrophenyl-D-cellobioside (pNPC), consistent with cellobiohydrolase activity. Bioinformatics tools were used to perform phylogeny studies of Exo8574 and to identify conserved families and domains. Exo8574 showed 48.8 % homology to a protein from a bacterium belonging to the phylum Firmicutes. The high-quality three-dimensional (3D) model of Exo8574 was obtained by protein structure prediction AlphaFold 2, a neural network-based method. After the heterologous expression of Exo8574 and its purification, biochemical experiments showed that the optimal activity of the enzyme was at a temperature of 55 ºC and pH 6.0, which was enhanced in the presence of metal ions, especially Fe[2 +]. The estimated kinetic parameters of Exo8574 using the synthetic substrate p-nithrophenyl-beta-D-cellobioside (pNPC) were: Vmax = 9.14 ± 0.2 x10[-5] μmol/min and Km = 248.27 ± 26.35 μmol/L. The thermostability test showed a 50 % loss of activity after 1 h incubation at 55 °C. The secondary structure contents of Exo8574 evaluated by Circular Dichroism were pH dependent, with greater structuring of protein in β-antiparallel and α-helices at pH 6.0. The similarity between the CD results and the Ramachandran plot of the 3D model suggests that a reliable model has been obtained. Altogether, the results of the biochemical and structural characterization showed that Exo8574 is capable of acting on p-nithrophenyl-beta-D-cellobioside (pNPC), a substrate that mimics bonds cleaved by cellobiohydrolases. These findings have significant implications for advancing in the field of biomass conversion while also contributing to efforts aimed at overcoming challenges in developing more efficient cellulase cocktails.}, }
@article {pmid40262432, year = {2025}, author = {Wu, G and Zhang, H and Huang, T and Song, Y and Liu, X and Liu, X and Wang, X and Pei, T and Xu, G and Wang, Z}, title = {Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model.}, journal = {Water research}, volume = {282}, number = {}, pages = {123626}, doi = {10.1016/j.watres.2025.123626}, pmid = {40262432}, issn = {1879-2448}, abstract = {Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.}, }
@article {pmid40261735, year = {2025}, author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD}, title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.}, journal = {Database : the journal of biological databases and curation}, volume = {2025}, number = {}, pages = {}, doi = {10.1093/database/baae112}, pmid = {40261735}, issn = {1758-0463}, mesh = {Animals ; *Chickens/microbiology ; *Microbiota ; *Salmon/microbiology ; *Databases, Genetic ; *Host Microbial Interactions ; Metadata ; *Gastrointestinal Microbiome ; }, abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.}, }
@article {pmid40261409, year = {2025}, author = {Zhao, S and Guo, H and Wang, Z and Zhang, B and Chen, H and Klitzsch, N and Yue, L and Xia, D}, title = {Clay mineral content modulates biogenic gas production in coal: divergent microbial responses in low- and medium-rank coals revealed by multi-omics.}, journal = {Bioprocess and biosystems engineering}, volume = {}, number = {}, pages = {}, pmid = {40261409}, issn = {1615-7605}, support = {23ZX015//Key Scientific Research Project of Colleges and Universities in Henan Province/ ; 42172195//National Natural Science Foundation of China/ ; 42172199//National Natural Science Foundation of China/ ; AQ20240302//Double First-Class Initiative for Safety Discipline Construction Project/ ; 2024B03002//Xinjiang Key R &amp; D Task Project/ ; }, abstract = {The influence of clay mineral content on biogenic gas production in coal seams remains insufficiently understood. This study systematically investigated the mechanisms by which clay minerals affect biogas production in low- and medium-rank coals by integrating simulated biogas production experiments with multidimensional analytical techniques, including infrared spectroscopy, X-ray diffraction, scanning electron microscopy, gas chromatography-mass spectrometry, fluorescence spectroscopy, and metagenomic analysis. The results demonstrated that in low-rank coal, increasing the clay content from 2.78 to 4.75 g per 20 g of coal reduced the biogas yield from 6.30 to 3.47 mL/g. Conversely, in medium-rank coal, increasing the clay content from 1.66 to 2.65 g per 20 g of coal enhanced the biogas yield from 3.45 to 5.28 mL/g. These contrasting outcomes are primarily attributed to the distinct mechanistic roles of clay minerals across coal ranks. In low-rank coal, the hydration-induced swelling of clay minerals intensified pore blockage, impeded gas diffusion, decreased the abundance of genes involved in propionate degradation, and suppressed microbial metabolic activity, ultimately limiting methane production. In contrast, in medium-rank coal, clay minerals facilitated the enrichment of key functional microbial taxa, such as Acetobacteroides and Methanoculleus, promoted the degradation of fatty acids, hydroxyls, and amines, and enhanced the activity of acidogenic and methanogenic pathways, thereby increasing methane yield. This study elucidates the microbial mechanisms underlying the regulatory role of clay minerals in biogas production, offering new theoretical insights into the origin of coalbed methane (CBM) and providing a scientific foundation for optimizing biogenic CBM recovery.}, }
@article {pmid40261207, year = {2025}, author = {Liao, X and Li, Y and Wu, Y and Li, X and Shang, X}, title = {Deep Learning-Based Classification of CRISPR Loci Using Repeat Sequences.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00174}, pmid = {40261207}, issn = {2161-5063}, abstract = {With the widespread application of the CRISPR-Cas system in gene editing and related fields, along with the increasing availability of metagenomic data, the demand for detecting and classifying CRISPR-Cas systems in metagenomic data sets has grown significantly. Traditional classification methods for CRISPR-Cas systems primarily rely on identifying cas genes near CRISPR arrays. However, in cases where cas gene information is absent, such as in metagenomes or fragmented genome assemblies, traditional methods may fail. Here, we present a deep learning-based method, CRISPRclassify-CNN-Att, which classifies CRISPR loci solely based on repeat sequences. CRISPRclassify-CNN-Att utilizes convolutional neural networks (CNNs) and self-attention mechanisms to extract features from repeat sequences. It employs a stacking strategy to address the imbalance of samples across different subtypes and uses transfer learning to improve classification accuracy for subtypes with fewer samples. CRISPRclassify-CNN-Att demonstrates outstanding performance in classifying multiple subtypes, particularly those with larger sample sizes. Although CRISPR loci classification traditionally depends on cas genes, CRISPRclassify-CNN-Att offers a novel approach that serves as a significant complement to cas-based methods, enabling the classification of orphan or distant CRISPR loci. The proposed tool is freely accessible via https://github.com/Xingyu-Liao/CRISPRclassify-CNN-Att.}, }
@article {pmid40261064, year = {2025}, author = {Žuštra, A and Leonard, VR and Holland, LA and Hu, JC and Mu, T and Holland, SC and Wu, LI and Begnel, ER and Ojee, E and Chohan, BH and Richardson, BA and Kinuthia, J and Wamalwa, D and Slyker, J and Lehman, DA and Gantt, S and Lim, ES}, title = {Longitudinal dynamics of the nasopharyngeal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their children.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0156824}, doi = {10.1128/msystems.01568-24}, pmid = {40261064}, issn = {2379-5077}, abstract = {UNLABELLED: The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest. The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coronavirus disease 2019 pandemic, on the nasopharyngeal microbiome among individuals living with HIV is not fully characterized. Here, we describe the nasopharyngeal microbiome before, during, and after SARS-CoV-2 infection in a longitudinal cohort of Kenyan women (21 living with HIV and 14 HIV-uninfected) and their children (18 HIV-exposed, uninfected and 7 HIV-unexposed, uninfected) between September 2021 and March 2022. We show using genomic epidemiology that mother and child dyads were infected with the same strain of the SARS-CoV-2 Omicron variant that spread rapidly across Kenya. We used metagenomic sequencing to characterize the nasopharyngeal microbiome of 20 women and children infected with SARS-CoV-2, six children negative for SARS-CoV-2 but experiencing respiratory symptoms, and 34 timepoint-matched SARS-CoV-2-negative mothers and children. Since individuals were sampled longitudinally before and after SARS-CoV-2 infection, we could characterize the short- (within a week of infection) and longer- (average of 38 days post-infection) term impact of SARS-CoV-2 infection on the nasopharyngeal microbiome. We found that mothers and children had significantly different microbiome composition and bacterial load (P-values < 0.0001). In both mothers and children, the nasopharyngeal microbiome did not differ before and after SARS-CoV-2 infection, regardless of HIV exposure status. Our results indicate that the nasopharyngeal microbiome is resilient to SARS-CoV-2 infection and was not significantly modified by HIV.<br><br>IMPORTANCE: The nasopharyngeal microbiome plays an important role in human health. The degree of impact that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has on the nasopharyngeal microbiome varies among studies and may be influenced by diverse SARS-CoV-2 variants and variations in the microbiome between individuals. Our results show that the nasopharyngeal microbiome was not altered substantially by SARS-CoV-2 infection nor by HIV infection in mothers or HIV exposure in children. Our findings highlight the resilience of the nasopharyngeal microbiome after SARS-CoV-2 infection. These findings advance our understanding of the nasopharyngeal microbiome and its interactions with viral infections.}, }
@article {pmid40261045, year = {2025}, author = {Doing, G and Shanbhag, P and Bell, I and Cassidy, S and Motakis, E and Aiken, E and Oh, J and Adams, MD}, title = {TEAL-Seq: targeted expression analysis sequencing.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0098424}, doi = {10.1128/msphere.00984-24}, pmid = {40261045}, issn = {2379-5042}, abstract = {Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed "targeted expression analysis sequencing" or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.IMPORTANCEThe gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step enables the profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.}, }
@article {pmid40260991, year = {2025}, author = {López-Gálvez, R and Orenes-Piñero, E and Rivera-Caravaca, JM and Pérez-Sanz, F and Ramos-Bratos, MP and Roca, MI and Mandaglio-Collados, D and López-García, C and Gil-Pérez, P and Esteve-Pastor, MA and Marín, F}, title = {Microbial Insights: The Role of Diet in Modulating Gut Microbiota and Metabolites After Acute Coronary Syndrome.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70046}, doi = {10.1002/mnfr.70046}, pmid = {40260991}, issn = {1613-4133}, support = {//Instituto de Salud Carlos III/ ; //Centro de investigaci&#xf3;n Biom&#xe9;dica en Red/ ; }, abstract = {Acute coronary syndrome (ACS) is a leading cause of global mortality, largely due to atherosclerosis influenced by lifestyle factors like diet. Gut microbiota impacts lipid metabolism, inflammation, and endothelial function, all vital in atherosclerosis. Dysbiosis increases intestinal permeability, causing inflammation and plaque instability, elevating cardiac event risk. This study investigates the impact of dietary improvements on gut microbiota and metabolite release in recent ACS patients versus healthy individuals. A cohort of 29 recent ACS patients receiving lipid-lowering therapy and dietary advice was analyzed alongside 56 healthy controls. Dietary habits, serum, and stool samples were collected at admission and after 3 months. Metagenomic analysis of stool and metabolomic analysis of serum were conducted. The results showed bacterial dysbiosis in ACS patients, characterized by a reduction in beneficial genera and an increase in potentially pro-inflammatory bacteria. After 3 months of dietary improvements, three metabolites with anti-inflammatory properties were significantly upregulated. The findings highlight the association between gut microbiota dysbiosis, fatty diets, and inflammation in ACS patients. The observed increase in anti-inflammatory metabolites following dietary changes underscore the following dietary interventions in modulating gut microbiota and improving cardiovascular and metabolic health.}, }
@article {pmid40260089, year = {2025}, author = {Xu, P and Pan, C and Yuan, M and Zhu, Y and Wei, S and Lu, H and Zhang, W}, title = {Viral metagenomics reveals diverse viruses in the fecal samples of children with acute respiratory infection.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1564755}, pmid = {40260089}, issn = {1664-302X}, abstract = {INTRODUCTION: Changes in the gut microbiome have been associated with the development of acute respiratory infection (ARI). However, due to methodological limitations, our knowledge of the gut virome in patients with ARIs remains limited.<br><br>METHODS: In this study, fecal samples from children with ARI were investigated using viral metagenomics.<br><br>RESULTS: The fecal virome was analyzed, and several suspected disease-causing viruses were identified. The five viral families with the highest abundance of sequence reads were Podoviridae, Virgaviridae, Siphoviridae, Microviridae, and Myoviridae. Additionally, human adenovirus, human bocavirus, human astrovirus, norovirus, and human rhinovirus were detected. The genome sequences of these viruses were respectively described, and phylogenetic trees were constructed using the gene sequences of the viruses.<br><br>DISCUSSION: We characterized the composition of gut virome in children with acute respiratory infections. However, further research is required to elucidate the relationship between acute respiratory infection and gut viruses.}, }
@article {pmid40260085, year = {2025}, author = {Perez, LJ and Perez-Restrepo, LS and Ciuoderis, K and Usuga, J and Moreno, I and Vargas, V and Arévalo-Arbelaez, AJ and Berg, MG and Cloherty, GA and Hernández-Ortiz, JP and Osorio, JE}, title = {Emergence, persistence, and positive selection of yellow fever virus in Colombia.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1548556}, pmid = {40260085}, issn = {1664-302X}, abstract = {Yellow fever virus (YFV) is an arbovirus that causes acute febrile illness (AFI), in tropical areas of South America and Africa. Through a 2020-2023 AFI study in Leticia, Colombia, leveraging metagenomic next-generation sequencing (mNGS), we identified and isolated YFV (LET1450). Phylogenetic analysis showed this strain belongs to South American genotype II (SamII), linked to Peruvian and Bolivian sequences emerging around 1989. Phylodynamic analysis indicates these strains, with a unique genetic makeup, could have reduced vaccine susceptibility, and due to positive Darwinian selection have an enhanced adaptive capacity. Antigenic analysis identified additional immune-evasive traits and this strain's potential for wider Latin American spread. Phylogeographic reconstruction demonstrated the persistence of YFV in Colombia is not due to repeated external introductions, but results from continuous, cryptic internal circulation. This study highlights the crucial role of mNGS in monitoring emerging strains and underscores the need for genomic surveillance of YFV and other arboviral infections.}, }
@article {pmid40260047, year = {2025}, author = {Guo, L and Wu, X and Cao, L}, title = {Clinical Characteristics of Miliary Pulmonary Tuberculosis in Pregnancy After In Vitro Fertilization-Embryo Transfer: A Retrospective Clinical Study.}, journal = {Health science reports}, volume = {8}, number = {4}, pages = {e70705}, pmid = {40260047}, issn = {2398-8835}, abstract = {BACKGROUND AND AIMS: Miliary pulmonary tuberculosis (MPTB) is rare in patients treated with In Vitro fertilization-embryo transfer (IVF-ET), and can be life-threatening to pregnant women and fetuses. We aimed to describe the clinical characteristics of MPTB after IVF-ET and pregnancy outcomes to provide reference for early diagnosis and treatment.<br><br>METHODS: Clinical data from patients who developed MPTB after IVF-ET from January 2018-December 2021 were retrospectively and statistically analyzed.<br><br>RESULTS: Ultimately, 21 patients (mean age: 29.81&#x2009;&#xb1;&#x2009;3.79 years) were included. Three patients had a history of pulmonary or extrapulmonary tuberculosis (TB), and were cured or showed no suggestive TB activity before pregnancy. Patients presented with atypical early symptoms, fever (39.16&#x2009;&#xb1;&#x2009;0.74&#xb0;C), and vaginal bleeding, and lung imaging changes. Patients became febrile 78.90&#x2009;&#xb1;&#x2009;26.04 days after IVF-ET; the time from fever to diagnosis was 17.76&#x2009;&#xb1;&#x2009;9.05 days. Patients were admitted 96.05&#x2009;&#xb1;&#x2009;25.33 days after IVF-ET. Sputum Mycobacterium tuberculosis smear and culture, purified protein derivative, TB polymerase chain reaction, and other routine TB examinations had low positivity rates; the erythrocyte sedimentation rate was generally within normal limits. Chest imaging during pregnancy is limited, further increasing the diagnosis time. Two critically ill patients were diagnosed by metagenomic next-generation sequencing. Seven patients had TB meningitis or encephalitis. Pregnancy was terminated in all but three patients. All patients received anti-TB therapy; however, two patients died during hospitalization (mean hospitalization: 58.29&#x2009;&#xb1;&#x2009;33.40 days).<br><br>CONCLUSIONS: Comprehensive TB screening before IVF-ET is necessary for infertile patients. MPTB develops after IVF-ET with atypical symptoms and poor pregnancy outcomes. Clinicians should use multiple methods to confirm TB diagnoses early on, without delaying chest imaging.}, }
@article {pmid40259990, year = {2025}, author = {Chen, Y and Liu, Y and Ji, M and Zhang, Z and Xing, T and Pan, H and Liu, K and Li, Y and Liu, P}, title = {Metabolic diversity and adaptation of carbon-fixing microorganisms in extreme glacial cryoconite.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf056}, pmid = {40259990}, issn = {2730-6151}, abstract = {Understanding the diversity and functionality of carbon-fixing microorganisms in glacial ecosystems is crucial for elucidating carbon cycling processes in extreme environments. This study investigates the composition, diversity, and metabolic potential of carbon-fixing microorganisms in Tibetan cryoconite. Through metagenomic sequencing, we identified 13 carbon-fixing metagenome-assembled genomes spanning ten known and three unclassified genera. Deoxyribonucleic acid -stable isotope probing experiments with [13]C-labeled sodium bicarbonate confirmed the metabolic activity of key genera, including Cyanobacteria (Microcoleus and Phormidesmis) and Proteobacteria (Rhizobacter and Rhodoferax). Our results reveal a diverse array of carbon fixation pathways, with the Calvin-Benson-Bassham cycle and 3-hydroxypropionate bicycle being the most prominent. In addition to photoautotrophic microorganisms, chemoautotrophic microorganisms also contribute to carbon fixation through mechanisms such as sulfur oxidation and atmospheric reducing gas utilization. The study highlights the adaptability of microbial communities to varying environmental conditions, including fluctuations in oxygen, light, and substrate availability. The findings underscore the complex interplay between carbon fixation pathways and environmental factors in cryoconite ecosystems. It also emphasizes the importance of exploring alternative carbon fixation pathways to gain a more comprehensive understanding of carbon cycling in these harsh and dynamic ecosystems.}, }
@article {pmid40259731, year = {2025}, author = {Sun, YS and Zhao, L and Zheng, CL and Yan, XT and Li, Y and Gao, XL and Xue, TF and Zhang, YM and Li, ZP and Heller, R and Feng, CG and Xu, C and Wang, K and Qiu, Q}, title = {Convergent musk biosynthesis across host and microbiota in musk deer and muskrat.}, journal = {Zoological research}, volume = {46}, number = {3}, pages = {505-517}, doi = {10.24272/j.issn.2095-8137.2025.094}, pmid = {40259731}, issn = {2095-8137}, mesh = {Animals ; *Deer/microbiology/metabolism ; *Fatty Acids, Monounsaturated/metabolism ; *Microbiota ; Scent Glands/metabolism ; *Arvicolinae/microbiology/metabolism ; }, abstract = {Mammalian scent glands mediate species-specific chemical communication, yet the mechanistic basis for convergent musk production remain incompletely understood. Forest musk deer and muskrat have independently evolved specialized musk-secreting glands, representing a striking case of convergent evolution. Through an integrated multi-omics approach, this study identified cyclopentadecanone as a shared key metabolic precursor in musk from both forest musk deer and muskrat, although downstream metabolite profiles diverged between the two lineages. Single-cell RNA sequencing revealed that these specialized apocrine glands possessed unique secretory architecture and exhibited transcriptional profiles associated with periodic musk production, distinct from those in conventional apocrine glands. Convergent features were evident at the cellular level, where acinar, ductal, and basal epithelial subtypes showed parallel molecular signatures across both taxa. Notably, acinar cells in both species expressed common genes involved in fatty acid and glycerolipid metabolism (e.g., ACSBG1, HSD17B12, HACD2, and HADHA), suggesting a conserved molecular framework for musk precursor biosynthesis. Metagenomic analysis of musk samples further revealed parallel microbial community structures dominated by Corynebacterium and enriched in lipid metabolic pathways. These findings suggest multi-level convergence in musk biosynthesis, from molecular pathways to microbial communities, providing novel insights into mammalian chemical signaling and artificial musk production.}, }
@article {pmid40259344, year = {2025}, author = {Zhang, Q and Hutchison, ER and Pan, C and Warren, MF and Keller, MP and Attie, AD and Lusis, AJ and Rey, FE}, title = {Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {101}, pmid = {40259344}, issn = {2049-2618}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Amylases/genetics/metabolism ; Genome-Wide Association Study ; Metagenomics/methods ; Male ; Bacteroidetes/genetics/classification/isolation &amp; purification ; Mendelian Randomization Analysis ; Firmicutes/genetics/classification/isolation &amp; purification ; Cecum/microbiology ; }, abstract = {BACKGROUND: Population studies have revealed associations between host genetic and gut microbiome in humans and mice. However, the molecular bases for how host genetic variation impacts the gut microbial community and bacterial metabolic niches remain largely unknown.<br><br>RESULTS: We leveraged 90 inbred hyperlipidemic mouse strains from the hybrid mouse diversity panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these, we detected a genetic locus surrounding multiple amylase genes that were associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar degrading capabilities. The genetic variants at the amylase gene locus were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes.<br><br>CONCLUSIONS: This work reveals novel relationships among host genetic variation, gut microbial enterotypes, and host metabolic traits and supports the notion that variation of host amylase may represent a key determinant of gut microbiome in mice. Video Abstract.}, }
@article {pmid40258842, year = {2025}, author = {Duru, IC and Lecomte, A and Laine, P and Shishido, TK and Suppula, J and Paulin, L and Scheperjans, F and Pereira, PAB and Auvinen, P}, title = {Comparison of phage and plasmid populations in the gut microbiota between Parkinson's disease patients and controls.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13723}, pmid = {40258842}, issn = {2045-2322}, support = {NNF22OC0080109//Novo Nordisk Foundation/ ; }, mesh = {Humans ; *Parkinson Disease/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/isolation &amp; purification ; Aged ; *Plasmids/genetics ; Male ; Female ; Middle Aged ; Feces/microbiology/virology ; Case-Control Studies ; Metagenomics/methods ; Machine Learning ; }, abstract = {The aging population worldwide is on the rise, leading to a higher number of Parkinson's disease (PD) cases each year. PD is presently the second most prevalent neurodegenerative disease, affecting an estimated 7-10 million individuals globally. This research aimed to identify mobile genetic elements in human fecal samples using a shotgun metagenomics approach. We identified over 44,000 plasmid contigs and compared plasmid populations between PD patients (n = 68) and controls (n = 68). Significant associations emerged between groups (control vs PD) based on plasmid alpha and beta diversity. Moreover, the gene populations present on plasmids displayed marked differences in alpha and beta diversity between PD patients and controls. We identified a considerable number of phage contigs that were differentially abundant in the two groups. We also developed a predictive machine learning model based on phage abundance data, achieving a mean Area Under the Curve (AUC) of 0.74 with a standard deviation of 0.105 and a mean F1 score of 0.68 with a standard deviation of 0.14 across cross-validation folds, indicating moderate discriminatory power. Additionally, when tested on external data, the model yielded an AUC of 0.74 and an F1 score of 0.8, further demonstrating the predictive potential of phage populations in Parkinson's disease. Further, we improved the continuity and identification of the protein coding regions of the phage contigs by implementing alternative genetic codes.}, }
@article {pmid40258509, year = {2025}, author = {Fang, C and Zhu, J and Xu, H and Qian, M and Jin, Y}, title = {Polystyrene microplastics and cypermethrin exposure interfered the complexity of antibiotic resistance genes and induced metabolic dysfunction in the gut of adult zebrafish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126288}, doi = {10.1016/j.envpol.2025.126288}, pmid = {40258509}, issn = {1873-6424}, abstract = {Environmental pollutants such as microplastics (MPs) and pesticides are becoming prevalent in aquatic ecosystems, posing risks to wildlife and human health. This study investigated the toxicological effects of polystyrene microplastics (PS-MPs) and cypermethrin (CYP) on adult female zebrafish (Danio rerio), focusing on intestinal microenvironment. Adsorption kinetics experimental results showed that PS-MPs can adsorb a certain amount of CYP on its surface, thereby forming a new type of composite pollutant. After exposure to red fluorescent PS-MPs for 4 days, it was found that the PS-MPs could enter the zebrafish and accumulate in the intestines. Five-month-old female zebrafish were exposed to PS-MPs, CYP, and a mixture of both for 21 days. After exposure, feces were collected and analyzed using metagenomic sequencing to determine microbial composition and functional changes. Metagenomic sequencing of naturally excreted feces showed that co-exposure synergistically reduced α-diversity and shifted community structure, with marked losses of beneficial Fusobacteriota, Firmicutes and Cetobacterium somerae and enrichment of pathogenic Preplasmiviricota. Functional annotation indicated that PS-MPs alone up-regulated glycoside hydrolases and glycosyl-transferases, whereas CYP and the co-exposure group suppressed a great number of the top 50 carbohydrate-active enzymes and decreased secondary metabolic pathways linked to amino-acid, lipid and carbohydrate metabolism pathways. Antibiotic-resistance gene (ARGs) profiling identified 57 ARG types (such as sul1, adeF, lnuC and mphA) after co-exposure. Finally, key genes related to amino acid metabolism, carbohydrate metabolism, and lipid metabolism in intestinal tissue were significantly altered. Collectively, our data demonstrated that PS-MPs and CYP exposure amplified gut dysbiosis, metabolic dysfunction and ARG complexity in zebrafish. Overall, the study highlighted the potential risks of combined environmental pollutants on intestinal microbiota, with implications for ecosystem health.}, }
@article {pmid40258462, year = {2025}, author = {He, R and Li, X and Zhang, X}, title = {Methane enhancing nitrous oxide consumption in microaerobic sludge systems.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121658}, doi = {10.1016/j.envres.2025.121658}, pmid = {40258462}, issn = {1096-0953}, abstract = {Nitrous oxide (N2O) reduction is traditionally known to be active under extremely low oxygen concentrations and hypoxic conditions. Herein, microaerobic sludge systems (∼38.2 and ∼12.1 μM dissolved oxygen) were conducted to investigate the performance of simultaneous methane (CH4) oxidation and N2O consumption compared with hypoxic conditions. During the whole experiment, the average N2O consumption rate in the high dissolved oxygen sludge system with CH4 was 3.4-4.9 times that of the others. A positively linear correlation was observed between the CH4 oxidation rate and the N2O consumption rate in the sludge systems. Compared to the treatment without CH4, the N2O consumption rate was higher in the treatment with CH4, indicating that aerobic CH4 oxidation might be related with the N2O consumption in the systems. The N2O consumption in the microaerobic system was influenced by the O2, CH4 and NH4[+]-N concentrations and was regulated by the microbial species. Type I methane-oxidizing bacteria (MOB) including Methylococcus, Methylocaldum, Methylomagnum, Methylosarcina, Methylobacter and Methylogaea, type II MOB Methylocystis and NC10 phylum Candidatus Methylomirabilis were the main methanotrophs in the systems. Compared with type II MOB, type I MOB were more abundant in the system. Anaerolinea and Lautropia were the main denitrifying bacteria in the microaerobic system with CH4 and N2O. Clad I nosZ and clad II nosZ were both rich in the microaerobic system. These findings suggest that an appropriate oxygen concentration would be favorable for simultaneous mitigation of CH4 and N2O emission in the sludge systems.}, }
@article {pmid40257249, year = {2025}, author = {Maggiori, C and John, Z and Bower, DM and Millan, M and Hahn, AS and McAdam, A and Johnson, SS}, title = {Draft genome sequence of a member of a putatively novel Rubrobacteraceae genus from lava tubes in Lava Beds National Monument.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0133524}, doi = {10.1128/mra.01335-24}, pmid = {40257249}, issn = {2576-098X}, abstract = {We report the draft genome sequence of a member of a potentially novel genus of Rubrobacteraceae isolated from Golden Dome Cave in Lava Beds National Monument. Members of this family are known to inhabit thermophilic environments. The metagenome-assembled genome presented here helps illuminate the genetic capacity of basaltic lava tube environments.}, }
@article {pmid40257199, year = {2025}, author = {Wang, X and Wang, M and Zhang, W and Li, H and Tiedje, JM and Zhou, J and Topp, E and Luo, Y and Chen, Z}, title = {Treatment of antibiotic-manufacturing wastewater enriches for Aeromonas veronii, a zoonotic antibiotic-resistant emerging pathogen.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf077}, pmid = {40257199}, issn = {1751-7370}, abstract = {Antibiotic-manufacturing wastewater treatment plants primarily target chemical pollutants, but their processes may select for antibiotic-resistant pathogens and antibiotic resistance genes. Here, leveraging the combined strengths of deep metagenomic sequencing, 16S rRNA gene sequencing, qPCR, and bacterial culturing, we investigated bacterial communities and antibiotic resistomes across eleven treatment units in a full-scale antibiotic-manufacturing wastewater treatment plant processing wastewater from a β-lactam manufacturing facility. We demonstrated that both bacterial communities and antibiotic resistance gene compositions varied across the treatment units, but were associated. Certain antibiotic resistance gene persisted through treatment, either carried by identical bacterial species, or linked to mobile genetic elements in different species. Despite the satisfactory performance in chemical removal, the antibiotic-manufacturing wastewater treatment plant continuously enriched zoonotic antibiotic-resistant Aeromonas veronii (an emerging pathogen responsible for substantial economic losses in aquaculture and human health) from influent to effluent, probably due to prolonged β-lactam selection pressure and aquatic nature of A. veronii. This enrichment resulted in a significantly higher abundance of A. veronii in the antibiotic-manufacturing wastewater treatment plant compared to other aquatic samples worldwide. Furthermore, the closest evolutionary relative to the antibiotic-manufacturing wastewater treatment plant derived A. veronii was an isolate obtained from the stool of a local diarrhea patient. These findings highlighted a substantial public health risk posed by antibiotic-manufacturing wastewater treatment plants, underlining their potential role in enriching and disseminating zoonotic antibiotic-resistant pathogens. Beyond chemical monitoring, enhanced surveillance of antibiotic-resistant pathogens and antibiotic resistance genes is needed in antibiotic-manufacturing wastewater treatment plants to avoid creating environmental hotspots of antibiotic resistant pathogens from discharging wastewater effluents.}, }
@article {pmid40256453, year = {2025}, author = {Shen, D and Ju, H and Wang, H and Wang, X and Li, G}, title = {The clinic application of mNGS and ENA-78 assays to identify intra-amniotic infection/inflammation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1510671}, pmid = {40256453}, issn = {2235-2988}, mesh = {Humans ; Female ; Pregnancy ; *Amniotic Fluid/microbiology/chemistry ; Adult ; *Chorioamnionitis/diagnosis ; *Inflammation/diagnosis ; *Pregnancy Complications, Infectious/diagnosis ; Biomarkers/analysis ; High-Throughput Nucleotide Sequencing ; Obstetric Labor, Premature/diagnosis ; Pregnancy Outcome ; Cerclage, Cervical ; Young Adult ; *Chemokine CXCL5/analysis ; }, abstract = {OBJECTIVE: The objective of this study is to explore whether metagenomic next-generation sequencing (mNGS) and Epithelial Neutrophil Activating Peptide-78 (ENA-78) assays in the amniotic fluid (AF) of patients with preterm labor (PTL) could be employed for diagnosing intra-amniotic infection/inflammation (IAI/I) and predict the outcomes of emergency cerclage in women with cervical insufficiency(CI).<br><br>METHODS: AF samples from 40 patients were subjected to PTL were subjected to mNGS and microbial culture to diagnose intra-amniotic infection known as microbial invasion of the amniotic cavity (MIAC); ELISA was used to analyze ENA-78 levels for prediction of intra-amniotic inflammation (IAI). Pregnancy outcomes were compared, the predictive performance of mNGS and ENA-78 were assessed to evaluate the efficacy of emergency cervical cerclage.<br><br>RESULTS: The diagnosis rate of MIAC was higher with mNGS (17.5%) compared to microbial culture (2.5%). AF ENA-78 levels were significantly higher in IAI patients than in non-IAI/I patients. ENA-78 demonstrated certain accuracy in identifying IAI, with sensitivity and specificity of 73.3% and 100%, respectively. Compared with non-IAI/I patients, patients with MIAC or IAI exhibited poor pregnancy outcomes after cervical cerclage.<br><br>CONCLUSIONS: mNGS and ENA-78 assays are valuable means for assessing the state of infection/inflammation in the amniotic cavity and predicting the outcomes of emergency cerclage.}, }
@article {pmid40255248, year = {2025}, author = {Favale, N and Costa, S and Summa, D and Sabbioni, S and Mamolini, E and Tamburini, E and Scapoli, C}, title = {Comparison of microbiome community structure and dynamics during anaerobic digestion of different renewable solid wastes.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100383}, pmid = {40255248}, issn = {2666-5174}, abstract = {This study analysed the effect of the different lignocellulose composition of two crop substrates on the structure and dynamics of bacterial communities during anaerobic digestion (AD) processes for biogas production. To this end, cereal grains and grape pomace biomasses were analysed in parallel in an experimental AD bench-scale system to define and compare their metagenomic profiles for different experimental time intervals. The bacterial community structure and dynamics during the AD process were detected and characterised using high-resolution whole metagenomic shotgun analyses. Statistical evaluation identified 15 strains as specific to two substrates. Some strains, like Clostridium isatidis, Methanothermobacter wolfeii, and Methanobacter sp. MB1 in cereal grains, and Acetomicrobium hydrogeniformans and Acetomicrobium thermoterrenum in grape pomace, were never before detected in biogas reactors. The presence of bacteria such as Acetomicrobium sp. and Petrimonas mucosa, which degrade lipids and protein-rich substrates, along with Methanosarcina sp. and Peptococcaceae bacterium 1109, which tolerate high hydrogen pressures and ammonia concentrations, suggests a complex syntrophic community in lignin-cellulose-enriched substrates. This finding could help develop new strategies for the production of a tailor-made microbial consortium to be inoculated from the beginning of the digestion process of specific lignocellulosic biomass.}, }
@article {pmid40255076, year = {2025}, author = {Buttler, L and Velázquez-Ramírez, DA and Tiede, A and Conradi, AM and Woltemate, S and Geffers, R and Bremer, B and Spielmann, V and Kahlhöfer, J and Kraft, ARM and Schlüter, D and Wedemeyer, H and Cornberg, M and Falk, C and Vital, M and Maasoumy, B}, title = {Distinct clusters of bacterial and fungal microbiota in end-stage liver cirrhosis correlate with antibiotic treatment, intestinal barrier impairment, and systemic inflammation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2487209}, doi = {10.1080/19490976.2025.2487209}, pmid = {40255076}, issn = {1949-0984}, mesh = {Humans ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Aged ; Dysbiosis/microbiology ; *Fungi/classification/isolation &amp; purification/genetics ; *Inflammation/microbiology ; *Liver Cirrhosis/microbiology ; *Mycobiome ; Prospective Studies ; Metagenomics ; Intestinal Mucosa/microbiology ; *End Stage Liver Disease/microbiology/drug therapy ; Adult ; }, abstract = {Decompensated liver cirrhosis (dLC) is associated with intestinal dysbiosis, however, underlying reasons and clinical consequences remain largely unexplored. We investigated bacterial and fungal microbiota, their relation with gut barrier integrity, inflammation, and cirrhosis-specific complications in dLC-patients. Competing-risk analyses were performed to investigate clinical outcomes within 90 days. Samples were prospectively collected from 95 dLC-patients between 2017 and 2022. Quantitative metagenomic analyses clustered patients into three groups (G1-G3) showing distinct microbial patterns. G1 (n = 39) displayed lowest diversity and highest Enterococcus abundance, G2 (n = 24) was dominated by Bifidobacteria, G3 (n = 29) was most diverse and clustered most closely with healthy controls (HC). Of note, bacterial concentrations were significantly lower in cirrhosis compared with HC, especially for G1 that also showed the lowest capacity to produce short chain fatty acids and secondary bile acids. Consequently, fungal overgrowth, dominated by Candida spp. (51.63%), was observed in G1. Moreover, G1-patients most frequently received antibiotics (n = 33; 86.8%), had highest plasma-levels of Zonulin (p = 0.044) and a proinflammatory cytokine profile along with numerically higher incidences of subsequent infections (p = 0.09). In conclusion, distinct bacterial clusters were observed at qualitative and quantitative levels and correlated with fungal abundances. Antibiotic treatment significantly contributed to dysbiosis, which translated into intestinal barrier impairment and systemic inflammation.}, }
@article {pmid40254830, year = {2025}, author = {Pham, CM and Rankin, TJ and Stinear, TP and Walsh, CJ and Ryan, FJ}, title = {TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf173}, pmid = {40254830}, issn = {1477-4054}, support = {GNT1194325//National Health and Medical Research Council of Australia/ ; }, mesh = {*Microbiota ; Humans ; *Software ; *Metagenomics/methods ; Diabetes Mellitus, Type 2/microbiology/genetics ; *Databases, Genetic ; *Computational Biology/methods ; Inflammatory Bowel Diseases/microbiology/genetics ; Metagenome ; }, abstract = {Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most current tools focus on detecting changes among individual taxa (e.g. species or genera), however in other omics fields, such as transcriptomics, enrichment analyses like gene set enrichment analysis are commonly used to uncover patterns not seen with individual features. Here, we introduce TaxSEA, a taxon set enrichment analysis tool available as an R package, a web portal (https://shiny.taxsea.app), and a Python package. TaxSEA integrates taxon sets from five public microbiota databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, and GMRepoV2) while also allowing users to incorporate custom sets such as taxonomic groupings. In silico assessments show TaxSEA is accurate across a range of set sizes. When applied to differential abundance analysis output from inflammatory bowel disease and type 2 diabetes metagenomic data, TaxSEA can rapidly identify changes in functional groups corresponding to known associations. We also show that TaxSEA is robust to the choice of differential abundance analysis package. In summary, TaxSEA enables researchers to efficiently contextualize their findings within the broader microbiome literature, facilitating rapid interpretation, and advancing understanding of microbiome-host and environmental interactions.}, }
@article {pmid40254787, year = {2025}, author = {Dame-Teixeira, N and Lynch, J and Yu, X and Cena, JA and Do, T}, title = {The Caries and Caries-Free Archaeome.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345251329343}, doi = {10.1177/00220345251329343}, pmid = {40254787}, issn = {1544-0591}, abstract = {The difficulty of establishing a relationship between archaea and oral diseases such as dental caries stems from the challenges of detecting, identifying, and isolating these microorganisms. This study aimed to detect archaea in publicly available datasets comprising caries and caries-free saliva and dental plaque by using a tailored bioinformatic pipeline for shotgun sequencing analysis. A systematic search was performed to identify studies using shotgun metagenomics or metatranscriptomics on samples obtained from individuals with dental caries. Two reviewers selected studies based on eligibility criteria. Sequencing and metadata from each study were retrieved from the SRA Bioproject. A count table was generated for each database by mapping reads against an archaea genome database, specifically tailored for this study, using stringent filtering parameters of greater than 97% similarity and 90% query coverage. Archaeal prevalence was determined using an arbitrary cutoff point (>500 reads). An effect size meta-analysis was performed to determine the overall prevalence. Phyloseq and DESeq2 packages were used to determine alpha and beta diversities, differential abundance in different taxonomic levels, and differential expression comparing caries and caries-free samples. Spearman correlation was performed with the bacteriome. The search yielded 154 titles, from which a collection of 7 datasets from 8 studies was obtained. Of 397 samples, N = 63 were positive for archaea using postfiltering, comprising a putative prevalence of 20% (confidence interval = 0%-40%) and identifying Euryarchaeota, Thermoplasmatota, and Nitrosphaeria. Methanogens were present in both the caries and caries-free groups (Methanobrevibacter spp., Methanosarcina, and Methanosphaera) and positively correlated with Stenotrophomonas, Streptococcus, Actinomyces, Abiotrophia, Gemella, and Corynebacterium. Several methanogenesis genes, including methyl-coenzyme M reductase, which catalyzes the final step of methane production in methanogens, were underexpressed in caries-active samples compared with caries-free samples. Saliva and dental plaque emerged as sites of low-abundance archaea, with methanogenesis genes underexpressed in caries-active samples.}, }
@article {pmid40254701, year = {2025}, author = {Zaharuddin, AM and Muslim, A and Aazmi, S and Idorus, MY and Almabhouh, FA and Lim, SY and Loganathan, AL and Ayub, Q and Chong, CW and Khalil, KA and Ghani, NA and Lim, SM and Ramasamy, K}, title = {Probiotic Lactobacillus rhamnosus GG Alleviates Prehypertension and Restores Gut Health and Microbiota in NaCl-Induced Prehypertensive Rats.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40254701}, issn = {1867-1314}, abstract = {Probiotics could be used as adjuvant treatments in prehypertension management to restore gut microbiota dysbiosis caused by a high-salt diet. This study investigated the antihypertensive effects of the probiotic Lactobacillus rhamnosus strain GG (LGG) on high-salt diet-induced prehypertensive rats. Eighteen Sprague-Dawley rats were assigned equally into three groups: normotensive fed on a normal diet (ND), prehypertensive induced on a 4% NaCl high-salt diet (HSD), and prehypertensive induced on an HSD treated with LGG at 1 × 10[9] CFU daily for 8 weeks (LGG). Weekly changes in water, food, body weight, diastolic blood pressure (DBP), systolic blood pressure (SBP), and mean arterial pressure (MAP) were monitored. Serum levels of Na, K, Cl, ALB, Ca, and TP were measured at the end of treatment, along with morphological and histomorphometric changes in the small intestine. Stool samples collected before (W0) and 8 weeks after treatment (W8) were sequenced for bacterial 16S rDNA metagenomics. Probiotic LGG significantly reduces average DBP, SBP, and MAP while improving gut integrity through intact intestine morphology, higher villus heights, and a V/C ratio. At the genus level, the LGG group's gut microbiota composition is more similar to the HSD profile at W0 but shifts to the ND profile after treatment at W8. Thus, probiotic LGG lowers blood pressure indices, improves serum biochemistry profile, restores small intestinal integrity barrier, and modulates gut microbiota profile, indicating its potential as an adjuvant treatment for prehypertension and the significance of gut health in blood pressure regulation.}, }
@article {pmid40254251, year = {2025}, author = {Chang, FM and Chen, YH and Hsu, PS and Wu, TH and Sung, IH and Wu, MC and Nai, YS}, title = {RNA metagenomics revealed insights into the viromes of honey bees (Apis mellifera) and Varroa mites (Varroa destructor) in Taiwan.}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108341}, doi = {10.1016/j.jip.2025.108341}, pmid = {40254251}, issn = {1096-0805}, abstract = {The honey bee (Apis mellifera) is a vital pollinator for crops. However, they are infested by a worldwide spread ecto-parasite, Varroa mite (Varroa destructor). The Varroa mite is a vector of various western honey bee viruses. In this study, the prevalence of seven honey bee viruses (Deformed wing virus, Lake Sinai virus, Acute bee paralysis virus, Sacbrood virus, Kashmir bee virus, Black queen cell virus, Israeli acute paralysis virus), was screened with the honey bees, which were collected from fourteen apiaries from March 2023 to January 2024, and the Varroa mites, which were collected from two apiaries from July to October 2023 by using RT-PCR. Subsequently, metagenomic analyses were conducted on seven honey bee samples and two Varroa mite samples using next-generation sequencing with poly-A capture and rRNA depletion library construction methods. The results showed that 50% to 85.7% of honey bee viruses in each sample were detected by both methods, with up to three additional viruses identified when combining the two approaches. These findings underscore the importance of integrating both methods for comprehensive virome analysis. According to the virome analysis, 28 honey bee viruses were identified in honey bees and 11 in Varroa mites. Among these, 23 viruses were newly recorded in Taiwanese honey bee populations. Notably, three of the newly recorded viruses, Acute bee paralysis virus, Israeli acute paralysis virus, and Apis mellifera filamentous virus, are known to cause symptoms in honey bees, posing potential risks to their health. Six of these viruses were also detected in Varroa mites, highlighting their role in viral transmission. This study represents the first virome analysis of honey bees and Varroa mites in Taiwan, providing critical insights into honey bee health and establishing a foundation for future health assessment indices and mitigation strategies.}, }
@article {pmid40253770, year = {2025}, author = {Zhu, Y and Tian, Q and Huang, Q and Wang, J}, title = {Bile-processed Rhizoma Coptidis alleviates type 2 diabetes mellitus through modulating the gut microbiota and short-chain fatty acid metabolism.}, journal = {International immunopharmacology}, volume = {156}, number = {}, pages = {114645}, doi = {10.1016/j.intimp.2025.114645}, pmid = {40253770}, issn = {1878-1705}, abstract = {BACKGROUND: Bile-Processed Rhizoma Coptidis (BPRC) is a processed products of Rhizoma Coptidis (RC) commonly used to treat type 2 diabetes mellitus (T2DM). However, the synergistic mechanism of its processing remains unknown. Current research indicates that the gut microbiota and its metabolites, such as short-chain fatty acids (SCFAs), are closely associated with the progression of T2DM.<br><br>PURPOSE: This study aims to investigate the effects of BPRC on the gut microbiota and its metabolite SCFAs in T2DM rats.<br><br>METHODS: T2DM rat model was induced by a high-fat diet (HFD) combined with streptozotocin (STZ), followed by a 4-week treatment with BPRC to observe its therapeutic effects. The impact of BPRC on the gut microbiota was studied through metagenomic sequencing. Quantitative analysis of SCFAs was conducted using GC-MS. Western blot and quantitative real-time PCR (qRT-PCR) were conducted to investigate the potential mechanisms of BPRC.<br><br>RESULTS: BPRC significantly improved insulin resistance in T2DM rats, downregulated levels of pancreatic cell apoptosis factors, and upregulated the abundance of Bacteroides uniformis, Bacteroides sp A1C1, Anaerostipes caccae, Alistipes finegoldii and Blautia sp.N6H1-15 in T2DM rats. Additionally, BPRC increased the levels of seven SCFAs in the intestines of T2DM rats. It activated intestinal TGR5, GPR41, GPR43, and GPR109a receptors, collectively upregulating GLP-1 protein expression, and exerted therapeutic effects on T2DM.<br><br>CONCLUSION: The results indicate that the synergistic mechanism of BPRC in treating T2DM is associated with modulating the gut microbiota, increasing SCFAs content in the intestines, and regulating intestinal GLP-1 production.}, }
@article {pmid40253436, year = {2025}, author = {Huang, J and Zheng, X and Yu, T and Ali, M and Wiese, J and Hu, S and Huang, L and Huang, Y}, title = {Diverse lifestyles and adaptive evolution of uncultured UBA5794 actinobacteria, a sister order of "Candidatus actinomarinales".}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {39}, pmid = {40253436}, issn = {2524-6372}, support = {92351301, 32470005, 42376238, and 32393970//National Natural Science Foundation of China/ ; 91751000//Major Research Plan of the National Natural Science Foundation of China/ ; GML20240002//the PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; }, abstract = {Uncultured UBA5794 actinobacteria are frequently found in marine and inland water environments by using metagenomic approaches. However, knowledge about these actinobacteria is limited, hindering their isolation and cultivation, and they are always confused with "Candidatus Actinomarinales" based on 16S rRNA gene classification. Here, to conduct genomic characterization of them, we obtained three high-quality UBA5794 metagenome-assembled genomes (MAGs) from a hydrothermal sediment on the Carlsberg Ridge (CR) and retrieved 131 high-quality UBA5794 genomes from public datasets. Phylogenomic analysis confirms UBA5794 as an independent order within the class Acidimicrobiia. Genome-based metabolic predictions reveal that flexible metabolism and diversified energy acquisition, as well as heavy metal(loid) detoxification capacity, are crucial for the ability of UBA5794 to thrive in diverse environments. Moreover, there is separation between sponge-associated and free-living UBA5794 groups in phylogeny and functional potential, which can be attributed to the symbiotic nature of the sponge-associated group and the extensive horizontal gene transfer (HGT) events observed in these bacteria. Ancestral state reconstruction suggests that the UBA5794 clade may have originated from a free-living environment and then some members gradually migrated to the sponge host. Overall, our study sheds light on the ecological adaptation and evolutionary history of the ubiquitous but poorly understood UBA5794 actinobacteria.}, }
@article {pmid40253169, year = {2025}, author = {Aryal, A and Nwachukwu, ID and Aryee, ANA}, title = {Examining the impact of crops and foods biofortified with micronutrients on the gut microbiome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {209}, number = {}, pages = {116189}, doi = {10.1016/j.foodres.2025.116189}, pmid = {40253169}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome/physiology ; *Micronutrients ; Humans ; *Crops, Agricultural ; *Biofortification ; *Food, Fortified ; Animals ; }, abstract = {Micronutrient deficiencies (MNDs) impact more than three billion individuals worldwide, particularly those in impoverished and marginalized communities, leading to adverse long-term health consequences. Biofortification, which focusses on enhancing the nutrient density of food crops, presents a promising strategy to address this challenge. Recent studies involving both model organisms and human subjects have demonstrated that, beyond remedying common dietary insufficiencies, micronutrients can modulate the composition and functionality of the gut microbiome. The microbiota, in turn, utilize these micronutrients, facilitating digestion, synthesizing essential nutrients, and modulating immune responses, thereby establishing a bidirectional relationship known as the micronutrient-microbiome axis. Numerous studies have also documented significant variations in these interactions, highlighting the complex dynamics of the micronutrient-microbiome relationship. The composition and interactions of the microbiota have been investigated using various methodologies, including 16S rRNA gene sequencing, RT-PCR, metagenomics, and metabolomics. This review explores recent advancements in understanding the reciprocal relationship between micronutrient levels and the gut microbiome, emphasizing key findings that provide critical insights for the development of targeted dietary strategies aimed at alleviating MNDs and improving overall health.}, }
@article {pmid40252922, year = {2025}, author = {Charya, AV and Jang, MK and Kong, H and Park, W and Tian, X and Keller, M and Phipps, K and Sanders, A and Shah, P and Mathew, J and Aryal, S and Berry, GJ and Marboe, C and Orens, JB and Nathan, SD and Agbor-Enoh, S}, title = {Donor-derived cell-free DNA is associated with the degree of immunosuppression in lung transplantation.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajt.2025.04.011}, pmid = {40252922}, issn = {1600-6143}, abstract = {Donor-derived cell-free DNA is increasingly used in clinical practice to monitor lung transplant patients for acute rejection. However, its association with conventional approaches to monitor immunosuppression remains unclear. This multicenter observational cohort study examines the association of donor-derived cell free DNA with surrogate measures of immunosuppression. Serial plasma samples were collected for quantification of donor-derived cell-free DNA and anellovirus abundance via shotgun and metagenomic sequencing. Adjudication committees reviewed clinical data to define acute cellular and antibody-mediated rejection. The association between ddcfDNA, anellovirus abundance, and serum tacrolimus trough concentrations over the study period and during episodes of acute rejection were examined via linear mixed effects modeling. Donor-derived cell-free DNA demonstrated a significant inverse association with tacrolimus troughs (p=0.027) and anellovirus abundance (p<0.001) over time. Acute rejection episodes were associated with significantly decreased anellovirus abundance (median, 0.042 vs. 0.708, p<0.001) and higher ddcfDNA levels (1.49% vs. 0.26%, p<0.001) compared to stable control timepoints. However, tacrolimus levels were similar between acute rejection and controls (10.1 ng/ml vs 10.3 ng/ml, p = 0.13). Our findings suggest donor-derived cell-free DNA correlates with measures of immunosuppression in lung transplant patients. Additional studies are needed to assess the utility of donor-derived cell-free DNA to assess immunosuppression adequacy.}, }
@article {pmid40252793, year = {2025}, author = {Yang, R and Guo, S and Huo, L and Yang, G and Tian, S}, title = {Impact of Watershed-Scale Land Restoration on Soil Microbial Communities and Their Functions: Insights from Metagenomic Analysis.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121609}, doi = {10.1016/j.envres.2025.121609}, pmid = {40252793}, issn = {1096-0953}, abstract = {Land restoration in the gully regions of China's Loess Plateau has significantly altered soil conditions and farming practices, yet its impact on soil microbes remains unclear. This study applied metagenomic sequencing and correlation analysis to examine microbial community shifts and key genes involved in carbon, nitrogen, and phosphorus cycling. Results show increased biodiversity and microbial activity, especially downstream, enhancing carbon metabolism and ecosystem resilience. Phosphorus activation improved, with related gene abundance rising by 27.45%-52.57%, facilitating phosphorus availability. Nitrogen cycling showed enhanced nitrification and nitrogen fixation, with reduced denitrification, promoting nitrogen retention. Soil organic carbon, total nitrogen, ammonium nitrogen, and available phosphorus (AP), particularly AP, strongly influenced microbial dynamics. These findings highlight the positive role of land restoration in improving soil health and nutrient cycling, supporting sustainable agriculture.}, }
@article {pmid40252750, year = {2025}, author = {Yang, M and Peng, L and Mu, M and Yang, F and Li, Z and Han, B and Zhang, K}, title = {Significant effects of earthworm species on antibiotic resistome in livestock manure as revealed by metagenomic analysis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126277}, doi = {10.1016/j.envpol.2025.126277}, pmid = {40252750}, issn = {1873-6424}, abstract = {Animal-derived antibiotic resistance genes (ARGs) have emerged as a critical threat, while vermicomposting has been recognized as an effective strategy for reducing ARGs. However, the efficacy of different earthworm species in reducing ARGs remains poorly understood. In this study, 72 vermicompost and earthworm gut samples were collected from various earthworm farms to evaluate the impact of vermicomposting with different earthworm species on ARGs via metagenomic analysis. Approximately 28 ARG types were detected in gut and vermicompost samples. There were significant differences in ARGs among the four species of earthworm composting systems (p < 0.05), and each species possessed its dominant ARGs and microbes. Proteobacteria represented the predominant bacterial phylum within the gut microbiota of Pheretima guillelmi (46.89%) and Eisenia fetida (48.42%), whereas Euryarchaeota (36.71%) and Actinobacteria (39.42%) were the most abundant in Perionyx excavatus and Eudrilus eugeniae, respectively. The overall abundance of ARGs in vermicompost processed by Eisenia fetida (0.18 copies16S rRNA gene copies) was lower than that observed in other earthworm species (0.23-0.39 copies/16S rRNA gene copies), with gut microbial identified as a key determinant of variations in ARG reduction. These findings provide valuable insights into selecting suitable earthworm species to promote ARG degradation, thus contributing to the decrease in ARG dissemination risks in agricultural ecosystems.}, }
@article {pmid40252553, year = {2025}, author = {Bariod, L and Fuentes, E and Millet, M and White, J and Jacquiod, S and Moreau, J and Monceau, K}, title = {Exposure to pesticides is correlated with gut microbiota alterations in a farmland raptor.}, journal = {Environment international}, volume = {199}, number = {}, pages = {109436}, doi = {10.1016/j.envint.2025.109436}, pmid = {40252553}, issn = {1873-6750}, abstract = {The gut microbiota is crucial for host health and can be impacted by various environmental disruptions, yet the effects of multiple pesticide exposures on farmland organisms' microbiomes remain largely unexplored. We assessed microbiota changes in a wild apex predator exposed to multiple pesticides in agricultural landscapes. Pesticides, including acetochlor and quinoxyfen, which are supposed to be banned, were significantly positively correlated with certain key bacteria from Actinobacteria, Alphaproteobacteria and Gammaproteobacteria classes. Our results light up the potential collateral effect of pesticides on gut bacterial assemblages through unknown mechanisms. These effects could result in dysbiosis and the promotion of potential pathogens and/or the selection of bacteria that might allow the organism to detoxify the organism. Although formal metagenomic analyses would be required soon, these microbial shifts underline the broader ecological consequences of pesticide exposure, emphasising the need for integrated biodiversity conservation and ecosystem management to protect environmental and public health.}, }
@article {pmid40252419, year = {2025}, author = {Ciuchcinski, K and Kaczorowska, AK and Biernacka, D and Dorawa, S and Kaczorowski, T and Park, Y and Piekarski, K and Stanowski, M and Ishikawa, T and Stokke, R and Steen, IH and Dziewit, L}, title = {Computational pipeline for sustainable enzyme discovery through (re)use of metagenomic data.}, journal = {Journal of environmental management}, volume = {382}, number = {}, pages = {125381}, doi = {10.1016/j.jenvman.2025.125381}, pmid = {40252419}, issn = {1095-8630}, abstract = {Enzymes derived from extremophilic organisms, also known as extremozymes, offer sustainable and efficient solutions for industrial applications. Valued for their resilience and low environmental impact, extremozymes have found use as catalysts in various processes, ranging from dairy production to pharmaceutical manufacturing. However, discovery of novel extremozymes is often hindered by challenges such as culturing difficulties, underrepresentation of extreme environments in reference databases, and limitations of traditional sequence-based screening methods. In this work, we present a computational pipeline designed to discover novel enzymes from metagenomic data derived from extreme environments. This pipeline represents a versatile and sustainable approach that promotes reuse and recycling of existing datasets and minimises the need for additional environmental sampling. In its core, the algorithm integrates both traditional bioinformatic techniques and recent advances in structural prediction, enabling rapid and accurate identification of enzymes. However, due to its design, the algorithm relies heavily on existing databases, which can limit its effectiveness in situations where reference data is scarce or when encountering novel protein families. As a proof-of-concept, we applied the pipeline to metagenomic data from deep-sea hydrothermal vents, with a focus on β-galactosidases. The pipeline identified 11 potential candidate proteins, out of which 10 showed in vitro activity. One of the selected enzymes, βGal_UW07, showed strong potential for industrial applications. The enzyme exhibited optimal activity at 70 °C and was exceptionally resistant to high pH and the presence of metal ions and reducing agents. Overall, our results indicate that the pipeline is highly accurate and can play a key role in sustainable bioprospecting, leveraging existing metagenomic datasets and minimising in situ interventions in pristine regions.}, }
@article {pmid40252413, year = {2025}, author = {Okamura, T and Hasegawa, Y and Ohno, Y and Saijo, Y and Nakanishi, N and Honda, A and Hamaguchi, M and Takano, H and Fukui, M}, title = {Oral exposure to nanoplastics and food allergy in mice fed a normal or high-fat diet.}, journal = {Chemosphere}, volume = {379}, number = {}, pages = {144401}, doi = {10.1016/j.chemosphere.2025.144401}, pmid = {40252413}, issn = {1879-1298}, abstract = {The global prevalence of food allergies, particularly IgE-mediated responses, is increasing at an alarming rate. This trend is likely driven by environmental factors such as nanoplastics (NPs) ingestion and the westernization of dietary and lifestyle habits. This study examines the impact of polystyrene nanoplastics (PS-NPs) on ovalbumin (OVA)-induced food allergies in mice subjected to either a normal diet (ND) or a high-fat diet (HFD). BALB/c mice were stratified into eight groups based on dietary regimen, NP exposure, and OVA sensitization. Food allergy was induced via OVA administration, and multiple physiological and immunological parameters were evaluated, including body weight, intestinal permeability, cytokine profiles, gut microbiota composition, and small intestinal gene expression. Mice in the HFD + OVA + NP group exhibited significant increases in intestinal permeability, diarrhea severity, and serum OVA-specific IgE levels compared to other groups. Flow cytometric analysis revealed an expansion of innate lymphoid cells (ILC2 and ILC1) within the lamina propria of the small intestine. Shotgun metagenomic sequencing demonstrated gut microbiota dysbiosis, characterized by a reduction in beneficial bacterial populations in the HFD + OVA + NP cohort. Weighted Gene Co-Expression Network Analysis (WGCNA) identified a negative correlation between NPs exposure or OVA sensitization and the expression of Slc1a1, Slc5a8, and Mep1a, while a positive correlation was observed with Aa467197 expression. These findings indicate that oral exposure to PS-NPs exacerbates OVA-induced food allergies, particularly in the context of an HFD, through mechanisms involving increased intestinal permeability, gut microbial dysbiosis, and gene expression modulation. This study highlights the potential health hazards posed by environmental microplastic contamination and its possible contribution to the escalating incidence of food allergies.}, }
@article {pmid40252307, year = {2025}, author = {Qian, L and Jiang, J and Zhang, Y and Huang, X and Che, Z and Chen, G and Liu, S}, title = {Sublethal exposure to boscalid induced respiratory abnormalities and gut microbiota dysbiosis in adult zebrafish.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {283}, number = {}, pages = {107370}, doi = {10.1016/j.aquatox.2025.107370}, pmid = {40252307}, issn = {1879-1514}, abstract = {Boscalid (BO), one of the frequently detected fungicides of succinate dehydrogenase inhibitor in water environments, has unknown effects on the respiratory function and gut health of aquatic organisms. Therefore, zebrafish were exposed to BO solutions (0.01-1.0 mg/L) for 21 days to assess its effects on zebrafish respiration and intestinal microbiota in this study. The results showed that exposure to 0.1 and 1.0 mg/L BO for 21 days resulted in zebrafish exhibiting aggregation of gill filaments, reduction of mucous cells, and significantly decreased opercular movement, linked to a marked decline in the activity of respiratory chain complex II. 16S rRNA gene sequencing revealed significant changes in the intestinal microbiota composition of zebrafish exposed to 1.0 mg/L BO. Specifically, the relative abundance of beneficial bacteria (Cetobacterium) was markedly reduced, while pathogenic bacteria (such as Ralstonia, Legionella, Acinetobacter, Escherichia/Shigella) associated with energy metabolism and immune pathways in zebrafish showed a significant increase in relative abundance. Accordingly, metagenomic functional prediction analysis further revealed the potential impact of BO-induced gut microbiota changes on energy metabolism and immune pathways in zebrafish. Furthermore, histopathological analysis of intestinal tissues revealed that exposure to BO resulted in necrosis and shedding of epithelial cells, as well as a decrease in goblet cell count, which exacerbated adverse effects on intestinal health. In conclusion, sublethal exposure to BO affects the respiratory function and intestinal health of zebrafish. Therefore, the impact of BO in aquatic environments on fish health warrants attention.}, }
@article {pmid40252261, year = {2025}, author = {Li, B and Liang, C and Xu, B and Song, P and Liu, D and Zhang, J and Gu, H and Jiang, F and Gao, H and Cai, Z and Zhang, T}, title = {Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer.}, journal = {Microbiological research}, volume = {297}, number = {}, pages = {128182}, doi = {10.1016/j.micres.2025.128182}, pmid = {40252261}, issn = {1618-0623}, abstract = {Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (Przewalskium albirostris), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, Rikenellaceae_RC9_gut_group, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including norank_f_p-2534-18B5_gut_group, Cellulosilyticum, and Paeniclostridium, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, Rikenellaceae_RC9_gut_group and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, norank_f_p-2534-18B5_gut_group contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.}, }
@article {pmid40251489, year = {2025}, author = {Bini, F and Soffritti, I and D'Accolti, M and Mazziga, E and Caballero, JD and David, S and Argimon, S and Aanensen, DM and Volta, A and Bisi, M and Mazzacane, S and Caselli, E}, title = {Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {382}, pmid = {40251489}, issn = {1471-2164}, support = {INV-004891/GATES/Gates Foundation/United States ; }, mesh = {*Bacillus/genetics/isolation &amp; purification/drug effects/classification/pathogenicity ; *Probiotics ; *Whole Genome Sequencing ; *Genome, Bacterial ; Polymorphism, Single Nucleotide ; *Sanitation ; Humans ; *Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Healthcare-associated infections (HAIs) caused by microbes that acquire antimicrobial resistance (AMR) represent an increasing threat to human health worldwide. The high use of chemical disinfectants aimed at reducing the presence of pathogens in the hospital environment can simultaneously favor the selection of resistant strains, potentially worsening AMR concerns. In the search for sustainable ways to control bioburden without affecting this aspect, probiotic-based sanitation (PBS) using Bacillus spp. was proposed to achieve stable reduction of pathogens, AMR, and associated HAIs. Although Bacillus probiotics are classified as nonpathogenic, comprehensive data about the potential genetic alterations of these probiotics following prolonged contact with surrounding pathogens are not yet available. This study aimed to assess in depth the genetic content of PBS-Bacillus isolates to evaluate any eventual variations that occurred during their usage.<br><br>RESULTS: WGS analysis was used for the precise identification of PBS-Bacillus species and detailed profiling of their SNPs, resistome, virulome, and mobilome. Analyses were conducted on both the original PBS detergent and 172 environmental isolates from eight hospitals sanitized with PBS over a 30-month period. The two species B. subtilis and B. velezensis were identified in both the original product and the hospital environment, and SNP analysis revealed the presence of two clusters in each species. No virulence/resistance genes or mobile conjugative plasmids were detected in either the original PBS-Bacillus strain or any of the analyzed environmental isolates, confirming their high genetic stability and their low/no tendency to be involved in horizontal gene transfer events.<br><br>CONCLUSIONS: The data obtained by metagenomic analysis revealed the absence of genetic sequences associated with PBS-Bacillus and the lack of alterations in all the environmental isolates analyzed, despite their continuous contact with surrounding pathogens. These results support the safety of the Bacillus species analyzed. Further metagenomic studies aimed at profiling the whole genomes of these and other species of Bacillus, possibly during longer periods and under stress conditions, would be of interest since they may provide further confirmation of their stability and safety.}, }
@article {pmid40251030, year = {2025}, author = {Chen, J and Zhang, S and Wang, M and Kang, G and Lu, L and Chang, N and Wang, N and Xie, Z and Liu, Y and Zhang, H and Shen, W}, title = {Investigating the Impact of Landfill Age and Season on the Occurrence and Dissemination of Antibiotic Resistance Genes in Leachate and the Underlying Mechanisms Using Metagenomics.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf091}, pmid = {40251030}, issn = {1365-2672}, abstract = {AIMS: Antibiotic resistance genes (ARGs) pose a critical public health concern, with landfill leachate serving as a significant environmental reservoir. While ARG dynamics in leachate have been investigated in various contexts, their occurrence and influence factors in semi-arid regions remain poorly understood. This study investigated the occurrence and influence factors of ARG profiles, their potential hosts, and underlying mechanisms driving their proliferation.<br><br>METHODS AND RESULTS: Comprehensive metagenomic analysis of leachate samples collected from landfills of varying landfill ages (5, 10, and 20 years) in Hohhot, Inner Mongolia-a representative semi-arid region of northern China-across three seasons (autumn, spring, and summer). Metagenomic analysis revealed distinct patterns in core ARG abundances modulated by both landfill age and seasonal variations. Notably, landfill age predominantly influenced tetracycline- and glycopeptide- ARGs, while seasonal fluctuations primarily affected glycopeptide- and multidrug- ARGs. Taxonomic analysis identified Pseudomonas aeruginosa and Pseudomonas fluorescens as the predominant resistant pathogens, with elevated prevalence during spring and winter compared to summer. Network analysis and metabolic pathway reconstruction demonstrated that landfill age maybe impacted ARG dissemination through modulation of carbohydrate and nitrogen metabolic pathways. This novel finding suggests a previously unrecognized mechanism linking waste decomposition stages to ARG proliferation.<br><br>CONCLUSIONS: Our study provides the first systematic characterization of ARG dynamics in semi-arid landfill leachate, offering crucial insights for developing targeted strategies to mitigate ARG dissemination in these distinct ecological contexts. These findings establish a theoretical framework for understanding ARG transmission in semi-arid environments while providing empirical evidence to inform environmental management practices.}, }
@article {pmid40251011, year = {2025}, author = {Dawson, SJT and Shibu, P and Garnett, S and Newberry, F and Brook, TC and Tijani, T and Kujawska, M and Hall, LJ and McCartney, AL and Negus, D and Hoyles, L}, title = {Weberviruses are gut-associated phages that infect Klebsiella spp.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf043}, pmid = {40251011}, issn = {1574-6941}, abstract = {Weberviruses are bacteriophages (phages) that can infect and lyse clinically relevant, multidrug-resistant (MDR) strains of Klebsiella. They are an attractive therapeutic option to tackle Klebsiella infections due to their high burst sizes, long shelf life and associated depolymerases. In this study we isolated and characterized seven new lytic phages and compared their genomes with those of their closest relatives. Gene-sharing network, ViPTree proteome and terL gene-sequence-based analyses incorporating all publicly available webervirus genomes [n=258 from isolates, n=65 from metagenome-assembled genome (MAG) datasets] confirmed the seven phages as members of the genus Webervirus and identified a novel genus (Defiantjazzvirus) within the family Drexlerviridae. Using our curated database of 265 isolated phage genomes and 65 MAGs (n=330 total), we found that weberviruses are distributed globally and primarily associated with samples originating from the gut: sewage (154/330, 47%), wastewater (83/330, 25%) and human faeces (66/330, 20%). We identified three distinct clusters of potential depolymerases encoded within the 330 genomes. Due to their global distribution, frequency of isolation and lytic activity against the MDR clinical Klebsiella strains used in this study, we conclude that weberviruses and their depolymerases show promise for development as therapeutic agents against Klebsiella spp.}, }
@article {pmid40250773, year = {2025}, author = {Wu, X and Li, Y and Li, P and Lu, G and Wu, J and Wang, Z and Wen, Q and Cui, B and Wang, J and Zhang, F}, title = {Structural variations in ulcerative colitis-associated E. coli reduce fructose utilization and aggravate inflammation under high fructose diet.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.03.039}, pmid = {40250773}, issn = {1528-0012}, abstract = {BACKGROUND AND AIMS: Structural variations (SVs) have significant effects on the microbial phenotypes. The underlying mechanism of functional changes caused by gut microbial SVs in the development of ulcerative colitis (UC) need further investigation.<br><br>METHODS: We performed long-read (ONT-based) and short-read (Illumina-based) metagenomic sequencing on stool samples from 93 UC patients and 100 healthy controls (HCs), and analyzed microbial SVs. A total of 648 Escherichia coli (E. coli) strains from fecal samples of UC patients (UC-strains) and HCs (HC-strains) were isolated. SV-associated scrK gene deletion was verified via whole-genome sequencing or targeted PCR. Then, representative UC-strains, HC-strains, and scrK-knockout E. coli were used for the in vitro and in vivo experiments to investigate the effects of specific SV in E. coli on fructose utilization ability and colitis.<br><br>RESULTS: E. coli in UC with the highest fold change had SVs-affected functional differences on fructose metabolism to that of HCs. The fructose utilization genes deletion was common in UC-strains, ostensibly reducing fructose utilization in vitro and leading to fructose-dependent aggravation of colitis in murine models. UC-strains and HC-strains induced comparable colitis under low fructose. However, high fructose exacerbated colitis severity exclusively in UC-strain-colonized mice, with elevated intestinal fructose residues, significant microbiome/metabolome changes, increased inflammation, and gut barrier disruption. These changes were mechanistically depended on the deletion of fructose utilization gene scrK.<br><br>CONCLUSIONS: SV-caused difference in fructose utilization and proinflammatory properties in E. coli from UC patients influence the development of UC, emphasizing the importance of fine-scale metagenomic studies in disease.}, }
@article {pmid40250459, year = {2025}, author = {Munroe, ES and Spicer, A and Castellvi-Font, A and Zalucky, A and Dianti, J and Graham Linck, E and Talisa, V and Urner, M and Angus, DC and Baedorf-Kassis, E and Blette, B and Bos, LD and Buell, KG and Casey, JD and Calfee, CS and Del Sorbo, L and Estenssoro, E and Ferguson, ND and Giblon, R and Granholm, A and Harhay, MO and Heath, A and Hodgson, C and Houle, T and Jiang, C and Kramer, L and Lawler, PR and Leligdowicz, A and Li, F and Liu, K and Maiga, A and Maslove, D and McArthur, C and McAuley, DF and Serpa Neto, A and Oosthuysen, C and Perner, A and Prescott, HC and Rochwerg, B and Sahetya, S and Samoilenko, M and Schnitzer, ME and Seitz, KP and Shah, F and Shankar-Hari, M and Sinha, P and Slutsky, AS and Qian, ET and Webb, SA and Young, PJ and Zampieri, FG and Zarychanski, R and Fan, E and Semler, MW and Churpek, M and Goligher, EC and ,  and , }, title = {Evidence-based personalised medicine in critical care: a framework for quantifying and applying individualised treatment effects in patients who are critically ill.}, journal = {The Lancet. Respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2213-2600(25)00054-2}, pmid = {40250459}, issn = {2213-2619}, abstract = {Clinicians aim to provide treatments that will result in the best outcome for each patient. Ideally, treatment decisions are based on evidence from randomised clinical trials. Randomised trials conventionally report an aggregated difference in outcomes between patients in each group, known as an average treatment effect. However, the actual effect of treatment on outcomes (treatment response) can vary considerably between individuals, and can differ substantially from the average treatment effect. This variation in response to treatment between patients-heterogeneity of treatment effect-is particularly important in critical care because common critical care syndromes (eg, sepsis and acute respiratory distress syndrome) are clinically and biologically heterogeneous. Statistical approaches have been developed to analyse heterogeneity of treatment effect and predict individualised treatment effects for each patient. In this Review, we outline a framework for deriving and validating individualised treatment effects and identify challenges to applying individualised treatment effect estimates to inform treatment decisions in clinical care.}, }
@article {pmid40250281, year = {2025}, author = {Chen, Y and Hu, S and Hu, B and Li, Y and Chen, Z}, title = {Functional insights into microbial community dynamics and resilience in mycorrhizal associated constructed wetlands under pesticide stress.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138315}, doi = {10.1016/j.jhazmat.2025.138315}, pmid = {40250281}, issn = {1873-3336}, abstract = {Arbuscular mycorrhizal fungi (AMF) are critical mutualistic symbionts in most terrestrial ecosystems, where they facilitate nutrient acquisition, enhance plant resilience to environmental stressors, and shape the surrounding microbiome. However, its contributions (especially for microorganisms) to constructed wetlands (CWs) under pesticide stress remain poorly understood. This study investigated the effects of AMF on microbial community composition, diversity, metabolic pathways, and functional genes by metagenomics in CWs exposed to pesticides stress. Using comparative analyses of AMF-colonized and non-colonized CWs, we found that AMF enhanced overall microbial diversity, as evidenced by increases of 2.22 % (Chao1) and 2.83 % (observed species). Under fungicide stress, nitrogen-cycling microorganisms (e.g., Nitrososphaerota and Mucoromycota) increased in relative abundance, while carbon cycle-related microorganisms (e.g., Pseudomonadota and Bacteroidota) generally declined. AMF colonization improved microbial resilience, demonstrated by a 312 % rise in Rhizophagus abundance and significant increases in phosphorus-cycling microorganisms (e.g., Bradyrhizobium and Mesorhizobium). Functional gene analysis further revealed that AMF helped mitigate fungicide-induced reductions in genes related to nitrogen and carbon cycling, lowering the average decline rates to 4.02 % and 1.44 %, respectively, compared to higher rates in non-AMF treatments. In summary, these findings highlight the crucial role of AMF in enhancing pesticide stress resilience, maintaining microbial community stability, and improving the bioremediation capacity of CWs.}, }
@article {pmid40250270, year = {2025}, author = {Yang, C and Xu, Y and Yu, T and Li, Y and Zeng, XC}, title = {Microbial reductive mobilization of As(V) in solid phase coupled with the oxidation of sulfur compounds: An overlooked biogeochemical reaction affecting the formation of arsenic-contaminated groundwater.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138234}, doi = {10.1016/j.jhazmat.2025.138234}, pmid = {40250270}, issn = {1873-3336}, abstract = {Dissimilatory As(V)-respiring prokaryotes (DARPs) are recognized as having a crucial role in the formation of arsenic-contaminated groundwater. DARPs use small-molecule organic acids as electron donor to directly reduce As(V) in solid phase to more mobile As(III). Therefore, DARPs are considered to be heterotrophic bacteria. However, these cannot explain why high concentrations of As(III) are produced in environments lacking soluble organic carbon. We thus propose that reduced sulfur compounds may also be utilized by DARPs and affect the DARPs-mediated arsenic mobilization. This study sought to confirm this hypothesis. Metagenomic investigations on the DARP population derived from As-contaminated soil indicated that approximately 84 % of DARP MAGs possess the enzymes potentially catalyzing the oxidation of S[2-], S[0], SO3[2-], or S2O3[2-]. Functional analysis of DARP population and a cultivable strain suggested that DARPs, in addition to small-molecule organic carbon, can effectively use sulfur compounds as electron donor to reduce As(V) to mobile As(III). Arsenic release experiments using DARP population and a cultivable DARP strain showed that DARPs indeed utilized sulfur compounds as the sole electron donors under autotrophic and anaerobic conditions to directly reduce adsorbed As(V) in the soils to mobile As(III). These findings provide new insights into the microbial mechanism responsible for the variation of As(III) concentrations in contaminated groundwater.}, }
@article {pmid40250268, year = {2025}, author = {Yang, JH and Huang, DQ and Wu, GG and Han, NN and Fan, NS and Jin, RC}, title = {Quorum sensing-mediated microecological homeostasis in anammox consortia.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138285}, doi = {10.1016/j.jhazmat.2025.138285}, pmid = {40250268}, issn = {1873-3336}, abstract = {Quorum sensing (QS) mediated by signal molecules regulates bacterial communication and further affects the performance and microbial physiological characteristics of anaerobic ammonium oxidation (anammox) process. The potential application of low concentrations of typical exogenous signal molecules into maintaining the long-term homeostasis of anammox consortia were evaluated in this study. The results of 150-d continuous-flow experiment showed that 30 μg L[-1]N-hexanoyl-homoserine lactone (C6-HSL) and diffusible signaling factor (DSF) could maintain the stable nitrogen removal efficiency of anammox systems (90.3 ± 3.6 % and 90.2 ± 3.8 %). C6-HSL and DSF also significantly promoted the anammox activity and the production of extracellular polymeric substances (EPS). Microbial community analysis indicated that the relative abundance of Candidatus Kuenenia fluctuated and finally maintained at 27.0 % and 39.3 %, which was still significantly higher than that of initial phase. Meanwhile, the abundances of functional genes related to anammox process (hzsA, hdh and nirS) increased significantly. Metagenomic analysis revealed that the abundances of main functional genes involved in nitrogen metabolism, amino acid metabolism and QS were significantly upregulated. The interspecies interactions were also enhanced through QS-mediated intercellular communication, which was beneficial to microecological homeostasis in anammox systems. In contrast, DSF exhibited the more significant and longer-lasting promotion impact, while the effect of C6-HSL was rapid. These findings reveal the potential regulatory mechanism of exogenous signaling molecules on anammox consortia and drive the potential application of signaling molecules in the anammox process to treat real wastewater.}, }
@article {pmid40250228, year = {2025}, author = {Wang, H and Yang, Q and Wang, S}, title = {Metagenomic insights into the impact of tillage practices on soil nutrient cycling and wheat yield.}, journal = {The Science of the total environment}, volume = {978}, number = {}, pages = {179427}, doi = {10.1016/j.scitotenv.2025.179427}, pmid = {40250228}, issn = {1879-1026}, abstract = {Decreasing tillage intensity (DT) are beneficial for soil health and crop yield; however, the relationship between microbial nutrient cycling function and crop yield remains poorly understood.The objective of this study was to investigate the impact of tillage practices of conventional tillage with rotary tillage (RT) and decreasing tillage intensity (DT) on the soil microbial community and the functions of carbon, nitrogen, and phosphorus cycles of wheat and examine the relationship between soil microbes and yield based on a four year field experiment. An increased maize yield of 9.3 % and 8.5 % in DT compared with that in RT in 2023 and 2024, respectively. Further analysis reveals that DT influences the availability of soil carbon, nitrogen, and phosphorus by altering microbial communities and their functions. Microbial function analysis indicates that DT leads to higher abundances of genes associated with glgP (starch degradation) and xynB (hemicellulose degradation), which play a crucial role in elevating POC levels (11.6 %-23.4 %). Additionally, DT shows increased abundances of genes related to organic nitrogen metabolism (glnA), nitrification (amoB), and nitrogen fixation (nifK), contributing to the rise in NO3[-]- N content (19.1 %-31.1 %). Furthermore, DT exhibits a high abundance of the organic phosphorus mineralization gene phnM, resulting in enhanced AP content (4.7 %-25.4 %). Moreover, among the microbial genera significantly influenced by DT, ten genera-Lysobacter, Luteimonas, Bradyrhizobium, Aromatoleum, Acidibacter, Variovorax, Polaromonas, Pseudorhodoplanes, Piscinibacter, and Ramlibacter-show increased abundance, positively impacting wheat yield. Our study offers a novel framework for comprehending the enhancement of wheat yield through the lens of microbial nutrient cycling functionality and mining of beneficial bacteria for wheat yield.}, }
@article {pmid40250042, year = {2025}, author = {Menichini, D and Seta, F and Mastrolia, SA and Cetin, I and Carafa, A and Santagni, S and Foschi, C and Cerboneschi, M and Smeazzetto, S and Neri, I and Facchinetti, F}, title = {Probiotics in pregnancy and group B streptococcus colonization: A multicentric, randomized, placebo-controlled, double-blind study with a focus on vaginal microbioma.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {310}, number = {}, pages = {113976}, doi = {10.1016/j.ejogrb.2025.113976}, pmid = {40250042}, issn = {1872-7654}, abstract = {OBJECTIVE: To evaluate the feasibility and effects of the use of probiotics in pregnancy, starting in the third trimester, on rectovaginal colonization of group B streptococcus (GBS) in women at low obstetric risk.<br><br>METHODS: A multicentre, randomized, placebo-controlled, double-blind, parallel-group study was conducted in three tertiary hospitals in northern Italy and included low-risk pregnant women. The intervention consisted of oral administration of two capsules of probiotics or placebo from 30&#xa0;weeks of pregnancy until 37&#xa0;weeks of pregnancy. The primary outcome was GBS colonization, evaluated with rectovaginal swabs. In a subgroup, selected at random, changes in the vaginal microbiome after treatment administration were evaluated using 16S Metagenomic Sequencing Library Preparation sequencing and analysis.<br><br>RESULTS: In total, 267 pregnant women were randomized to receive probiotics (n&#xa0;=&#xa0;133) or placebo (n&#xa0;=&#xa0;134). The two groups were similar at baseline. After treatment, no differences were found in the rates of positive rectovaginal swabs (p&#xa0;=&#xa0;0.24) and antibiotic administration (p&#xa0;=&#xa0;0.27). Only one case of postpartum fever (>38&#xa0;&#xb0;C) was found in the placebo group. Labour and delivery outcomes and neonatal outcomes were similar in both groups. Analysis of the vaginal microbiota showed that the relative abundance of Lactobacillus spp. was not modified significantly by the probiotics, but the relative abundance of Gardnerella spp. decreased significantly (3.6&#xa0;&#xb1;&#xa0;7.9 vs 5.5&#xa0;&#xb1;&#xa0;10.2; p&#xa0;=&#xa0;0.03). Interestingly, the relative abundance of Lactobacillus spp. reduced significantly in women who subsequently presented with partial rupture of membranes (46.9&#xa0;&#xb1;&#xa0;43.6 vs 77.7&#xa0;&#xb1;&#xa0;24.9; p&#xa0;=&#xa0;0.02).<br><br>CONCLUSION: Although the clinical outcomes were unaffected, administration of probiotics led to favourable changes in vaginal microbiota. It remains to be established how this effect could be translated into clinical advantage.}, }
@article {pmid40249976, year = {2025}, author = {Zhang, WG and Liang, S and Liao, Y and Ran, G and Ji, S and Gao, Y and Lei, Z}, title = {Insights into the impact of different phytoremediation strategies on antibiotic resistance genes at the metagenomic level in real scenarios.}, journal = {Ecotoxicology and environmental safety}, volume = {296}, number = {}, pages = {118211}, doi = {10.1016/j.ecoenv.2025.118211}, pmid = {40249976}, issn = {1090-2414}, abstract = {Engineered phytoremediation strategies provide cost effective options for eliminating antibiotics and antibiotic resistance genes (ARGs) from wastewater. However, there is a knowledge gap in understanding the impact of these phytoremediation strategies on the on the diversity and composition of ARGs as well as the key driving biotic and biological factors of ARGs at the metagenomic level in real scenarios. Through metagenomic sequencing, this study demonstrates that phytoremediation with Iris pseudacorus L., Myriophyllum verticillatum L., Eichhornia crassipes (Mart.) Solms and Oenanthe javanica (Bl. DC) significantly alters the pattern of antibiotic resistome. This study is the first to reveal, at the omics level, that phytoremediation enhances the diversity of ARGs (3.2 %∼11.6 % improvement), despite reducing their absolute abundances. Furthermore, this study highlights that plant varieties have a significant impact on the performance of phytoremediation in mitigating ARGs. The non-dominant bacterial taxa, specifically Verrucomicrobia, Planctomycetes, and Actinobacteria, play a crucial role in shaping the pattern of the antibiotic resistome during the wastewater treatment. The changes in the total organic carbon, total nitrogen and antibiotics robustly influence the environmental behaviors of antibiotic resistome and microbiome. In summary, this study gives insight into the impact of different phytoremediation strategies on mitigating ARGs at the omics level in real scenarios.}, }
@article {pmid40249811, year = {2025}, author = {Huss, P and Kieft, K and Meger, A and Nishikawa, K and Anantharaman, K and Raman, S}, title = {Engineering bacteriophages through deep mining of metagenomic motifs.}, journal = {Science advances}, volume = {11}, number = {16}, pages = {eadt6432}, doi = {10.1126/sciadv.adt6432}, pmid = {40249811}, issn = {2375-2548}, mesh = {*Metagenomics/methods ; *Bacteriophage T7/genetics ; *Metagenome ; *Bacteriophages/genetics ; *Genetic Engineering ; }, abstract = {Bacteriophages can adapt to new hosts by altering sequence motifs through recombination or convergent evolution. Where these motifs exist and what fitness advantage they confer remains largely unknown. We report a new method, Metagenomic Sequence Informed Functional Scoring (Meta-SIFT), to find sequence motifs in metagenomic datasets to engineer phage activity. Meta-SIFT uses experimental deep mutational scanning data to create sequence profiles to mine metagenomes for functional motifs invisible to other searches. We experimentally tested ~17,000 Meta-SIFT-derived sequence motifs in the receptor binding protein of the T7 phage. The screen revealed thousands of T7 variants with novel host specificity with motifs sourced from distant families. Position, substitution, and location preferences dictated specificity across a panel of 20 hosts and conditions. To demonstrate therapeutic utility, we engineered active T7 variants against foodborne pathogen Escherichia coli O121. Meta-SIFT is a powerful tool to unlock the potential encoded in phage metagenomes to engineer bacteriophages.}, }
@article {pmid40249033, year = {2025}, author = {Wei, Q and Chen, L and Yin, Y and Pai, M and Duan, H and Zeng, W and Hu, X and Xu, M and Li, S}, title = {Analysis of Blood Microbiome From People Living With HIV and Donors by 16S rRNA Metagenomic Sequencing.}, journal = {Journal of medical virology}, volume = {97}, number = {4}, pages = {e70341}, doi = {10.1002/jmv.70341}, pmid = {40249033}, issn = {1096-9071}, support = {//This work was supported by the Chinese Society of Blood Transfusion Weigao Research Fund Project (CSBT-MWG-2020-02) and the Chinese Academy of Medical Sciences Medical and Health Science and Technology Innovation Project (CAMS-2021-I2M-1-060)./ ; }, mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *HIV Infections/microbiology/blood/drug therapy ; *Microbiota ; Metagenomics ; *Blood Donors ; *Bacteria/genetics/classification/isolation &amp; purification ; Male ; Adult ; Female ; Middle Aged ; Sequence Analysis, DNA ; *Blood/microbiology ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; }, abstract = {Utilize 16S rRNA sequencing technology to characterize bacterial species susceptible to people living with HIV (PLWH) across different stages. This mapping aims to establish a foundational framework for preventing secondary HIV infections, prolonging patient survival, enhancing quality of life, and advancing the diagnosis, treatment, and research of bacterial co-infections. In this study, we classified the participants into three groups: The blood of donors living with HIV (DI group), AIDS patients who have received ART treatment (PI group), and healthy blood donors as the control group (DH group). Each group was divided into three parallel subgroups, with 30 samples pooled from each parallel group for plasma extraction. As initial processing steps, the nine parallel subgroups were subjected to nucleic acid extraction and PCR amplification targeting the 16SV34 region. The resulting amplified products were subsequently forwarded to a sequencing company. It can be seen from the Venn diagram that the DI groups showed significantly higher bacterial diversity than the PI group and the DH group. The PI group had lower bacterial relative abundance and diversity compared to the DI group, with a community structure more similar to the control group. The DI group is particularly susceptible to several significant pathogens, including Ralstonia, Pseudomonas, Acinetobacter, Methyloversatilis, and Vibrio. The study revealed a greater quantity and diversity of bacteria in the DI blood compared to the PI and DH groups. This observation may be attributed to PI group patients in this study being hospitalized and receiving treatment.}, }
@article {pmid40248366, year = {2025}, author = {Lu, X and Lu, Q and Zhu, R and Sun, M and Chen, H and Ge, Z and Jiang, Y and Wang, Z and Zhang, L and Zhang, W and Dai, Z}, title = {Metagenomic analysis reveals the diversity of the vaginal virome and its association with vaginitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1582553}, pmid = {40248366}, issn = {2235-2988}, mesh = {Female ; Humans ; *Virome/genetics ; *Vagina/virology/microbiology ; *Metagenomics ; Phylogeny ; *Vaginitis/virology/microbiology ; Adult ; Microbiota ; Bacteriophages/genetics/classification ; *Viruses/classification/genetics/isolation &amp; purification ; Middle Aged ; Biodiversity ; Young Adult ; Bacteria/classification/genetics ; }, abstract = {INTRODUCTION: The human vaginal virome is an essential yet understudied component of the vaginal microbiome. Its diversity and potential contributions to health and disease, particularly vaginitis, remain poorly understood.<br><br>METHODS: We conducted metagenomic sequencing on 24 pooled vaginal swab libraries collected from 267 women, including both healthy individuals and those diagnosed with vaginitis. Viral community composition, diversity indices (Shannon, Richness, and Pielou), and phylogenetic characteristics were analyzed. Virus-host associations were also investigated.<br><br>RESULTS: DNA viruses dominated the vaginal virome. Anelloviridae and Papillomaviridae were the most prevalent eukaryotic viruses, while Siphoviridae and Microviridae were the leading bacteriophages. Compared to healthy controls, the vaginitis group exhibited significantly reduced alpha diversity and greater beta diversity dispersion, indicating altered viral community structure. Anelloviruses, detected in both groups, showed extensive lineage diversity, frequent recombination, and pronounced phylogenetic divergence. HPV diversity and richness were significantly elevated in the vaginitis group, alongside an unbalanced distribution of viral lineages. Novel phage-bacterial associations were also identified, suggesting a potential role for bacteriophages in shaping the vaginal microbiome.<br><br>DISCUSSION: These findings provide new insights into the composition and structure of the vaginal virome and its potential association with vaginal dysbiosis. The distinct virome characteristics observed in women with vaginitis highlight the relevance of viral communities in reproductive health. Future studies incorporating individual-level sequencing and metatranscriptomics are warranted to explore intra-host viral dynamics, assess viral activity, and clarify the functional roles of vaginal viruses in host-microbiome interactions.}, }
@article {pmid40247828, year = {2025}, author = {Doorenspleet, K and Mailli, AA and van der Hoorn, BB and Beentjes, KK and De Backer, A and Derycke, S and Murk, AJ and Reiss, H and Nijland, R}, title = {Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19158}, pmid = {40247828}, issn = {2167-8359}, mesh = {*Biodiversity ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; North Sea ; Nanopores ; Belgium ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodiversity assessments. In this study, we compared three DNA-based techniques for assessing the diversity of bulk macrobenthos samples from the Belgian North Sea. Specifically, we compared amplicon sequencing using Illumina MiSeq and portable real-time sequencing of Oxford Nanopore versus shotgun sequencing using Illumina NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served as the target region for the metabarcoding analysis. Our results indicate that Oxford Nanopore and MiSeq metabarcoding had similar performances in terms of alpha and beta diversity, revealing highly similar location-specific community compositions. The NovaSeq metagenomics method also resulted in similar alpha diversity, but slightly different community compositions compared to the metabarcoding approach. Despite these differences, location-specific community compositions were maintained across all platforms. Notably, read counts from the NovaSeq metagenomic analysis showed the weakest correlation to size corrected morphological abundance and there were mismatches between morphological identification and all DNA based findings which are likely caused by a combination of factors such as primer efficiency and an incomplete reference database. Our findings underscore the critical importance of database completeness prior to implementing DNA-based techniques as standardized monitoring method, especially for metagenomics. Nevertheless, our findings emphasize that Oxford Nanopore metabarcoding proves to be a viable alternative to the conventional Illumina MiSeq metabarcoding platform for macrobenthos biodiversity monitoring.}, }
@article {pmid40247824, year = {2025}, author = {Chen, P and Yu, Q and Wang, C and Montoya, L and West, PT and Xu, L and Varoquaux, N and Cole, B and Hixson, KK and Kim, YM and Liu, L and Zhang, B and Zhang, J and Li, B and Purdom, E and Vogel, J and Jansson, C and Hutmacher, RB and Dahlberg, JA and Coleman-Derr, D and Lemaux, PG and Taylor, JW and Gao, C}, title = {Holo-omics disentangle drought response and biotic interactions among plant, endophyte and pathogen.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70155}, pmid = {40247824}, issn = {1469-8137}, support = {32022002//National Natural Science Foundation of China/ ; 32101286//National Natural Science Foundation of China/ ; 32170129//National Natural Science Foundation of China/ ; 32322053//National Natural Science Foundation of China/ ; 2022YFC2303100//National Key Research and Development Program of China/ ; XDA28030401//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, abstract = {Holo-omics provide a novel opportunity to study the interactions among fungi from different functional guilds in host plants in field conditions. We address the entangled responses of plant pathogenic and endophytic fungi associated with sorghum when droughted through the assembly of the most abundant fungal, endophyte genome from rhizospheric metagenomic sequences followed by a comparison of its metatranscriptome with the host plant metabolome and transcriptome. The rise in relative abundance of endophytic Acremonium persicinum (operational taxonomic unit 5 (OTU5)) in drought co-occurs with a rise in fungal membrane dynamics and plant metabolites, led by ethanolamine, a key phospholipid membrane component. The negative association between endophytic A. persicinum (OTU5) and plant pathogenic fungi co-occurs with a rise in expression of the endophyte's biosynthetic gene clusters coding for secondary compounds. Endophytic A. persicinum (OTU5) and plant pathogenic fungi are negatively associated under preflowering drought but not under postflowering drought, likely a consequence of variation in fungal fitness responses to changes in the availability of water and niche space caused by plant maturation over the growing season. Our findings suggest that the dynamic biotic interactions among host, beneficial and harmful microbiota in a changing environment can be disentangled by a blending of field observation, laboratory validation, holo-omics and ecological modelling.}, }
@article {pmid40247698, year = {2025}, author = {Zhao, J and Pachiadaki, M and Conrad, RE and Hatt, JK and Bristow, LA and Rodriguez-R, LM and Rossello-Mora, R and Stewart, FJ and Konstantinidis, KT}, title = {Promiscuous and genome-wide recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf072}, pmid = {40247698}, issn = {1751-7370}, abstract = {Surveys of microbial communities (metagenomics) or isolate genomes have revealed sequence-discrete species. That is, members of the same species show >95% Average Nucleotide Identity (ANI) of shared genes among themselves vs. <83% ANI to members of other species while genome pairs showing between 83-95% ANI are comparatively rare. In these surveys, aquatic bacteria of the ubiquitous SAR11 clade (Class Alphaproteobacteria) are an outlier and often do not exhibit discrete species boundaries, suggesting the potential for alternate modes of genetic differentiation. To explore evolution in SAR11, we analyzed high-quality, single-cell amplified genomes (SAGs) and companion metagenomes from an oxygen minimum zone (OMZ) in the Eastern Tropical Pacific Ocean, where the SAR11 make up ~20% of the total microbial community. Our results show that SAR11 do form several sequence-discrete species, but their ANI range of discreteness is shifted to lower identities between 86-91%, with intra-species ANI ranging between 91-100%. Measuring recent gene exchange among these genomes based on a recently developed methodology revealed higher frequency of homologous recombination within compared to between species that affects sequence evolution at least twice as much as diversifying point mutation across the genome. Recombination in SAR11 appears to be more promiscuous compared to other prokaryotic species, likely due to the deletion of universal genes involved in the mismatch repair, and has facilitated the spreading of adaptive mutations within the species (gene sweeps), further promoting the high intra-species diversity observed. Collectively, these results implicate rampant, genome-wide homologous recombination as the mechanism of cohesion for distinct SAR11 species.}, }
@article {pmid40247632, year = {2025}, author = {Lee, JS and Kao, DJ and Worledge, CS and Villamaria, ZF and Wang, RX and Welch, NM and Kostelecky, RE and Colgan, SP}, title = {E. coli genetically modified for purine nucleobase release promotes butyrate generation and colonic wound healing during DSS insult.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2490211}, doi = {10.1080/19490976.2025.2490211}, pmid = {40247632}, issn = {1949-0984}, mesh = {Animals ; *Escherichia coli/genetics/metabolism ; *Wound Healing ; Gastrointestinal Microbiome ; Mice ; *Purines/metabolism ; *Colon/microbiology/metabolism/pathology ; *Butyrates/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; *Colitis/chemically induced/microbiology ; Intestinal Mucosa/metabolism/microbiology ; Male ; }, abstract = {The gut microbiota transforms energy stored as undigestible carbohydrates into a remarkable number of metabolites that fuel intestinal bacterial communities and the host tissue. Colonic epithelial cells at the microbiota-host interface depend upon such microbiota-derived metabolites (MDMs) to satisfy their energy requisite. Microbial dysbiosis eliciting MDM loss contributes to barrier dysfunction and mucosal disease. Recent work has identified a role for microbiota-sourced purines (MSPs), notably hypoxanthine, as an MDM salvaged by the colonic epithelium for nucleotide biogenesis and energy balance. Here, we investigated the role of MSPs in mice during disease-modeled colonic energetic stress using a strain of E. coli genetically modified for enhanced purine nucleobase release (E. coli Mutant). E. coli Mutant colonization protected against DSS-induced tissue damage and permeability while promoting proliferation for wound healing. Metabolite and metagenomic analyses suggested a colonic butyrate-purine nucleobase metabolic axis, wherein the E. coli Mutant provided purine substrate for Clostridia butyrate production and host purine salvage, altogether supplying the host substrate for efficient nucleotide biogenesis and energy balance.}, }
@article {pmid40246700, year = {2025}, author = {Iguchi, H and Watanabe, A}, title = {Honey flavors formed via yeast fermentation in honey from Japanese honeybees.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/bbb/zbaf057}, pmid = {40246700}, issn = {1347-6947}, abstract = {Honey is formed from floral nectar through bee-derived substances, dehydration, and chemical reactions during storage in beehives. While bacteria and fungi inhabit honey and beehives, their roles in honey maturation remain unclear. In this study, we characterized the fermentation process of honey from Apis cerana japonica (Japanese honeybee) with respect to its microbial and flavor compound profiles. Metagenomic analysis revealed that the fungi in Japanese honeybee honey are dominated by Zygosaccharomyces siamensis, with minor members of Talaromyces, Oidiodendron, Starmerella, and Priceomyces. Fermentation of diluted raw honey increased the population of Z. siamensis. Inoculating honey with Z. siamensis produced aromatic compounds, including isoamyl alcohol, hotrienol, 2-phenylethanol, and 2-phenylethyl acetate, as well as the organic acid succinate. These results indicate that fermentation by Z. siamensis can generate favorable flavor compounds, offering the potential for enhancing honey's sensory qualities and applications in the food industry.}, }
@article {pmid40246602, year = {2025}, author = {Zeng, S and Wang, S and Mu, D}, title = {Metagenomics for IgA-coated gut microbiota: from taxonomy to function.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.04.001}, pmid = {40246602}, issn = {1878-4380}, abstract = {Immunoglobulin A (IgA) establishes intricate interactions with human gut microbiota, thereby forming IgA-coated microbiota. This forum first explores state-of-the-art metagenomic techniques for characterizing IgA-coated microbiota. Thereafter, metagenomic insights into its taxonomic diversity and microbial genomic functions that mediate IgA coating are provided. Finally, clinical implications for human health are highlighted.}, }
@article {pmid40246210, year = {2025}, author = {Wani, AK and Qadir, F and Elboughdiri, N and Rahayu, F and Saefudin,  and Pranowo, D and Martasari, C and Kosmiatin, M and Suhara, C and Sudaryono, T and Prayogo, Y and Yadav, KK and Muzammil, K and Eltayeb, LB and Alreshidi, MA and Singh, R}, title = {Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {108580}, doi = {10.1016/j.biotechadv.2025.108580}, pmid = {40246210}, issn = {1873-1899}, abstract = {Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.}, }
@article {pmid40245994, year = {2025}, author = {Yang, R and Liu, Z and Liu, Y and Yang, Z and Zhang, Y and Lei, J and Wang, J and Zhang, A and Li, Z}, title = {High-throughput community and metagenomic elucidate systematic performance variation and functional transition mechanisms during morphological evolution of aerobic sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132550}, doi = {10.1016/j.biortech.2025.132550}, pmid = {40245994}, issn = {1873-2976}, abstract = {In this study, high-throughput sequencing and metagenomics were used to investigate the microbial succession and functional gene dynamics during aerobic sludge granulation from activated sludge (AS) to aerobic granular sludge (AGS) to algal-bacterial granular sludge (ABGS). It was found that the settleability and pollutant removal efficiency of the sludge system increased with the sludge morphology evolution. Extracellular polymeric substances (EPS) analysis showed a rise in protein from 2.1 to 17.4 mg/gSS during stage of AGS and polysaccharides from 3.3 to 5.9 mg/gSS during stage of ABGS. Microbial community analysis revealed that the sludge evolution reduced species richness but enriched functional bacteria for nitrogen/phosphorus removal, while increasing the complexity of community structure and close interactions between species. Key genes involved in the tricarboxylic acid cycle, nitrogen/phosphorus and EPS metabolism were also upregulated. This study revealed the continuity mechanism and stage dependence of the functional transition during sludge morphology evolution.}, }
@article {pmid40245993, year = {2025}, author = {Zhang, J and Zhang, B and Duan, F and Xuan, Z and Sun, T and Lu, L}, title = {Metagenomic exploration of novel β-galactosidases for glycosylation engineering.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132546}, doi = {10.1016/j.biortech.2025.132546}, pmid = {40245993}, issn = {1873-2976}, abstract = {β-Galactosidases are important enzymatic tools for glycosylation, but their properties vary greatly with the source. Here, ten putative β-galactosidase genes, designated as bga1 to bga10, encoding proteins Bga1 to Bga10, were mined from an environmental metagenomic dataset comprising 119,152 sequences. Five of the encoded enzyme proteins exhibited less than 80% sequence similarity to known enzymes, but displayed conserved catalytic sites in their predicted three-dimensional models. After heterologous expression and characterization, two recombinant enzymes showed specific hydrolysis activity toward o-nitrophenyl-β-d-galactopyranoside. One of them, Bga4R, exhibited remarkable activity at pH 7.4 and 50℃, with excellent alkaline stability. Notably, Bga4R tolerated a wide range of acceptors for transglycosylation. It catalyzed galactosyl transfer to various monosaccharides and sugar alcohols, and enabling the synthesis of diverse glycosylated derivatives. This study identifies a novel GH 1 β-galactosidase as a powerful tool for glycosylation engineering, with promising potential for synthesizing galactosides valuable to food and pharmaceutical industries.}, }
@article {pmid40245807, year = {2025}, author = {Wang, J and Zhang, Y and Meng, Q and Hu, Z and Fu, J and Dang, C}, title = {New perspectives on bacterial chlorine resistance: Phages encoding chlorine resistance genes improve bacterial adaptation.}, journal = {Water research}, volume = {282}, number = {}, pages = {123607}, doi = {10.1016/j.watres.2025.123607}, pmid = {40245807}, issn = {1879-2448}, abstract = {Bacterial resistance to chlorine disinfectant reduces its effectiveness in killing pathogenic bacteria and poses a severe threat to environmental and health safety. The interaction between bacteria and phages is the most frequent biological activity in Earth's biosphere, but little is known about what role and mechanism phages play in the resistance of bacterial communities to chlorine disinfectants. Here, we investigated the changes in the abundance, activity and function of the bacterial-phage community under the effect of chlorine disinfectants in a 92-day running anaerobic-anoxic-oxic system, using metagenomics and metatranscriptomics sequencing. We found that transcriptional activities of both bacteria and phage are highly sensitive to chlorine disinfectants, although their relative abundance was not obviously altered. The increase in both phage diversity and the ratio of temperate to lytic phages' average activity indicated phages, especially temperate, could play a crucial role in the response to chlorine disinfectants. Interestingly, the phages that carry chlorine resistance genes (CRGs) were the drivers of the phage and microbial community when chlorine disinfectants were present, but they followed the dynamics of community in the absence of chlorine disinfectants. Based on the association bipartite network, we further found that phages directly mediated the horizontal transfer of CRGs among bacteria, facilitating the spread of CRGs in the bacterial community. Moreover, the 4 CRGs related to cell wall repair, redox balance regulation, and efflux pumps that were carried by the phages but lacking in the hosts suggest the potential compensatory effects of the phage for the chlorine resistance of their hosts. Our findings reveal the important role of phages in improving the resistance of bacterial communities to chlorine disinfectants, providing a new perspective on the co-evolution of phages and bacteria to adapt to environments.}, }
@article {pmid40245806, year = {2025}, author = {Li, J and Zuo, X and Chen, Q and Lin, Y and Meng, F}, title = {Genome-resolved metagenomic analysis reveals a novel denitrifier with truncated nitrite reduction pathway from the genus SC-I-84.}, journal = {Water research}, volume = {282}, number = {}, pages = {123598}, doi = {10.1016/j.watres.2025.123598}, pmid = {40245806}, issn = {1879-2448}, abstract = {Understanding the genomic and ecological traits of partial denitrification (PD) bacteria is of high importance for developing wastewater treatment technologies. In this study, a PD-based bioreactor was operated, resulting in a mixed culture dominated by a potentially novel PD functional bacterium (SC-I-84). Progressively increased activity in both nitrate reduction and nitrite production were observed in the SC-I-84 enrichment system, whereas the nitrite reduction activity was always negligible. The phylogenetic analysis indicated that SC-I-84 was closely related to an uncultured beta-proteobacterium (99 %), whereas its denitrification functional genes (napA, napB, narV, and narY) exhibited evidence of co-evolution with chromosomal genes from the genus Cupriavidus, order Burkholderiales. In the genetic sketch of SC-I-84, only nitrate-reduction genes (nar and nap) were identified, whereas nitrite-reduction genes (nir) were absent. Notably, nitrate reduction genes were adjacent to carbon metabolism genes (sucB/C, mdh, idh) and a high abundance of tricarboxylic acid (TCA) cycling genes were found. This can promote the utilization efficiency of electron donors by nitrate reduction genes in SC-I-84, thus enhancing the denitrification activity. Furthermore, SC-I-84 positively cooperated with some bacteria that participate in nitrogen and carbon metabolism and other PD bacteria, but negatively interacted with full-denitrification bacteria. These results indicate that the enrichment of SC-I-84 restricted the growth of full-denitrification bacteria, aiding in the maintenance of a stable PD process. Taken together, the meta-genomic analysis of the novel PD functional bacterium is expected to enhance our understanding of PD processes and aid in the development of PD-based wastewater treatment processes.}, }
@article {pmid40245686, year = {2025}, author = {Simó, C and Mamani-Huanca, M and Hernández-Hernández, O and Redondo-Río, &#xc1; and Muñoz, S and García-Cañas, V}, title = {Application of nanopore long-read sequencing and metabolomics in an in vitro dynamic intestinal digestion model: A genome-centric metatranscriptomic approach to investigating microbial TMA and SCFA metabolism.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {262}, number = {}, pages = {116896}, doi = {10.1016/j.jpba.2025.116896}, pmid = {40245686}, issn = {1873-264X}, abstract = {The gut microbiota plays a relevant role in human health by metabolizing dietary components into bioactive molecules, including short-chain fatty acids and trimethylamine. Understanding how dietary interventions modulate microbial metabolism is key to developing strategies for reducing harmful metabolites such as TMA, a precursor of the pro-atherogenic trimethylamine-N-oxide. In this study, we integrated a dynamic in vitro gastrointestinal model (simgi®) with nanopore sequencing technology and metabolomics to investigate the impact of red thyme extract on microbial trimethylamine metabolism from L-carnitine. Metabarcoding, metagenomic, and metatranscriptomic analyses were performed alongside targeted metabolite quantification. Our results showed that microbial trimethylamine production primarily occurred in the transverse and descending colon compartments, coinciding with increased transcriptional activity of taxa harboring gbu cluster, associated with trimethylamine production. The administration of red thyme extract transiently reduced L-carnitine utilization but had a limited effect on overall trimethylamine levels. In parallel, short-chain fatty acids analysis revealed a shift in microbial fermentation patterns, with Acidaminococcus emerging as a dominant butyrate producer. Carbohydrate-active enzyme profiling identified Bacteroides and Parabacteroides genera as key mucin utilizers under the simulation conditions. These findings highlight the metabolic plasticity of the gut microbiota in response to the presence of L-carnitine and reduced complex carbohydrates availability, and provide new insights into microbial functional responses to dietary interventions targeting trimethylamine metabolism. Additionally, this study represents the first integration of nanopore-based metagenomics and genome-centric metatranscriptomics with targeted metabolomics in a dynamic in vitro gastrointestinal model. This multi-omics approach enabled a detailed reconstruction of the microbial metabolic network involved in L-carnitine utilization and trimethylamine formation, offering a powerful tool for mechanistic studies of gut microbiota-diet interactions.}, }
@article {pmid40245533, year = {2025}, author = {Zhao, J and Wang, Y and Zhang, D and Du, J and Gao, Y and Lu, MY and Guo, JY and Su, HT and Chen, XF and Wen, DH and Jia, SY and Xu, YC and Chen, J and Yang, QW}, title = {Uncovering the unseen: Metagenomic next-generation sequencing improves liver abscess diagnostics.}, journal = {Journal of infection and public health}, volume = {18}, number = {7}, pages = {102708}, doi = {10.1016/j.jiph.2025.102708}, pmid = {40245533}, issn = {1876-035X}, abstract = {BACKGROUND: This study retrospectively analyzed the metagenomic next-generation sequencing (mNGS) results and clinical data from patients with liver abscess (LA) to investigate the clinical value of mNGS in the diagnosis of LA.<br><br>METHODS: This retrospective observational study included patients with LA who were admitted to Peking Union Medical College Hospital (PUMCH) between April 2022 and July 2024. We comprehensively analyzed the final clinical etiological diagnosis, traditional pathogen detection through conventional microbiological testing (CMT), and mNGS results in terms of pathogen type and specimen turnaround time.<br><br>RESULTS: Among 60 patients with LA, 19 types of pathogens were identified. Using clinical etiological diagnosis as the standard, mNGS identified all pathogens, whereas CMT identified only 42.11&#x202f;% of pathogens. The true-positivity rate of mNGS (86.67&#x202f;%) was significantly higher than that of CMT (58.33&#x202f;%; P&#x202f;<&#x202f;0.001). The average specimen turnaround time for mNGS (57.66&#x202f;h) was shorter than that for CMT (86.54&#x202f;hours, P&#x202f;<&#x202f;0.001).<br><br>CONCLUSIONS: Compared with existing CMT, mNGS offers higher true-positive rates, broader pathogen coverage, and shorter specimen turnaround time. These advantages contribute to more accurate clinical diagnosis and treatment.}, }
@article {pmid40245502, year = {2025}, author = {Zhong, Y and Teo, JQ and Guo, S and Schlundt, J and Kwa, AL and Ong, RT}, title = {Characterization of mobile resistance elements in extended-spectrum β-lactamase producing gram-negative bacteria from aquatic environment.}, journal = {The Science of the total environment}, volume = {978}, number = {}, pages = {179353}, doi = {10.1016/j.scitotenv.2025.179353}, pmid = {40245502}, issn = {1879-1026}, abstract = {Extended-spectrum β-lactamase producing (ESBL) bacteria from aquatic environments can pose potential threats to public health due to their capability of spreading antimicrobial resistance (AMR) genes through mobile genetic elements (MGEs), such as plasmids, insertion sequences (ISs), transposons, and integrons. Currently, there is no policy for routine monitoring of AMR genes in aquatic environments and their roles in transmission are therefore unknown. Previous metagenomic and PCR-based culture-independent approaches are limited in recovering AMR resistant aquatic bacteria isolates and the data resolution generated are not able to provide detailed genetic comparison with known human pathogens particularly for determining genetic islands harbouring AMR genes. To address these gaps, we thus investigated the genetic profiles of ESBL-producing gram-negative aquatic bacteria found from water body sites within Singapore, examining the AMR genes carried and their associated MGEs. In total, 16 ESBL-producing gram-negative bacteria were identified, of which 8 were Escherichia coli, 3 Klebsiella pneumoniae, and 5 Aeromonas spp. Whole genome sequencing (WGS) analysis revealed the presence of 12 distinct classes of AMR genes, including 16 distinct variants of β-lactamase, of which blaCTX-M was the dominant beta-lactamase genotype in all 11 Enterobacterales. The AMR genetic islands in the aquatic bacteria were also found to share similar genetic structures similar to those of circulating ESBL bacteria causing human infections. These findings underscore the potential role of aquatic ESBL bacteria as AMR reservoirs for human pathogens, suggesting that aquatic bacteria may facilitate the hidden transmission of AMR mediated by MGEs through horizontal gene transfer across different sources and species, highlighting the importance of integrating environmental AMR monitoring into local surveillance strategies.}, }
@article {pmid40244604, year = {2025}, author = {Koyanagi, Y and Sajiki, AF and Yuki, K and Ushida, H and Kawano, K and Fujita, K and Shimizu, H and Okuda, D and Kosaka, M and Yamada, K and Suzumura, A and Kachi, S and Kaneko, H and Komatsu, H and Usui, Y and Goto, H and Nishiguchi, KM}, title = {Application of Metagenomic Long-Read Sequencing for the Diagnosis of Herpetic Uveitis.}, journal = {Investigative ophthalmology &amp; visual science}, volume = {66}, number = {4}, pages = {50}, doi = {10.1167/iovs.66.4.50}, pmid = {40244604}, issn = {1552-5783}, mesh = {Humans ; *Aqueous Humor/virology ; Female ; Male ; *Uveitis/diagnosis/virology ; Middle Aged ; *Metagenomics/methods ; *DNA, Viral/analysis/genetics ; *Eye Infections, Viral/diagnosis/virology ; Adult ; Sensitivity and Specificity ; Aged ; Multiplex Polymerase Chain Reaction ; *Herpesviridae/genetics/isolation &amp; purification ; Young Adult ; }, abstract = {PURPOSE: To investigate the sensitivity and specificity of herpes virus detection by nanopore metagenomic analysis (NMA) compared with multiplex polymerase chain reaction (mPCR)-positive and -negative controls.<br><br>METHODS: This study included 43 patients with uveitis who had been screened for intraocular herpes virus infection using mPCR from aqueous humor samples. Aqueous humor samples stored after mPCR were subjected to whole-genome amplification, long-read sequencing, and analysis of the phylogenetic microorganism composition using a Flongle flow cell on the Oxford Nanopore MinION platform. For samples that tested positive with mPCR and negative with the Flongle flow cell, additional long-read sequencing was performed using a MinION flow cell, which enabled acquisition of more sequence data. The sensitivity and specificity of herpes virus detection by NMA were compared with the mPCR-positive and -negative controls.<br><br>RESULTS: NMA using a Flongle flow cell detected the pathogenic virus in 60.0% of those who tested positive by mPCR (12/20). Further analysis using the MinION flow cell successfully identified viral DNA fragments in three out of the eight initially undetected samples, yielding a collective sensitivity of 75.0% (15/20). All of the virus detected with the long-read sequencing were identical to those diagnosed by mPCR testing, and none of the samples that tested negative by mPCR revealed herpes viral DNA with the use of long-read sequencing.<br><br>CONCLUSIONS: For the detection of etiologic herpes virus DNA fragments, NMA revealed a reasonable sensitivity and high specificity. Our study highlights the potential of nanopore sequencing to facilitate further advances in uveitis diagnosis.}, }
@article {pmid40244481, year = {2025}, author = {Klangnurak, W and Hinthong, W and Aue-Umneoy, D and Yomla, R}, title = {Assessment of Bacterial Community and Other Microorganism Along the Lam Takhong Watercourse, Nakhon Ratchasima, Thailand.}, journal = {Current microbiology}, volume = {82}, number = {6}, pages = {248}, pmid = {40244481}, issn = {1432-0991}, support = {grant number FRB650039/0240 project number 165430//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; contract number FF-65/008//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; }, mesh = {Thailand ; *Bacteria/classification/genetics/isolation &amp; purification ; *Water Microbiology ; *Rivers/microbiology ; Metagenomics ; *Microbiota ; Water Quality ; Environmental Monitoring ; }, abstract = {Lam Takhong, a vital watercourse in Nakhon Ratchasima province, Thailand, supports agricultural, recreational, and urban activities. Originating in a national park, it flows through urban areas before discharging into a dam and running off via the sluice gate. While water quality monitoring is routine, microbial community data have never been reported. This study assesses the microorganism diversity and functional genes in Lam Takhong watercourse using a shotgun sequencing metagenomics approach. Water samples were collected from the upstream, midstream, and downstream sections. The midstream area exhibited the highest abundance of fecal coliform bacteria, plankton, and benthos, suggesting elevated pollution levels. Genes related to metabolism, particularly carbohydrate and amino acid pathways, were predominant. Proteobacteria was the most abundant phylum found in the water, with Limnohabitans as the dominant planktonic bacteria. Bacteria such as Staphylococcus, Mycobacterium, Escherichia, Pseudomonas, Enterococcus, Neisseria, Streptomyces, and Salmonella were detected, along with antibiotic resistance genes, raising public health concerns. These findings emphasize the need for microbial monitoring in the Lam Takhong to determine the potential water quality bioindicator and prevent potential disease spread through the water system.}, }
@article {pmid40244477, year = {2025}, author = {Li, J and Zhang, Y and He, L}, title = {The role of urine microbiota in culture-negative patients with pyuria.}, journal = {World journal of urology}, volume = {43}, number = {1}, pages = {227}, pmid = {40244477}, issn = {1433-8726}, mesh = {Humans ; *Pyuria/microbiology/virology/urine ; Retrospective Studies ; Male ; Female ; *Microbiota ; Middle Aged ; *Urine/microbiology/virology ; Aged ; Adult ; }, abstract = {BACKGROUND: Pyuria is usually caused by bacteria and usually results in antibiotic prescriptions. However, traditional urine culture is time-consuming and has a high false negative possibility. Additionally, the role of urine viruses in pyuria is unclear. Metagenomics can enhance the precision and efficiency of diagnosis by directly sequencing the microbiota in urine. We aimed to determine the association of urine microbiota in patients with or without pyuria and culture negative.<br><br>METHODS: In this retrospective study, we screened urine samples from patients who received whole genome sequencing (WGS) and had a negative urine culture from October 2021 to May 2024. We compared differences in the top 10 detected genera of urine microbiota between the pyuria group and the non-pyuria group. Multivariable analysis was used for correlation analysis and performed to odds ratio (OR) and OR with 95% confidence interval (CI). The receiver operating characteristic (ROC) curve analyses tested the predictive ability of associated microbiota to pyuria.<br><br>RESULTS: We found 29 microbial genera including 2 viral genera. Escherichia [OR 11.688 (95%CI 2.190-62.362), p&#x2009;=&#x2009;0.004], Gardnerella [OR 9.904 (95%CI 2.180-45.005), p&#x2009;=&#x2009;0.003] or Polyomavirus [OR 5.205 (95%CI 1.295-20.919), p&#x2009;=&#x2009;0.020] was associated with the independent risk factors of pyuria, while Lactobacillus was associated with a decreased risk of pyuria [OR 17.273 (95%CI 1.297-230.061), p&#x2009;=&#x2009;0.031]. An integrated logistic regression model of Escherichia, Gardnerella, Polyomavirus, and Lactobacillus exhibited a predictive power for pyuria with the area under curve (AUC) of 0.8132 [95%CI (0.7098-0.9167), p&#x2009;<&#x2009;0.001].<br><br>CONCLUSION: Urine microbiota is diverse. Escherichia, Gardnerella, or Polyomavirus are independently associated with pyuria, while Lactobacillus is a positive factor against pyuria.}, }
@article {pmid40244062, year = {2025}, author = {Stevens, EJ and Li, JD and Hector, TE and Drew, GC and Hoang, K and Greenrod, STE and Paterson, S and King, KC}, title = {Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf071}, pmid = {40244062}, issn = {1751-7370}, support = {COEVOPRO 802242//European Research Council Starting/ ; }, abstract = {Pathogens newly invading a host must compete with resident microbiota. This. within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a native microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but maintained its virulence across generations. Conversely, pathogen populations and microbiota passaged in isolation caused more host harm relative to their respective no-host controls. For the evolved pathogens, this increase in virulence was partly mediated by enhanced biofilm formation and expression of the global virulence regulator agr. Whole genome sequencing revealed shifts in the mode of selection from directional (on pathogens evolving in isolation) to fluctuating (on pathogens evolving in host microbiota). This approach also revealed that competitive interactions with the microbiota drove early pathogen genomic diversification. Metagenome sequencing of the passaged microbiota shows that evolution in pathogen-infected hosts caused a significant reduction in community stability (dysbiosis), along with restrictions on the co-existence of some species based on nutrient competition. Our study reveals how microbial competition during novel infection could determine the patterns and processes of evolution with major consequences for host health.}, }
@article {pmid40243577, year = {2025}, author = {Paradzik Simunovic, M and Degoricija, M and Korac-Prlic, J and Lesin, M and Stanic, R and Puljak, L and Olujic, I and Marin Lovric, J and Vucinovic, A and Ljubic, Z and Thissen, J and Reen Kok, C and Jaing, C and Bucan, K and Terzic, J}, title = {Potential Role of Malassezia restricta in Pterygium Development.}, journal = {International journal of molecular sciences}, volume = {26}, number = {7}, pages = {}, doi = {10.3390/ijms26072976}, pmid = {40243577}, issn = {1422-0067}, support = {IP-2020-02-8921//Croatian Science Foundation/ ; }, mesh = {Humans ; *Pterygium/microbiology/pathology/genetics ; *Malassezia/genetics/isolation &amp; purification ; Male ; Female ; Middle Aged ; Conjunctiva/microbiology/pathology ; Microbiota ; Aged ; Gene Expression Profiling ; }, abstract = {Pterygium is a condition affecting the ocular surface, marked by a triangular-shaped growth of fibrotic tissue extending from the nasal conjunctiva toward the corneal center, potentially causing visual impairment. While ultraviolet (UV)light exposure is the primary risk factor for pterygium, its underlying cause remains unclear. In order to better understand the true genesis of pterygium development, we investigated pterygium tissue and compared it with healthy conjunctiva controls. Given the eye's direct environmental exposure, we analyzed the microbiota composition using metagenomic sequencing of pterygium tissue to identify microbes potentially associated with this condition. Metagenomic sequencing revealed a higher prevalence of the fungus Malassezia restricta in five pterygium samples, confirmed by in situ hybridization. The CHIT1 gene, which plays a role in antifungal defenses, displayed the highest expression in five pterygium tissue samples compared to healthy conjunctiva controls, suggesting the potential involvement of Malassezia restricta in pterygium development. Gene expression profiling of pterygium highlighted an IL-33 and IL-4 gene expression signature, along with an increased presence of M2 macrophages, emphasizing their role in promoting fibrosis-a hallmark feature of pterygium. The detection of Malassezia restricta in the pterygium samples and associated molecular changes provides novel insights into the ocular microbiome and raises the possibility of Malassezia's involvement in pterygium pathology.}, }
@article {pmid40243351, year = {2025}, author = {Li, Y and Liu, S and Han, P and Lei, J and Wang, H and Zhu, W and Dong, Z and Zhang, Y and Jiang, Z and Zheng, B and Rao, G and Yu, Z and Li, A}, title = {Performance and hypothetical clinical impact of an mNGS-based machine learning model for antimicrobial susceptibility prediction of five ESKAPEE bacteria.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0259224}, doi = {10.1128/spectrum.02592-24}, pmid = {40243351}, issn = {2165-0497}, abstract = {UNLABELLED: Antimicrobial resistance is an escalating global health crisis, underscoring the urgent need for timely and targeted therapies to ensure effective clinical treatment. We developed a machine learning model based on metagenomic next-generation sequencing (mNGS) for rapid antimicrobial susceptibility prediction (mNGS-based AST), which was tailored to five ESKAPEE bacteria: Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. However, the clinical utility remained unvalidated. Assuming that mNGS-based AST results were obtained during clinical management, we assessed its clinical utility using data from a previous observational cohort study of clinical mNGS applications. We collected the data from 114 patients infected with five ESKAPEE bacteria from 07/2021 to 03/2023 and incorporated the sequencing data into the model. We evaluated the performance and hypothetical impact of the method by comparing its results and therapy recommendations with those based on traditional culture-based AST. The primary outcome was the performance of mNGS-based AST (n = 113 strains). mNGS-based AST displayed an overall accuracy of 93.84% and shorter turnaround time (1.12 ± 0.33 days vs 2.81 ± 0.57 days for culture-based AST, t = -27.31, P < 0.05). The secondary outcomes included the proportion of patients who could benefit from mNGS-based AST. It could allow earlier and suitable antibacterial adjustments in 32.05% of culture-positive patients (25/78) and offer actionable antimicrobial susceptibility results in 16.67% of culture-negative cases (6/36). mNGS-based AST offers a promising approach for individualized antibacterial therapy.<br><br>IMPORTANCE: Metagenomic next-generation sequencing (mNGS)-based antimicrobial susceptibility prediction (AST) is a novel method for predicting the antimicrobial susceptibility of ESKAPEE bacteria using a machine learning approach and short-read sequencing data. Assuming that mNGS-based AST results were obtained during clinical management, it could significantly reduce turnaround time while maintaining a high level of accuracy, allowing for earlier therapeutic adjustments for patients. Furthermore, mNGS-based AST can be integrated with clinical mNGS to maximize the utility of short-read data without substantial cost increases. This study demonstrates the potential of mNGS-based AST for precise, individualized antibacterial selection and highlights its broader applicability in enhancing clinical antimicrobial use for various infections.}, }
@article {pmid40243342, year = {2025}, author = {Gruninger, RJ and McCormack, ML and Chomistek, NC and Zaheer, R and McAllister, TA}, title = {Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of the Bacteroides found in hepatic lesions.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0042325}, doi = {10.1128/spectrum.00423-25}, pmid = {40243342}, issn = {2165-0497}, abstract = {UNLABELLED: Liver abscesses in cattle reduce animal performance, increase the environmental footprint of beef production, and cause significant economic losses. The low pH of the rumen resulting from the consumption of high grain diets damages the rumen epithelium and facilitates the translocation of opportunistic pathogens from the gastrointestinal tract into the bloodstream where they can colonize the liver, causing infection. Recently, 16s rRNA sequencing has revealed that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides. Due to the inability to reliably classify amplicon sequences beyond the genus level, the identity of these microbes remains unknown. We have employed a combination of culture-independent and culture-based methods to isolate and identify the Bacteroides associated with liver abscesses in cattle. Shotgun metagenomic sequencing and assembly of metagenome-assembled genomes generated four high-quality genomes, two of which were putatively identified as Bacteroides. These microbes were subsequently isolated from the purulent material of liver abscesses. Whole-genome sequencing conclusively identified these isolates as Bacteroides pyogenes and a previously unknown species of Bacteroides, revealing distinct differences from Bacteroides typically found in the gut. Carbohydrate utilization assays revealed that both organisms metabolize glycogen and glycosaminoglycans found in the extracellular matrix of the liver but display differences in substrate specificity. These data not only identify Bacteroides found in bovine liver abscesses but also provide new insights into the potential role that these organisms may play in this production-limiting disease.<br><br>IMPORTANCE: Liver abscesses (LAs) are commonly found in cattle raised in feedlots and result from a bacterial infection of the liver. Not only are LAs a concern for animal health, but they also impact growth efficiency, animal welfare, and cost the North American beef industry upwards of $120 million per annum. Recently, it has been found that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides; however, to date, the biological relevance in LA pathogenesis and the identity of these bacteria are unknown. This research describes the isolation, identification, and genomic characterization of the Bacteroides found in bovine liver abscesses. These data provide a critical foundation for expanding our knowledge of the potential role Bacteroides play in liver abscess development and could contribute to the identification of novel targets for developing treatments to prevent this important production-limiting disease.}, }
@article {pmid40243306, year = {2025}, author = {Wang, Z and Sun, Y and Wang, H and Yun, J and Du, W}, title = {Metagenome-assembled genome of a novel Pseudoalteromonas species from South Mid-Atlantic Ridge deep-sea water suggests potential for chitin degradation.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0018925}, doi = {10.1128/mra.00189-25}, pmid = {40243306}, issn = {2576-098X}, abstract = {We report a high-quality metagenome-assembled genome (MAG) of a novel Pseudoalteromonas species recovered from deep-sea water of the South Mid-Atlantic Ridge. This MAG encodes key chitinase-related genes, suggesting potential involvement in chitin degradation and organic matter remineralization in the deep sea.}, }
@article {pmid40242593, year = {2025}, author = {Sun, S and He, R and Chen, S and Ren, J and Ma, X and Yang, J}, title = {Odontogenic brain abscess caused by Porphyromonas gingivalis and Streptococcus constellatus: a case report and review article.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2485197}, pmid = {40242593}, issn = {2000-2297}, abstract = {BACKGROUND: Odontogenic brain abscess is a rare, but potentially fatal, central nervous system infection, with insidious onset and unclear etiology.<br><br>METHODS: This case reports a 70-year-old male patient who developed an odontogenic brain abscess secondary to periodontal infection and underwent neurological surgery. Extract pus during surgery for the metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: The mNGS of pus samples obtained from brain abscess aspiration identified the periodontal pathogens Porphyromonas gingivalis and Streptococcus constellatus. Consequently, he was referred to the department of stomatology for further examination and treatment.<br><br>CONCLUSIONS: Our study found that major periodontal pathogens including P. gingivalis and S. constellatus were essential in the development of odontogenic brain abscesses; thus, timely intervention and preventive measures are important for treatment.}, }
@article {pmid40242244, year = {2025}, author = {Kang, Z and Zhang, R and Li, S and Wang, J and Huang, M and Li, W}, title = {Preliminary investigation of gut microbiota and associated metabolic pathways in the pathogenesis of primary central nervous system lymphoma.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1548146}, pmid = {40242244}, issn = {2234-943X}, abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) is a rare and highly aggressive form of non-Hodgkin lymphoma, primarily confined to the central nervous system. In recent years, growing evidence has indicated that dysbiosis of the gut microbiota is closely associated with the development of various malignancies. This study aims to systematically explore the potential role of gut microbiota and their metabolic pathways in the pathogenesis of PCNSL by integrating metagenomic and metabolomic approaches.<br><br>MATERIALS AND METHODS: A total of 33 PCNSL patients and 32 healthy controls were enrolled in this study, and fecal samples were collected from each participant. The fecal samples were analyzed using metagenomic and metabolomic techniques, followed by KEGG pathway enrichment analysis to investigate the biological pathways enriched by the differential gut microbiota and metabolites.<br><br>RESULTS: Significant differences were observed in the composition of gut microbiota and metabolites between PCNSL patients and healthy controls. In the gut microbiota of PCNSL patients, the abundance of the phylum Proteobacteria was markedly increased, while the Firmicutes/Bacteroidetes (F/B) ratio was significantly elevated. Metabolomic analysis revealed that the abundance of oleamide was significantly reduced in the PCNSL group, while the relative abundance of deoxycholic acid was significantly elevated. KEGG pathway analysis indicated that the differential gut microbiota and metabolites were primarily involved in key metabolic pathways such as nitrogen metabolism, phenylalanine metabolism, purine metabolism, and pyrimidine metabolism, with these pathways being more active in PCNSL patients.<br><br>CONCLUSION: This study is the first to systematically investigate the differences in gut microbiota and their metabolites between PCNSL patients and healthy individuals, highlighting the potential role of gut microbiota alterations in the pathogenesis of PCNSL.}, }
@article {pmid40241899, year = {2025}, author = {Chen, L and Weng, W and Li, D and Xie, W and Lu, L and Li, S}, title = {Case Report: A clinically relevant isolation of Gardnerella leopoldii guided by morphological and molecular evidence from a urinary tract infection case.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1548067}, pmid = {40241899}, issn = {2296-858X}, abstract = {BACKGROUND: The genus Gardnerella is commonly found in the vaginal ecosystem and is considered a covert pathogen of the urinary tract. However, Gardnerella vaginalis had been the only recognized species of the genus Gardnerella for decades. Cases regarding the clinical relevance of Gardnerella leopoldii have rarely been reported, which is crucial for fully understanding the various species within the genus Gardnerella.<br><br>CASE PRESENTATION: A 72-year-old female patient was admitted to the hospital with gross hematuria and complaints of waist soreness. Physical examinations, including those of the head, chest, and abdomen, along with routine laboratory tests such as white blood cell (WBC) count and proportion, liver function, and renal function, yielded normal results. However, the patient also exhibited significantly elevated levels of serum C-reactive protein (CRP) and abnormal urinary test findings, which revealed positive results for occult blood and leukocyte esterase, and increased counts of erythrocyte and leukocyte. To further evaluate the urinary system, computerized tomography urography (CTU) was performed. The CTU results revealed multiple weakly enhanced foci in the right kidney and thickening of the right ureter, renal pelvis, calyces, and bladder walls. Based on the above findings, the initial diagnosis included hematuria, hydronephrosis, and urinary tract infection (UTI). To identify the causative pathogens, we employed a comprehensive approach that included microscopic morphology, Sanger sequencing, and metagenomic next-generation sequencing (mNGS). Finally, both Mycobacterium tuberculosis and G. leopoldii were identified as the co-infecting etiological agents responsible for the patient's urinary tract infection.<br><br>CONCLUSION: This case represents the first documented isolation of clinically relevant G. leopoldii, guided by morphological and molecular evidence from a clinical urine sample. It highlights the potential of mNGS as a promising tool for identifying previously unrecognized species and offers valuable insights to enhance the understanding of clinically relevant microorganisms.}, }
@article {pmid40241768, year = {2025}, author = {Yao, XQ and Bao, H and La, NT and Jiang, GS and Zhai, PH and Liu, CB and Yu, L}, title = {Gut microbiota contribute to cold adaptation in mammals-primates and ungulates.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112245}, pmid = {40241768}, issn = {2589-0042}, abstract = {Gut microbiota play an influential role in how animals adapt to extreme environments. Two phylogenetically distant mammals, Yunnan snub-nosed monkey and reindeer both adapted to frigid environments. Metagenomic analyses revealed they developed similar cold adaptation strategies in response to food scarcity (enhanced fiber degradation and nitrogen balance maintenance), energy shortages (increased short-chain fatty acid [SCFA] synthesis), and a constant body temperature sustainment (stimulation of non-shivering thermogenesis [NST]). Moreover, they evolved distinct adaptation strategies to cope with different cold ecosystems. Yunnan snub-nosed monkey adapt to high-altitude hypoxia environment through enhancing ability to synthesize lactate and metabolize purine, while reindeer adapt to extreme cold environment through increasing blood flow, strengthening urea cycling, and enriching fat storage associated bacteria. Notably, reindeer microbiota uniquely enriched cholesterol-degrading bacteria, potentially mitigating cardiovascular risks from lipid storage. Our study expands the knowledge of how gut microbiome promotes cold adaptation through shared and specialized mechanisms shaped by different phylogenetic and ecological contexts.}, }
@article {pmid40241748, year = {2025}, author = {Liu, T and Kress, AM and Debelius, J and Zhao, N and Smirnova, E and Bandyopadhyay, S and Bonham, K and Comstock, SS and Gill, S and Gern, JE and Koinis-Mitchell, D and Klepac-Ceraj, V and Lee-Sarwar, K and Litonjua, AA and McKee, K and McCauley, K and O'Connor, TG and Rosas-Salazar, C and Scheible, K and Stanford, JB and Moore, B and Jacobson, LP and Mueller, NT and , }, title = {Maternal vaginal and fecal microbiota in later pregnancy contribute to child fecal microbiota development in the ECHO cohort.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112211}, pmid = {40241748}, issn = {2589-0042}, abstract = {There is growing interest in the use of microbial-seeding interventions to mitigate the impacts of prenatal antibiotics, C-section, and lack of breastfeeding on mother-child microbe sharing. However, the relative importance of maternal vaginal vs. fecal microbiota in this process is unclear. Analyzing 16S rRNA sequences from five US birth cohorts, we found that maternal vaginal and fecal microbiota became more similar as pregnancy progressed, and both niches influenced the child's fecal microbiota. The relative contribution of maternal vaginal microbiota increased when vaginal sampling occurred later in gestation. As children aged from birth to 5 years, their fecal microbiota increasingly resembled their mother's fecal microbiota as compared to vaginal microbiota. Patterns of sharing appeared to differ by prenatal antibiotic use, birth mode (C-section vs. vaginal), and breastfeeding. Our findings enhance understanding of niche-specific mother-child microbe sharing and may inform microbial-seeding interventions. Metagenomic studies are needed to identify specific shared strains.}, }
@article {pmid40241728, year = {2025}, author = {Xie, L and Wang, X and Wang, X and Liu, X}, title = {Changes in microbial community succession and volatile compounds during the natural fermentation of bangcai.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1581378}, pmid = {40241728}, issn = {1664-302X}, abstract = {INTRODUCTION: Fermented bangcai (Brassica juncea var. crassicaulis) is a traditional Chinese food with unique flavor. However, the formation mechanism of flavor compounds related to the fermentation process of bangcai has not been thoroughly studied.<br><br>METHODS: Gas chromatography-ion mobility spectrometry technology combined with metagenomics was used to analyze the characteristic volatile flavor compounds and microbial community structure of bangcai before and after fermentation in this study.<br><br>RESULTS: A total of 91 types of volatile organic compounds were detected in this study. The pungent odor brought by allyl isothiocyanate, 1-butene isothiocyanate, and other substances in the raw materials was removed through fermentation. This process led to the formation of flavor substances such as propyl acetate, ethyl acetate, and 2-methyl-3-furanthiol, which imparted bangcai with flavors of flower and fruit, roast meat, and fried coffee. In addition, our study found that after air drying, bangcai mainly contained &#x3b3;-butyrolactone, nonanal and other flavor compounds, giving the bangcai products a richer floral and fruity flavor profile. Citrobacter, Lactobacillus, and Leuconostoc were the dominant bacteria in the fermentation process of bangcai. They were significantly related to the formation of differential flavor compounds such as &#x3b3;-butyrolactone, ethyl 2-methylpropanoat, and benzaldehyde-D.<br><br>DISCUSSION: These results provide a theoretical basis for improving the flavor quality of fermented vegetable products.}, }
@article {pmid40241696, year = {2025}, author = {Yang, Z and Xie, Y and Zhu, Y and Lei, M and Chen, X and Jin, W and Fu, C and Yu, L}, title = {Unraveling the flavor formation process of mellow and thick-type ripened Pu-erh tea through non-targeted metabolomics and metagenomics.}, journal = {Food chemistry: X}, volume = {27}, number = {}, pages = {102424}, pmid = {40241696}, issn = {2590-1575}, abstract = {Ripened Pu-erh tea (RPT) is renowned for its distinctive flavor and health benefits. However, its complex fermentation process poses challenges in ensuring consistency in production. This study investigated RPT flavor formation through sensory evaluation, multi-omics analysis, and multivariate statistical approaches. By day 24, the tea exhibited a reddish-brown infusion and a mellow, thick taste (MT_RPT), achieving the highest sensory score (94.0, P < 0.05). Sixteen flavor-related chemical components exhibited significant changes (P < 0.05). The contents of free amino acids, L-theanine, tea polyphenols, flavonoids, catechins, and thearubigins decreased. In contrast, the contents of total soluble sugars, caffeine, theobromine, epicatechin, and theabrownins (TBs) increased, reaching 74.1 mg/g, 65.38 mg/g, 3.13 mg/g, 3.33 mg/g, and 134.84 mg/g, respectively. Additionally, 33 nonvolatile metabolites (e.g., pelargonidin 3-O-glucoside, dihydroisorhamnetin, and puerarin) were significantly correlated with MT_RPT flavor (VIP > 1, |r| ≥ 0.8, P < 0.05) and influenced by key functional microbes, including Pantoea, Aspergillus, Brachybacterium, and Staphylococcus. By day 30, the infusion darkened, and sensory scores declined (81.4, P < 0.05), attributed to the dominance of Brevibacterium. This microbial shift reduced water-soluble pectin, free amino acids, and 11 metabolites while increasing TBs and theophylline (219.33 mg/g and 0.09 mg/g, respectively). Therefore, TBs were identified as a crucial indicator of optimal fermentation. Moreover, redundancy analysis indicated that the tea pile's central temperature, moisture content, and pH were essential fermentation parameters (P < 0.05). These findings deepen our understanding of MT_RPT flavor development mechanisms and provide valuable insights into precise fermentation control.}, }
@article {pmid40241220, year = {2025}, author = {Yang, K and Li, G and Li, Q and Wang, W and Zhao, X and Shao, N and Qiu, H and Liu, J and Xu, L and Zhao, J}, title = {Distribution of gut microbiota across intestinal segments and their impact on human physiological and pathological processes.}, journal = {Cell &amp; bioscience}, volume = {15}, number = {1}, pages = {47}, pmid = {40241220}, issn = {2045-3701}, support = {82272812//National Natural Science Foundation of China/ ; 82360018//National Natural Science Foundation of China/ ; }, abstract = {In recent years, advancements in metagenomics, metabolomics, and single-cell sequencing have enhanced our understanding of the intricate relationships between gut microbiota and their hosts. Gut microbiota colonize humans from birth, with their initial composition significantly influenced by the mode of delivery and feeding method. During the transition from infancy to early childhood, exposure to a diverse diet and the maturation of the immune system lead to the gradual stabilization of gut microbiota's composition and distribution. Numerous studies have demonstrated that gut microbiota can influence a wide range of physiological functions and pathological processes by interacting with various tissues and organs through the gut-organ axis. Different intestinal segments exhibit unique physical and chemical conditions, which leads to the formation of vertical gradients along the intestinal tract: aerobes and facultative aerobes mainly live in the small intestine and anaerobic bacteria mainly live in the large intestine, and horizontal gradients: mucosa-associated microbiota and lumen-associated microbiota. In this review, we systematically summarize the distribution characteristics of gut microbiota across six intestinal segments: duodenum, jejunum, ileum, cecum, colon, and rectum. We also draw a conclusion that gut microbiota distributed in different intestinal segments affect the progression of different diseases. We hope to elucidate the role of microbiota at specific anatomic sites within the gut in precisely regulating the processes of particular diseases, thereby providing a solid foundation for developing novel diagnostic and therapeutic strategies for related diseases.}, }
@article {pmid40240641, year = {2025}, author = {Muñoz-Rivera, MP and Martínez-Morales, F and Guzmán-Morales, D and Rivera-Ramírez, A and Sánchez-Reyes, A and Trejo-Hernández, MR}, title = {Population dynamics of a bacterial consortium from a marine sediment of the Gulf of Mexico during biodegradation of the aromatic fraction of heavy crude oil.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40240641}, issn = {1618-1905}, abstract = {In the marine environment, uncontained crude oil is dispersed and degraded by abiotic or biotic processes; native bacterial populations gradually adapt to integrate interspecific and intraspecific metabolic networks for efficient and dynamic utilization of xenobiotic substrates as carbon source. Aromatic compounds accumulate in marine sediments and bacterial populations at these sites play a crucial role in the mobilization of those complex molecules into the global geochemical cycles. The aim of this work was to use native bacteria from a marine sediment sample in the Gulf of Mexico to enhance the biodegradation of the aromatic fraction from a heavy crude oil, as the sole carbon source, during a 200-day microcosm experiment. This process involved the gradual increase of the aromatic fraction into the culture to promote bacterial enrichment; the increase in viable cells correlated well with a biodegradation pattern of the aromatic fraction at some points. Bacterial biodiversity, as revealed by metagenomic and microbiological approaches, indicates that bacterial groups are present at all fraction concentrations, but with changes in abundance, richness and dominance. Population dynamics revealed the presence of bacteria that modify emulsification and surface tension reduction values, which could promote the incorporation of the highly hydrophobic polyaromatic compounds into the culture aqueous phase for their biodegradation by hydrocarbonoclastic bacteria present. On the other hand, the presence of non-hydrocarbonoclastic bacteria probably is sustained by cross-feeding events involving sugars, amino acids, short carbon compounds, lipids produced by the former bacteria by co-metabolism of complex aromatic substrates, which are transformed into diverse biomolecules for biofilm development to promote a bacterial population dynamics adapted to this environment.}, }
@article {pmid40240456, year = {2025}, author = {Bahetjan, K and Yu-Xia,  and Lin, S and Aili, N and Yang, H and Du, S}, title = {Analysis of the bronchoalveolar lavage fluid microbial flora in COPD patients at different lung function during acute exacerbation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13179}, pmid = {40240456}, issn = {2045-2322}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Microbiota ; Bacteria/classification/genetics/isolation &amp; purification ; *Lung/microbiology/physiopathology ; Dysbiosis/microbiology ; }, abstract = {There is a correlation between the dysbiosis of the respiratory microbiota and the occurrence, severity, frequency, and mortality of Chronic Obstructive Pulmonary Disease (COPD). However, it is not unclear if there are differences in the bronchoalveolar lavage fluid (BALF) microbiota among patients at differente lung function. In this study, BALF samples were collected from 70 COPD patients experiencing acute exacerbations (AECOPD). The patients were divided into a mild group (FEV1/pre ≥ 50; PFT I, n = 50) and a severe group (FEV1/pre < 50; PFT II, n = 20) according to the lung function: or a frequent exacerbation (FE, n = 41) group and a non-frequent exacerbation (NFE, n = 29) group according to their exacerbation history. Microbiota analysis of BALF samples was conducted using mNGS and bioinfromatic analysis. Compared to PFT I group, PFT II group exhibited a significant decrease in species diversity (Shannon index), as well as a significant reduction in total species count and richness (Chao1, ACE indices). NFE group demonstrated diversity similar to that of FE group. Conversely, the microbial diversity of NFE group was comparable to that of FE group. The most abundant bacterial genera were Streptococcus, Prevotella, Veillonella, Rod-shaped Bacillus, and Rothia. Aspergillus was the most dominant fungal genus in AECOPD. Lymphocryptovirus was the most prevalent virus in AECOPD.Compared to the PFT I group, Corynebacterium's abundance significantly increased in PFT II group. Furthermore, FE group showed a notable increase in Streptococcus mitis abundance relative to NFE group. Bubble plot analysis revealed a significant increase in Moraxella, Fusobacterium, Haemophilus, Pseudomonas, Streptomyces, and Klebsiella in PFT II group, including a notable increase in typical Veillonella, Actinomyces, and Gordonia. The NFE group exhibited a significant increase in Bacteroides and Prevotella's relative abundance. Spearman correlation analysis revealed strong positive correlations among certain microbial communities. There exists a significant variation in microbial composition across groups of AECOPD patients at different lung function. Specifically, patients with severe airflow limitations exhibit a significant reduction in microbial diversity. Additionally, distinct bacterial taxa are enriched in patients characterized by varying levels of airflow limitation and exacerbation frequency. These observations offer vital insights into the pathogenesis of AECOPD, suggesting a potentially crucial role for the microbiota in its development. Such findings pave the way for identifying potential therapeutic targets and intervention strategies, ultimately aiming to improve treatment outcomes for AECOPD patients.}, }
@article {pmid40240384, year = {2025}, author = {Pinto, OHB and Biazotti, BB and de Souza, RSC and Yassitepe, J&#xc9;CT and Arruda, P and Dante, RA and Gerhardt, IR}, title = {Seasonal bacterial profiles of Vellozia with distinct drought adaptations in the megadiverse campos rupestres.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {636}, pmid = {40240384}, issn = {2052-4463}, support = {2022/08797-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (S&#xe3;o Paulo Research Foundation)/ ; 2022/08797-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (S&#xe3;o Paulo Research Foundation)/ ; }, mesh = {*Droughts ; Seasons ; *Soil Microbiology ; Brazil ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; *Microbiota ; Bacteria/genetics/classification ; }, abstract = {Microbial communities can vary as a function of seasonal precipitation and the phenotypic characteristics of the prevailing plant species in an ecosystem. The Brazilian campos rupestres (CRs) host a unique flora adapted to harsh conditions, including severe droughts and nutrient-poor soils. Velloziaceae, a dominant angiosperm family in CRs, exhibit contrasting drought adaptive strategies, prominently desiccation tolerance and dehydration avoidance. Here, we created a comprehensive dataset of microbial composition and dynamics of bulk soil and distinct plant compartments (leaf blade, dry sheath, aerial root, and underground root) from two desiccation-tolerant and two dehydration-avoiding, non-desiccation-tolerant Vellozia species, across four seasons (beginning and end of rainy and dry seasons) through 16S rRNA gene sequencing of 374 samples. This dataset also includes 38 soil metagenomes encompassing dry and rainy seasons from both drought adaptive strategies. Exploring an overlooked aspect of CRs biology offers significant potential for understanding plant-microbial associations and adaptations to water availability in tropical regions. The genetic data and metadata support further research for hypothesis testing and cross-study comparisons.}, }
@article {pmid40240311, year = {2025}, author = {Liu, D and Abdellah, YAY and Dou, T and Keiblinger, KM and Zhou, Z and Bhople, P and Jiang, J and Shi, X and Zhang, F and Yu, F and Xing, B}, title = {Livestock-Crop-Mushroom (LCM) Circular System: An Eco-Friendly Approach for Enhancing Plant Performance and Mitigating Microbiological Risks.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12517}, pmid = {40240311}, issn = {1520-5851}, abstract = {Mushroom production using agroforestry biowaste is a great green cycling agriculture alternative. Therefore, the current study explored the Livestock-Crop-Mushroom (LCM) circular production model, starting with co-composting of straw and cow manure as a'St' biofertilizer further used for mushroom cultivation that ultimately produced a'StM' biofertilizer. The two biofertilizers were tested for their impacts on plant growth and potential microbial risks. The results show significant growth of oats stimulated by biofertiliser use. Both'St' and'StM' increased plant biomass, while with the latter, the crude protein content (+5.1%) and root biomass were also higher. Reduced abundances of resistome genes (30%) and pathogens (25%) were observed during the oat growth. Further, metagenomics analysis also indicated a reduction in antibiotic-resistance genes by -20% in soils with oats treated by'St' and -46% in'StM' biofertilizer treatment. The'StM' had a three-fold stronger inhibitory effect on oat rhizosphere soil pathogens than'St'. Moreover, compared to'St','StM' suppressed pathogens in seeds and stems, with specific beneficial biomarker microbes in different plant parts. Overall, the antibiotic resistance gene related to oxytetracycline decreased more than three-fold in the LCM system. This study demonstrates the substantial potential and scalability of the LCM circular system within the agricultural domain.}, }
@article {pmid40239498, year = {2025}, author = {Chen, M and Grégoire, DS and St-Germain, P and Berdugo-Clavijo, C and Hug, LA}, title = {Microbial diversity and capacity for arsenic biogeochemical cycling in aquifers associated with thermal mobilization.}, journal = {The Science of the total environment}, volume = {977}, number = {}, pages = {179357}, doi = {10.1016/j.scitotenv.2025.179357}, pmid = {40239498}, issn = {1879-1026}, abstract = {Thermal recovery technologies for in-situ bitumen extraction can result in the heating of surrounding aquifers, potentially mobilizing arsenic naturally present in the sediments to the groundwater. The relative toxicity of dissolved arsenic is related to its speciation, with As(V) being less toxic than As(III). Microorganisms have various mechanisms of arsenic detoxification and metabolism, which include genes for efflux, methylation, and reduction/oxidation of As(V)/As(III). We characterized the microbial communities along two aquifer transects associated with thermally mobilized arsenic near Northeastern Alberta oil sands deposits. 16S rRNA amplicons and metagenomic sequencing data of biomass from filtered groundwater indicated major changes in the dominant taxa between wells, especially those currently experiencing elevated arsenic concentrations. Annotation of arsenic-related genes indicated that efflux pumps (arsB, acr3), intracellular reduction (arsC) and methylation (arsM) genes were widespread among community members but comparatively few organisms encoded genes for arsenic respiratory reductases (arrA) and oxidases (arxA, aioA). While this indicates that microbes have the capacity to exacerbate arsenic toxicity by increasing the relative concentration of As(III), some populations of iron oxidizing and sulfate reducing bacteria (including novel Gallionella and Thermodesulfovibrionia populations) show potential for indirect bioremediation through formation of insoluble iron/sulfide minerals which adsorb or coprecipitate arsenic. An unusually high proportional abundance of a single Paceibacteria population that lacked arsenic resistance genes was identified in one high‑arsenic well, and we discuss hypotheses for its ability to persist. Overall, this study describes how aquifer microbial communities respond to thermal and arsenic plumes, and predicts potential contributions of microbes to arsenic biogeochemical cycling under this disturbance.}, }
@article {pmid40238917, year = {2025}, author = {Trepka, KR and Kidder, WA and Kyaw, TS and Halsey, T and Olson, CA and Ortega, EF and Noecker, C and Upadhyay, V and Stanfield, D and Steiding, P and Guthrie, BGH and Spanogiannopoulos, P and Dumlao, D and Turnbaugh, JA and Stachler, MD and Van Blarigan, EL and Venook, AP and Atreya, CE and Turnbaugh, PJ}, title = {Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity.}, journal = {Science translational medicine}, volume = {17}, number = {794}, pages = {eadq8870}, doi = {10.1126/scitranslmed.adq8870}, pmid = {40238917}, issn = {1946-6242}, mesh = {Animals ; Humans ; *Operon/genetics ; *Fluorouracil/therapeutic use/toxicity/adverse effects ; Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Colorectal Neoplasms/drug therapy/microbiology ; *Pyrimidines/toxicity ; *Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; }, abstract = {Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Here, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal profiling of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. Substantial shifts in gut microbial community structure during oral fluoropyrimidine treatment across multiple patient cohorts, in mouse small and large intestinal contents, and in patient-derived ex vivo communities were revealed by 16S rRNA gene sequencing. Metagenomic sequencing revealed marked shifts in pyrimidine-related gene abundance during oral fluoropyrimidine treatment, including enrichment of the preTA operon, which was sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). preTA[+] bacteria depleted 5-FU in gut microbiota grown ex vivo and in the mouse distal gut. Germ-free and antibiotic-treated mice experienced increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA[+] Escherichia coli, or preTA-high stool from patients with CRC. Last, preTA abundance was negatively associated with fluoropyrimidine toxicity in patients. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach may be generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.}, }
@article {pmid40238748, year = {2025}, author = {da Silva-Álvarez, E and Gómez-Arrones, V and Correa-Fiz, F and Martín-Cano, FE and Gaitskell-Phillips, G and Carrasco, JJ and Rey, J and Aparicio, IM and Peña, FJ and Alonso, JM and Ortega-Ferrusola, C}, title = {Metagenomic and proteomic analyses reveal similar reproductive microbial profiles and shared functional pathways in uterine immune regulation in mares and jennies.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0321389}, doi = {10.1371/journal.pone.0321389}, pmid = {40238748}, issn = {1932-6203}, mesh = {Animals ; Female ; Horses/microbiology/immunology ; *Uterus/microbiology/immunology/metabolism ; Proteomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Vagina/microbiology/immunology ; Bacteria/genetics/classification ; Proteome ; }, abstract = {This study aims to unveil potential differences in the vaginal and uterine microbiomes in mares and jennies, and to identify possible mechanisms involved in uterine immune homeostasis. The microbiota was characterized using 16S rRNA sequencing, and the uterine proteome was analyzed using UHPLC/MS/MS in 18 samples from healthy mares and 14 from jennies. While taxonomic analysis revealed high interspecies similarities, β-diversity analysis showed distinct clustering, with only two vaginal taxa and five uterine taxa differing between species. Despite compositional differences, PICRUSt analysis suggested minimal variations in predicted functional pathways across species. Comparing vaginal and uterine microbiota within the same species revealed overlapping bacterial taxa, but significant differences in α- and β-diversity and functional pathways. The uterine microbiota of both species was dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with abundant taxa like Streptococcus, Pseudomonas, Bacillus, Corynebacterium, and Staphylococcus, many of which are frequently associated with endometritis. The presence of Lactobacillus in the equine reproductive tract was minimal or non-existent. KEGG functional pathway analysis predicted that uterine microbiota of both species utilize metabolic pathways with potential immunomodulatory effects. Proteomic enrichment analysis showed that numerous overexpressed uterine proteins in both species are linked to adaptive and innate immune regulation and defense mechanisms against symbionts. Gene enrichment analysis identified several enriched Gene Ontology terms, including response to bacterial stimuli, humoral immune regulation, and TGF-beta receptor signaling, underscoring microbial-host interactions. The uterine microbiota may play a vital role in maintaining immune balance. Further research is required to confirm its interaction with the uterine immune system and clarify the mechanisms involved.}, }
@article {pmid40238740, year = {2025}, author = {Wang, J and Yin, J and Liu, X and Liu, Y and Jin, X}, title = {Gut commensal bacterium Bacteroides vulgatus exacerbates helminth-induced cardiac fibrosis through succinate accumulation.}, journal = {PLoS pathogens}, volume = {21}, number = {4}, pages = {e1013069}, doi = {10.1371/journal.ppat.1013069}, pmid = {40238740}, issn = {1553-7374}, mesh = {Animals ; *Succinic Acid/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/physiology ; *Trichinellosis/complications/metabolism/pathology ; *Trichinella spiralis ; *Bacteroides/metabolism ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/metabolism ; Myocardium/pathology/metabolism ; Male ; }, abstract = {Trichinella spiralis (Ts) is known to cause cardiac fibrosis, which is a critical precursor to various heart diseases, and its progression is influenced by metabolic changes. However, the metabolic mechanisms remain unclear. Here, we observed that Ts-infected mice exhibited cardiac fibrosis along with elevated succinate levels in the heart using metabolomic analysis. Administration of succinate exacerbated fibrosis during Ts infection, while deficiency in succinate receptor 1 (Sucnr1) alleviated the condition, highlighting the role of the succinate-Sucnr1 axis in fibrosis development. Furthermore, metagenomics sequencing showed that Ts-infected mice had a higher abundance ratio of succinate-producing bacteria to succinate-consuming bacteria in the intestines. Notably, the succinate-producer Bacteroides vulgatus was enriched in Ts group. Oral supplementation with B. vulgatus aggravated Ts-induced cardiac fibrosis. In summary, our findings underscore the succinate-Sucnr1 axis as a critical pathway in helminth-induced cardiac fibrosis and highlight the potential of targeting this axis for therapeutic interventions. This study presents novel insights into the gut-heart axis, revealing innovative strategies for managing cardiovascular complications associated with helminth infections.}, }
@article {pmid40238414, year = {2025}, author = {Magnano San Lio, R and Maugeri, A and Barchitta, M and Favara, G and La Rosa, MC and La Mastra, C and Agodi, A}, title = {Monitoring Antibiotic Resistance in Wastewater: Findings from Three Treatment Plants in Sicily, Italy.}, journal = {International journal of environmental research and public health}, volume = {22}, number = {3}, pages = {}, doi = {10.3390/ijerph22030351}, pmid = {40238414}, issn = {1660-4601}, support = {MUR-PNRR project SAMOTHRACE (ECS00000022)//European Union (NextGeneration EU)/ ; }, mesh = {*Wastewater/microbiology ; Sicily ; *Drug Resistance, Microbial/genetics ; *Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; }, abstract = {Antimicrobial resistance (AMR) poses a global public health threat. Wastewater analysis provides valuable insights into antimicrobial resistance genes (ARGs), identifying sources and trends and evaluating AMR control measures. Between February 2022 and March 2023, pre-treatment urban wastewater samples were collected weekly from treatment plants in Pantano D'Arci, Siracusa, and Giarre (Sicily, Italy). Monthly composite DNA extracts were prepared by combining weekly subsamples from each site, yielding 42 composite samples-14 from each treatment plant. Real-time PCR analysis targeted specific ARGs, including blaSHV, erm(A), erm(B), blaOXA, blaNDM, blaVIM, blaTEM, and blaCTX-M. The preliminary findings revealed that blaERM-B, blaOXA, blaTEM, and blaCTX-M were present in all samples, with erm(B) (median value: 8.51; range: 1.67-30.93), blaSHV (0.78; 0.00-6.36), and blaTEM (0.72; 0.34-4.30) showing the highest relative abundance. These results underscore the importance of integrating ARG data with broader research to understand the persistence and proliferation mechanisms of ARGs in wastewater environments. Future studies should employ metagenomic analyses to profile resistomes in urban, hospital, agricultural, and farm wastewater. Comparing these profiles will help identify contamination pathways and inform the development of targeted ARG surveillance programs. Monitoring shifts in ARG abundance could signal cross-sectoral contamination, enabling more effective AMR control strategies.}, }
@article {pmid40238256, year = {2025}, author = {Rueangsri, N and Roytrakul, S and Muangnoi, C and Tongkhao, K and Sae-Tan, S and Treesuwan, K and Sirivarasai, J}, title = {Metaproteomic Analysis of Fermented Vegetable Formulations with Lactic Acid Bacteria: A Comparative Study from Initial Stage to 15 Days of Production.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/foods14071148}, pmid = {40238256}, issn = {2304-8158}, support = {C02F660008//Mahidol University and the Office of National Higher Education Science Research and Innova-tion Policy Council through the Program Management Unit for Competitiveness, Thailand/ ; }, abstract = {Research in metagenomics and metaproteomics can reveal how microbiological interactions in fermented foods contribute to their health benefits. This study examined three types of fermented vegetables: a standard formulation, a probiotic formulation with Lacticaseibacillus rhamnosus GG, and a polyphenol formulation with vitexin from Mung bean seed coat. Measurements were taken at day 0 (after 36 h of fermentation at room temperature) and after 15 days. We applied 16S rRNA sequencing to evaluate microbial diversity and utilized LC-MS/MS to investigate the proteomic profiles of specific genera (Lactobacillus and Weissella) and species (Lacticaseibacillus rhamnosus and Levilactobacillus brevis) of lactic acid bacteria (LAB). All of these taxa demonstrated significant relative abundance between 0 and 15 days of fermentation in our metagenomic analysis. Our findings from principal component analysis and clustering analysis categorically distinguished protein expression patterns at various stages of fermentation. By comparing samples from day 0 to day 15, we identified proteins associated with DNA replication and repair mechanisms, including transcription elongation factor GreA, tRNA pseudouridine synthase B, and helicases. We also observed their roles in protein synthesis, which encompasses oxidoreductases and aspartokinase. Furthermore, we identified strong correlations of specific proteins across the three formulations with antioxidant markers. In conclusion, the results of this study decisively enhance our understanding of the role of the proteins related to specific LAB in fermented foods, highlighting their potential to improve texture, flavor, nutritional quality, and health benefits.}, }
@article {pmid40238219, year = {2025}, author = {Cadamuro, RD and Elois, MA and Pilati, GVT and Savi, BP and Pessi, L and Jempierre, YFSH and Rodríguez-Lázaro, D and Fongaro, G}, title = {Role of Lysogenic Phages in the Dissemination of Antibiotic Resistance Genes Applied in the Food Chain.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/foods14071082}, pmid = {40238219}, issn = {2304-8158}, abstract = {Bacteriophages, first discovered in 1915, have re-emerged as critical players in microbial ecosystems, particularly in food production. Their ability to lysogenize bacterial hosts raises concerns about their role in the horizontal transfer of antibiotic resistance genes (ARGs) and virulence factors, contributing to the global challenge of antimicrobial resistance. Key studies reveal that ARG-carrying phages are prevalent across various stages of the food chain, including soil, vegetables, meat, dairy, and wastewater associated with food production. These findings demonstrate the potential for lysogenic phages to act as vectors for resistance gene dissemination, posing risks to public health. The review also explores emerging genetic elements, such as phage-inducible chromosomal islands and gene transfer agents, that further enhance the mobility of resistance and virulence genes. Advancements in metagenomic tools have improved our understanding of phage-mediated gene transfer, but significant knowledge gaps remain. Future research should aim to quantify these processes in real-world settings and develop strategies to mitigate the risks associated with lysogenic phages in food systems.}, }
@article {pmid40238218, year = {2025}, author = {Zhadyra, S and Tao, F and Xu, P}, title = {Exploring the Microbiome and Functional Metabolism of Fermented Camel Milk (Shubat) Using Metagenomics.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/foods14071102}, pmid = {40238218}, issn = {2304-8158}, abstract = {Shubat is a traditional fermented camel milk drink that originated in Central Asia, with especially deep cultural roots in Kazakhstan. However, systematic studies on the microbial ecology and functional genes of Shubat remain scarce. As a distinctive fer-mented food, its microbial diversity and functional properties have not been fully ex-plored. This study investigates the microbial diversity and functional potential of Shubat by using advanced metagenomic techniques. Its microbial community is mainly composed of bacteria (96.6%), with Lactobacillus, Lactococcus, and Streptococcus being the dominant genera. Functional annotations through EggNOG, KEGG, and CAZy databases highlighted the metabolic versatility of Shubat's microbiota. Key pathways included amino acid and carbohydrate metabolism, vitamin biosynthesis, and central carbon metabolism, emphasizing their roles in fermentation and nutritional enhancement. The identification of various enzymes related to chemical synthesis further emphasizes the contribution of the microbiota to Shubat's unique flavor and texture. This study not only provides an important basis for the scientific understanding of Shubat but also expands the application possibilities of fermented food in the field of health and nutrition and confers modern value and significance to traditional food. This integration of science and tradition has not only facilitated the development of food microbiology but also paved new pathways for the global dissemination of traditional foods and the development of functional foods.}, }
@article {pmid40238191, year = {2025}, author = {Ren, C and Zhao, M and Xue, T and Geng, T and Nie, X and Han, C and Wen, Y and Jia, L}, title = {Metagenomic and Physicochemical Analyses Reveal Microbial Community and Functional Differences Between Three Different Grades of Hongxin Low-Temperature Daqu.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/foods14071104}, pmid = {40238191}, issn = {2304-8158}, support = {202302140601016//Key R&amp;D Program of Shanxi Province/ ; }, abstract = {Hongxin (HX) is an indispensable Daqu in the production of light-flavor Baijiu (LFB). However, the classification method of HX is highly subjective, and the classification and functional differences in microorganisms in different grades of HX are still unclear. In this study, metagenomics and physiochemical analysis were used to compare three grades of HX (top, first, second) and clarify their brewing functions in LFB. The results showed that a total of 1556 genera and 5367 species were detected in all samples. Bacteria and fungi are the main microorganisms in HX, and the relative abundance of bacteria and fungi is above 4.5:1. Kroppenstedtia (11.43%), Leuconostoc (10.52%), Fructilactobacillus (9.00%) were the top three genera in HX. Although the microbial community composition of the three grades of HX is highly similar, each HX has a specific microbial community structure and macrogene functional characteristics, indicating that they have different brewing functions. The dominant microorganisms in top-grade HX and first-grade HX were mainly positively correlated with energy metabolism and lipid metabolism, while the dominant microorganisms in second-grade HX were mainly positively correlated with carbohydrate metabolism and amino acid metabolism. This study revealed the different fermentation effects of different grades of HX in LFB and provided suggestions for the scientific classification and quality control of HX.}, }
@article {pmid40238188, year = {2025}, author = {Ugarcina Perovic, S and Ramji, V and Chong, H and Duan, Y and Maguire, F and Coelho, LP}, title = {argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO).}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf173}, pmid = {40238188}, issn = {1367-4811}, abstract = {SUMMARY: Currently available and frequently used tools for annotating antimicrobial resistance genes (ARGs) in genomes and metagenomes provide results using inconsistent nomenclature. This makes the comparison of different ARG annotation outputs challenging. The comparability of ARG annotation outputs can be improved by mapping gene names and their categories to a common controlled vocabulary such as the Antibiotic Resistance Ontology (ARO). We developed argNorm, a command line tool and Python library, to normalize all detected genes across 6 ARG annotation tools (8 databases) to the ARO. argNorm also adds information to the outputs using the same ARG categorization so that they are comparable across tools.<br><br>argNorm is available as an open-source tool at: https://github.com/BigDataBiology/argNorm. It can also be downloaded as a PyPI package and is available on Bioconda and as an nf-core module.}, }
@article {pmid40237937, year = {2025}, author = {Maimaris, J and Payne, J and Roa-Bautista, A and Breuer, J and Storey, N and Morfopoulou, S and Bamford, A and D'Arco, F and Gilmour, K and Aquilina, K and Hassell, J and Hacohen, Y and Silva, AHD and Merve, A and Jacques, TS and Rao, K and Chiesa, R and Amrolia, P and Silva, J and Braggins, H and Xu-Bayford, J and Goldblatt, D and Worth, A and Booth, C and Ip, W and Qasim, W and Kusters, M and Kaliakatsos, M and Brown, JR and Elfeky, R}, title = {Safety and Diagnostic Utility of Brain Biopsy and Metagenomics in Decision-Making for Patients with Inborn Errors of Immunity (IEI) and Unexplained Neurological Manifestations.}, journal = {Journal of clinical immunology}, volume = {45}, number = {1}, pages = {86}, pmid = {40237937}, issn = {1573-2592}, support = {GN-000707//Brain Tumour Charity/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Brain/pathology ; Male ; Biopsy ; Female ; Child, Preschool ; Infant ; Child ; Retrospective Studies ; *Nervous System Diseases/diagnosis/etiology ; Clinical Decision-Making ; Adolescent ; High-Throughput Nucleotide Sequencing ; }, abstract = {Unexplained neurological symptoms can pose a diagnostic challenge in patients with inborn errors of immunity (IEI) where the aetiology can be varied, and diverse pathologies may require contrasting treatments. Brain biopsy, the process of sampling brain tissue directly, has historically provided histological and microbiological information and can now be exploited for deep metagenomic next generation analysis (mNGS). We conducted a retrospective analysis of clinical and diagnostic data on paediatric patients with IEI who had a brain biopsy between 2010 and 2022 at a UK tertiary centre where 14 patients fulfilled our search criteria. We report on clinical characteristics, adverse events and the additional impact of mNGS of brain biopsies, where these were conducted. We found that brain biopsy enabled diagnostics with manageable complications in most cases, either by tissue or metagenomics analysis (n = 11/14, 79%). We found that mNGS analysis improved the diagnostic yield of brain biopsy in 29% of IEI cases (n = 4/14). Brain biopsy enabled a change in management in 71% of cases (n = 10/14). This series provides compelling evidence for the safe and purposeful use of brain biopsy in children with IEI.}, }
@article {pmid40237802, year = {2025}, author = {Lei, W and Huang, R and Qu, L and Ma, K and Li, J}, title = {Exogenous Mogroside V Drove Microbial Carbohydrate Metabolism and Consequently Enhanced Fruity Aroma in Greengage Wine.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c10783}, pmid = {40237802}, issn = {1520-5118}, abstract = {The microbial community is essential for the formation of aroma development in high-acidity greengage wine fermentation. Recent observations also highlight positive effects of mogroside V (MG V) on microorganisms in fermented foods, but the underlying chemical and biological mechanisms remain inadequate. The results indicated differences in the physicochemical properties among greengage wines, particularly a 50% increase in the ethanol conversion rate. Concurrently, GC-MS and sensory analyses demonstrated that MG V augmented carbohydrate conversion into ethyl esters (twice as much as in the control group), exhibiting tropical fruit and floral aroma profiles. The perceived intensity of these aromatic compounds increased by over 30%, thereby enriching the overall aromatic harmony of the wine. Integrated analysis of KEGG pathways and CAZymes annotations demonstrated that the enhancement of ethyl ester formation by MG V depends on improvement of the transport of carbohydrates and MG V, as well as accelerating the flux of pyruvate to acetyl-CoA in yeast. In conclusion, our study presents a targeted strategy for the high-acidity fruit wine industry of modulating this metabolic node in yeast, thereby achieving a focused enhancement of tropical fruit aroma characteristics in fruit wines.}, }
@article {pmid40237492, year = {2025}, author = {Hu, T and Meng, Y and Zhao, C and Sheng, D and Yang, S and Dai, J and Wei, T and Zhang, Y and Zhao, G and Liu, Y and Wang, Q and Zhang, L}, title = {Genome-scale metabolic modeling reveals specific vaginal Lactobacillus strains and their metabolites as key inhibitors of Candida albicans.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0298424}, doi = {10.1128/spectrum.02984-24}, pmid = {40237492}, issn = {2165-0497}, abstract = {As the predominant constituents of the vaginal microbiome in healthy women, Lactobacillus species are considered essential in maintaining a homeostatic vaginal microbiome. Specific Lactobacillus species can produce beneficial metabolites to support their persistence within the host environment and inhibit Candida albicans colonization. Due to the extensive diversity of Lactobacillus species and their metabolites, comprehensively investigating all possible interactions remains challenging. This study employed an integrative approach combining genome-scale metabolic modeling, metagenomic sequencing, and in vitro validation to explore Lactobacillus and C. albicans interactions. Pairwise simulations of 159 Lactobacillus strains with C. albicans revealed that most strains exhibit inhibitory effects, altering fungal amino acid and carbohydrate metabolism. Key inhibitory metabolites identified included formate, L-lactate, and L-malate. Metagenomic analysis of vaginal swabs from 20 vulvovaginal candidiasis (VVC) patients and 20 healthy women showed a correlation between Lactobacillus species abundance and reduced C. albicans colonization. In vitro experiments confirmed the inhibitory effects of these metabolites and the selected Lactobacillus strains on C. albicans growth, thereby validating our computational predictions. These findings provide insights into the metabolic interactions within the vaginal microbiome and pave the way for targeted microbial or metabolite-based therapeutic strategies to manage VVC.IMPORTANCEVulvovaginal candidiasis is a prevalent fungal infection with significant implications for women's health, caused primarily by Candida albicans. Although the protective role of a Lactobacillus-dominated vaginal microbiome is well established, the metabolic mechanisms underlying the interactions between Lactobacillus species and C. albicans remain inadequately understood. Specifically, the Lactobacillus species that effectively inhibit C. albicans and the metabolic pathways involved warrant further investigation. This study offers novel insights into the metabolic mechanisms underlying Lactobacillus antagonism against C. albicans. By identifying critical metabolic pathways and inhibitory metabolites, this study enhances our understanding of vaginal microbiome dynamics and host-microbe interactions. The findings suggest that key Lactobacillus strains and their metabolites could significantly reduce harmful levels of C. albicans, paving the way for future therapeutic strategies that leverage these microbial characteristics to promote vaginal health.}, }
@article {pmid40237489, year = {2025}, author = {Rybicka, I and Kaźmierczak, Z}, title = {The human phageome: niche-specific distribution of bacteriophages and their clinical implications.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0178824}, doi = {10.1128/aem.01788-24}, pmid = {40237489}, issn = {1098-5336}, abstract = {Bacteriophages (phages) play a crucial role in shaping the composition and diversity of the human microbiome across various body niches. Recent advancements in high-throughput sequencing technologies have enabled comprehensive analysis of the human phageome in different body sites. This review comprehensively analyzes phage populations across major human body niches, examining their distribution and dynamics through recent metagenomic discoveries. We explore how phage-bacteria interactions within different body sites contribute to homeostasis and disease development. Emerging evidence demonstrates that phageome perturbations can serve as early indicators of various disorders, particularly in the gut microbiome. Understanding these complex microbial interactions offers promising opportunities for developing novel diagnostic markers and therapeutic approaches. However, the causal relationship between phages, bacteria, and disease development remains unclear. Further research is needed to elucidate the role of phages in human health and disease and to explore their potential as diagnostic or therapeutic tools. Understanding the intricate interactions between phages, bacteria, and the human host is crucial for unraveling the complexities of the human microbiome and its impact on health and disease.}, }
@article {pmid40237482, year = {2025}, author = {Zhang, C and Bosma, TNP and Atashgahi, S and Smidt, H}, title = {Genome-resolved transcriptomics reveals novel PCE-dehalogenating bacteria from Aarhus Bay sediments.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0150324}, doi = {10.1128/msystems.01503-24}, pmid = {40237482}, issn = {2379-5077}, abstract = {Organohalide-respiring bacteria (OHRB) are keystone microbes in bioremediation of sites contaminated with organohalides and in natural halogen cycling. Known OHRB belong to distinct genera within the phyla Chloroflexota, Proteobacteria, and Firmicutes, whereas information about novel OHRB mediating natural halogen cycling remains scarce. In this study, we applied a genome-resolved transcriptomic approach to characterize the identity and activity of OHRB from tetrachloroethene respiring cultures previously enriched from sediments of Aarhus Bay. Combining short- and long-read sequencing approaches, we assembled 37 medium-quality bins with over 75% completeness and less than 5% contamination. Sixteen bins harbored RDase genes and were affiliated taxonomically to the class of Bacilli and phyla of Bacteroidota, Synergistota, and Spirochaetota, which have not been reported to catalyze reductive dehalogenation. Among the 16 bins, bin.26, phylogenetically close to the genus Vulcanibacillus (phylum Firmicutes), contained an unprecedented 97 reductive dehalogenase (RDase) genes. Of these, 84 RDase genes of bin.26 were transcribed during tetrachloroethene dechlorination in addition to RDase genes from the members of Synergistales (bin.5 and bin.32) and Bacteroidales (bin.18 and bin.24). Moreover, metatranscriptome analysis suggested that the RDase genes were likely under the regulation of transcriptional regulators not previously associated with organohalide respiration, such as HrcA and SigW, which are known to respond to abiotic environmental stresses, such as temperature changes. Combined application of genomic methods enabled us to pinpoint novel OHRB from pristine environments not previously known to mediate reductive dechlorination and to add to the current knowledge of the diversity, activity, and regulation of RDase genes.IMPORTANCEPristine marine environment is the major reservoir for naturally produced organohalides, in which reductive dehalogenation underneath plays an important role in the overall cycling of these compounds. Here, we obtain some novel OHRB genomes from Aarhus Bay marine sediments, which are phylogenetically distant to the well-documented OHRB and widely distributed across the bacterial phyla, such as Bacteroidota, Synergistota, and Spirochaetota. Furthermore, transcriptional profiles unravel that these RDase genes are induced differently, and their activity is controlled by diverse regulatory systems. Accordingly, elucidating the reductive dehalogenation of pristine marine environments substantially advances our understanding of the diversity, phylogeny, and regulatory variety of dehalogenating bacteria contributing to the global halogen cycle.}, }
@article {pmid40237336, year = {2025}, author = {Naspolini, NF and Schüroff, PA and Vanzele, PAR and Pereira-Santos, D and Valim, TA and Bonham, KS and Fujita, A and Passos-Bueno, MR and Beltrão-Braga, PCB and Carvalho, ACPLF and Klepac-Ceraj, V and Polanczyk, GV and Campos, AC and Taddei, CR}, title = {Exclusive breastfeeding is associated with the gut microbiome maturation in infants according to delivery mode.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2493900}, doi = {10.1080/19490976.2025.2493900}, pmid = {40237336}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Brazil ; Feces/microbiology ; Metagenomics ; *Delivery, Obstetric/methods ; Cohort Studies ; Infant, Newborn ; }, abstract = {Exclusive breastfeeding (EBF) plays a crucial role in infant gut microbiome assembly and development. However, few studies have investigated the effects of EBF in restoring a perturbed microbiome. In this study, we applied whole metagenomic sequencing to assess the gut microbiome assembly in 525 Brazilian infants from 3 to 9 months of age of the Germina Cohort, demonstrating the early determinants of microbial taxonomy and function modulation. Our analysis shows that EBF alters the relative abundance of genes related to the microbiome taxonomy and function, with effects varying by delivery mode. EBF alters the pattern of carbohydrates, lipid metabolism, and cell structure pathways depending on the delivery mode. The microbiome age is closer to chronological infant age in EBF than in non-EBF infants, meaning a lower microbiome maturation index (MMI). Using a complementary machine learning approach, we show that Escherichia coli, Ruminococcus gnavus, and Clostridium neonatale, as well as vitamin K and o-antigen pathways contribute strongly to EBF prediction. Moreover, EBF influences the microbiome maturation in early life, toward a microbiome age more similar to the chronological infant's age.}, }
@article {pmid40236771, year = {2025}, author = {Liu, W and Lau, HCH and Ding, X and Yin, X and Wu, WKK and Wong, SH and Sung, JJY and Zhang, T and Yu, J}, title = {Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects.}, journal = {iMeta}, volume = {4}, number = {2}, pages = {e70008}, pmid = {40236771}, issn = {2770-596X}, abstract = {Antimicrobial resistance is a major global health concern. However, the source of gut resistome remains unsolved. We aimed to analyze the contribution of environmental antimicrobial resistance genes (ARGs) to colorectal cancer (CRC) patients. Here, we collected metagenomic data from 1,605 human stool samples (CRC = 748; healthy = 857) and 1,035 city-matched environmental samples, in which 110 CRC, 112 healthy, and 56 environmental samples were newly collected. Compared to healthy subjects, CRC patients had significantly higher ARG burden (p < 0.01) with increased levels of multidrug-resistant ARGs. Gut ARGs in CRC also had a closer similarity to environmental ARGs (p < 0.001). By comparing environmental and gut ARGs, 28 environmental ARGs were identified as CRC-specific ARGs, including SUL2 and MEXE, which were not identified in healthy subjects. Meanwhile, more mobile ARGs (mARGs) from the environment were observed in CRC patients compared to healthy subjects (p < 0.05). The hosts of mARGs were mainly pathogenic bacteria (e.g., Escherichia coli (E. coli) and Clostridium symbiosum (C. symbiosum)). Compared to healthy subjects, CRC patients showed elevated horizontal gene transfer efficiency from the environment to gut. Consistently, the abundance of pathobionts carrying specific mARGs (e.g., E. coli-SUL2 and C. symbiosum-SUL2) were significantly increased in CRC patients compared to healthy subjects (p < 0.05). We thus reveal a route of ARG dissemination from the environment into the gut of CRC patients.}, }
@article {pmid40236770, year = {2025}, author = {Zhang, C and Chen, Y and Duan, R and Zhang, Y and Zheng, H and Zhang, J and Zhang, T and Xu, J and Li, K and Pei, F and Duan, L}, title = {Preconception maternal gut dysbiosis affects enteric nervous system development and disease susceptibility in offspring via the GPR41-GDNF/RET/SOX10 signaling pathway.}, journal = {iMeta}, volume = {4}, number = {2}, pages = {e70012}, pmid = {40236770}, issn = {2770-596X}, abstract = {Maternal health, specifically changes in the gut microbiota, can profoundly impact offspring health; however, our understanding of how gut microbiota alterations during the preconception period influence the offspring remains limited. In this study, we investigated the impact and mechanisms of preconception maternal gut dysbiosis on the development of the enteric nervous system (ENS) in mice. We found that preconception maternal exposure to antibiotics led to the abnormal development of the ENS in offspring, increasing their susceptibility to water avoidance stress at the adult stage. Metagenomic, targeted metabolomic, and transcriptomic analyses revealed that preconception antibiotic exposure disrupted the expression of genes crucial for embryonic ENS development by altering maternal gut microbiota composition. Multi-omics analysis combined with Limosilactobacillus reuteri and propionate gestational supplementation demonstrated that the maternal gut microbiota and metabolites may influence embryonic ENS development via the GPR41-GDNF/RET/SOX10 signaling pathway. Our findings highlight the critical importance of maintaining a healthy maternal gut microbiota before conception to support normal ENS development in offspring.}, }
@article {pmid40236767, year = {2025}, author = {Huang, L and Wang, P and Liu, S and Deng, G and Qi, X and Sun, G and Gao, X and Zhang, L and Zhang, Y and Xiao, Y and Gao, T and Maitiabula, G and Wang, X}, title = {Gut microbiota-derived tryptophan metabolites improve total parenteral nutrition-associated infections by regulating Group 3 innate lymphoid cells.}, journal = {iMeta}, volume = {4}, number = {2}, pages = {e70007}, pmid = {40236767}, issn = {2770-596X}, abstract = {Clinical nutritional support is recognized by Klinefner's Surgery as one of the four pivotal advancements in surgical practice during the 20th century. Surgeons regard clinical nutrition as a "life-saving" discipline, pivotal in preserving the lives of numerous critically ill patients and facilitating the success of many surgical procedures. Parenteral nutrition (PN) support serves as a crucial component of clinical nutritional therapy, while a range of complications associated with total parenteral nutrition (TPN) can significantly undermine the efficacy of patient treatment. Impaired intestinal homeostasis is strongly associated with the occurrence and progression of TPN-related infections, yet the underlying mechanisms remain poorly understood. In this study, RNA sequencing and single-cell RNA sequencing (scRNA-Seq) revealed that reduced secretion of interleukin-22 (IL-22) by intestinal Group 3 innate lymphoid cells (ILC3s) is a significant factor contributing to the onset of TPN-related infections. Additionally, through 16S ribosomal RNA (16S rRNA) gene sequencing of the gut microbiota from patients with chronic intestinal failure and metagenomic sequencing analysis of the gut microbiota from mice, we observed that TPN reduced the abundance of Lactobacillus murinus (L. murinus), while supplementation with L. murinus could promote IL-22 secretion by ILC3s. Mechanistically, L. murinus upregulates indole-3-carboxylic acid, which activates the nuclear receptor Rorγt to stimulate IL-22 secretion by ILC3s. This pathway strengthens gut barrier integrity and reduces infection susceptibility. Our findings enhance our understanding of the mechanisms driving the onset of TPN-related infections, highlighting the critical role of gut microbiota in maintaining immune homeostasis and improving clinical outcomes.}, }
@article {pmid40236616, year = {2025}, author = {Lu, Y and Zhang, C and Wu, J and Xu, X and Lu, A and Huang, H and Chen, M}, title = {Explore the Application Value of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid in the Early Diagnosis of Pulmonary Tuberculosis.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1837-1845}, pmid = {40236616}, issn = {1178-6973}, abstract = {OBJECTIVE: Compare the diagnostic efficacy of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) with that of four traditional methods in the diagnosis of pulmonary tuberculosis (PTB), and explore the application value of BALF mNGS in the early diagnosis of PTB.<br><br>METHODS: A retrospective analysis was performed on 102 patients with suspected PTB in Wuming Hospital Affiliated with Guangxi Medical University from January 2021 to August 2024, among which 61 cases were PTB and 41 cases were non - PTB. Diagnostic performance metrics (sensitivity, specificity, positive/negative predictive value [PPV/NPV], accuracy) were calculated for BALF mNGS, sputum TB-DNA, sputum acid-fast bacilli (AFB) smear, BALF AFB smear, and BALF TB-DNA, using clinical diagnosis as the reference standard.<br><br>RESULTS: BALF mNGS demonstrated a sensitivity of 75.41% (46/61), specificity of 87.80% (36/41), PPV of 90.20% (46/51), NPV of 70.59% (36/51), and accuracy of 80.39% (82/102). Its accuracy was significantly higher than sputum-based methods (53.03-58.82%, P < 0.0125) and second only to BALF TB-DNA (84.13%, P > 0.0125). BALF mNGS exhibited superior sensitivity compared to sputum TB-DNA (38.00%), sputum AFB smear (41.67%), and BALF AFB smear (41.50%) (P < 0.0125). While specificity and PPV showed no significant differences among methods, BALF mNGS had a higher NPV than sputum-based assays (53.03-54.17%) but lower than BALF TB-DNA (82.53%, P < 0.0125). Both BALF mNGS (Kappa = 0.608, P < 0.001) and BALF TB-DNA (Kappa = 0.670, P < 0.001) showed strong concordance with clinical diagnosis.<br><br>CONCLUSION: BALF mNGS demonstrates high sensitivity and accuracy for PTB diagnosis, outperforming conventional sputum-based methods. Although BALF TB-DNA achieved the highest specificity and NPV, BALF mNGS serves as a robust supplementary tool, particularly for early-stage or paucibacillary PTB. Integration of these molecular techniques may optimize diagnostic workflows in high-TB-burden settings.}, }
@article {pmid40236150, year = {2025}, author = {Bommana, S and Olagoke, S and Hu, Y and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, T and Dean, D}, title = {Effect of Azithromycin treatment on the microbial composition, functional dynamics and resistomes of endocervical, vaginal and rectal microbiomes of women in Fiji with Chlamydia trachomatis infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.04.02.646699}, pmid = {40236150}, issn = {2692-8205}, abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes with Chlamydia trachomatis (Ct) infection remain poorly understood. Some data exist on vaginal microbiomes pre- and post-treatment, but none are available for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples from women who, overtime, had Ct persistence, clearance, or no infection to evaluate azithromycin-induced changes in microbial composition, function, and the resistome. Our results show a shift in composition and function that support Ct post-treatment with azithromycin resistance mutations in the Ct rplV gene and significant endocervical enrichment of azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis, the strains of which have moderate/high potential for biofilm formation. These findings highlight the unintended ecological consequences of azithromycin, including resistance gene propagation and microbiome shifts that support persistent/recurrent Ct, emphasizing the need for novel treatment and microbiome-preserving strategies.}, }
@article {pmid40235649, year = {2025}, author = {Mohamed, AYA and Gill, L and Monleon, A and Pronk, M and van Loosdrecht, M and Saikaly, PE and Ali, M}, title = {Genome-resolved metatranscriptomics unveils distinct microbial functionalities across aggregate sizes in aerobic granular sludge.}, journal = {Environmental science and ecotechnology}, volume = {25}, number = {}, pages = {100560}, pmid = {40235649}, issn = {2666-4984}, abstract = {Microbial aggregates of different sizes in aerobic granular sludge (AGS) systems have been shown to exhibit distinct microbial community compositions. However, studies comparing the microbial activities of different-sized aggregates in AGS systems remain limited. In this study, genome-resolved metatranscriptomics was used to investigate microbial activity patterns within differently sized aggregates in a full-scale AGS plant. Our analysis revealed a weak correlation between the relative abundance of metagenome-assembled genomes (MAGs) and their transcriptomic activity, indicating that microbial abundance does not directly correspond to metabolic activity within the system. Flocculent sludge (FL; <0.2 mm) predominantly featured active nitrifiers and fermentative polyphosphate-accumulating organisms (PAOs) from Candidatus Phosphoribacter, while small granules (SG; 0.2-1.0 mm) and large granules (LG; >1.0 mm) hosted more metabolically active PAOs affiliated with Ca. Accumulibacter. Differential gene expression analysis further supported these findings, demonstrating significantly higher expression levels of key phosphorus uptake genes associated with Ca. Accumulibacter in granular sludge (SG and LG) compared to flocculent sludge. Conversely, Ca. Phosphoribacter showed higher expression of these genes in the FL fraction. This study highlights distinct functional roles and metabolic activities of crucial microbial communities depending on aggregate size within AGS systems, offering new insights into optimizing wastewater treatment processes.}, }
@article {pmid40234711, year = {2025}, author = {Wu, M and Liu, X and Musat, F and Guo, J}, title = {Microbial oxidation of short-chain gaseous alkanes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40234711}, issn = {2058-5276}, abstract = {Short-chain gaseous alkanes (SCGAs), including ethane, propane and butane, are major components of natural gas and their atmospheric emissions impact global air quality and tropospheric chemistry. Many microbial taxa can degrade SCGAs aerobically and anaerobically to CO2, acting as the major biological sink of these compounds and reducing their negative impacts on climate. Environmental metagenomics and cultivation efforts have expanded our understanding of SCGA-oxidizing microorganisms. In this Review, we discuss recent discoveries in the diversity, physiology and metabolism of aerobic and anaerobic SCGA-oxidizing microorganisms, highlight their climate implications and discuss how knowledge of these processes can help develop biotechnologies for environmental remediation and value-added chemical production.}, }
@article {pmid40234093, year = {2025}, author = {Block, MS and Nelson, GD and Chen, J and Johnson, S and Yang, L and Flotte, TJ and Grewal, EP and McWilliams, RR and Kottschade, LA and Domingo-Musibay, E and Markovic, SN and Dimou, A and Montane, HN and Piltin, MA and Price, DL and Khariwala, SS and Hui, JYC and Erskine, CL and Strand, CA and Zahrieh, D and Dong, H and Hieken, TJ}, title = {Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for stage III melanoma: outcomes and the impact of the microbiome from the NeoACTIVATE trial.}, journal = {Journal for immunotherapy of cancer}, volume = {13}, number = {4}, pages = {}, doi = {10.1136/jitc-2025-011706}, pmid = {40234093}, issn = {2051-1426}, mesh = {Humans ; *Melanoma/drug therapy/pathology/mortality ; Female ; Male ; *Azetidines/therapeutic use/pharmacology ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; *Neoadjuvant Therapy/methods ; *Piperidines/pharmacology/therapeutic use ; *Vemurafenib/pharmacology/therapeutic use ; Aged ; Neoplasm Staging ; Adult ; Gastrointestinal Microbiome ; Treatment Outcome ; *Skin Neoplasms/drug therapy ; }, abstract = {BACKGROUND: Neoadjuvant treatment has become standard for patients with high-risk operable stage III melanoma, but the optimal regimen is unknown. Targeted therapy approaches yield high pathological response rates, while immunotherapy regimens show favorable recurrence-free survival (RFS). NeoACTIVATE was designed to address whether a neoadjuvant combination of both targeted therapy and immunotherapy might leverage the benefits of each.<br><br>METHODS: We tested neoadjuvant treatment with 12 weeks of vemurafenib, cobimetinib, and atezolizumab for patients with BRAF-mutated (BRAFm) melanoma (cohort A) and cobimetinib and atezolizumab for patients with BRAF-wild-type (BRAFwt) melanoma (cohort B), regimens which we have shown generate a substantial major pathological response. After therapeutic lymph node dissection, patients received 24 weeks of adjuvant atezolizumab. Here, we report survival outcomes and their association with biomarkers assayed among the gut microbiome and peripheral blood immune subsets.<br><br>RESULTS: With 49 months median follow-up, the median RFS was not reached for cohort A and was 40.8 months for cohort B. At 24 months after operation, 2 of 14 cohort A patients and 4 of 13 cohort B patients had experienced distant relapse. Key findings from correlative analyses included diversity, taxonomic and functional metagenomic gut microbiome signals associated with distant metastasis-free survival at 2 years. Notably, we observed a strong correlation between low microbial arginine biosynthesis (required for T-cell activation and effector function) and early distant recurrence (p=0.0005), which correlated with taxonomic differential abundance findings. Peripheral blood immune monitoring revealed increased double-positive (CD4+CD8+) T cells in patients with early recurrence.<br><br>CONCLUSIONS: Neoadjuvant treatment with cobimetinib and atezolizumab&#xb1;vemurafenib was associated with a low rate of distant metastasis in patients with high-risk stage III melanoma. Freedom from early distant metastasis was highly associated with taxonomic differences in gut microbiome structure and with functional pathway alterations known to modulate T cell immunity. Identification of predictive biomarkers will permit optimization of neoadjuvant therapy regimens for individual patients.<br><br>TRIAL REGISTRATION NUMBER: NCT03554083.}, }
@article {pmid40233994, year = {2025}, author = {Jenkins, R and Samec, M and Arment, C and Warrington, KJ and Davis, JM and Koster, MJ}, title = {Use of Metagenomic Microbial Plasma Cell-Free DNA Next-Generation Sequencing Assay in Outpatient Rheumatology Practice.}, journal = {The Journal of rheumatology}, volume = {}, number = {}, pages = {}, doi = {10.3899/jrheum.2024-1211}, pmid = {40233994}, issn = {1499-2752}, abstract = {OBJECTIVE: To assess the utility of a metagenomic microbial plasma cell-free DNA next-generation sequencing assay (Karius TestTM; KT) in the evaluation of patients in an outpatient rheumatology practice.<br><br>METHODS: All patients with a KT ordered and obtained by a rheumatology provider in the outpatient setting from 1 January 2020 through 31 December 2022 were retrospectively identified. Demographic, clinical, laboratory, radiologic, histopathology, and microbial studies were abstracted. Indication for KT testing was categorized. KT results were defined based on positive result and clinical relevance regarding the symptoms under investigation at the time of the rheumatologic investigation. Review of cases three months after KT was undertaken to determine clinical outcome.<br><br>RESULTS: 150 patients with a KT were included (52.7% female, mean age 52 years). The reason for KT was evaluation of atypical presentation of rheumatic disease (80.0%), assessing flare versus infection in patient on immunosuppression (16.7%), and fever of unknown origin (3.3%). 24 (16.0%) KTs were positive, six of which were considered clinically relevant and altered the final diagnosis and treatment. Of the 126 negative KTs, 5 (4.0%) were found to have a clinically relevant infection by conventional testing methodologies.<br><br>CONCLUSION: In this large retrospective cohort study, the most frequent reason for KT utilization was an atypical presentation of rheumatic disease. Twenty-five percent of positive KTs altered the final diagnosis and treatment, whereas a false-negative rate of 4.0% was observed. KT has utility in the outpatient rheumatology assessment. Further delineation of which patients are best suited for KT testing remains to be defined.}, }
@article {pmid40233938, year = {2025}, author = {Kolokotronis, SO and Bhattacharya, C and Panja, R and Quate, I and Seibert, M and Jorgensen, E and Mason, CE and Hénaff, EM}, title = {Metagenomic interrogation of urban Superfund site reveals antimicrobial resistance reservoir and bioremediation potential.}, journal = {Journal of applied microbiology}, volume = {136}, number = {4}, pages = {}, doi = {10.1093/jambio/lxaf076}, pmid = {40233938}, issn = {1365-2672}, support = {80NSSC24K0728/NASA/NASA/United States ; R01AI125416/NH/NIH HHS/United States ; 1758800//National Science Foundation/ ; }, mesh = {Biodegradation, Environmental ; Metagenomics ; *Microbiota/genetics ; Metals, Heavy/metabolism ; *Geologic Sediments/microbiology ; *Bacteria/genetics/metabolism/drug effects/isolation &amp; purification/classification ; Water Pollutants, Chemical/metabolism ; Polychlorinated Biphenyls/metabolism ; *Drug Resistance, Bacterial/genetics ; Metagenome ; }, abstract = {AIMS: We investigate the bioremediation potential of the microbiome of the Gowanus Canal, a contaminated waterway in Brooklyn, NY, USA, designated a Superfund site by the US Environmental Protection Agency due to high concentrations of contaminants, including polychlorinated biphenyls, petrochemicals, and heavy metals.<br><br>METHODS AND RESULTS: We present a metagenomic analysis of the Gowanus Canal sediment, consisting of a longitudinal study of surface sediment and a depth-based study of sediment core samples. We demonstrate that the resident microbiome includes 455 species, including extremophiles across a range of saltwater and freshwater species, which collectively encode 64 metabolic pathways related to organic contaminant degradation and 1171 genes related to heavy metal utilization and detoxification. Furthermore, our genetic screening reveals an environmental reservoir of antimicrobial resistance markers falling within 8 different classes of resistance, as well as de-novo characterization of 2319 biosynthetic gene clusters and diverse groups of secondary metabolites with biomining potential.<br><br>CONCLUSION: The microbiome of the Gowanus Canal is a biotechnological resource of novel metabolic functions that could aid in efforts for bioremediation, AMR reservoir mapping, and heavy metal mitigation.}, }
@article {pmid40037519, year = {2025}, author = {Jawale, N and Shenberger, JS and Rodriguez, RJ and Shetty, AK and Garg, PM}, title = {The Nonbacterial Infant Microbiome and Necrotizing Enterocolitis.}, journal = {American journal of perinatology}, volume = {}, number = {}, pages = {}, doi = {10.1055/a-2549-6551}, pmid = {40037519}, issn = {1098-8785}, support = {U54GM115428/GM/NIGMS NIH HHS/United States ; U54GM115428//NIGMS of the NIH/ ; }, abstract = {Necrotizing enterocolitis (NEC) is among the most devastating neonatal illnesses of premature infants. Although it is a disease of multifactorial etiology associated with bacterial dysbiosis, several reports of viral and some fungal infections associated with NEC have been published. Despite the abundance of viruses-primarily bacteriophages, and "virus-like particles" in the normal infant gut flora, there is limited understanding of the contribution of these elements to newborn gut health and disease. This study aims to review existing evidence on normal newborn virome and mycobiome development and present insights into the complex inter-kingdom interactions between gut bacteria, viruses, and fungi in the intestinal ecosystem, exploring their potential role in predisposing the preterm infant to NEC. · We have reviewed a number of viral and fungal infections reported in association with NEC-like illnesses.. · Bacteriophages play a crucial role in the gut microbiome development, but their role in pathogenesis of NEC and potential for therapeutic use is unknown.. · Development of next-gen metagenomic tools are needed to enhance our understanding of viral diversity, bacteriophages, and the gut virome in the context of neonatal health and disease..}, }
@article {pmid40233768, year = {2025}, author = {Tinker, KA and Anthony, W and Brandi, M and Flett, S and Bagwell, CE and Smallwood, C and Davis, R and Gulliver, D}, title = {Identifying Potential Geochemical and Microbial Impacts of Hydrogen Storage in a Deep Saline Aquifer.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70076}, doi = {10.1111/1758-2229.70076}, pmid = {40233768}, issn = {1758-2229}, support = {//U.S. Department of Energy's (DOE) Office of Fossil Energy and Carbon Management's Hydrogen with Carbon Management Program and executed through the National Energy Technology Laboratory (NETL) Research &amp; Innovation Center's Natural Gas Decarbonization and Hydrogen Technologies Multi-Year Research Plan/ ; }, mesh = {*Hydrogen/metabolism ; *Groundwater/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Illinois ; Methane/metabolism ; Microbiota ; Metagenomics ; }, abstract = {Hydrogen is valuable commodity and a promising energy carrier for variable energy production. Storage of hydrogen may occur through injection of hydrogen or a hydrogen/methane gas blend in subsurface reservoirs. However, the geochemical and biological reactions that may impact the stored hydrogen are not yet understood. Therefore, we collected samples from a deep storage aquifer located in the St. Peter Formation in southern Illinois. The reservoir material was primarily quartz with sulphur and iron deposits, while the major constituents of the fluid were chloride and sulphate. 16S rRNA gene amplicon sequencing revealed a low biomass microbial community that contained no obvious hydrogen-consuming bacteria. Next, we enriched a field sample to increase the biomass and completed a metagenomic analysis, finding a low number of genes present that are associated with hydrogen consumption. Then, we completed a series of reactor experiments under reservoir conditions with 15% H2/85% CH4 gas simulating a short-term hydrogen storage, high withdrawal scenario. We found minimal changes in the geochemistry or microbiology for the reactor experiments. This work suggests that short-term storage may be highly successful, although significant additional work needs to be completed in order to accurately evaluate the risks associated with long-term hydrogen storage scenarios. It is essential we continue to expand our understanding of the dynamics present in saline aquifers and provide new insights into how hydrogen storage may impact underground geological storage environments.}, }
@article {pmid40233618, year = {2025}, author = {Fan, C and Hou, D and Zhang, L and Li, C and Chen, L and Zhang, P and Wu, Y and Zou, J}, title = {Bioaugmentation using HN-AD consortia for high salinity wastewater treatment: Synergistic effects of halotolerant bacteria and nitrogen removal bacteria.}, journal = {Journal of environmental management}, volume = {381}, number = {}, pages = {125355}, doi = {10.1016/j.jenvman.2025.125355}, pmid = {40233618}, issn = {1095-8630}, abstract = {Bioaugmentation shows promise in enhancing nitrogen removal efficiency of high-salt wastewater, yet the impact of microbial associations on ecosystem function and community stability remains unclear. This study innovatively introduced a novel heterotrophic nitrification-aerobic denitrification bacterial consortium to improve the performance of SBR reactor for removing nitrogen from saline wastewater. The results revealed that the bioaugmented reactor (R2) exhibited superior removal performance, achieving maximum removal efficiencies of 87.8 % for COD and 97.8 % for NH4[+]-N. Moreover, proper salinity (2 % and 4 %) promoted the secretion of EPS and ectoine, further enhancing the resistance and stability of bacterial consortia. 16S rRNA gene sequencing and metagenomics analysis revealed the key denitrifying bacteria Pseudomonas and salt-tolerant bacteria Halomonas were successfully coexistence and the relative abundances of crucial genes (napB, nirS, norB, norC and nosZ) were increased obviously, which were benefit for the excellent nitrogen removal performance in R2. These findings elucidate microbial interactions in response to salinity in bioaugmentation, providing a valuable reference for the efficient treatment of high-saline wastewater.}, }
@article {pmid40233040, year = {2025}, author = {Pomej, K and Frick, A and Scheiner, B and Balcar, L and Pajancic, L and Klotz, A and Kreuter, A and Lampichler, K and Regnat, K and Zinober, K and Trauner, M and Tamandl, D and Gasche, C and Pinter, M}, title = {Study protocol: Fecal Microbiota Transplant combined with Atezolizumab/Bevacizumab in Patients with Hepatocellular Carcinoma who failed to achieve or maintain objective response to Atezolizumab/Bevacizumab - the FAB-HCC pilot study.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0321189}, doi = {10.1371/journal.pone.0321189}, pmid = {40233040}, issn = {1932-6203}, mesh = {Humans ; *Liver Neoplasms/therapy/drug therapy ; *Carcinoma, Hepatocellular/therapy/drug therapy ; Pilot Projects ; *Fecal Microbiota Transplantation/methods ; *Bevacizumab/therapeutic use/administration &amp; dosage ; *Antibodies, Monoclonal, Humanized/therapeutic use/administration &amp; dosage ; Male ; Female ; Gastrointestinal Microbiome ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Aged ; }, abstract = {BACKGROUND: The gut microbiota is often altered in chronic liver diseases and hepatocellular carcinoma (HCC), and increasing evidence suggests that it may influence response to cancer immunotherapy. Strategies to modulate the gut microbiome (i.e., fecal microbiota transplant (FMT)) may help to improve efficacy of immune checkpoint inhibitors (ICIs) or even overcome resistance to ICIs. Here, we describe the design and rationale of FAB-HCC, a single-center, single-arm, phase II pilot study to assess safety, feasibility, and efficacy of FMT from patients with HCC who responded to PD-(L)1-based immunotherapy or from healthy donors to patients with HCC who failed to achieve or maintain a response to atezolizumab plus bevacizumab.<br><br>METHODS: In this single-center, single-arm, phase II pilot study (ClinicalTrials.gov identifier: NCT05750030), we plan to include 12 patients with advanced HCC who failed to achieve or maintain a response to atezolizumab/bevacizumab. Patients will receive a single FMT via colonoscopy from donors with HCC who responded to PD-(L)1-based immunotherapy or from healthy individuals, followed by atezolizumab/bevacizumab every 3 weeks. The primary endpoint is safety, measured by incidence and severity of treatment-related adverse events. The main secondary endpoint is efficacy, as assessed by best radiological response according to RECISTv1.1 and mRECIST. Additional exploratory endpoints include data on the effect of FMT on recipient gut microbiota, as well as metagenomic analysis of stool samples, analyses of circulating immune cells and serum and stool proteomic, metabolomic and lipidomic signatures.<br><br>DISCUSSION: The results of this study will help to define the potential of FMT as add-on intervention in the systemic treatment of advanced HCC, with the potential to improve efficacy of immunotherapy or even overcome resistance.<br><br>TRIAL REGISTRATION: EudraCT Number: 2022-000234-42 Clinical trial registry &amp; ID: ClinicalTrials.gov identifier: NCT05750030 (Registration date: 16.01.2023).}, }
@article {pmid40232948, year = {2025}, author = {Leech, SM and Barrett, HL and Dorey, ES and Mullins, T and Laurie, J and Nitert, MD}, title = {Consensus approach to differential abundance analysis detects few differences in the oral microbiome of pregnant women due to pre-existing type 2 diabetes mellitus.}, journal = {Microbial genomics}, volume = {11}, number = {4}, pages = {}, doi = {10.1099/mgen.0.001385}, pmid = {40232948}, issn = {2057-5858}, mesh = {Humans ; Female ; Pregnancy ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Microbiota/genetics ; Adult ; *Diabetes, Gestational/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Oral microbiome dysbiosis has been proposed as a potential contributing factor to rising rates of diabetes in pregnancy, with oral health previously associated with an increased risk of numerous chronic diseases and complications in pregnancy, including gestational diabetes mellitus (GDM). However, whilst most studies examining the relationship between GDM and the oral microbiome identify significant differences, these differences are highly variable between studies. Additionally, no previous research has examined the oral microbiome of women with pre-existing type 2 diabetes mellitus (T2DM), which has greater risks of complications to both mother and baby. In this study, we compared the oral microbiome of 11 pregnant women with pre-existing T2DM with 28 pregnant normoglycaemic controls. We used shotgun metagenomic sequencing to examine buccal swab and saliva rinse samples at two time points between 26 and 38 weeks of gestation. To reduce variation caused by the choice of differential abundance analysis tool, we employed a consensus approach to identify differential taxa and pathways due to diabetes status. Differences were identified at the late time point only. In swab samples, there was increased Flavobacteriaceae, Capnocytophaga, Capnocytophaga gingivalis SGB2479, Capnocytophaga leadbetteri SGB2492 and Neisseria elongata SGB9447 abundance in T2DM as well as increased Shannon diversity and richness. In rinse samples, there was an increased abundance of Haemophilus, Pasteurellaceae, Pasteurellales and Proteobacteria. In contrast to studies of the oral microbiome in T2DM or GDM that use a single differential abundance analysis tool, our consensus approach identified few differences between pregnant women with and without T2DM.}, }
@article {pmid40232107, year = {2025}, author = {Ravizza, T and Volpedo, G and Riva, A and Striano, P and Vezzani, A}, title = {Intestinal microbiome alterations in pediatric epilepsy: Implications for seizures and therapeutic approaches.}, journal = {Epilepsia open}, volume = {}, number = {}, pages = {}, doi = {10.1002/epi4.70037}, pmid = {40232107}, issn = {2470-9239}, support = {PE0000006/DN.1553//National Recovery and Resilience Plan (NRRP)/ ; //AICE-FIRE/ ; }, abstract = {The intestinal microbiome plays a pivotal role in maintaining host health through its involvement in gastrointestinal, immune, and central nervous system (CNS) functions. Recent evidence underscores the bidirectional communication between the microbiota, the gut, and the brain and the impact of this axis on neurological diseases, including epilepsy. In pediatric patients, alterations in gut microbiota composition-called intestinal dysbiosis-have been linked to seizure susceptibility. Preclinical models revealed that gut dysbiosis may exacerbate seizures, while microbiome-targeted therapies, including fecal microbiota transplantation, pre/pro-biotics, and ketogenic diets, show promise in reducing seizures. Focusing on clinical and preclinical studies, this review examines the role of the gut microbiota in pediatric epilepsy with the aim of exploring its implications for seizure control and management of epilepsy. We also discuss mechanisms that may underlie mutual gut-brain communication and emerging therapeutic strategies targeting the gut microbiome as a novel approach to improve outcomes in pediatric epilepsy. PLAIN LANGUAGE SUMMARY: Reciprocal communication between the brain and the gut appears to be dysfunctional in pediatric epilepsy. The composition of bacteria in the intestine -known as microbiota- and the gastrointestinal functions are altered in children with drug-resistant epilepsy and animal models of pediatric epilepsies. Microbiota-targeted interventions, such as ketogenic diets, pre-/post-biotics administration, and fecal microbiota transplantation, improve both gastrointestinal dysfunctions and seizures in pediatric epilepsy. These findings suggest that the gut and its microbiota represent potential therapeutic targets for reducing drug-resistant seizures in pediatric epilepsy.}, }
@article {pmid40232020, year = {2025}, author = {Zhang, X and Chi, H and Peng, D and Jiang, M and Wang, C and Zhang, H and Kang, W and Li, L}, title = {Integrated Metagenomic and LC-MS/MS Analysis Reveals the Biogenic Amine-Producing Strains of Two Typical Chinese Traditional Fish Products: Fermented Mandarin Fish (Siniperca chuatsi) and Semi-Dried Yellow Croaker (Larimichthys crocea).}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/foods14061016}, pmid = {40232020}, issn = {2304-8158}, support = {2022TD02//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; }, abstract = {Two typical fish products-fermented mandarin fish and semi-dried yellow croaker-are associated with biogenic amines (BAs), which are harmful to human health. The objective of this study was to investigate the bacterial ecology of the two fish products and to determine their capacity for producing BAs. Putrescine and cadaverine were major BAs detected in the fish products. Concentrations of BAs were significantly corrected with microbial count (p < 0.05). BA-producing isolates (33) in the two fish products were all multiple BA producers. Several of them, including Lactobacillus sakei, Bacillus cereus and Hafnia alvei isolated from fermented mandarin fish, as well as Shewanella baltica, Aeromonas veronii, and Photobacterium phosphoreum isolated from semi-dried yellow croaker, showed remarkable BA-producing capacity. Hafnia alvei produced the greatest abundance of putrescine, cadaverine, tyramine and 2-phenylethylamine. Lactobacillus sakei mainly produced tryptamine and putrescine. Photobacterium phosphoreum showed the strongest histamine-producing capacity.}, }
@article {pmid40231916, year = {2025}, author = {A'yuni, Q and Mok, K and Nakphaichit, M and Jangchud, K and Pirak, T}, title = {Thai Cannabis sativa Leaves as a Functional Ingredient for Quality Improvement and Lactic Acid Bacterial Growth Enhancement in Kombucha.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/foods14060942}, pmid = {40231916}, issn = {2304-8158}, support = {FF(KU)25.66//Fundamental fund of Kasetsart University/ ; //Kasetsart's Agro-Industry Scholarship from Department of Product Development, Faculty of Agro-Industry, Kasetsart University/ ; }, abstract = {Kombucha is a well-known fermented drink that gained interest due to its gut health benefits. However, it has a harsh taste of acetic acid and is hard to consume. Thai Cannabis leaves (Cannabis sativa sp. Hang Kra Rog Phu phan ST1) contain high protein and phytochemicals which can improve the growth of lactic acid bacteria (LAB) and enhance the organoleptic quality of the Kombucha. This study revealed the effect of infusing assam green tea leaves with cannabis leaves on the fermentation rate, microbial communities, volatile compounds, and overall quality and taste of the kombucha. The high protein content (23.10%) of Cannabis leaves was found. Phytonutrients and phytochemicals found in the leaves promotes LAB growth, which resulted in the higher number of LAB in the treatment with cannabis leaves. At the end of fermentation (day 7), the highest LAB count (5.53 log CFU mL[-1]) was presented in kombucha infused with 30% cannabis leaves. Kombucha with better quality, higher pH, and less acidity was obtained in a dose manner. The change in microbial communities was detected using metagenomic analysis. The prominence of Dekkera and Komagataeibacter, with low abundance of Zygosaccharomyces and Weissella were identified. These microorganisms improved flavor by lessening strong fermented odor and harsh acidic taste. From volatile compounds, HS-SPME-GCMS revealed that kombucha infused with 30% cannabis leaves possessed less acetic acid, ethanol, and carbon dioxide and gave a better odor and taste. Hence, cannabis leaves was the novel substrate for kombucha fermentation by enhancing LAB growth and improving the overall qualities.}, }
@article {pmid40231684, year = {2025}, author = {Glenna, S and Birkeland, EE and Orr, RJ and Gilfillan, GD and Dalland, M and Økstad, OA and Voie, &#xd8;A and Rounge, TB}, title = {Skin bacterial community dynamics of hands and forearms before and after military field exercise.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0295324}, doi = {10.1128/spectrum.02953-24}, pmid = {40231684}, issn = {2165-0497}, abstract = {The human skin microbiome is crucial for health and immunity, especially under the extreme conditions military personnel face. Soldiers often encounter unique stressors and hygienic challenges that can alter their skin's microbial composition, particularly in field environments. In this study, we aimed to investigate the impact of military field exercises on the diversity and composition of the skin bacterial microbiota using 16S rRNA sequencing. We conducted a longitudinal study of Norwegian soldiers (n = 19) participating in outdoor training operations during the NATO winter exercise Cold Response 2022. Skin swabs were taken from soldiers' hands and forearms before and after the 10-day military exercise, and following a 3-week post-exercise leave. Our results reveal hand- and forearm-specific shifts in bacterial populations associated with the exercise, likely influenced by environmental exposure, reduced hygiene, and heightened social contact. Alpha diversity increased on forearms while remaining stable on hands, which appeared more resilient to perturbations. Both sites exhibited temporal changes in composition, with soil- and water-associated bacteria enriched post-exercise; most being transient on hands but more sustained on forearms. The soldiers' microbiomes converged during the exercise, then diverged in the post-exercise leave period, and neither skin site returned to baseline composition at follow-up. Our findings highlight the impact of collaborative outdoor activities on microbial communities and suggest that resilience and stability differ between skin sites.IMPORTANCEOptimizing soldier health and resilience is critical for maintaining military readiness and operational effectiveness. The skin, as the body's first line of defense, is subjected to numerous challenges in military environments. Unique environmental and hygiene challenges can disrupt the skin microbiome and increase susceptibility to skin and soft tissue infections. This longitudinal research provides valuable insights into the effects of military service on the bacterial dynamics of the skin microbiome but can also inform hygiene management and disease prevention in comparable situations.}, }
@article {pmid40230845, year = {2025}, author = {Gao, Q and Li, Z and Geng, J and Han, B and Yang, T and Feng, S and Zhao, L and Teng, Y and Li, Y and Zhao, R and Zhang, W and Wang, Y and Wang, Y}, title = {The type of pathogen is associated with organ failure and legacy dysfunction in patients with sepsis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1541634}, pmid = {40230845}, issn = {1664-3224}, mesh = {Humans ; *Sepsis/mortality/microbiology/complications ; Male ; Female ; *Multiple Organ Failure/mortality/microbiology/etiology ; Middle Aged ; Aged ; High-Throughput Nucleotide Sequencing ; Adult ; Retrospective Studies ; }, abstract = {INTRODUCTION: Is there a difference in pathogen infection among sepsis patients with different organ dysfunction and Post-sepsis persistent organ dysfunction? Is this related to survival? It is currently unclear.<br><br>METHODS: This study reviewed 1982 sepsis patients between December 2019 and September 2023, and included 619 patients after removing patients with missing data. Of these, 332 were tested for metagenomic next-generation sequencing (mNGS). First, the pathogens distribution was assessed in all NGS-positive patients, followed by patients with different organ dysfunction (excluding those who died during hospitalization). Lastly, the survival analysis was conducted on patients infected with different pathogens.<br><br>RESULTS: The results showed that the mortality rate in our cohort was 27.63% in patients with sepsis, and patients with Respiratory, Liver, Circulatory, Hematologic, Neurological, and Renal dysfunction had poor survival. And patients with post-sepsis persistent organ dysfunction after sepsis have worse survival rates. In addition, we found the infection rates of Legionella and Betapapillomavirus were higher in patients with liver dysfunction. The infection rates of Mastadenovirus, Enterococcus, and Candida were higher in patients with neurological dysfunction. The infection rates of Candida were higher in patients with renal dysfunction and hematologic dysfunction. The infection rates of Moraxella were higher in patients with circulatory dysfunction. The infection rates of Enterococcus, Pneumocystis, and Acinetobacter were higher in patients with Post-sepsis cardiac dysfunction.The infection rates of Enterococcus, Acinetobacter, and Morganella were higher in patients with Post-sepsis liver dysfunction. The infection rates of Enterococcus, Acinetobacter, and Staphylococcus were higher in patients with Post-sepsis respiratory dysfunction. The infection rates of Enterococcus, Candida, Pneumocystis, Staphylococcus, and Listeria were higher in patients with Post-sepsis renal dysfunction. In addition, we found that patients with Escherichia infection in sepsis had the lowest survival rate. The survival rate of patients with Enterococcus infection combined with post-sepsis persistent respiratory dysfunction is also worse.<br><br>DISCUSSION: In conclusion, there are differences in the types and proportions of pathogens infected in patients with different organ dysfunction and Post-sepsis persistent organ dysfunction. The combination of Escherichia infection and Enterococcus infection with post-sepsis persistent respiratory dysfunction can affect the survival of patients. We should strengthen the management of sepsis patients, especially those with Post-sepsis persistent organ dysfunction.}, }
@article {pmid40230330, year = {2025}, author = {Cui, T and Kushmaro, A and Barak, H and Poehlein, A and Daniel, R and Mägert, HJ}, title = {Enhanced discovery of bacterial laccase-like multicopper oxidase through computer simulation and metagenomic analysis of industrial wastewater.}, journal = {FEBS open bio}, volume = {}, number = {}, pages = {}, doi = {10.1002/2211-5463.70037}, pmid = {40230330}, issn = {2211-5463}, abstract = {Laccases belong to the superfamily of multicopper oxidases (MCO), a group of enzymes with the ability to reduce oxygen to water in a reaction without producing harmful byproducts. Laccase activity is influenced by many factors, such as structure; the number, location and binding status of copper ions; and the substrate-binding status. A large number of sequences that have not been experimentally characterized yet have been annotated as laccases. However, the biological functions of the characterized MCOs are considered to vary, and the substrate spectrum overlaps with that of other MCOs. Here, we identified 34 putative bacterial laccase sequences from metagenome data for industrial wastewater. We used machine-learning tools to screen enzymes with laccase activity by combining the T1 copper-binding capacity, the overall copper-binding capacity and the substrate-binding capacity. We also used the software comparisons to remove sequences with large discrepancies between different software applications. Three-dimensional structures of identified enzymes were predicted using alphafold, the positions of metal ions within the proteins were predicted by metal3d and autodock-vina, and their docking with ABTS [i.e. 2,2'-azinobis(3‑ethylbenzo-6‑thiazolinesulfonic acid)] as a substrate was predicted by rosetta and autodock-vina. Based on the docking results, we selected 10 high-scoring proteins, two low-scoring proteins and one composite protein for expression using the pET-21d (+) vector. In line with our predictions, all selected high-scoring proteins exhibited activity towards ABTS. Overall, we describe a method for discovering and designing novel bacterial laccase-like multicopper oxidases, offering increased possibilities for the degradation of various harmful components derived from environmental pollution.}, }
@article {pmid40230307, year = {2025}, author = {Liu, B and He, N and Li, H and Yang, Z and Lin, Y and Wu, X and Zhang, H and Zhang, Z and Zhang, Z and Tian, Y and Wu, Z and Zou, Y and Peng, J and Li, S}, title = {3-Fucosyllactose Prevents Nonalcoholic Fatty Liver Disease by Modulating the Gut Microbiota-Derived Pantothenate in Mice.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c00079}, pmid = {40230307}, issn = {1520-5118}, abstract = {Nonalcoholic fatty liver disease (NAFLD) is a growing global health threat. Human milk oligosaccharides (HMOs) exhibit prebiotic properties that may alleviate NAFLD progression. Herein, our study demonstrates that 3-fucosyllactose (3-FL), a distinctive and crucial HMO, significantly attenuates body weight gain, enhances hepatic lipid metabolism, and reduces inflammation in a high-fat diet (HFD)-induced NAFLD mouse model. These findings suggest its potential as a dietary supplement for preventing and alleviating NAFLD progression. Subsequently, fecal metagenomic and nontargeted metabolomics analyses revealed that 3-FL treatment significantly alleviated HFD-induced gut microbiota dysbiosis, with a specific enhancement of the pantothenate (vitamin B5) metabolic pathways. Our targeted metabolite analysis further revealed a significant increase in both hepatic and fecal pantothenate concentrations, which contributed to the enhancement of the coenzyme A (CoA)-mediated lipid metabolism pathway. Furthermore, the subsequent population cohort analyses revealed a significant correlation between serum pantothenate levels and the progression of NAFLD, thereby reinforcing its candidacy as a noninvasive diagnostic biomarker. These findings show that 3-FL acts as an effective prebiotic to alleviate NAFLD symptoms, in part by enhancing the gut microbiota-mediated pantothenate/CoA metabolic pathway.}, }
@article {pmid40230133, year = {2025}, author = {Chen, HD and Gao, S and Wang, LJ and Zhao, B and Lu, MQ and Song, YM and Cui, JS and Zhang, LL}, title = {[Spatial and Temporal Differences and Influencing Factors of Mobile Genetic Elements in Urban and Suburban River Sediments in Shijiazhuang City].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {4}, pages = {2250-2262}, doi = {10.13227/j.hjkx.202403034}, pmid = {40230133}, issn = {0250-3301}, mesh = {*Rivers ; China ; *Geologic Sediments/microbiology ; *Interspersed Repetitive Sequences/genetics ; Cities ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Spatio-Temporal Analysis ; }, abstract = {With the widespread use of antibiotics in medicine and agriculture, the spread of antibiotic resistance genes （ARGs） in the environment has become a serious threat to ecological balance and human health, particularly for its role in facilitating the emergence of multidrug-resistant pathogens. The study of riverine environments as a major transmission route for ARGs and closely related mobile genetic elements （MGEs） is of great importance. MGEs exacerbate the spread of resistance genes by facilitating the horizontal transfer of ARGs in bacterial populations. Although studies have been conducted to explore the interactions between MGEs and ARGs, there is still a relative lack of research on the spatial and temporal differences in the distribution of MGEs in rivers and their drivers. This study selected two rural rivers （with a total of six sampling points） and three urban rivers （with a total of nine sampling points） within Shijiazhuang as research subjects, and sediment samples were collected in December 2020 and April 2021. By employing metagenomic sequencing technology, this study comprehensively compared and analyzed the spatiotemporal distribution characteristics and influencing factors of MGEs in the sediment of urban and rural rivers. The results showed that： ① In December, 1 738 types of MGEs （60572 RPKM） and 1 604 types of MGEs （26916 RPKM） were detected in urban and rural rivers, respectively. In April, 1 790 types of MGEs （74354 RPKM） and 1 631 types of MGEs （32062 RPKM） were detected in urban and rural rivers, respectively. ② The types and abundance of MGEs in urban rivers were greater than those in rural rivers, and the types and abundance of MGEs in April were greater than those in December. ③ ISPa38, IS26, and tnpA were the most significantly different typical MGEs among the rivers in urban and suburban Shijiazhuang. ④ PCoA and NMDS analyses showed significant spatiotemporal differences in MGEs between urban and rural rivers. ⑤ Correlation analysis and co-occurrence results indicated that the abundance of MGEs in urban rivers was significantly positively correlated with antibiotic concentration, industrial enterprises, sewage treatment plants, total population, livestock farming, and aquaculture. In suburban rivers, the abundance of MGEs was mainly significantly positively correlated with antibiotic concentration, livestock farming, aquaculture, and total population. Overall, by comparing the spatiotemporal heterogeneity of MGEs in urban and rural rivers and identifying the main driving factors of MGEs in urban and suburban rivers, this study provides data support for subsequent risk management and control of antibiotic resistance in different rivers.}, }
@article {pmid40229213, year = {2025}, author = {Hoops, SL and Moutsoglou, D and Vaughn, BP and Khoruts, A and Knights, D}, title = {Metagenomic source tracking after microbiota transplant therapy.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2487840}, doi = {10.1080/19490976.2025.2487840}, pmid = {40229213}, issn = {1949-0984}, mesh = {Humans ; *Metagenomics/methods ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/genetics ; Colitis, Ulcerative/therapy/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Bayes Theorem ; Feces/microbiology ; }, abstract = {Reliable engraftment assessment of donor microbial communities and individual strains is an essential component of characterizing the pharmacokinetics of microbiota transplant therapies (MTTs). Recent methods for measuring donor engraftment use whole-genome sequencing and reference databases or metagenome-assembled genomes (MAGs) to track individual bacterial strains but lack the ability to disambiguate DNA that matches both donor and patient microbiota. Here, we describe a new, cost-efficient analytic pipeline, MAGEnTa, which compares post-MTT samples to a database comprised MAGs derived directly from donor and pre-treatment metagenomic data, without relying on an external database. The pipeline uses Bayesian statistics to determine the likely sources of ambiguous reads that align with both the donor and pre-treatment samples. MAGEnTa recovers engrafted strains with minimal type II error in a simulated dataset and is robust to shallow sequencing depths in a downsampled dataset. Applying MAGEnTa to a dataset from a recent MTT clinical trial for ulcerative colitis, we found the results to be consistent with 16S rRNA gene SourceTracker analysis but with added MAG-level specificity. MAGEnTa is a powerful tool to study community and strain engraftment dynamics in the development of MTT-based treatments that can be integrated into frameworks for functional and taxonomic analysis.}, }
@article {pmid40228816, year = {2025}, author = {Chen, J and Liu, X and Bai, Y and Tang, X and Xue, K and Zhu, Z and Liu, W and Wang, J and Wang, C and Qiao, H and Dang, E and Yin, W and Wang, G and Shao, S}, title = {Tonsillar Microbiota Alterations Contribute to Immune Responses in Psoriasis by Skewing Aged Neutrophils.}, journal = {The British journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1093/bjd/ljaf134}, pmid = {40228816}, issn = {1365-2133}, abstract = {BACKGROUND: The interplay between microbiota and the onset of immune-mediated diseases is increasingly coming to light. However, the role of tonsillar microbiota in cutaneous inflammation remains largely unknown.<br><br>OBJECTIVE: We aimed to determine how tonsillar microbiota influence skin inflammation in psoriasis and to uncover the underlying molecular mechanisms.<br><br>METHODS: Tonsillar microbiota samples were collected from 24 healthy controls and 28 psoriasis patients. Microbial community composition was analyzed using 16S rRNA sequencing and metagenomic sequencing. Serum levels of short-chain fatty acids (SCFAs) were measured via liquid chromatography-mass spectrometry in 10 healthy controls and 14 psoriasis patients. Peripheral blood neutrophils from both groups were then exposed to a representative microbial metabolite, and key pro-inflammatory markers were evaluated using functional immune assays.<br><br>RESULTS: We found significant alterations in the diversity and composition of the tonsillar microbial community in psoriasis group, with an increased prevalence of Bacteroidales and a decreased prevalence of Burkholderiales, Micrococcales, and Pasteurellales relative to healthy controls. Notably, a marked reduction in Rothia mucilaginosa correlated inversely with systemic inflammation (neutrophil-to-lymphocyte ratio) and disease severity (psoriasis area and severity index). Metagenomic analysis revealed disruptions in pathways critical for SCFAs production, including propanoate, pyruvate, and butanoate metabolism, which was supported by significantly lower serum SCFAs levels in psoriasis patients. Functional assays demonstrated that SCFAs inhibited neutrophil aging, pro-inflammatory cytokine secretion, and neutrophil extracellular traps (NETs) formation.<br><br>CONCLUSION: Our findings reveal that changes in tonsillar microbiota and their metabolic outputs contribute to psoriasis by modulating immune responses, highlighting potential clinical implications.}, }
@article {pmid40228693, year = {2025}, author = {Ma, JY and Liu, JH and Chen, CZ and Zhang, YZ and Guo, ZS and Song, MP and Jiang, F and Chai, ZT and Li, Z and Lv, SX and Zhen, YJ and Wang, L and Liang, ZL and Jiang, ZY}, title = {Characteristics of microbial carbon pump in the sediment of kelp aquaculture zone and its contribution to recalcitrant dissolved organic carbon turnover: insights into metabolic patterns and ecological functions.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121559}, doi = {10.1016/j.envres.2025.121559}, pmid = {40228693}, issn = {1096-0953}, abstract = {The study delves into the microbial carbon pump (MCP) within the sediments of kelp aquaculture zones, focusing on its influence on the turnover of recalcitrant dissolved organic carbon (RDOC). Following kelp harvest, significant alterations in the microbial community structure were noted, with a decrease in complexity and heterogeneity within co-occurrence networks potentially impacting RDOC production efficiency. Metabolic models constructed identified four key microbial lineages crucial for RDOC turnover, with their abundance observed to decrease post-harvest. Analysis of metabolic complementarity revealed that RDOC-degrading microorganisms exhibit broad substrate diversity and are engaged in specific resource exchange patterns, with cross-feeding interactions possibly enhancing the ecological efficiency of the MCP. Notably, the degradation of RDOC was found not to deplete the RDOC pool; as aromatic compounds break down, new ones are released into the environment, thus supporting the renewal of the RDOC pool. The research highlights the pivotal role of microbial communities in RDOC turnover and offers fresh insights into their cross-feeding behavior related to RDOC cycling, providing valuable data to support the future development and application of MCP theory.}, }
@article {pmid40228470, year = {2025}, author = {Zhang, Y and Ye, Y and Fang, M and Xiang, Y and Chen, J and Tang, X and Yang, Z and Qian, Q}, title = {Biogas production enhancement from anaerobic digestion with magnetic biochar: Insights into the functional microbes and DIET.}, journal = {Journal of environmental management}, volume = {381}, number = {}, pages = {125347}, doi = {10.1016/j.jenvman.2025.125347}, pmid = {40228470}, issn = {1095-8630}, abstract = {The application of magnetic biochar in anaerobic digestion (AD) has gained increasing attention. However, the underlying mechanisms remain insufficiently understood. This study systematically investigated the effects of magnetic biochar on functional microbial communities involved in methanogenesis and elucidated its role in promoting direct interspecies electron transfer (DIET) within AD systems. The addition of 40 mg g[-1] TSadded of magnetic biochar significantly enhanced methane production by 42.21 %, reaching 223.08 mL g[-1] TS with highest organic matter degradation efficiency. Microbial community analysis showed that magnetic biochar significantly enriched microorganisms associated with hydrolysis, acidogenesis, and methanogenesis, as well as electroactive microorganisms' abundance such as Geobacter spp., Syntrophus spp., P. aestuarii, and M. harundinacea, providing direct evidence for the DIET process of AD with magnetic biochar. Furthermore, the abundance of key genes involved in the DIET, including pilA, Fpo, and the genes encoded outer-membrane c-type cytochromes, was respectively upregulated by 44.49 %, 22.04 %, and 37.6 % in the presence of magnetic biochar. These findings suggest that magnetic biochar enhances the production of conductive pili and cytochrome c, facilitating extracellular electron transfer between syntrophic microorganisms. This accelerated electron transfer promotes CO2 reduction to CH4, ultimately improving methane production efficiency in the AD system. Moreover, the enhancement of hydrogenotrophic methanogenesis was particularly pronounced with magnetic biochar, further contributing to the improved AD performance. This study provides novel mechanistic insights into biochar-mediated DIET, offering a theoretical basis for optimizing biochar applications in AD.}, }
@article {pmid40226917, year = {2025}, author = {Lai, Q and Yao, S and Zha, Y and Zhang, H and Zhang, H and Ye, Y and Zhang, Y and Bai, H and Ning, K}, title = {Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model.}, journal = {Nucleic acids research}, volume = {53}, number = {7}, pages = {}, doi = {10.1093/nar/gkaf305}, pmid = {40226917}, issn = {1362-4962}, support = {2021YFA0910500//National Key R&amp;D Program of China/ ; 32071465//National Natural Science Foundation of China/ ; }, mesh = {*Multigene Family ; *Biosynthetic Pathways/genetics ; *Neural Networks, Computer ; *Genome, Microbial ; Phylogeny ; Metagenome ; Secondary Metabolism/genetics ; Genome, Bacterial ; }, abstract = {Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC prediction and classification. Leveraging the transformer encoder, BGC-Prophet captures location-dependent relationships between genes. As one of the pioneering ultrahigh-throughput tools, BGC-Prophet significantly surpasses existing methods in efficiency and fidelity, enabling comprehensive pan-phylogenetic and whole-metagenome BGC screening. Through the analysis of 85 203 genomes and 9428 metagenomes, BGC-Prophet has profiled an extensive array of sub-million BGCs. It highlights notable enrichment in phyla like Actinomycetota and the widespread distribution of polyketide, NRP, and RiPP BGCs across diverse lineages. It reveals enrichment patterns of BGCs following important geological events, suggesting environmental influences on BGC evolution. BGC-Prophet's capabilities in detection of BGCs and evolutionary patterns offer contributions to deeper understanding of microbial secondary metabolites and application in synthetic biology.}, }
@article {pmid40226542, year = {2025}, author = {Cao, J and Wang, S and Ding, R and Liu, Y and Yuan, B}, title = {Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19260}, pmid = {40226542}, issn = {2167-8359}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; China ; *Arvicolinae/microbiology ; *Murinae/microbiology ; *Metagenome ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Proteobacteria/genetics/isolation &amp; purification ; Firmicutes/genetics/isolation &amp; purification ; Sympatry ; Bacteroidetes/genetics/isolation &amp; purification ; }, abstract = {The gut microbiota is integral to an animal's physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China's temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome's composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota's contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning.}, }
@article {pmid40226095, year = {2025}, author = {Ho, JY and Koh, XQ and Kang, DY and Low, A and Hu, D and Haryono, MAS and Williams, RBH and Case, RJ and Boucher, YF}, title = {Discovery of a phylogenetically novel tropical marine Gammaproteobacteria elucidated from assembled genomes and the proposed transfer of the genus Umboniibacter from the family Cellvibrionaceae to Umboniibacteraceae fam. nov.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1437936}, pmid = {40226095}, issn = {1664-302X}, abstract = {Marine heterotrophic bacteria in coastal waters respond to the influx of carbon from natural and anthropogenic sources. We identified two nearly identical, (99.9% average nucleotide identity; 100% amino acid identity; same DNA G + C content of 52.3 mol%) high-quality (≥99% CheckM completeness and ≤ 1.3% contamination) draft metagenome-assembled genomes (MAGs; SJ0813 and SJ0972) from seawater microbiomes of a southern island of Singapore that is in a protected marine park. The MAGs were only assigned to the Cellvibrionaceae family according to Genome Taxonomy Database. Overall genome related indices to Pseudomaricurvus alkylphenolicus KU41G[T] as the closest phylogenetic relative revealed no more than 70.45% average nucleotide identity (ANIcutoff < 95%), below the 50% percentage of conserved proteins (POCPcutoff = 43.54%) for genera cutoff and low digital DNA-DNA hybridization values (DDH = 20.6 and 20.8%). The major respiratory quinone is predicted to be ubiquinone-9 from the annotation of 3-demethylubiquinone-9 3-methyltransferase (ubiG, K00568) involved in the last step of the ubiquinone biosynthesis pathway (M00117), which differed from the ubiquinone-8 utilized by known members of Cellvibrionaceae. Both MAGs contained a complete pathway for dissimilatory nitrate reduction to ammonia, which increases bioavailability of nitrogen in seawater. An identical choline dehydrogenase found in both MAGs have a low amino-acid identity (≤64.47%) compared to existing GMC family oxidoreductases, expanding on the diversity of this family of enzymes. The MAGs meet nearly all the minimum requirements but lack a 16S rRNA gene of sufficient length required for the proposed novel genus and species under SeqCode. Nevertheless, phylogenetic trees based on core-genome and RpoB as an alternative phylogenetic marker are congruent with the taxon standing as a monophyletic clade to other taxa of the order Cellvibrionales. Taken together, the MAGs (SJ0813 and SJ0972) represent an uncultured, undescribed genus and species in which we tentatively propose the name Candidatus Pelagadaptatus aseana gen. nov., sp. nov. and strain SJ0813[TS] (=BAABNI000000000.1[TS]) as type sequence. Phylogenetic inference from core-genome and RpoB phylogenetic trees placed Umboniibacter marinipuniceus KMM 3891[T] outside Cellvibrionaceae. We, therefore, propose the transfer of the genus Umboniibacter from the family Cellvibrionaceae to a new family Umboniibacteraceae according to the International Code of Nomenclature of Prokaryotes.}, }
@article {pmid40225905, year = {2025}, author = {Lambisia, AW and Mwita Morobe, J and Moraa, E and Mwarumba, S and K N Korir, F and Seif Athman, R and Kiptui, R and Mbee, M and Mugo, N and Amoth, P and Muange, P and J Houldcroft, C and Barasa, E and Mwangangi, J and Githinji, G and C Holmes, E and Isabella Ochola-Oyier, L and N Agoti, C}, title = {Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {28}, pmid = {40225905}, issn = {2398-502X}, abstract = {BACKGROUND: In early 2024, a surge in acute hemorrhagic conjunctivitis (AHC), also referred as "red eye" disease, was observed in coastal Kenya, prompting the Ministry of Health to issue an outbreak alert. Herein, we investigated the etiology of this outbreak.<br><br>METHODS: Ocular swabs were obtained from 13 individuals presenting with AHC at a Mombasa clinic in early February 2024. Ten of these were analyzed using bacterial cultures, and all 13 using a pan-adenovirus quantitative PCR (qPCR) and metagenomic sequencing. Potential viral etiology was confirmed by a specific qPCR, amplicon sequencing and phylogenetic analysis.<br><br>RESULTS: Bacterial cultures yielded no growth except in three samples where non-pathogenic bacteria were detected. All 13 samples were adenovirus qPCR negative. Metagenomic sequencing detected coxsackievirus A24 variant (CA24v) in three of the 13 samples. CV-A24v detections were confirmed by both CV-A24v specific qPCR and amplicon sequencing of an approximately 450 nucleotide long VP4/2 junction genomic region. Phylogenetic analysis of the VP4/2 sequences showed that they were closely related to CV-A24v genotype IV.<br><br>CONCLUSION: The AHC epidemic in coastal Kenya in early 2024 was likely caused by CA24v. Metagenomic sequencing is a powerful tool for identifying potential causative agents of new disease outbreaks.}, }
@article {pmid40225898, year = {2025}, author = {Liu, H and Wang, H and Sun, J and Yang, T and Mo, Z and Huang, H and Pan, Y}, title = {High-Altitude Open-Pit Coal Mining has Changed the Sulfur Cycle and Ecological Network of Plant Rhizosphere Microorganisms.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71183}, pmid = {40225898}, issn = {2045-7758}, abstract = {Ecological restoration of mining sites has a considerable effect on microbial community dynamics; however, its impact on sulfur cycling is unclear. This study explored the changes in functional genes related to sulfur cycling and microbial diversity during different stages of succession following the ecological restoration of a mining site in a cold arid area. A total of three succession stages were selected-natural, secondary, and artificial. The expression of sulfur cycle-related genes and associated microbial drivers was investigated using metagenomics and network analysis. The dominant bacteria in the secondary succession were found to be r-strategy-adopting Proteobacteria and Cyanobacteria. Natural succession primarily comprised Aspergillus and Thermus, whereas artificial succession comprised Proteobacteria, Chlorophyta, and Actinobacteria. Mining disturbances were determined to significantly reduce the abundance of sulfur-cycling archaea. Secondary succession was primarily influenced by soil total phosphorus in the sulfur-cycle gene network. The key bacteria and archaea involved in the sulfur cycle were found to be Bradyrhizobium and Nitrosopumilus, respectively. The abundance of Streptomyces was significantly higher in natural succession than in artificial or secondary succession. Burkholderia, which has biological control and bioremediation effects, was abundant during artificial succession. These results provide a theoretical basis for restoring the sulfur cycle and promoting a positive succession of ecosystems in mining areas.}, }
@article {pmid40225105, year = {2025}, author = {He, W and Wang, S and Xiong, X and Dai, W}, title = {[18]F-FDG PET/CT Imaging of Talaromyces marneffei Infection with Bone Destruction in an HIV-Negative Patient: Case Report and Review.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1745-1752}, pmid = {40225105}, issn = {1178-6973}, abstract = {BACKGROUND: Talaromycosis is an opportunistic fungal infection caused by Talaromyces marneffei (T. marneffei), commonly occurs in HIV-positive individuals. While less common, it can also affect HIV-negative individuals. We reported a T. marneffei infection in an HIV-negative patient, whose imaging findings and diagnostic process offer valuable clinical insights.<br><br>CASE PRESENTATION: An HIV-negative male adult patient with an intermittent cough for more than two years and worsened for more than one month. Enhanced CT scan indicated lung cancer with rib and lymph nodes metastasis. The lower respiratory tract and bronchial lavage fluid culture of the patient were negative. He received two bronchoscopies, two biopsies and two metagenomic next-generation sequencing (mNGS) tests, which failed to find the malignant cell but sequentially identified the presence of Pasteurella multocida and the Epstein-Barr virus. His condition did not improve after anti-infective treatment for 2weeks. An 18-fluorodeoxy glucose ([18]F-FDG) PET/CT scan revealed increased radioactivity in right supraclavicular lymph node, left lung and the right tenth rib. Ultimately, a biopsy at the hypermetabolic lesion of left lung, and a third mNGS test confirmed the presence of Talaromyces marneffei. Subsequently, the patient started antifungal therapy with amphotericin B and itraconazole and showed a favorable response.<br><br>CONCLUSION: We reviewed all reported PET/CT findings of T. marneffei infection patients, suggesting that fungus T. marneffei should be considered in patients identified as infection and exhibited bone destruction and also highlight the role of PET/CT in guiding the biopsy site.}, }
@article {pmid40224142, year = {2025}, author = {Caille, A and Connan, C and Lyon Belgy, N and Borezée, E and Cherbuy, C and Meunier, N and Meslier, V}, title = {Positive nutritional selection of adults with healthy lifestyle and high daily fiber consumption for the isolation of beneficial intestinal bacteria: The iTARGET cohort study protocol.}, journal = {MethodsX}, volume = {14}, number = {}, pages = {103268}, pmid = {40224142}, issn = {2215-0161}, abstract = {Recent advances in the study of the gut microbiota has pointed to its under-utilized source of potentially beneficial bacteria, known as next generation probiotics, offering a promising avenue to restore or compensate impaired gut microbiota toward a healthy state. Aside from the difficulties to achieve in-lab adequate culture conditions, the use of beneficial bacterial isolates is also limited by their bioavailability in the donor itself. In the iTARGET study, we positively selected donors based on their diet enriched in fiber, that has been shown to increase the prevalence of bacterial species associated with health. The iTARGET study is a monocenter, prospective, observational study of adults with healthy lifestyle and high daily fiber consumption. We aim to recruit individuals in two phases, the first one for all individuals that will permit the identification of carriers for bacteria of interest and the second phase for a subset of individuals to allow for culture and isolation of previously identified potentially beneficial bacteria. Our primary outcome is the isolation and culture of at least one potentially beneficial isolate. The secondary outcomes comprised the high throughput metagenomic profiles of the intestinal microbiota and the characterization of the cultured isolates. The study was approved by the French Research Ethics Committees (Comité de Protection des Personnes Sud-Est I) under the National reference ID 2023-A01677-38. Study findings and results will be published in peer-reviewed Open Access journals. (Trial registration number on ClinicalTrials.gov: NCT06166810).}, }
@article {pmid40223813, year = {2025}, author = {Alp-Baltakesmez, D and Ertürkmen, P and Bulantekin, &#xd6;}, title = {Diversity and Functional Roles of Microorganisms in Anatolian Black Pine Cone Vinegar Fermentation.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {4}, pages = {e70155}, pmid = {40223813}, issn = {2048-7177}, abstract = {The parts of some pine species are a rich source of bioactive compounds that can be used in various food products. The current work, the physicochemical, bioactive, antimicrobial, sensory, and aromatic properties of traditional vinegar produced from Anatolian Black Pine Cones from different provinces of Turkey were determined, as well as the cultivable microbial diversity and metagenomic analysis. The total phenolic content of the vinegars ranged from 163.88 to 174.79 mg GAE/L. Antioxidant activity, measured via DPPH and ABTS assays, varied among the samples. CnB vinegar, made from Burdur province cones, stood out for its bioactive compounds, including terpenes, acetic acid, ascorbic acid, and the highest α-terpineol content (3.13%). CnB also exhibited the strongest antimicrobial activity, with the largest inhibition zone (44.91 mm) against E. coli type A, while CnM showed the lowest activity. Sensory evaluations favored CnB for its balanced flavor, while CnV was criticized for excessive sharpness, and CnM was deemed too mild. The bacterial microbiome of CnB was predominantly composed of acetic acid bacteria, with an average concentration of 7.36 log CFU/mL in the enumeration of culturable microorganisms. The dominant bacterial taxa at the phyla level included Proteobacteria (72.296%), Firmicutes (22.062%), Bacteroidota (3.665%), followed by Acetobacteraceae (71.47%), Clostridia (13.187%), Bacilli (5.066%), Bacteroidetes (3.665%), and C. negativicutes (3.737%) at the phylum level. The fungal microbiome was mainly represented by Ascomycota (78.717%) and Eukaryota Incertae sedis (15.840%). The findings demonstrate that pine cone vinegar can be employed in a multitude of applications, including food preservation and health promotion.}, }
@article {pmid40223739, year = {2025}, author = {El Mouzan, M and Savidge, TC and Al Sarkhy, A and Badu, S and Alsaleem, B and Al Mofarreh, M and Almasood, A and Assiri, A}, title = {Gut virome profile in new onset treatment naïve Saudi children with ulcerative colitis.}, journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association}, volume = {}, number = {}, pages = {}, doi = {10.4103/sjg.sjg_24_25}, pmid = {40223739}, issn = {1998-4049}, abstract = {BACKGROUND: Gut microbiome imbalance is well established in ulcerative colitis (UC) in Western populations. Significantly less is known about the gut virome and whether geography impacts the UC-associated microbiome. The aim of this study was to characterize gut bacteriophage changes, as well as to identify phage-bacterial associations that can serve as potential biomarkers of UC.<br><br>METHODS: Twenty children with UC and 20 healthy controls were enrolled in the study. Inclusion criteria included newly diagnosed treatment-na&#xef;ve children with UC with no antibiotic exposure for at least six months prior to sample collection. Deoxyribonucleic acid (DNA) was extracted from stool and rectal biopsies and was processed for shotgun metagenomic sequencing. Bioinformatics and statistical analyses were performed to assess phage diversity and their associations with gut bacteria. Candidate biomarkers were identified using the random forest classifier.<br><br>RESULTS: In fecal samples, bacteriophage diversity was not significantly altered, but 72 species were significantly altered in UC, five of which (Salmonella_phage_SEN4, uncultured_crAssphage, Staphylococcus_phage_SPbeta-like, Streptococcus_phage_YMC-2011 and Siphoviridae_u_s) were identified as candidate biomarker signatures.<br><br>CONCLUSIONS: We found a significantly altered bacteriophage signature in children with new onset, treatment na&#xef;ve UC in Saudi children, a Middle Eastern population. These changes differed from previously reported Western UC cases, indicating that demographic bias needs to be considered when developing microbiota-based diagnostics and therapeutic applications for non-Western populations.}, }
@article {pmid40223703, year = {2025}, author = {Gao, M and Zhang, Q and Chen, B and Lei, C and Xia, Q and Sun, L and Li, T and Zhou, NY and Lu, T and Qian, H}, title = {Global Geographic Patterns of Soil Microbial Degradation Potential for Polycyclic Aromatic Hydrocarbons.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c00306}, pmid = {40223703}, issn = {1520-5851}, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are toxic and persistent pollutants that are widely distributed in the environment. PAHs are toxic to microorganisms and pose ecological risks. Bacteria encode enzymes for PAH degradation through specific genes, thereby mitigating PAH pollution. However, due to PAHs' complexity, information on the global degradation potential, diversity, and associated risks of PAH-degrading microbes in soils is lacking. In this study, we analyzed 121 PAH-degrading genes and selected 33 as marker genes to predict the degradation potential within the soil microbiome. By constructing a Hidden Markov Model, we identified 4990 species carrying PAH-degrading genes in 40,039 soil metagenomic assembly genomes, with Burkholderiaceae and Stellaceae emerging as high-potential degraders. We demonstrated that the candidate PAH degraders predominantly emerged in artificial soil and farmland, with significantly fewer present in extreme environments, driven by factors such as average annual rainfall, organic carbon, and human modification of terrestrial systems. Furthermore, we comprehensively quantified the potential risks of each potential host in future practical applications using three indicators (antibiotic resistance genes, virulence factors, and pathogenic bacteria). We found that the degrader Stellaceae has significant application prospects. Our research will help determine the biosynthetic potential of PAH-degrading enzymes globally and further identify potential PAH-degrading bacteria at lower risk.}, }
@article {pmid40223273, year = {2025}, author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW}, title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2412001}, doi = {10.4014/jmb.2412.12001}, pmid = {40223273}, issn = {1738-8872}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; }, abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.}, }
@article {pmid40223231, year = {2025}, author = {Lin, H and Chen, Y and Zhou, M and Wang, H and Chen, L and Zheng, L and Wang, Z and Zheng, X and Lu, S}, title = {Comprehensive analysis of faecal metagenomic and serum metabolism revealed the role of gut microbes and related metabolites in detecting colorectal lateral spreading tumours.}, journal = {Virulence}, volume = {16}, number = {1}, pages = {2489154}, doi = {10.1080/21505594.2025.2489154}, pmid = {40223231}, issn = {2150-5608}, mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology/pathology/metabolism/blood ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; Metagenomics ; Aged ; Metabolomics ; Dysbiosis/microbiology ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metabolic Networks and Pathways ; Case-Control Studies ; Adult ; }, abstract = {Colorectal lateral spreading tumours (LST), early-stage lesions of colorectal cancer (CRC), are associated with gut microbiota dysbiosis. However, the functional alterations in gut microbiota and their metabolic pathways remain inadequately understood. This study employed propensity score matching to compare 35 LST patients with 35 healthy controls. Metagenomic and metabolomic analyses revealed notable differences in gut microbiota composition and metabolic pathways. LST patients exhibited a marked reduction in short-chain fatty acid (SCFA)-producing probiotics, such as Roseburia, Clostridium, and Butyricicoccus sp-OF13-6, alongside anti-inflammatory metabolites. In contrast, potential intestinal pathogens linked to inflammatory bowel disease (IBD), including Escherichia and Citrobacter amalonaticus, were significantly enriched. Orthogonal partial least squares discriminant analysis (OPLS-DA) highlighted significant metabolic disparities between the groups, with enrichment in pathways associated with cholesterol metabolism, choline metabolism in cancer, and amino acid metabolism - all relevant to cancer progression. Key biomarkers identified for LST included fumarate, succinate, glutamic acid, glycine, and L-aspartic acid, which were closely linked to these pathways. Functional studies demonstrated that these metabolites promoted the proliferation and invasion of HCT-116 and SW480 human colorectal cancer cells in vitro. Metagenomic and metabolomic analysis revealed a strong positive correlation between Escherichia and Ruminococcus sp-AM41-2AC abundance and the enriched pathways, whereas reductions in Roseburia species, including Roseburia-OF03-24 and Roseburia intestinalis_CAG13-exhibited negative correlations. These results suggest that gut microbiota and metabolite alterations in LST contribute to intestinal inflammation and CRC development, underscoring their potential as biomarkers for early detection and therapeutic targets.}, }
@article {pmid40223096, year = {2025}, author = {Yang, Z and Zhou, Y and Lin, J and Wang, X and Huang, C and Gao, J and Wang, G and Yang, B and Liu, G and Duan, H and Cui, J and Zhao, J and Luo, W and Cheng, S and Liu, Y}, title = {Identification and characterization of pigeon adenovirus 1 as an emerging pathogen in pigeons from Northern and Northwest China.}, journal = {BMC veterinary research}, volume = {21}, number = {1}, pages = {266}, pmid = {40223096}, issn = {1746-6148}, support = {BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; QNJJ202234//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; QNJJ202234//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; }, mesh = {Animals ; *Columbidae/virology ; China/epidemiology ; *Adenoviridae Infections/veterinary/virology/epidemiology/pathology ; *Bird Diseases/virology/epidemiology/pathology ; *Aviadenovirus/genetics/isolation &amp; purification ; Phylogeny ; Genome, Viral ; *Communicable Diseases, Emerging/veterinary/virology/epidemiology ; }, abstract = {BACKGROUND: In 2022, a new infectious disease characterized by severe acute hepatitis, sudden death, and high mortality among breeding pigeons, was reported in China.<br><br>RESULTS: In naturally infected pigeons, key necropsy findings comprised hepatic swelling with patchy hemorrhage and pericardial effusion. Histopathological examination further revealed degeneration, necrosis, and basophilic intranuclear inclusion bodies affecting hepatocytes, cardiomyocytes, and vascular endothelial cells. Transmission electron microscopy revealed a typical icosahedral virus structure and crystal-like arrangement of viral particles in the nucleus. Metagenomic next-generation sequencing (mNGS) of pericardial effusion samples revealed the presence of pigeon adenovirus. Sequencing analysis of the hexon and fiber-2 genes suggested that it constituted pigeon adenovirus 1 (PiAdV-1). The complete genome of CH/BJ/1/2022 was determined to be 48,071 nucleotides in length, with a 10-amino acid deletion in the fiber-2 gene at residues 627-636 and a 95-animo acid insertion in the 100&#xa0;K gene at residue 75. The same disease was reproduced in pigeons by experimental infection.<br><br>CONCLUSION: Collectively, our analyses confirmed that the etiological agent was PiAdV-1, an emerging pathogen that causes severe acute hepatitis and high mortality in pigeons. This virus merits close attention because it could be catastrophic for the pigeon industry.}, }
@article {pmid40222673, year = {2025}, author = {Fu, CM and Luo, SQ and Tang, DR and Zhang, YM and Xu, JW and Lin, LB and Zhang, QL}, title = {Effect of bacteriocin RSQ01 on milk microbiota during pasteurized milk preservation.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-26395}, pmid = {40222673}, issn = {1525-3198}, abstract = {Milk has high risk for microbial contamination. RSQ01, a bacteriocin, previously has shown potentiality for pasteurized milk preservation. This study analyzed the effects of RSQ01 on milk microbiota by comparison of bacterial number and composition in 3 pasteurized milk groups: controls without RSQ01, treatment group with the addition of 2 × MIC (low concentration) and 4 × MIC RSQ01 (high concentration). Integrated 16S rDNA sequencing and metagenomics of these groups after 3 d of storage showed inhibition of RSQ01 on microbiota diversity. Pathogenic bacteria such as Salmonella showed a decrease in relative abundance after RSQ01 treatment, while probiotic bacteria such as Lactococcus showed an increase, indicating that RSQ01 contributed to milk preservation by maintaining a low abundance of pathogens and a relatively high abundance of probiotics. Further investigations revealed that milk preservation was primarily attributed to the ability of RSQ01 to decrease the relative abundance of genes related to metabolism of energy and nutrients (e.g., vitamins, lipids, and amino acids) of microbiota, with change of genetic, environmental, and cellular processes. Interestingly, RSQ01 generally reduced the relative abundance of virulence factors- and quorum-sensing-related genes in microbiota, likely reducing virulence and resistance. The findings provided insights into microbiomics mechanisms regarding pasteurized milk preservation of bacteriocins.}, }
@article {pmid40222492, year = {2025}, author = {Xia, Y and Chen, X and Jiang, X and Shen, J}, title = {Enhanced denitrification under saline Conditions: Glycine betaine as a key osmoprotectant.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132517}, doi = {10.1016/j.biortech.2025.132517}, pmid = {40222492}, issn = {1873-2976}, abstract = {Biological denitrification is significantly inhibited by salinity, which adversely affects microbial activity and reduces efficiency. This study aimed to evaluate the impact of salinity on denitrification performance and assess the potential of glycine betaine (GB) as an osmotic pressure regulator and protective agent. Results indicated that under the optimal conditions, including an influent nitrate concentration of 51.03 mg L[-1], C/N ratio of 5.42, pH value of 8.95, and salinity of 1.05 %, the nitrate removal efficiency was predicted to reach 100 %. However, a sharp decline (56.09 ± 4.52 %) in nitrate removal efficiency occurred when salinity increased from 0 % to 3 % within the initial 6 h. This inhibition was mitigated by adding 25 mg L[-1] GB, which enhanced nitrate removal efficiency by 2.19 times. GB promoted the secretion of extracellular polymeric substances (EPS), especially polymeric protein, a critical contributor to salinity resistance. Metagenomics analysis revealed that GB improved denitrification process by upregulating key genes involved in nitrogen and carbon metabolism. Furthermore, the relative abundance of Na[+] transporter genes, K[+] transporter genes, and GB absorption and synthesis genes rose with GB addition, underscoring the indispensable role of GB in alleviating osmotic stress and accelerating microbial metabolism. These findings emphasize the detrimental effects of salinity on denitrification and demonstrate the potential of GB as an osmoprotectant, enabling efficient nitrogen removal under saline conditions.}, }
@article {pmid40222473, year = {2025}, author = {Jing, K and Li, Y and Li, Y and Meng, Q and Guan, Q}, title = {The treated wastewater enhances the biodegradation of sulfonamide antibiotics in biofilm-sediment downstream of the receiving river outlet.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121600}, doi = {10.1016/j.envres.2025.121600}, pmid = {40222473}, issn = {1096-0953}, abstract = {Although the treated wastewater meets the discharge standards, it can still become a potential transmitted stressor that affects aquatic organisms in receiving rivers. Biofilms and sediments as the main solid-phase substances in natural aquatic environments can biodegrade micropollutants. However, most of the current studies have selected a single solid-phase material, and there are relatively few studies that comprehensively consider the effect of treated wastewater on the dissipation of micropollutants in a composite biofilm-sediment system. Therefore, this study investigated the dissipation pathways of six sulfonamide antibiotics (SAs) in biofilm-sediment and the effect of treated wastewater on SAs dissipation. The results showed that biodegradation was the main pathway for SAs dissipation in biofilm-sediment. The input of treated wastewater increased the abundance of dominant degradation bacteria Burkholderiales and Pseudomonadale, thereby improving the biodegradation rate of SAs (approximately 1.5 times higher than upstream degradation rate). These genera could also be further integrated into downstream communities to continuously mediate the biodegradation of SAs. Through mass spectrometry and metagenomic sequencing analysis, it was found that the common degradation pathways of SAs in biofilm-sediment affected by treated wastewater are acetylation, formylation, hydroxylation, and bond cleavage. Acetyltransferase played an important role in the biodegradation of SAs. In addition, the enrichment of antibiotic resistant genes during biodegradation increased the risk of their spread in the aquatic environment. These findings provide new insights into the fate of antibiotics in aquatic environments and the impact of treated wastewater on downstream bacterial communities.}, }
@article {pmid40222470, year = {2025}, author = {Yang, X and Yu, X and Ming, Y and Liu, H and Zhu, W and Yan, B and Huang, H and Ding, L and Qian, X and Wang, Y and Wu, K and Niu, M and Yan, Q and Huang, X and Wang, C and Wang, Y and He, Z}, title = {The vertical distribution and metabolic versatility of complete ammonia oxidizing communities in mangrove sediments.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121602}, doi = {10.1016/j.envres.2025.121602}, pmid = {40222470}, issn = {1096-0953}, abstract = {Recently discovered complete ammonia-oxidizing (comammox) microorganisms can completely oxidize ammonia to nitrate and play an important role in the nitrogen (N) cycle across various ecosystems. However, little is known about the vertical distribution and metabolic versatility of comammox communities in mangrove ecosystems. Here we profiled comammox communities from deep sediments (up to 5 m) in a mangrove wetland by combining metagenome sequencing and physicochemical properties analysis. Our results showed that the relative abundance of comammox bacteria (23.2%) was higher than ammonia-oxidizing bacteria (AOB, 12.0%), but lower than ammonia-oxidizing archaea (AOA, 64.8%). The abundance of comammox communities significantly (p < 0.01) decreased with the sediment depth, and dissolved organic carbon and total sulfur appeared to be major environmental factors influencing the nitrifying microbial community structure. We also recovered a high-quality metagenome-assembled genome (MAG) of comammox bacteria (Nitrospira sp. bin2030) affiliated with comammox clade A. Nitrospira sp. bin2030 possessed diverse metabolic processes, not only the key genes for ammonia oxidation and urea utilization in the N cycle, but also key genes involved in carbon and energy metabolisms, sulfur metabolism, and environmental adaptation (e.g., oxidative stress, salinity, temperature, heavy metal tolerance). The findings advance our understanding of vertical distribution and metabolic versatility of comammox communities in mangrove sediments, having important implications for quantifying their contribution to nitrification processes in mangrove ecosystems.}, }
@article {pmid40222255, year = {2025}, author = {Bobrovska, S and Newcomer, E and Gottlieb, M and McSorley, VE and Kittner, A and Hayden, MK and Green, S and Barbian, HJ}, title = {Hospital air sampling enables surveillance of respiratory virus infections and genomes.}, journal = {The Science of the total environment}, volume = {977}, number = {}, pages = {179346}, doi = {10.1016/j.scitotenv.2025.179346}, pmid = {40222255}, issn = {1879-1026}, abstract = {There is an urgent need for early detection and comprehensive surveillance of respiratory pathogens. Environmental surveillance may be key to timely responses for newly emerging pathogens and infections that are unreported or underreported. Here, we employed air sampling in a large urban hospital. Air samples (n = 358) were collected weekly at five locations, including two in the emergency department, two in hospital common areas and one in a storage room, for two respiratory virus seasons (November 2022 to June 2024). Air samples were tested for eight respiratory pathogens by qPCR, including RNA and DNA viruses and a bacterium. Air samples had an average of four detected pathogens per sample and 97 % samples contained SARS-CoV-2. Air sample pathogen positivity and quantity were strongly correlated with clinical surveillance for four seasonal respiratory pathogens: influenza A and B, respiratory syncytial virus, and human metapneumovirus. Targeted amplicon sequencing of SARS-CoV-2 showed that lineages detected in air samples reflected those in contemporaneous regional clinical specimens. Metagenomic sequencing with viral capture enrichment detected myriad human pathogens, including respiratory-associated viruses with recovery of full viral genomes. Detection of viral pathogens correlated well between virus capture sequencing and qPCR. Overall, this suggests air sampling can be an agile and effective tool for pathogen early warning, surveillance and genome characterization.}, }
@article {pmid40222247, year = {2025}, author = {Suzuki, M and Hayashi, T and Takahashi, K and Nozaki, K and Kasuya, KI}, title = {Exploring biodegradation limits of n-alkanes as polyethylene models using multi-omics approaches.}, journal = {The Science of the total environment}, volume = {977}, number = {}, pages = {179365}, doi = {10.1016/j.scitotenv.2025.179365}, pmid = {40222247}, issn = {1879-1026}, abstract = {Polyethylene (PE) is widely regarded as non-biodegradable in natural environments, despite reports suggesting partial biotic degradation. Using multi-omics analysis, this study investigated the biodegradation mechanisms of n-alkanes-structural analogs of PE-to determine the threshold carbon number in PE that allows for environmental biodegradation. n-Alkanes with 6-40 carbons (C6-C40) were biodegraded in the soil, whereas C44 and PE were not. 16S rRNA gene amplicon sequence analysis identified distinct microbial communities associated with non-degradable compounds (PEs and C44) and biodegradable alkanes (C6-C40). Notably, the microbial community composition for C40 differed from those associated with biodegradable alkanes below C36. Multi-omics analysis identified the genera Aeromicrobium, Nocardia, Nocardioides, Rhodococcus, Acinetobacter, and Fontimonas as key degraders of n-alkanes at C36 and below, utilizing alkane hydroxylases such as alkane monooxygenase (AlkB), LC-alkane monooxygenase from Acinetobacter (AlmA), and cytochrome P450 (CYP153). Conversely, the biodegradation of C40 was facilitated by taxa, including the order Acidimicrobiales and the genera, Acidovorax, Sphingorhabdus, Prosthecobacter, and Roseimicrobium using AlmA and CYP153-type hydroxylases. This difference in key degraders and alkane hydroxylases may explain the reduced biodegradability of n-alkanes above C40, including PE.}, }
@article {pmid40222078, year = {2025}, author = {Xu, A and Gao, D and Wu, WM and Gong, X and Liang, H}, title = {Enhanced denitrification using iron modified biochar under low carbon source condition: Modulating community assembly, allocating carbon metabolism and facilitating electron transfer.}, journal = {Journal of environmental management}, volume = {381}, number = {}, pages = {125354}, doi = {10.1016/j.jenvman.2025.125354}, pmid = {40222078}, issn = {1095-8630}, abstract = {Biochar can modulate microbial community structure to enhance denitrification but the activity is still restricted by the availability of electron transfer (ETS) under metabolic imbalance conditions. Here we developed iron (Ⅲ) modified biochar (FeBC) to substantially mitigate this electron limitation, enhance ETS and accelerate denitrification reaction via intracellular metabolism and community interaction. The results demonstrated that FeBC could significantly improve the denitrification performance, the nitrate removal rate was significantly increased by 30 % at C/N ratio of 3 (W/W) with little nitrite and nitrous oxide accumulation, attributing to the enhanced activities of the ETS and denitrifying reductases and complex microbial interactions via increased abundance of microorganisms involved in carbon and nitrogen transformations. Biochemical quantification and electrochemical analysis, revealed that FeBC activated the acceleration of the ETS process. Comparative metagenome analyses indicated that upregulating key enzymes in the tricarboxylic acid cycle was the potential respiratory enzyme associated with FeBC-mediated ETS. NADH/NAD[+] circulation stimulate the startup of carbon metabolism. This energy-linked mechanism could provide ATP for denitrification. This study revealed the functional roles of FeBC in mediating ETS and regulating the bacterial community to achieve enhanced denitrification.}, }
@article {pmid40221653, year = {2025}, author = {Babalola, OO and Adebayo, AA and Enagbonma, BJ}, title = {Shotgun metagenomics dataset of the core rhizo-microbiome of monoculture and soybean-precedent carrot.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {26}, pmid = {40221653}, issn = {2730-6844}, mesh = {*Daucus carota/microbiology ; *Metagenomics/methods ; *Rhizosphere ; *Glycine max/microbiology/growth &amp; development ; *Microbiota ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {OBJECTIVES: Carrot is a significant vegetable crop contributing to agricultural diversity and food security, but less is known about the core microbiome associated with its rhizosphere. More so, the effect of preceding crop and cropping history on the composition and diversity of carrot rhizo-microbiome remains largely unknown. With shotgun metagenomics, the study unveils how cropping systems direct rhizo-microbiome structure and functions, previously limited by other methods.<br><br>DATA DESCRIPTION: Metagenomic-DNA molecule was extracted from four replicates each (12 samples) of a distant bulk soil and the rhizosphere soils from monoculture and soybean-precedent carrots, with the Power soil&#xae; DNA Isolation kit. The DNA samples were subjected to Next Generation Sequencing using the Illumina Novaseq X Plus (PE 150) platform. Raw sequencing reads were assembled and annotated with MEGAHIT and LCA algorithms in MEGAN software respectively, before a quality control check was done with FASTP. CD-Hit was used to de-replicate the sequences and the removal of host genomic-DNA and contaminant sequences was done with Bowtie2. The clean sequence data, in FastQ files, were analyzed for taxonomic classification and functional diversity of the rhizosphere microbiome using the Micro_NR and KEGG database respectively. The findings provide insights into microbiome dynamics, with potential implications for sustainable agricultural practices.}, }
@article {pmid40221647, year = {2025}, author = {Zhang, N and Dou, H and Guo, P and Sun, J and Zhang, F and Chen, T and Gao, C and Wang, Z}, title = {Concurrent invasive disseminated Nocardia farcinica and Candida infections in a patient undergoing long-term glucocorticoid therapy for autoimmune thrombocytopenia: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {520}, pmid = {40221647}, issn = {1471-2334}, support = {gxgnfx2022035//Domestic Visiting Training Program for Outstanding Young Backbone Teachers/ ; 2023SYKFZ05//Open project of Anhui Biochemical Drug Engineering Technology Research Center in 2023/ ; }, mesh = {Humans ; Female ; *Nocardia Infections/drug therapy/diagnosis/microbiology/complications ; Middle Aged ; *Nocardia/isolation &amp; purification ; *Candidiasis/drug therapy/diagnosis/microbiology/complications ; *Purpura, Thrombocytopenic, Idiopathic/drug therapy/complications ; *Glucocorticoids/therapeutic use/adverse effects ; Antifungal Agents/therapeutic use ; Candida albicans/isolation &amp; purification ; Anti-Bacterial Agents/therapeutic use ; *Coinfection/microbiology ; Prednisone/therapeutic use/adverse effects ; Immunocompromised Host ; }, abstract = {BACKGROUND: Nocardia farcinica is a virulent organism known for its high resistance to many antibiotics and its ability to cause disseminated life-threatening infections, particularly in immunocompromised patients or those undergoing organ transplantation. Candida albicans can cause disseminated candidiasis with a mortality rate ranging from 30% to 60%. Cases involving concurrent disseminated N. farcinica and C. albicans, particularly in patients with autoimmune thrombocytopenia, are extremely rare. The presence of two disseminated pathogens complicates both diagnosis and treatment, creating substantial challenges for healthcare providers.<br><br>CASE PRESENTATION: A 50-year-old woman who had a history of autoimmune thrombocytopenia and was being treated with prednisone (60&#xa0;mg qd). She presented with a 40-day history of high-grade fevers (40&#x2103;), cough, headache, and multiple abscesses in the skin structure. N. farcinica was found in her skin structure, cerebrospinal fluid, and blood, and C. albicans was cultured in cerebrospinal fluid, sputum, and urine. She was diagnosed with disseminated nocardiosis and disseminated candidiasis. The patient received a prolonged course of multiple anti-bacterial and anti-fungal medications and eventually recovered.<br><br>CONCLUSIONS: Due to the atypical clinical presentations, the diagnosis of concurrent invasive disseminated N. farcinica and C. albicans infections might be delayed. A variety of diagnostic testing, including metagenomics next-generation sequencing, can help to identify the pathogen rapidly. Drug susceptibility test can guide the selection and adjustment of antibiotics, which should be in companion with surgical interventions to save lives in affected patients.}, }
@article {pmid40221512, year = {2025}, author = {Yong, Y and Zhou, L and Zhang, X and Ran, X and Guo, Y and Gai, W and Chen, Y}, title = {The clinical value of metagenomic next-generation sequencing in the diagnosis of pulmonary tuberculosis and the exploration of lung microbiota characteristics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12568}, pmid = {40221512}, issn = {2045-2322}, support = {82104236//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Lung/microbiology ; *Microbiota/genetics ; Adult ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; }, abstract = {The lung microbiota plays a critical role in many important physiological processes and is linked with various pulmonary infectious diseases. The present study aimed to characterize the lung microbiota in patients with pulmonary tuberculosis (PTB), and to explore the association between the abundance of Mycobacterium tuberculosis complex (MTBC) and the lung microbiota. This retrospective study included 190 patients with MTBC infection. The enrolled patients were classified into three groups based on the abundance results of bronchoalveolar lavage fluid (BALF) mNGS: low [reads per ten million (RPTM) = 1 ~ 1000], medium (RPTM = 1001 ~ 10000) and high (RPTM > 10000). In the high-abundance group, there were more bilateral lobar involvement and symptoms of cavitation. In addition to mNGS, the highest positivity rates were T-spot (92.36%), GeneXpert (71.58%), culture (68.95%) and AFB smear (17.84%). The positive rates of culture, AFB smear and GeneXpert increased with the increase of MTBC abundance, and the positive rates were highest in the high-abundance MTBC group. Both the alpha and beta diversity showed significant difference between the three groups, with the high-abundance MTBC groups showed lowest alpha diversity. The increased abundance of MTBC positively associated with the longer time of hospital stay. To sum up, the lung microbiota of patients with PTB were significantly distinct between groups with different abundant levels of MTBC. Combined with imaging features, a high abundance of MTBC suggests the patient is more severely ill and has a poorer prognosis.}, }
@article {pmid40221485, year = {2025}, author = {Wu, Q and Gao, J and Sa, B and Cong, H and Deng, W and Zhang, Y and Zhong, X and Zhang, J and Wang, L and Liu, H and Yan, Y and Zhang, Y and Liu, D and Yan, W}, title = {Genomes of Prochlorococcus, Synechococcus, bacteria, and viruses recovered from marine picocyanobacteria cultures based on Illumina and Qitan nanopore sequencing.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {612}, pmid = {40221485}, issn = {2052-4463}, support = {42188102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42293292//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Prochlorococcus/genetics ; *Synechococcus/genetics ; *Genome, Bacterial ; Nanopore Sequencing ; *Genome, Viral ; Metagenome ; Pacific Ocean ; Indian Ocean ; Seawater/microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Prochlorococcus and Synechococcus are key contributors to marine primary production and play essential roles in global biogeochemical cycles. Despite the ecological importance of these two picocyanobacterial genera, current genomic datasets still lack comprehensive representation of under-sampled ocean regions, associated bacteria and viruses. To address this gap, we used a combination of second- and third-generation sequencing technologies to assemble comprehensive genomic data from 105 Picocyanobacterial enrichment cultures isolated from the Indian Ocean, the South China Sea, and the western Pacific Ocean. This dataset includes 55 Prochlorococcus and 50 Synechococcus genomes with high completeness (>98%) and low contamination (<2%), along with 308 non-redundant associated bacterial genomes derived from 1,457 medium- and high-quality non-cyanobacteria metagenome-assembled genomes (MAGs, completeness ≥50% and contamination ≤10%). Additionally, 2,113 non-redundant viral operational taxonomic units (vOTUs) were derived from a total of 7632 qualified viral contigs. This dataset provides a valuable resource for improving our understanding of the complex interactions among Prochlorococcus, Synechococcus, and their associated bacteria and viruses in marine ecosystems, offering a foundation to study their ecological roles and evolutionary dynamics.}, }
@article {pmid40221450, year = {2025}, author = {Kim, KS and Noh, J and Kim, BS and Koh, H and Lee, DW}, title = {Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {57}, pmid = {40221450}, issn = {2055-5008}, support = {RS-2021-NR056579//National Research Foundation of Korea (NRF)/ ; RS-2023-KH141436//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; 200118770//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; Colitis, Ulcerative/microbiology ; DNA, Bacterial/genetics ; Republic of Korea ; Phylogeny ; Feces/microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; }, abstract = {Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition and functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for gut microbiome analysis compared to the merging approach across various regions of the 16S rRNA gene. We assessed this approach in both mock communities and Korean cohorts with or without ulcerative colitis. Our results indicate that using the direct joining method for the V1-V3 or V6-V8 regions improves taxonomic resolution compared to merging paired-end reads (ME) in post-sequencing data. While predicting microbial function based on 16S rRNA sequencing has inherent limitations, integrating sequencing reads from both the V1-V3 and V6-V8 regions enhanced functional predictions. This was confirmed by whole metagenome sequencing (WMS) of Korean cohorts, where our approach improved taxa detection that was lost using the ME method. Thus, we propose that the integrated dual 16S rRNA sequencing technique serves as a valuable tool for microbiome research by bridging the gap between amplicon sequencing and WMS.}, }
@article {pmid40220806, year = {2025}, author = {Ye, G and Li, M and Huang, H and Avellán-Llaguno, RD and Chen, J and Chen, G and Huang, Q}, title = {Polystyrene microplastic exposure induces selective accumulation of antibiotic resistance genes in gut microbiota and its potential health risks.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {142983}, doi = {10.1016/j.ijbiomac.2025.142983}, pmid = {40220806}, issn = {1879-0003}, abstract = {As emerging pollutants, antibiotic resistance genes (ARGs) and microplastics threaten the environment and human health. Gut microbiota is a hotspot for ARG emergence and spread. However, effects of microplastic exposure on the emergence and spread of gut microbial ARGs are unclear. Therefore, metagenomics was used to characterize polystyrene microplastics (PS)-induced ARG alterations in rat gut microbiota and their health risks, and to identify key ARG hosts and pathways as intervention targets. We found that PS exposure not only induced selective accumulation of glycopeptide and aminoglycoside ARGs, but also promoted mobility risks of glycopeptide and macrolide-lincosamide-streptogramin ARGs in gut microbiota. Metagenomic reassembly identified microbes belonging to Firmicutes (particularly order Clostridiales, such as speices Lachnospiraceae bacterium 3-1 and MD335) as major ARG hosts. Meanwhile, genera Enterococcus, Clostridioides and Streptococcus were main ARG hosts among human pathogens. Furthermore, glycopeptide and aminoglycoside ARGs were highly correlated with VanS/VanR signaling and its regulatory pathways of vancomycin resistance and peptidoglycan metabolism, amino sugar and nucleotide sugar metabolism, and CpxR signaling and its regulatory remodeling of cell envelope peptidoglycans and proteins in gut microbiota upon PS exposure. This study provides novel insights and intervention targets involved in PS-induced changes in gut microbial ARGs and their health risks.}, }
@article {pmid40220770, year = {2025}, author = {Venkatesan, P}, title = {UK launch metagenomic pathogen surveillance programme.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101143}, doi = {10.1016/j.lanmic.2025.101143}, pmid = {40220770}, issn = {2666-5247}, }
@article {pmid40220715, year = {2025}, author = {Chen, Y and Chen, Z and Liang, L and Li, J and Meng, L and Yuan, W and Xie, B and Zhang, X and Feng, L and Jia, Y and Fu, Z and Su, P and Tong, Z and Zhong, J and Liu, X}, title = {Multi-kingdom gut microbiota dysbiosis is associated with the development of pulmonary arterial hypertension.}, journal = {EBioMedicine}, volume = {115}, number = {}, pages = {105686}, doi = {10.1016/j.ebiom.2025.105686}, pmid = {40220715}, issn = {2352-3964}, abstract = {BACKGROUND: Gut microbiota dysbiosis has been implicated in pulmonary arterial hypertension (PAH). However, the exact roles and underlying mechanisms of multi-kingdom gut microbiota, including bacteria, archaea, and fungi, in PAH remain largely unclear.<br><br>METHODS: The shotgun metagenomics was used to analyse multi-kingdom gut microbial communities in patients with idiopathic PAH (IPAH) and healthy controls. Furthermore, fecal microbiota transplantation (FMT) was performed to transfer gut microbiota from IPAH patients or monocrotaline (MCT)-PAH rats to normal rats and from normal rats to MCT-PAH rats.<br><br>FINDINGS: Gut microbiota analysis revealed substantial alterations in the bacterial, archaeal, and fungal communities in patients with IPAH compared with healthy controls. Notably, FMT from IPAH patients or MCT-PAH rats induced PAH phenotypes in recipient rats. More intriguingly, FMT from normal rats to MCT-PAH rats significantly ameliorated PAH symptoms; restored gut bacteria, archaea, and fungi composition; and shifted the plasma metabolite profiles of MCT-PAH rats toward those of normal rats. In parallel, RNA-sequencing analysis demonstrated the expression of genes involved in key signalling pathways related to PAH. A panel of multi-kingdom markers exhibited superior diagnostic accuracy compared with single-kingdom panels for IPAH.<br><br>INTERPRETATION: Our findings established an association between multi-kingdom gut microbiota dysbiosis and PAH, thereby indicating the therapeutic potential of FMT in PAH. More importantly, apart from gut bacteria, gut archaea and fungi were also significantly associated with PAH pathogenesis, highlighting their indispensable role in PAH.<br><br>FUNDING: This work was supported by Noncommunicable Chronic Diseases-National Science and Technology Major Projects No. 2024ZD0531200, No. 2024ZD0531201 (Research on Prevention and Treatment of Cancer, Cardiovascular and Cerebrovascular Diseases, Respiratory Diseases, and Metabolic Diseases), the National Natural Science Foundation of China of China (No. 82170302, 82370432), Financial Budgeting Project of Beijing Institute of Respiratory Medicine (Ysbz2025004, Ysbz2025007), National clinical key speciality construction project Cardiovascular Surgery, Reform and Development Program of Beijing Institute of Respiratory Medicine (Ggyfz202417, Ggyfz202501), Clinical Research Incubation Program of Beijing Chaoyang Hospital Affiliated to Capital Medical University (CYFH202209).}, }
@article {pmid40220662, year = {2025}, author = {Yuan, Q and Ng, C and Goh, SG and Khor, WC and Ong, GHM and Aung, KT and Gin, KY}, title = {Evaluation of public health impact risks associated with bacterial antimicrobial resistome in tropical coastal environments.}, journal = {Water research}, volume = {282}, number = {}, pages = {123621}, doi = {10.1016/j.watres.2025.123621}, pmid = {40220662}, issn = {1879-2448}, abstract = {This study investigated antimicrobial resistance genes (ARGs) and microbial communities in Singapore's tropical coastal environments, comparing natural marine waters with aquaculture sites using metagenomic analysis. Results show consistently low ARG levels in natural ecosystems, whereas aquaculture sites exhibit elevated ARG concentrations, particularly those relevant to human pathogens, with considerably temporal fluctuations likely driven by human activities and seasonal factors. Additionally, aquaculture sites were found to host mobile genetic elements (MGEs) that may facilitate ARG spread, identifying aquaculture as a key reservoir of resistance genes with potential public health implications. These findings underscore distinct prevalence of ARG between natural and managed marine environments and highlight the need for continued surveillance to monitor ARG dynamics in coastal areas. By elucidating the potential for ARGs to transfer from aquaculture environments to the human food chain, this research emphasizes the importance of sustainable aquaculture practices and proactive ARG management strategies to mitigate antimicrobial resistance risks posed by tropical coastal ecosystem.}, }
@article {pmid40220550, year = {2025}, author = {Silva, CJFD and Silva, CVFD and Cardoso, AM and de Oliveira Santos, E}, title = {Exploring clinical parameters and salivary microbiome profiles associated with metabolic syndrome in a population of Rio de Janeiro, Brazil.}, journal = {Archives of oral biology}, volume = {175}, number = {}, pages = {106251}, doi = {10.1016/j.archoralbio.2025.106251}, pmid = {40220550}, issn = {1879-1506}, abstract = {OBJECTIVES: This study investigates for the first time the association between metabolic syndrome and oral microbial profiles in a population-based sample from Rio de Janeiro, Brazil.<br><br>DESIGN: We assessed 66 volunteers, collecting detailed sociodemographic, anthropometric, and clinical data alongside salivary samples for metagenomic analysis.<br><br>RESULTS: Our findings reveal significant differences in anthropometric parameters, including waist circumference, glycemia, High-Density Lipoprotein (HDL), and triglycerides between the metabolic syndrome and control groups. Increased abundance of Bacteroidetes and Bacteroidia was observed in the metabolic syndrome group, suggesting a potential link between these phyla and metabolic dysregulation. While no significant differences in alpha diversity were found between the overall groups, stratification by body mass index (BMI) indicated that the normal weight subgroup without Metabolic Syndrome exhibited notable variations compared to overweight and obese individuals.<br><br>CONCLUSIONS: This study identifies specific shifts in oral microbiota composition that are associated with metabolic syndrome, highlighting their potential as microbial biomarkers for this condition. These findings suggest a link between oral dysbiosis and metabolic dysregulation, providing new insights into the pathophysiology of metabolic syndrome. Additionally, the results pave the way for the development of non-invasive diagnostics tools and targeted therapies that leverage the oral microbiome's role in systemic health.}, }
@article {pmid40220395, year = {2025}, author = {Zhu, Y and Zhang, X and Tao, W and Yang, S and Qi, H and Zhou, Q and Su, W and Zhang, Y and Dong, Y and Gan, Y and Lei, C and Zhang, A}, title = {Mitigating the risk of antibiotic resistance and pathogenic bacteria in swine waste: The role of ectopic fermentation beds.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138221}, doi = {10.1016/j.jhazmat.2025.138221}, pmid = {40220395}, issn = {1873-3336}, abstract = {The ectopic fermentation bed (EFB) is used to recycle animal waste, but the fate and dynamic change of antibiotic resistance genes (ARGs) with biocide or heavy metal resistance genes (B/MRGs) and pathogens remain unclear. We performed metagenomic sequencing on 129 samples to study the resistome and bacteriome in pig feces from 24 farms, comparing these profiles with EFBs from five farms, and one farm's EFB was monitored for 154 days. Results showed pig feces from different cities (Chengdu, Meishan, and Chongqing) shared 284 of 311 ARG subtypes, with over 70 % being high-risk ARGs, and 106 of 114 pathogenic bacteria. Swine farms were heavily contaminated with co-occurrences of risky ARGs, B/MRGs, and pathogenic hosts, particularly Escherichia coli and Streptococcus suis being hosts of multidrug ARGs. The application of EFBs markedly mitigated these risks in feces, showing a 3.09-fold decrease in high-risk ARGs, a 72.22 % reduction in B/MRGs, a 3.95-fold drop in prioritized pathogens, an 89.09 % decline in the relative abundance of pig pathogens, and a simplification of their correlation networks and co-occurrence patterns. A mantel analysis revealed that metal contents (Fe, Mn, and Cu) and time influenced pathogen and ARG profiles. Pathogens, ARGs, and risk ARGs exhibited periodic variations, peaking at days 14, 84, and 154, with 70-day intervals. This study provides a comprehensive assessment of the risks associated with pig feces and EFBs and demonstrates that EFBs reduce ARG risks by inhibiting their associations with B/MRGs and pathogens. These findings can help guide and improve the management of antimicrobial resistance and pathogenic contaminants in EFB applications to reduce environmental pollution.}, }
@article {pmid40219113, year = {2025}, author = {Vinskienė, J and Tamošiūnė, I and Andriūnaitė, E and Gelvonauskienė, D and Rugienius, R and Hakim, MF and Stanys, V and Buzaitė, O and Baniulis, D}, title = {Inoculum of Endophytic Bacillus spp. Stimulates Growth of Ex Vitro Acclimatised Apple Plantlets.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/plants14071045}, pmid = {40219113}, issn = {2223-7747}, support = {S-MIP-22-54//Lietuvos Mokslo Taryba/ ; }, abstract = {In vitro shoot culture and cryopreservation (CP) are techniques essential for the ex situ preservation of genetic resources and the production of plant propagation material of clonally propagated horticultural crops. Changes in plant-associated microbiota diversity and composition induced by in vitro cultivation and CP treatment could have a negative effect on the growth and ex vitro adaptation of the in vitro propagated shoots. Therefore, the aim of the present study was to assess changes in endophytic bacteria diversity in domestic apple tissues induced by in vitro cultivation and CP treatment and to investigate the potential of the bacterial inoculum to improve the rooting and ex vitro acclimatisation of the propagated shoots. Metataxonomic analysis revealed a variation in the endophytic bacteria diversity and taxonomic composition between the field-grown tree dormant bud and the in vitro propagated or CP-treated shoot samples of apple cv. Gala. Whereas Sphingobacteriaceae, Sphingomonadaceae, Pseudomonadaceae, and Beijerinckiaceae families were the most prevalent families in the bud samples, Enterobacteriaceae, Bacillaceae, and Lactobacillaceae were dominant in the in vitro shoots. The bacterial inoculum effect on rooting and ex vitro acclimatisation was assessed using four isolates selected by screening the endophytic isolate collection. Bacillus sp. L3.4, B. toyonensis Nt18, or a combined inoculum resulted in a 21%, 36%, and 59% increase in cumulative root length and a 41%, 46%, and 35% increase in the biomass accumulation of ex vitro acclimatised plantlets, respectively. Root zone microbiota functional diversity analysis implied that growth stimulation was not related to improved nutrient uptake but could involve a pathogen-suppressing effect. The results demonstrate that the application of plant growth-promoting bacteria can potentially improve the performance of the in vitro propagated germplasm.}, }
@article {pmid40219101, year = {2025}, author = {Fouad, N and El-Zayat, EM and Amr, D and El-Khishin, DA and Abd-Elhalim, HM and Hafez, A and Radwan, KH and Hamwieh, A and Tadesse, W}, title = {Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/plants14071033}, pmid = {40219101}, issn = {2223-7747}, abstract = {Salinity is one of the most important abiotic stress factors affecting wheat production. Salt in the soil is a major environmental stressor that can affect the bacterial community in the rhizosphere of wheat. The bacteria in the plant's rhizosphere promote growth and stress tolerance, which vary by variety and location. Nevertheless, the soil harbors some of the most diverse microbial communities, while the rhizosphere selectively recruits according to the needs of plants in a complex harmonic regulation. The microbial composition and diversity under normal and saline conditions were assessed by comparing the rhizosphere of wheat with soil using 16S rRNA gene amplicon sequencing, highlighting the number of operational taxonomic units (OTUs). Taxonomic analyzes showed that the bacterial community was predominantly and characteristically composed of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Fibrobacteres, representing the usual microbial profile for the rhizosphere of wheat. Idiomarinaceae, Rheinheimera, Halomonas, and Pseudomonas (a strain of Proteobacteria), together with Gracilibacillus (a strain of Firmicutes Bacilli), were recognized as microbial signatures for the rhizosphere microbiome under saline conditions. This was observed even with unchanged soil type and genotype. These patterns occurred despite the same soil type and genotype, with salinity being the only variable. The collective action of these bacterial phyla in the rhizosphere not only improves nutrient availability but also induces systemic resistance in the plants. This synergistic effect improves plant resistance to salt stress and supports the development of salt-tolerant wheat varieties. These microbial signatures could improve our understanding of plant-microbe interactions and support the development of microbiome-based solutions for salt stress.}, }
@article {pmid40218354, year = {2025}, author = {Zhu, F and Ma, J and Xue, M and Xu, W and Liu, W and Zhou, Y and Liu, M and Fan, Y}, title = {Seasonal and Regional Dynamics of the Intestinal Microbiota in Schizothorax nukiangensis from the Nujiang River.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/ani15070961}, pmid = {40218354}, issn = {2076-2615}, support = {2023TD46, 2023TD09//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences (CAFS)/ ; }, abstract = {The dynamic alterations in intestinal microbiota can provide insights into the adaptive relationships between these microorganisms and their hosts in response to environmental changes. Schizothorax nukiangensis is widely distributed throughout the Nujiang River and exhibits numerous unique adaptations. In this study, we collected samples of S. nukiangensis across different seasons and regions within the Nujiang River to comprehensively elucidate the diversity and composition of its intestinal microbiota using metagenomic technology. The results indicated that Firmicutes and Proteobacteria predominated at the phylum level, while Priestia, Bacillus, and Aeromonas were the most abundant genera identified. Notably, the relative abundance of these microorganisms varied significantly across different seasons and regions. From autumn through spring and into summer, the predominant microorganisms shifted from Firmicutes to Proteobacteria. Biomarker analysis revealed that Firmicutes (including the class bacilli and the genera Priestia and Bacillus) exhibited a higher relative abundance within the upstream group, where categories related to amino acid metabolism and carbohydrate metabolism were significantly enriched. Conversely, Proteobacteria (including several potential pathogens, such as Saezia, Pantoea, Lelliotia, and Aeromonas genera) showed an increased relative abundance within downstream groups, where disease-related categories exhibited significant enrichment. Our findings significantly enhance our understanding of how S. nukiangensis adapts to its environment, providing valuable data support for the conservation of S. nukiangensis and for ecological security assessment of the Nujiang River.}, }
@article {pmid40218343, year = {2025}, author = {Ajmi, N and Duman, M and Coskun, B and Esen, C and Sonmez, O and Tasci, G and Coskuner-Weber, O and Ay, H and Yoyen-Ermis, D and Yibar, A and Desbois, AP and Saticioglu, IB}, title = {Unraveling Genomic and Pathogenic Features of Aeromonas ichthyocola sp. nov., Aeromonas mytilicola sp. nov., and Aeromonas mytilicola subsp. aquatica subsp. nov.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/ani15070948}, pmid = {40218343}, issn = {2076-2615}, support = {TGA-2024-1797 and 124Z735//The Research Fund of Bursa Uludag University and T&#xdc;B&#x130;TAK/ ; }, abstract = {The Gram-negative genus Aeromonas contains diverse bacterial species that are prevalent in aquatic environments. This present study describes three novel Aeromonas strains: A. ichthyocola sp. nov. A-5[T] and A. mytilicola subsp. aquatica subsp. nov. A-8[T] isolated from rainbow trout (Oncorhynchus mykiss), and A. mytilicola sp. nov. A-7[T] isolated from mussels (Mytilus galloprovincialis), respectively. Genomic analyses revealed that strains A-5[T] and A-7[T] shared the highest 16S rRNA gene sequence similarity with A. rivipollensis P2G1[T] (99.7% and 99.8%, respectively), while strain A-8[T] exhibited 99.7% identity with A. media RM[T]. Together with morphological, physiological, and biochemical data, genome-based analyses provided additional evidence for species differentiation. Digital DNA-DNA hybridization (dDDH; 56.8-65.9%) and average nucleotide identity (ANI; 94.2-95.7%) values fell below the species delineation thresholds, confirming that these isolates represent distinct taxa. Pathogenicity assays using greater wax moth (Galleria mellonella) larvae demonstrated strain-specific virulence profiles. Further genomic analyses identified biosynthetic gene clusters for nonribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs), which often have roles in secondary metabolite production. Ecological analyses, based on genomic comparisons and metagenomic database searches, revealed the adaptability of the strains to diverse habitats, including freshwater, wastewater, and activated sludge. Based on the genetic and phenotypic data, the novel taxa Aeromonas ichthyocola sp. nov. A-5ᵀ (LMG 33534ᵀ = DSM 117488ᵀ), Aeromonas mytilicola sp. nov. A-7ᵀ (LMG 33536ᵀ = DSM 117490ᵀ), and Aeromonas mytilicola subsp. aquatica subsp. nov. A-8ᵀ (LMG 33537ᵀ = DSM 117493ᵀ) are proposed.}, }
@article {pmid40217586, year = {2025}, author = {Komoróczy, B and Váncsa, S and Váradi, A and Hegyi, P and Vágási, V and Baradács, I and Szabó, A and Nyirády, P and Benkő, Z and Ács, N}, title = {Optimal Aspirin Dosage for the Prevention of Preeclampsia and Other Adverse Pregnancy Outcomes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.}, journal = {Journal of clinical medicine}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/jcm14072134}, pmid = {40217586}, issn = {2077-0383}, abstract = {Background/Objectives: This systematic review and meta-analysis aimed to determine the effectiveness of different aspirin dosages in preventing preeclampsia and its effect on other pregnancy-associated conditions. Methods: A comprehensive search of three databases (Pubmed, Embase, and Cochrane Library) was conducted for randomized controlled trials without time interval criteria, comparing aspirin at various doses with placebo or no specific preeclampsia prophylaxis. Eligible randomized controlled trials (RCTs) examined pregnant women receiving aspirin at any dose and time during their pregnancy, while the control group received a placebo, or placebo and a different dose of aspirin, or no specific preeclampsia prevention. No exclusion criteria were established regarding the population, study size, study site, or length of aspirin prophylaxis. Studies examining additional preventive medication (such as low-molecular-weight heparin) compared to aspirin without a placebo group were excluded. For all outcomes, the risk ratios (RRs) and mean differences (MDs) with 95% confidence intervals (CIs) were calculated. Meta-regression was performed to examine the relation between aspirin dosage and preeclampsia. Results: Based on the analysis of 31 studies involving 28,318 pregnancies and 20 studies involving 26,551 pregnancies, the early initiation of aspirin significantly reduced the overall incidence of preeclampsia (RR = 0.63, CI: 0.47-0.84) and perinatal death risk (RR = 0.82, CI: 0.72-0.93), respectively. Based on our meta-regression model, we could not establish a dose-dependent correlation between aspirin dosage and the risk of preeclampsia. Conclusions: Early-initiated aspirin prophylaxis is effective in preventing preeclampsia, without raising the incidence of placental abruption or increasing the amount of peripartum bleeding. No specific dose was superior to others; thus, further research should explore higher doses and focus on preterm preeclampsia, maternal-fetal complications, and bleeding.}, }
@article {pmid40217292, year = {2025}, author = {Diop, K and Mbaye, B and Nili, S and Filin, A and Benlaifaoui, M and Malo, J and Renaud, AS and Belkaid, W and Hunter, S and Messaoudene, M and Lee, KA and Elkrief, A and Routy, B}, title = {Coupling culturomics and metagenomics sequencing to characterize the gut microbiome of patients with cancer treated with immune checkpoint inhibitors.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {21}, pmid = {40217292}, issn = {1757-4749}, abstract = {BACKGROUND: The gut microbiome represents a novel biomarker for melanoma and non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICI). Gut microbiome metagenomics profiling studies of patients treated with immunotherapy identified bacteria associated with ICI efficacy, while others have been linked to resistance. However, limitations of metagenomics sequencing, such as complex bioinformatic processing requirements, necessity of a threshold for positive detection, and the inability to detect live organisms, have hindered our ability to fully characterize the gut microbiome. Therefore, combining metagenomics with high-throughput culture-based techniques (culturomics) represents an ideal strategy to fully characterize microbiome composition to more robustly position the microbiome as a biomarker of response to ICI.<br><br>METHODS: We performed culturomics using fecal samples from 22 patients from two academic centres in Canada and the United Kingdom with NSCLC and cutaneous melanoma treated with ICI (cancer group), comparing their microbiome composition to that of 7 healthy volunteers (HV), along with matching shotgun metagenomics sequencing.<br><br>RESULTS: For culturomics results, 221 distinct species were isolated. Among these 221 distinct species, 182 were identified in the cancer group and 110 in the HV group. In the HV group, the mean species richness was higher compared to the cancer group (34 vs. 18, respectively, p&#x2009;=&#x2009;0.002). Beta diversity revealed separate clusters between groups (p&#x2009;=&#x2009;0.004). Bifidobacterium spp. and Bacteroides spp. were enriched in HV, while cancer patients showed an overrepresentation of Enterocloster species, as well as Veillonella parvula. Next, comparing cancer patients' clinical outcomes to ICI, we observed that among the 20 most abundant bacteria present in non-responder patients, 2 belonged to the genus Enterocloster, along with an enrichment of Hungatella hathewayi and Cutibacterium acnes. In contrast, responders to ICI exhibited a predominance of Bacteroides spp. In NSCLC patients, metagenomics analysis revealed that of the 154 bacteria species isolated through culturomics, 61/154 (39%) were also identified by metagenomics sequencing. Importantly, 94 individual species were uniquely detected by culturomics.<br><br>CONCLUSION: These findings highlight that culturomics and metagenomics can serve as complementary tools to characterize the microbiome in patients with cancer. This integrated approach uncovers specific microbiome signatures that differentiate HV from cancer patients, and identifies specific species associated with therapy response and resistance.}, }
@article {pmid40216789, year = {2025}, author = {Shekarriz, S and Szamosi, JC and Whelan, FJ and Lau, JT and Libertucci, J and Rossi, L and Fontes, ME and Wolfe, M and Lee, CH and Moayyedi, P and Surette, MG}, title = {Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3469}, pmid = {40216789}, issn = {2041-1723}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Metagenomics/methods ; *Colitis, Ulcerative/therapy/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Placebos ; Adult ; Middle Aged ; }, abstract = {Fecal microbiota transplantation (FMT) has shown efficacy for the treatment of ulcerative colitis but with variable response between patients and trials. The mechanisms underlying FMT's therapeutic effects remains poorly understood but is generally assumed to involve engraftment of donor microbiota into the recipient's microbiome. Reports of microbial engraftment following FMT have been inconsistent between studies. Here, we investigate microbial engraftment in a previous randomized controlled trial (NCT01545908), in which FMT was sourced from a single donor, using amplicon-based profiling, shotgun metagenomics, and culture-enriched metagenomics. Placebo samples were included to estimate engraftment noise, and a significant level of false-positive engraftment was observed which confounds the prediction of true engraftment. We show that analyzing engraftment across multiple patients from a single donor enhances the accuracy of detection. We identified a unique set of genes engrafted in responders to FMT which supports strain displacement as the primary mechanism of engraftment in our cohort.}, }
@article {pmid40216686, year = {2025}, author = {Fan, Q and Zhang, Y and Lian, J and Liang, D and Yu, J and Liu, X and Zhang, N}, title = {Screening and community succession and functional prediction of high-efficiency degradation microbial communities for rice straw at low-temperature.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {2}, pages = {20}, pmid = {40216686}, issn = {1433-4909}, support = {2023YFD2100803//National Key R&amp;D Programme Project of China/ ; }, mesh = {*Oryza/microbiology/metabolism ; *Microbiota ; *Cold Temperature ; Lignin/metabolism ; }, abstract = {Traditional straw return relies on microbial degradation, but cold winters delay it, risking crops. Therefore, a microbial community adapted to rice straw degradation in cold regions was constructed by restrictive consecutively sub-cultured under low-temperature limitations. The capabilities of the microbial community, such as adaptability, stability, and degradation power, were evaluated by analyzing straw degradation features, Characterization experiments and lignocellulose enzyme activities across multiple generations. 16S amplicon sequencing was used to monitor the changes in its structure over generations. Metagenomic sequencing uses CAZy and KEGG to classify gene functions. The results showed that the highest degradation efficiencies and enzyme activities were observed in the E and F generations, dominated by Proteobacteria, Bacteroidetes, and Fungi The stable microbial community was designated as LJ-7. Metagenomic analysis showed that functional genes of LJ-7 were mainly concentrated in glycoside hydrolase (GHs) and glycosyl transferase (GTs) related genes which contained many fiber and lignin-degrading enzyme genes. It is speculated that microbial enzymes degrade straw by breaking down its complex structure into monosaccharides or metabolizing quinone compounds for energy. This experiment successfully screened a microbial community capable of degrading rice straw at low temperatures, thus offering novel research insights and pathways for straw degradation in cold conditions.}, }
@article {pmid40216167, year = {2025}, author = {Sangfuang, N and Xie, Y and McCoubrey, LE and Taub, M and Favaron, A and Mai, Y and Gaisford, S and Basit, AW}, title = {Investigating the bidirectional interactions between senotherepeutic agents and human gut microbiota.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {}, number = {}, pages = {107098}, doi = {10.1016/j.ejps.2025.107098}, pmid = {40216167}, issn = {1879-0720}, abstract = {Biological ageing is a time-dependent process that has implications for health and disease. Cellular senescence is a key driver in ageing and age-related diseases. Senotherapeutic agents have been shown to slow biological ageing by eliminating senescent mammalian cells. Given the increasing awareness of the gut microbiome in regulating human health, this study aimed to investigate the effects of senotherapeutic agents as pharmacological interventions on the human gut microbiota. In this study, the bidirectional effects of four senotherapeutic agents, quercetin, fisetin, dasatinib, and sirolimus, with the gut microbiota sourced from healthy human donors were investigated. The results revealed that quercetin was completely biotransformed by the gut microbiota within six hours, while dasatinib was the most stable of the four compounds. Additionally, metagenomic analysis confirmed that all four compounds increased the abundance of bacterial species associated with healthy ageing (e.g., Bacteroides fragilis, Bifidobacterium longum, and Veillonella parvula), and decreased the abundance of pathogenic bacteria primarily associated with age-related diseases (e.g., Enterococcus faecalis and Streptococcus spp.). The findings from this study provide a comprehensive understanding of the pharmacobiomics of senotherapeutic interventions, highlighting the potential of microbiome-targeted senolytics in promoting healthy ageing.}, }
@article {pmid40216056, year = {2025}, author = {Liu, S and Li, J and Zhang, Z and Tuo, J and Zhang, Q and Zhou, J and Liu, P and Zhang, XX}, title = {Exploring phylogenetic diversity of antibiotic resistance genes in activated sludge: A host and genomic location perspective.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121588}, doi = {10.1016/j.envres.2025.121588}, pmid = {40216056}, issn = {1096-0953}, abstract = {Antibiotic resistance has emerged as a significant global public health issue. The environmental behaviors of antibiotic resistance genes (ARGs), such as their persistence and horizontal transfer, have been extensively investigated. However, the genetic diversity characteristics of ARGs remain underexplored, which limits a comprehensive analysis of their roles in the environment. In this study, we examined the genetic diversity of ARGs in activated sludge from 44 wastewater treatment plants in five countries. Most ARGs detected in activated sludge possessed multiple variants, with a median of 48. The number of variants of gd-ARGs varied among different resistance mechanisms and ARG types. The number of potential variants of ARGs was strongly correlated with host diversity. Pseudomonas spp. and Klebsiella pneumoniae, identified as pathogenic bacteria, harbored multiple ARGs and had the most variants. Most ARG subtypes on plasmids and chromosomes showed divergent evolution. Molecular docking of AdeH proteins revealed that genomic location affects tetracycline binding energy. The findings underscore the intricate interplay between genetic variation and environmental adaptation in ARGs, offering a novel perspective on the spread of antibiotic resistance.}, }
@article {pmid40215877, year = {2025}, author = {Saeed, M and Al-Khalaifah, H and Al-Nasser, A and Al-Surrayai, T}, title = {Feeding the future: A new potential nutritional impact of Lactiplantibacillus plantarum and its promising interventions in future for poultry industry.}, journal = {Poultry science}, volume = {104}, number = {6}, pages = {105130}, doi = {10.1016/j.psj.2025.105130}, pmid = {40215877}, issn = {1525-3171}, abstract = {The increasing demand for sustainable and efficient chicken production has intensified the interest in functional feed additives such as probiotics. Lactiplantibacillus plantarum (formerly known as Lactobacillus plantarum) is an important probiotic bacterium that has become an essential component in poultry nutrition owing to its diverse advantages. This bacterium improves gut health by regulating the intestinal microbiota, increasing food absorption, and strengthening the immune system. It also alleviates the detrimental impacts of pathogenic bacteria, thereby reducing the reliance on antibiotics and promoting antibiotic-free poultry production. Additionally, Lactobacillus plantarum enhances growth performance, feed conversion efficiency, and total flock productivity. Adding Lactobacillus plantarum to chicken feed helps the gut microbiota by encouraging good bacterial communities (e.g., Eubacterium, Faecalibacterium, Ligilactobacillus, Limosilactobacillus, Blautia and Clostridium). This leads to increased growth in chickens and helps maintain the balance of their gut flora. Lactobacillus plantarum has been extensively investigated as a potential feed additive to replace in-feed antibiotics. Published literature have revealed that a dietary additive of Lactobacillus plantarum improved the health and growth of broilers by improving the balance of bacteria and the metabolism of nutrients in the gut. This study explores the incorporation of Lactobacillus plantarum into poultry diets and its importance in sustainable and healthy poultry production. This study will encourage poultry scientists to investigate further before encapsulation. Innovations in Lactiplantibacillus plantarum, including its intestine colonization methods and novel strategies to improve its colonization, have the potential to transform the industry. Rapid development of tools and techniques (microencapsulated, nanotechnology, metagenomics, and transcriptome for L. plantarum) could help cover research and application shortages.}, }
@article {pmid40215446, year = {2025}, author = {Allioni, GA and de Souza, GSM and Labello, JH and Torres, GSA and da Costa, DL and Casal, YR and Duarte-Neto, AN and Dorlass, EG and Amgarten, D and Malta, FM and Doi, AM and Peres Fernandes, GB and Rebello Pinho, JR and Vieira, GT and Castro, LH and Guedes, BF}, title = {Chronic Dengue Virus Encephalitis: A Case Study and Metagenomic Analysis.}, journal = {Neurology(R) neuroimmunology &amp; neuroinflammation}, volume = {12}, number = {3}, pages = {e200394}, doi = {10.1212/NXI.0000000000200394}, pmid = {40215446}, issn = {2332-7812}, mesh = {Humans ; Male ; *Dengue/complications/diagnosis ; Young Adult ; Metagenomics ; *Dengue Virus/genetics ; *Encephalitis, Viral/virology/pathology/diagnosis/complications ; Chronic Disease ; }, abstract = {BACKGROUND AND OBJECTIVES: Dengue virus (DENV) infection can cause acute encephalitis. Chronic encephalitis with progressive dementia is rarely reported.<br><br>METHODS: We present a case of chronic encephalitis with rapidly progressive dementia, in which a potential DENV brain infection was identified with brain tissue metagenomic next-generation sequencing. Brain pathology and molecular diagnosis are also presented.<br><br>RESULTS: A 20-year-old man from SP, Brazil, presented with rapidly progressive dementia, speech apraxia, and apathy in June 2022. By January 2023, cognitive testing showed severe global impairment (MMSE score of 18/30). MRI revealed white matter abnormalities and atrophy; CSF analysis disclosed a mild lymphocytic pleocytosis, mildly elevated protein levels, and positive CSF oligoclonal bands. Despite extensive testing ruling out common infectious and inflammatory causes, the patient's condition worsened with executive dysfunction, language impairment, tremors, and myoclonus. In August 2023, a brain biopsy and next-generation sequencing identified DENV-1 genotype V, linked to Brazilian sequences from 2000 to 2022.<br><br>DISCUSSION: This case highlights a challenging instance of encephalitis with unknown etiology, where metagenomic analysis detected DENV-1 RNA in brain tissue, suggesting a possible cause.}, }
@article {pmid40215391, year = {2025}, author = {Gómez, &#xc1; and Rodríguez-Largo, A and Pérez, E and García Freire, S and Hundehege, C and Berberich, E and Luján, L and Cortés, D}, title = {Clinicopathological progression and molecular characterization of intestinal dilatation syndrome in commercial brown layers.}, journal = {Veterinary pathology}, volume = {}, number = {}, pages = {3009858251331106}, doi = {10.1177/03009858251331106}, pmid = {40215391}, issn = {1544-2217}, abstract = {Intestinal dilatation syndrome (IDS) is a poorly described condition affecting layers and breeder hens globally. Its prevalence is increasing, particularly in free-range systems, but the cause remains unknown. This retrospective study examined 35 hens from 3 flocks: free-range flock A (n = 20) and enriched-caged flock B (n = 5), both affected by IDS, and enriched-caged flock C (n = 10), with no history of IDS. Clinicopathological studies were performed on these hens, and metagenomic analysis was conducted on the proventriculus and jejunum of hens from flock A (n = 2) and flock C (n = 2). Based on clinical signs and lesions, 3 progressive stages of IDS were identified. In the first stage, although hens were without clinical signs, proventricular dilatation and lymphoplasmacytic and heterophilic jejunitis and duodenitis were observed. The second stage was marked by cachexia, pale and small combs and wattles, and severe egg production drop. Jejunal dilatation was observed, with microscopic evidence of necrotic, lymphoplasmacytic and heterophilic jejunitis; ganglioneuritis; and mineralization of the jejunal nervous plexuses and subserosal ganglia. In the third stage, spontaneous death occurred due to jejunal volvulus and vascular involvement. Affected hens (stage 2) also exhibited elevated cloacal temperatures (>0.9°C) and marked heterophilia. Metagenomic analysis identified sequences consistent with Megrivirus C in IDS-affected hens and a disruption of the gut microbiota, with increased abundance of Fusobacterium mortiferum and Megamonas funiformis. In conclusion, this study describes in detail the clinicopathological progression of the IDS and suggests that Megrivirus C, in combination with opportunistic intestinal bacteria, could play a role in the pathogenesis of this disease.}, }
@article {pmid40214404, year = {2025}, author = {Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Snipen, LG and Sundt, M&#xd8; and Rudi, K}, title = {Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12464}, pmid = {40214404}, issn = {1520-5851}, abstract = {Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.}, }
@article {pmid40214102, year = {2025}, author = {Cernooka, E and Zrelovs, N and Kazaks, A}, title = {C-terminal anchor endolysins-proposing a third class of tailed bacteriophage endolysins.}, journal = {FEBS letters}, volume = {}, number = {}, pages = {}, doi = {10.1002/1873-3468.70042}, pmid = {40214102}, issn = {1873-3468}, support = {lzp-2021/1-0050//Latvijas Zin&#x101;tnes Padome/ ; }, abstract = {Endolysins-enzymes produced by tailed bacteriophages to degrade bacterial cell walls-have traditionally been classified as canonical or signal-anchor-release (SAR) endolysins. However, analysis of expanding viral (meta)genomic data has revealed a third class, which we designate as C-terminal anchor (CTA) endolysins. These enzymes feature an N-terminal enzymatic domain, a C-terminal transmembrane domain, and typically lack signal sequences, distinguishing them from SAR endolysins. CTA endolysins span all known enzymatic activities and exhibit diverse architectures, though most have a single transmembrane helix and an N-out, C-in topology, consistent with periplasmic activity. While their functional mechanisms remain to be elucidated, our findings suggest that CTA endolysins are nearly as prevalent as SAR endolysins and represent a distinct, previously unrecognized branch of the endolysin world.}, }
@article {pmid40213331, year = {2025}, author = {Wang, X and Zhao, Z and Zhao, F and Li, Y and Liang, Y and Zhou, R and Shen, S and Yu, J and Liu, W and Menghe, B}, title = {Dual-omics strategy for selecting optimal fermentation strains in traditional koumiss production.}, journal = {Food chemistry: X}, volume = {27}, number = {}, pages = {102407}, pmid = {40213331}, issn = {2590-1575}, abstract = {Koumiss is a fermented mare's milk beverage with a long history. However, due to the current lack of specialized starters, the product quality is unstable. Therefore, we used dual-omics combined with pure culture technology to screen out strains with excellent fermentation performance for koumiss. The results showed that: (1) The dominant species in koumiss were mainly Lactobacillus and Lactococcus, and metabolites such as arachidonic acid and ascorbic acid were significantly enriched in koumiss. (2) There was a significant correlation between specific microbial species and metabolites. (3) Through preliminary screening using experiments such as milk-based curdling experiments and acid resistance tests, and then rescreening through fermentation tests, five strains with excellent fermentation characteristics were screened out. They are Lacticaseibacillus paracasei SXM-5, Lactobacillus kefianofaciens MGE42-8, Lactobacillus helveticus CFS12-11-1, Saccharomyces cerevisiae PFD-2, and Kluyveromyces marxianus PYM-1. The screened strains supply microbial resources for koumiss products and boost the development of milk beverages.}, }
@article {pmid40212922, year = {2025}, author = {Wang, C and Li, C and You, F and Zhou, Y and Tu, G and Liu, R and Yi, P and Wu, X and Nie, H}, title = {Multi-Omics Analysis of Gut Microbiome and Host Metabolism in Different Populations of Chinese Alligators (alligator sinensis) During Various Reintroduction Phases.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71221}, pmid = {40212922}, issn = {2045-7758}, abstract = {Reintroduction plays a significant role in the self-maintenance and reconstruction of wild animal populations, serving as a communication bridge between captive and wild animals. The Chinese alligator (Alligator sinensis) is a distinct and endangered reptile species found in China. The mechanisms by which artificially bred Chinese alligators adapt following their release into the wild remain poorly understood. This study aims to elucidate the alterations in gut microbiomes and metabolic phenotypes of Chinese alligators during their reintroduction. During the Chinese alligator's reintroduction, Fusobacterium and Cetobacterium became more abundant, while typical pathogens declined significantly. The gut type of the Chinese alligator changed from Acinetobacter to Cetobacterium. The construction of the gut microbial community was dominated by neutral (random) processes and shifted towards deterministic processes with the progression of reintroduction. In terms of species function, reintroduction significantly upregulated the expression of host immune-related genes and significantly decreased the expression of gut bacterial pathogenic genes and antibiotic resistance genes. Metagenomic and metabolomic KEGG enrichment analyses indicate that glucoside hydrolase families 13 and 23-alongside glycolysis and gluconeogenesis pathways-may play pivotal roles in energy metabolism, host-pathogen interactions, and homeostasis maintenance for Chinese alligators. Differential metabolite analysis identified significant upregulation of metabolites related to neuroendocrine immune modulation and significant down-regulation of anti-inflammatory metabolites during Chinese alligator reintroduction. Association analysis showed that there were significant co-metabolic effects between microorganisms and metabolites, which coordinated host adaptive interaction. This study provides insights into the synergistic mechanisms of host adaptation and wild environment adaptation for Chinese alligators.}, }
@article {pmid40212663, year = {2025}, author = {Natasha, A and Pye, SE and Park, K and Rajoriya, S and Yang, I and Park, J and Pangestu, HS and Kim, J and Oh, Y and López, CB and Song, JW and Kim, WK}, title = {Detection and characterization of Langya virus in Crocidura lasiura (the Ussuri white-toothed shrew), Republic of Korea.}, journal = {One health (Amsterdam, Netherlands)}, volume = {20}, number = {}, pages = {101017}, pmid = {40212663}, issn = {2352-7714}, abstract = {Langya virus (LayV) is the only documented zoonotic agent within the shrew borne Parahenipavirus genus. Other Parahenipavirus species, including Gamak virus and Daeryeong virus, have been discovered in the Republic of Korea, highlighting the prevalence of this genus in the region. We retrospectively analyzed metagenomic next-generation sequencing of two Crocidura lasiura (the Ussuri white-toothed shrew) kidney samples from 2017, followed by paramyxovirus screening of 24 kidney samples from the same species collected in 2023. The LayV positivity rate was 12.5 % (3 of 24). Amplicon-based sequencing was subsequently developed to obtain the complete viral sequences. Five complete genomes of Langya virus Korea (LayV KOR) were identified: two from 2017 samples and three from 2023 samples. LayV KOR exhibited approximately 80 % and 95.5 % homology at the nucleotide and amino acid levels, respectively. Phylogenetic analysis underscored the close relationship between LayV KOR and LayV from China. This study represents the first detection of LayV complete sequences in shrews outside of China.}, }
@article {pmid40212081, year = {2024}, author = {Tuerhongjiang, G and Guo, M and Qiao, X and Liu, J and Xi, W and Wei, Y and Liu, P and Lou, B and Wang, C and Sun, L and Yuan, X and Liu, H and Xiong, Y and Ma, Y and Li, H and Zhou, B and Li, L and Yuan, Z and Wu, Y and She, J}, title = {Gut Microbiota Regulate Saturated Free Fatty Acid Metabolism in Heart Failure.}, journal = {Small science}, volume = {4}, number = {9}, pages = {2300337}, pmid = {40212081}, issn = {2688-4046}, abstract = {AIMS: Heart failure (HF) is associated with profound changes in cardiac metabolism. At present, there is still a lack of relevant research to explore the key microbiome and their metabolites affecting the progression of HF. Herein, the interaction of gut microbiota and circulating free fatty acid (FFA) in HF patients and mice is investigated.<br><br>METHODS AND RESULTS: In HF patients, by applying metagenomics analysis and targeted FFA metabolomics, enriched abundance of Clostridium sporogenes (C.sp) in early and late stage of HF patients, which negatively correlated to saturated free fatty acid (SFA) levels, is identified. KEGG analysis further indicates microbiota gene enrichment in FFA degradation in early HF, and decreased gene expression in FFA synthesis in late HF. In HF mice (C57BL/6J) induced by isoproterenol (ISO), impaired intestinal permeability is observed, and decreased fecal C.sp and increased SFA are further validated. At last, by supplementing C.sp to ISO-induced HF mice, the cardiac function, fibrosis, and myocardial size are partially rescued, together with decreased circulating SFA levels.<br><br>CONCLUSIONS: Clostridium abundance is increased in HF, compensating cardiac function deterioration via downregulation of circulating SFA levels. The results demonstrate that the gut microbiota-SFA axis plays an important role in HF protection, which may provide a strategic advantage for the probiotic therapy development in HF.}, }
@article {pmid40211978, year = {2025}, author = {Duan, C and Zang, Z and Xu, Y and He, H and Li, S and Liu, Z and Lei, Z and Zheng, JS and Li, SZ}, title = {FGeneBERT: function-driven pre-trained gene language model for metagenomics.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf149}, pmid = {40211978}, issn = {1477-4054}, support = {2022ZD0115101//National Science and Technology Major Project/ ; U21A20427//National Natural Science Foundation of China Project/ ; WU2023C019//Center of Synthetic Biology and Integrated Bioengineering of Westlake University/ ; //Westlake University Industries of the Future Research Funding/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Models, Genetic ; Metagenome ; Algorithms ; }, abstract = {Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the capture of structurally and functionally relevant gene contexts. Moreover, these approaches struggle with encoding biologically meaningful genes and fail to address the one-to-many and many-to-one relationships inherent in metagenomic data. To overcome these challenges, we introduce FGeneBERT, a novel metagenomic pre-trained model that employs a protein-based gene representation as a context-aware and structure-relevant tokenizer. FGeneBERT incorporates masked gene modeling to enhance the understanding of inter-gene contextual relationships and triplet enhanced metagenomic contrastive learning to elucidate gene sequence-function relationships. Pre-trained on over 100 million metagenomic sequences, FGeneBERT demonstrates superior performance on metagenomic datasets at four levels, spanning gene, functional, bacterial, and environmental levels and ranging from 1 to 213 k input sequences. Case studies of ATP synthase and gene operons highlight FGeneBERT's capability for functional recognition and its biological relevance in metagenomic research.}, }
@article {pmid40211688, year = {2025}, author = {Ge, SX and Niu, YM and Ren, LL and Zong, SX}, title = {Inheritance or Recruitment? The Assembly Mechanisms and Functional Dynamics of Microbial Communities in the Life Cycle of a Wood-Feeding Beetle.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17751}, doi = {10.1111/mec.17751}, pmid = {40211688}, issn = {1365-294X}, support = {2021YFD1400900//National Key R&amp;D Program of China/ ; }, abstract = {Microbial partners enhance the metabolic capabilities of insects, enabling their adaptation to diverse ecological niches. Xylophagous insects have larvae that can digest lignocellulose and cope with plant secondary metabolites (PSMs). However, there is little information in terms of microbiome sources, dynamics and species contributions. This limits our understanding of the interaction between xylophagous insects and the microbiome. Monochamus saltuarius (Cerambycidae) is a significant borer of conifers. We used combined qPCR, host genomic and microbiome metagenomic datasets, as well as in vitro validation experiments to study the dynamics of the associated microbiome and its interactions with M. saltuarius. We evaluated microbial metabolic/biosynthetic contributions and validated their related functions. Our findings revealed that insect growth and development altered the quantity and community composition of associated bacteria and fungi. The egg microbiome was particularly susceptible to alteration due to oviposition pits. Bacterial transmission largely persisted between developmental stages, while fungal re-acquisition primarily originated from the external environment. By reconstructing community pathway maps, we identified the cooperative interactions between the insect and its gut microbiome. As larvae transitioned from phloem to xylem feeding, the functional role of the gut microbiome in various pathways was weakened. Remarkably, high-contribution bacterial species largely overlapped across different functional roles, and these species also showed considerable overlap between phloem and xylem feeding periods. Overall, our study highlights the unique interaction between xylophagous insects and their microbiome, which enhances their ability in lignocellulose digestion, PSMs degradation and the acquisition of essential amino acids, as well as vitamins.}, }
@article {pmid40211685, year = {2025}, author = {Kim, JW and Choi, EC and Lee, KJ}, title = {Standardizing the approach to clinical-based human microbiome research: from clinical information collection to microbiome profiling and human resource utilization.}, journal = {Osong public health and research perspectives}, volume = {}, number = {}, pages = {}, doi = {10.24171/j.phrp.2024.0319}, pmid = {40211685}, issn = {2210-9099}, abstract = {OBJECTIVES: This study presents the standardized protocols developed by the Clinical-Based Human Microbiome Research and Development Project (cHMP) in the Republic of Korea.<br><br>METHODS: It addresses clinical metadata collection, specimen handling, DNA extraction, sequencing methods, and quality control measures for microbiome research.<br><br>RESULTS: The cHMP involves collecting samples from healthy individuals and patients across various body sites, including the gastrointestinal tract, oral cavity, respiratory system, urogenital tract, and skin. These standardized procedures ensure consistent data quality through controlled specimen collection, storage, transportation, DNA extraction, and sequencing. Sequencing encompasses both amplicon and whole metagenome methods, followed by stringent quality checks. The protocols conform to international guidelines, ensuring that the data generated are both reliable and comparable across microbiome studies.<br><br>CONCLUSION: The cHMP underscores the importance of methodological standardization in enhancing data integrity, reproducibility, and advancing microbiome-based research with potential applications for improving human health outcomes.}, }
@article {pmid40211121, year = {2025}, author = {Polizel, GHG and Diniz, WJS and Cesar, ASM and Ramírez-Zamudio, GD and Cánovas, A and Dias, EFF and Fernandes, AC and Prati, BCT and Furlan, &#xc9; and Pombo, GDV and Santana, MHA}, title = {Impacts of prenatal nutrition on metabolic pathways in beef cattle: an integrative approach using metabolomics and metagenomics.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {359}, pmid = {40211121}, issn = {1471-2164}, support = {2021/03265-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/12105-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Animals ; Cattle ; Female ; *Metabolomics/methods ; Pregnancy ; *Metabolic Networks and Pathways ; *Metagenomics/methods ; Male ; Metabolome ; Rumen/microbiology ; Microbiota ; *Prenatal Nutritional Physiological Phenomena ; *Animal Nutritional Physiological Phenomena ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: This study assessed the long-term metabolic effects of prenatal nutrition in Nelore bulls through an integrated analysis of metabolome and microbiome data to elucidate the interconnected host-microbe metabolic pathways. To this end, a total of 126 cows were assigned to three supplementation strategies during pregnancy: NP (control)- only mineral supplementation; PP- protein-energy supplementation during the last trimester; and FP- protein-energy supplementation throughout pregnancy. At the end of the finishing phase, blood, fecal, and ruminal fluid samples were collected from 63 male offspring. The plasma underwent targeted metabolomics analysis, and fecal and ruminal fluid samples were used to perform 16 S rRNA gene sequencing. Metabolite and ASV (amplicon sequence variant) co-abundance networks were constructed for each treatment using the weighted gene correlation network analysis (WGCNA) framework. Significant modules (p ≤ 0.1) were selected for over-representation analyses to assess the metabolic pathways underlying the metabolome (MetaboAnalyst 6.0) and the microbiome (MicrobiomeProfiler). To explore the metabolome-metagenome interplay, correlation analyses between host metabolome and microbiome were performed. Additionally, a holistic integration of metabolic pathways was performed (MicrobiomeAnalyst 2.0).<br><br>RESULTS: A total of one and two metabolite modules associated with the NP and FP were identified, respectively. Regarding fecal microbiome, three, one, and two modules for the NP, PP, and FP were identified, respectively. The rumen microbiome demonstrated two modules correlated with each of the groups under study. Metabolite and microbiome enrichment analyses revealed the main metabolic pathways associated with lipid and protein metabolism, and regulatory mechanisms. The correlation analyses performed between the host metabolome and fecal ASVs revealed 13 and 12 significant correlations for NP and FP, respectively. Regarding the rumen, 16 and 17 significant correlations were found for NP and FP, respectively. The NP holistic analysis was mainly associated with amino acid and methane metabolism. Glycerophospholipid and polyunsaturated fatty acid metabolism were over-represented in the FP group.<br><br>CONCLUSIONS: Prenatal nutrition significantly affected the plasma metabolome, fecal microbiome, and ruminal fluid microbiome of Nelore bulls, providing insights into key pathways in protein, lipid, and methane metabolism. These findings offer novel discoveries about the molecular mechanisms underlying the effects of prenatal nutrition.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40210868, year = {2025}, author = {Fu, Y and Guzior, DV and Okros, M and Bridges, C and Rosset, SL and González, CT and Martin, C and Karunarathne, H and Watson, VE and Quinn, RA}, title = {Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3434}, pmid = {40210868}, issn = {2041-1723}, support = {1R01DK140854//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; }, mesh = {Animals ; *Bile Acids and Salts/metabolism ; Humans ; Gastrointestinal Microbiome/genetics ; Mice, Knockout ; Mice ; Amidohydrolases/metabolism/genetics ; Hydrolysis ; Acyltransferases/genetics/metabolism ; Taurocholic Acid/pharmacology/metabolism ; Disease Models, Animal ; *Colitis/metabolism/pathology/microbiology ; Male ; Inflammatory Bowel Diseases/metabolism/microbiology ; Female ; Mice, Inbred C57BL ; Clostridiales/metabolism/genetics ; Crohn Disease/metabolism/microbiology/genetics ; }, abstract = {Conjugated bile acids (BAs) are multi-functional detergents in the gastrointestinal (GI) tract produced by the liver enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT) and by the microbiome from the acyltransferase activity of bile salt hydrolase (BSH). Humans with inflammatory bowel disease (IBD) have an enrichment in both host and microbially conjugated BAs (MCBAs), but their impacts on GI inflammation are not well understood. We investigated the role of host-conjugated BAs in a mouse model of colitis using a BAAT knockout background. Baat[-/-] KO mice have severe phenotypes in the colitis model that were rescued by supplementation with taurocholate (TCA). Gene expression and histology showed that this rescue was due to an improved epithelial barrier integrity and goblet cell function. However, metabolomics also showed that TCA supplementation resulted in extensive metabolism to secondary BAs. We therefore investigated the BSH activity of diverse gut bacteria on a panel of conjugated BAs and found broad hydrolytic capacity depending on the bacterium and the amino acid conjugate. The complexity of this microbial BA hydrolysis led to the exploration of bsh genes in metagenomic data from human IBD patients. Certain bsh sequences were enriched in people with Crohn's disease particularly that from Ruminococcus gnavus. This study shows that both host and microbially conjugated BAs may provide benefits to those with IBD, but this is dictated by a delicate balance between BA conjugation/deconjugation based on the bsh genes present.}, }
@article {pmid40210629, year = {2025}, author = {Park, JW and Yun, YE and Cho, JA and Yoon, SI and In, SA and Park, EJ and Kim, MS}, title = {Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3427}, pmid = {40210629}, issn = {2041-1723}, support = {2020R1A5A8017671//National Research Foundation of Korea (NRF)/ ; 2019R1C1C1009664//National Research Foundation of Korea (NRF)/ ; 2018R1D1A3B07050366//National Research Foundation of Korea (NRF)/ ; 2021R1F1A1064222//National Research Foundation of Korea (NRF)/ ; }, mesh = {Humans ; *Virome/genetics ; *Vegetables/virology ; *Gastrointestinal Microbiome/genetics ; Feces/virology ; *Plant Leaves/virology ; Metagenome ; Bacteriophages/genetics/classification/isolation &amp; purification ; Phylogeny ; Metagenomics ; }, abstract = {Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigate the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 10[7] viruses are present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses are taxonomically unclassified. Virome compositions are distinct among vegetable types and exhibit temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) are more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1498 human fecal VLP metagenomes reveals that approximately 10% of vegetable viruses are present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses are enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.}, }
@article {pmid40210439, year = {2025}, author = {Smith, BJ and Zhao, C and Dubinkina, V and Jin, X and Zahavi, L and Shoer, S and Moltzau-Anderson, J and Segal, E and Pollard, KS}, title = {Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.279543.124}, pmid = {40210439}, issn = {1549-5469}, abstract = {Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding the causes and consequences of this intraspecific diversity. The enormous size of pangenome references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pangenome profiler, now released as version 3, and developed StrainPGC, an approach to strain-specific gene content estimation that combines strain tracking and correlations across multiple samples. We validate our integrated analysis using a complex synthetic community of strains from the human gut and find that StrainPGC outperforms existing approaches. Analyzing a large, publicly available metagenome collection from inflammatory bowel disease patients and healthy controls, we catalog the functional repertoires of thousands of strains across hundreds of species, capturing extensive diversity missing from reference databases. Finally, we apply StrainPGC to metagenomes from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify two Escherichia coli strains, from two different donors, that are both frequently transmitted to patients but have notable differences in functional potential. StrainPGC and MIDAS v3 together enable precise, intraspecific pangenomic investigations using large collections of metagenomic data without microbial isolation or de novo assembly.}, }
@article {pmid40210403, year = {2025}, author = {Africa, AJ and Setati, ME and Hitzeroth, AC and Blancquaert, EH}, title = {Exploring the evolution of microbial communities from the phyllosphere and carposphere to the grape must of Vitis vinifera L. cv's Chardonnay and Pinot noir.}, journal = {Food microbiology}, volume = {130}, number = {}, pages = {104780}, doi = {10.1016/j.fm.2025.104780}, pmid = {40210403}, issn = {1095-9998}, mesh = {*Vitis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Fungi/classification/genetics/isolation &amp; purification ; *Plant Leaves/microbiology ; *Fruit/microbiology ; Wine/microbiology/analysis ; South Africa ; }, abstract = {Microbial communities associated with the grapevine phyllosphere and carposhere are a fundamental determinant of grape and wine quality. High throughput amplicon sequencing was used to profile the fungal and bacterial communities on the associated phylloplane and carposphere of Vitis vinifera L. cv's Chardonnay and Pinot noir in the Elgin and Hemel-en-Aarde wine districts of South Africa in the 2021-2022 growing season. The subsequent grape must was analysed to determine the prevalent microbiome. The most abundant bacterial and fungal genera found in both the phylloplane and carposphere of Chardonnay and Pinot noir were Pseudomonas and Filobasidium. The LEfSe (Linear discriminant analysis Effect Size) revealed significant differences in fungal and bacterial biomarkers from leaf, berry and grape must samples; however, no biomarkers were identified for cultivar nor location. Fungal β-diversity was significantly similar at different phenological stages, whereas bacterial β-diversity was significantly similar regardless of the site of colonisation. However, skin integrity of the grapes was may have influenced the microbial diversity.}, }
@article {pmid40210162, year = {2025}, author = {Gao, X and Yuan, S and Li, X and Xing, W}, title = {Non-synergistic effects of microplastics and submerged macrophytes on sediment microorganisms involved in carbon and nitrogen cycling.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126213}, doi = {10.1016/j.envpol.2025.126213}, pmid = {40210162}, issn = {1873-6424}, abstract = {Submerged macrophyte communities play a crucial role in regulating sediment carbon and nitrogen cycling in lake ecosystems. However, their interactions with emerging pollutants such as polystyrene microplastics (PS-MPs) remain poorly understood. In this study, we employed metagenomic analysis to examine the combined effects of submerged macrophyte communities and PS-MPs on sediment microbial communities, focusing on microbial populations, functional genes, and metabolic pathways involved in carbon and nitrogen cycling. Our results revealed a non-synergistic interaction between macrophyte communities and PS-MPs in shaping sediment biogeochemical processes. While increasing PS-MPs concentrations (from 0.5 to 2.5% w/w) significantly enhanced microbial diversity (species richness increased from 533 to 1,301), the presence of macrophytes moderated this response. Notably, we observed differential selective pressures on functional genes involved in key carbon and nitrogen cycling steps, particularly amoAB and amoC, nirS, and nirK, indicating distinct shifts in microbial functional groups. Furthermore, we identified complex substrate-pathway interactions: nitrate and ammonium differentially influenced fermentation and methanogenesis, while inorganic carbon positively regulated nitrate dissimilatory reduction. These findings provide novel insights into the regulatory mechanisms of submerged macrophytes in sediment biogeochemical cycling under microplastic stress, highlighting their potential role in maintaining ecosystem functions in contaminated aquatic environments.}, }
@article {pmid40210157, year = {2025}, author = {Li, C and Zhu, YX and Shen, XX and Gao, Y and Xu, M and Chen, MK and An, MY}, title = {Exploring the distribution and transmission mechanism of ARGs in crab aquaculture ponds and ditches using metagenomics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126209}, doi = {10.1016/j.envpol.2025.126209}, pmid = {40210157}, issn = {1873-6424}, abstract = {Aquaculture provides notable economic benefits; however, the excessive use of antibiotics has resulted in the production and spread of antibiotic resistance genes (ARGs). The intricate pollution dynamics in aquaculture areas complicate the comprehension of the distribution and transmission of ARGs in aquaculture systems. Using metagenomic sequencing technology, this study used eight ponds and four ditches in a large crab aquaculture area in Taizhou City, where Proteobacteria (61.58%) and Acidobacteria (6.04%) were identified as the dominant phyla and Thiobacillus (1.84%) and Lysobacter (0.99%) were the dominant genera. Network and linear discriminant analysis effect size (LEfse) analyses showed that Proteobacteria and Lysobacter were the main host phyla of ARGs, and Lysobacter, which are key host bacteria in ponds, played an important role in determining the abundance of ARGs in ponds. Co-occurrence network analysis (spearman r>0.7, p<0.01) revealed that prophages can dominate the spread of ARGs by carrying several ARG subtypes (rsmA, OXA-21, THIN-B and lnuF). Analysis of variance demonstrated that functions related to the horizontal gene transfer (HGT) of ARGs, such as EPS synthesis (lptF), oxidative stress (gor and ompR), ATP synthesis (lapB and vcaM), and cell membrane permeability (yajC and gspJ), were significantly expressed in the pond (p<0.05), confirming that ARGs had stronger transmission potential in the pond. The Mantel test and partial least squares path modeling (PLS-PM) analysis showed that ARGs exist in bacteria and spread among them through mobile genetic elements and HGT. This study revealed the distribution and transmission mechanism of ARGs in the ponds and ditches of a crab aquaculture system and provided a theoretical basis for controlling the spread of ARGs in crab aquaculture in this area.}, }
@article {pmid40209695, year = {2025}, author = {Yamane, T and Masaoka, T and Ishii, C and Masuoka, H and Suda, W and Kurokawa, S and Kishimoto, T and Mikami, Y and Fukuda, S and Kanai, T}, title = {Factors contributing to the efficacy of fecal microbiota transplantation for diarrhea-dominant functional bowel disorders.}, journal = {Digestion}, volume = {}, number = {}, pages = {1-22}, doi = {10.1159/000545183}, pmid = {40209695}, issn = {1421-9867}, abstract = {INTRODUCTION: In cases of effective fecal microbiota transplantation (FMT) for irritable bowel syndrome (IBS), donor feces have been observed to be enriched in Bifidobacterium spp., and FMT for functional bowel disease improved psychiatric symptoms. Although intestinal dysbiosis has received attention as one of the pathophysiologies of IBS, the efficacy of FMT for IBS has not yet been established. In this study, we performed a post-hoc analysis of the efficacy of FMT, focusing on metabolites in donor feces.<br><br>METHODS: FMT was performed in 12 patients, 8 with refractory diarrhea-predominant IBS and 4 with functional diarrhea (FDr), who were refractory to medical therapy. The donors were family members within the second degree of kinship and were different for each transplant. Fecal characteristics were evaluated before and 12 weeks after transplantation using the Bristol stool scale (BS). BS scores of 3-5 at 12 weeks after transplantation were considered indicative of responders, while BS scores of 6 and 7 were indicative of non-responders. Metagenomic and metabolomic analyses of all 12 donor fecal samples were performed to compare the responder and non-responder groups.<br><br>RESULTS: Before transplantation, all 12 patients had BS scores of 6-7, but 12 weeks after transplantation, 6 were in the responder group and 6 were in the non-responder group. Metagenomic analysis showed that effective donor feces contained significantly higher levels of Prevotella than ineffective donor feces. Metabolomic analysis showed that effective donor feces contained significantly higher levels of propionate and butyrate and significantly lower lactate levels than ineffective donor feces.<br><br>CONCLUSION: Propionate-, butyrate-, or Prevotella-rich donor feces may contribute to successful FMT in patients with diarrhea-dominant functional gastrointestinal disorders.}, }
@article {pmid40209677, year = {2025}, author = {Lin, Y and Lau, HC and Liu, C and Ding, X and Sun, Y and Rong, J and Zhang, X and Wang, L and Yuan, K and Miao, Y and Wu, WK and Wong, SH and Sung, JJ and Yu, J}, title = {Multi-cohort analysis reveals colorectal cancer tumor location-associated fecal microbiota and their clinical impact.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {4}, pages = {589-601.e3}, doi = {10.1016/j.chom.2025.03.012}, pmid = {40209677}, issn = {1934-6069}, mesh = {Humans ; *Feces/microbiology ; *Colorectal Neoplasms/microbiology/pathology/diagnosis ; *Gastrointestinal Microbiome ; Cohort Studies ; Metagenome ; Male ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; Aged ; Fusobacterium nucleatum/isolation &amp; purification ; Biomarkers, Tumor ; ROC Curve ; }, abstract = {Microbial alterations in different tumor locations of colorectal cancer (CRC) remain unclear. Here, 1,375 fecal metagenomes from six in-house and published datasets were analyzed, including 128 right-sided CRC (rCRC), 168 left-sided CRC (lCRC), 250 rectal cancer (RC), and 829 controls. Firmicutes progressively increase from rCRC, lCRC, to RC, in contrast to the gradual decrease of Bacteroidetes. Tumor location-associated fecal microbes are identified, including Veillonella parvula for rCRC, Streptococcus angionosus for lCRC, and Peptostreptococcus anaerobius for RC, while Fusobacterium nucleatum is enriched in all tumor locations. Tumor location-associated bacteria correlate with patient survival. Clinically, we establish a microbial biomarker panel for each tumor location that accurately diagnoses rCRC (area under the receiver operating characteristic curve [AUC] = 91.59%), lCRC (AUC = 91.69%), or RC (AUC = 90.53%) from controls. Tumor location-specific biomarkers also have higher diagnostic accuracy (AUC = 91.38%) than location-non-specific biomarkers (AUC = 82.92%). Overall, we characterize fecal microbes associated with different CRC tumor locations, highlighting that tumor location should be considered in non-invasive diagnosis.}, }
@article {pmid40209409, year = {2025}, author = {Cheng, Y and Zheng, X and Jiang, Y and Xiao, Q and Luo, Q and Ding, Y}, title = {Key genes and microbial ecological clusters involved in organophosphate ester degradation in agricultural fields of a typical watershed in southwest China.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138076}, doi = {10.1016/j.jhazmat.2025.138076}, pmid = {40209409}, issn = {1873-3336}, abstract = {Organophosphate esters (OPEs) are widely used as flame retardants and plasticizers, and they have raised global concern due to their persistence, bioaccumulation, and potential toxicity. However, OPE contamination characteristics and microbial degradation mechanisms in agricultural soils remain poorly understood. This study investigated agricultural soils from the riparian zone of the Anning River Basin in southwest China. The concentrations of 12 OPEs were determined using gas chromatography-tandem mass spectrometry. The results revealed that the total OPE concentration was moderate, with triethyl phosphate being the most abundant compound. Metagenomic techniques and Bayesian linear regression analysis were employed in combination with the Kyoto Encyclopedia of Genes and Genomes database to identify potential degradation pathways for triethyl phosphate and tris (2-chloroethyl) phosphate. The phoA, phoB, phoD, and glpQ genes, which encode phosphatases, catalyze ester bond cleavage, thereby facilitating the degradation of OPEs. Further microbial interaction network analysis identified core OPE-degrading microorganisms, including Pimelobacter simplex, Nocardioides sp. JS614, Nocardioides daphniae, and Methylocystis heyeri. Additionally, neutral community models indicated that environmental selection drives microbial community structure. In conclusion, this study provides an in-depth understanding of OPE contamination and its microbial degradation mechanisms in agricultural soils, offering theoretical insights for pollution management and remediation strategies.}, }
@article {pmid40209382, year = {2025}, author = {Su, C and Kang, J and Liu, S and Li, C}, title = {Exploring the influence of fruit ripeness on the microbiome, bioactive components, and flavor profiles of naturally fermented noni (Morinda citrifolia L.) juice.}, journal = {Food chemistry}, volume = {482}, number = {}, pages = {144192}, doi = {10.1016/j.foodchem.2025.144192}, pmid = {40209382}, issn = {1873-7072}, abstract = {Raw fruit ripeness is an important factor affecting fermented noni fruit juice (FNJ). This study investigated the physicochemical properties, active and volatile components, microbiota, and functional characteristics of FNJ prepared from noni fruits at varying ripening stages. The results showed that deacetylasperulosidic acid (203.54-805.89 mg/L) and asperulosidic acid (102.78-393.41 mg/L) were detected across in all FNJs during fermentation. As noni fruit ripens, the levels of octanoic acid and hexanoic acid in FNJs gradually decreased, while the content of esters significantly increased, particularly during the final stage of ripeness. Metagenomic analysis revealed that Acetobacter sp. and Gluconobacter sp. were core microbes responsible for FNJs, primarily contributing to fatty acid metabolism. Correlation analysis further indicated that the fruit's ripeness significantly influenced its functional properties and volatile components of FNJs. This study offered new insights into selecting the optimal ripeness of noni fruits for the preparation of FNJ and its potential industrial applications.}, }
@article {pmid40209373, year = {2025}, author = {Wang, L and Pei, H and Xing, T and Chen, D and Chen, Y and Hao, Z and Tian, Y and Ding, J}, title = {Gut bacteria and host metabolism: The keys to sea cucumber (Apostichopus japonicus) quality traits.}, journal = {Food chemistry}, volume = {482}, number = {}, pages = {144178}, doi = {10.1016/j.foodchem.2025.144178}, pmid = {40209373}, issn = {1873-7072}, abstract = {Gut bacteria have a significant impact on modern genetics and contribute to the improvement of aquatic germplasm, which is a key focus for breeders. However, the effects of complex interactions between gut bacteria community and phenotypic trait of aquatic products remain largely unknown. Here, we unravel the association between phenotypic trait, gut microbiota and host metabolic variables of 216 sea cucumbers (Apostichopus japonicus) by Metagenome-wide association studies (MWAS) and Weighted correlation network analysis (WGCNA) methods. Our findings reveal that a total of 14 microbial biomarkers and 201 metabolic markers considered being associated with polysaccharide and collagen content. Among them, Desulfobacterota has the capacity to facilitate the synthesis of octopamine within the neuroactive ligand-receptor metabolic pathway, subsequently influencing polysaccharide content. Additionally, the Lachnospiraceae_NK4A136_group was shown to enhance collagen content through the facilitation of glycine synthesis. In conclusion, this research indicating that precision microbiome management could be a strategy for develop strategies for cultivating high-quality aquatic germplasm.}, }
@article {pmid40209228, year = {2025}, author = {Den Uyl, PA and Kiledal, EA and Errera, RM and Chaganti, SR and Godwin, CM and Raymond, HA and Dick, GJ}, title = {Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c10888}, pmid = {40209228}, issn = {1520-5851}, abstract = {Saxitoxins (STXs), a group of closely related neurotoxins, are among the most potent natural toxins known. While genes encoding STX biosynthesis have been observed in Lake Erie, the organism(s) responsible for producing STXs in the Laurentian Great Lakes have not been identified. We identified a full suite of STX biosynthesis genes in a Dolichospermum metagenome-assembled genome (MAG). The content of sxt genes suggest that this organism can produce STX, decarbamoyl and deoxy-decarbamoyl saxitoxins, and other congeners. The absence of sxtX indicates this organism is unable to produce neosaxitoxin, a potent congener. However, a distinct, lower abundance sxt operon from an unidentified organism did contain sxtX, indicating neosaxitoxin biosynthesis potential. Metatranscriptomic data confirmed STX biosynthesis gene expression. We also recovered highly similar Dolichospermum MAGs lacking sxt genes, implying gene loss or horizontal gene transfer. sxtA was detected by quantitative polymerase chain reaction during 47 of 76 sampling dates between 2015 and 2019, demonstrating higher sensitivity than metagenomic approaches. sxtA gene abundance was positively correlated with temperature and particulate nitrogen:phosphorus ratio and negatively correlated with ammonium concentration. All Dolichospermum MAGs had genes required for nitrogen fixation. Collectively, this study provides a foundation for understanding potential new threats to Lake Erie water quality.}, }
@article {pmid40208400, year = {2025}, author = {Bourgon, N and Padioleau, I and Guibon, J and Fourgeaud, J and Lermine, A and Meurice, G and Guilleminot, T and Bussieres, L and Leruez-Ville, M and Dupont, JM and Ville, Y}, title = {Metagenomic analysis of NIPT raw data suggests high negative predictive value for congenital cytomegalovirus infection screening.}, journal = {Ultrasound in obstetrics &amp; gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology}, volume = {}, number = {}, pages = {}, doi = {10.1002/uog.29221}, pmid = {40208400}, issn = {1469-0705}, }
@article {pmid40207985, year = {2025}, author = {Zhang, Q and Wang, Q and Zhang, F and Li, X and Sun, Y and Wang, L and Zhang, Z}, title = {Diagnostic value of metagenomic next-generation sequencing in patients with osteoarticular infections: a prospective study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0106424}, doi = {10.1128/spectrum.01064-24}, pmid = {40207985}, issn = {2165-0497}, abstract = {Due to the limits of traditional microbiological methods and the complexity of osteoarthritis pathogens, only a few pathogens can be detected. We evaluated metagenomic next-generation sequencing (mNGS) for detecting pathogens in osteoarthritis infection samples. We prospectively included 150 patients with osteoarthritis infection who visited the Orthopedics Department of Shandong Provincial Public Health Center from 2023 to 2024, including 124 cases of primary osteoarthritis (POI) and 26 cases of invasive osteoarthritis (IOI). The most common pathogenic bacteria were Mycobacterium tuberculosis complex, Staphylococcus aureus, and Brucella melitensis. mNGS (75.33%) significantly improved the detection of pathogens in osteoarticular infections compared to conventional tests (CT) methods (36.67%). mNGS could detect a wider spectrum of pathogens compared to CT methods, especially for mixed and rare pathogens. The treatment strategies for patients with osteoarthritis infection could be adjusted based on the results obtained from mNGS testing. Furthermore, the abundance of M. tuberculosis complex, B. melitensis, and Staphylococcus epidermidis was significantly correlated with clinical indicators.IMPORTANCEIdentifying the microorganisms responsible for osteoarthritis infection could help with early diagnosis and treatment. In this study, we compared the pathogen detection rate of metagenomic next-generation sequencing (mNGS) and CT methods in patients with osteoarthritis infection and found that mNGS had a higher microbial detection rate and a broader spectrum of pathogens (especially for mixed pathogens). This study demonstrates that mNGS is an ideal tool for detecting pathogens in patients with osteoarticular infections.}, }
@article {pmid40207938, year = {2025}, author = {Zhao, D and Salas-Leiva, DE and Williams, SK and Dunn, KA and Shao, JD and Roger, AJ}, title = {Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.}, journal = {mBio}, volume = {}, number = {}, pages = {e0069925}, doi = {10.1128/mbio.00699-25}, pmid = {40207938}, issn = {2150-7511}, abstract = {UNLABELLED: Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities enables the discovery of the functions, physiologies, and evolutionary histories of prokaryotic and eukaryotic microbes. However, metagenomic studies of microbial eukaryotes lag due to challenges in identifying and assembling high-quality genomes from WGS data. To address this problem, we developed Eukfinder, a bioinformatics pipeline that identifies potential eukaryotic sequences from WGS metagenomic data, with a complementary binning workflow for recovering nuclear and mitochondrial genomes. Eukfinder uses two specialized databases for read/contig classification, customizable to specific data sets or environments. We tested Eukfinder on simulated gut microbiome data sets which included varying numbers of reads from the protist Blastocystis, a human gut commensal. We also applied Eukfinder to previously published human gut microbiome WGS metagenomic data to recover new genomes of Blastocystis. Compared to other workflows, Eukfinder offers the potential to recover high-quality, near-complete genomes of diverse eukaryotes, including different Blastocystis subtypes, without relying on a reference genome. With sufficient sequencing depth, Eukfinder outperforms similar tools for recovering eukaryotic genomes from metagenomic data. Eukfinder is a valuable tool for reference-independent and cultivation-free studies of eukaryotic microbial genomes from environmental WGS metagenomic samples.<br><br>IMPORTANCE: Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from various environments. Thousands of new prokaryotic genomes have been characterized; however, the large size and complexity of protistan genomes have hindered the use of WGS metagenomics to sample microbial eukaryotic diversity. Eukfinder enables the recovery of eukaryotic microbial genomes from environmental WGS metagenomic samples. Retrieval of high-quality protistan genomes from diverse metagenomic samples increases the number of reference genomes available. This aids future metagenomic investigations into the functions, physiologies, and evolutionary histories of eukaryotic microbes in the gut microbiome and other ecosystems.}, }
@article {pmid40207877, year = {2025}, author = {Huang, L and Chen, C and Meng, J and Yan, Q and Luo, G and Sha, S and Xing, Y and Liu, C and Xu, M and Zhao, L and Guo, S and Wu, X and Chen, H and Ma, J and You, W and Zhang, Y and Guo, R and Li, S and Yao, X and Ma, W and Kong, X and Zhou, P and Sun, W}, title = {Metagenome-Based Characterization of the Gut Virome Signatures in Patients With Gout.}, journal = {Journal of medical virology}, volume = {97}, number = {4}, pages = {e70336}, doi = {10.1002/jmv.70336}, pmid = {40207877}, issn = {1096-9071}, support = {//This study was supported by 2024 High-quality Development Project of Shenzhen Bao'an Public Hospital (BAGZL2024138 and BAGZL2024130), National Natural Science Foundation of China (82370563), Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding (JCH22023017), the Key Laboratory of Guizhou Provincial Education Department (Guizhou Education Technology [2023] No. 017), National and Provincial Science and Technology Innovation Talent Team Cultivation Program of Guizhou University of Traditional Chinese Medicine (GZUTCM-TD[2022]004)./ ; }, mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; *Gout/virology ; Male ; Middle Aged ; Feces/virology ; Female ; *Metagenome ; Metagenomics ; *Viruses/classification/genetics/isolation &amp; purification ; Adult ; Aged ; Longitudinal Studies ; }, abstract = {The gut microbiome has been implicated in the development of autoimmune diseases, including gout. However, the role of the gut virome in gout pathogenesis remains underexplored. We employed a reference-dependent virome approach to analyze fecal metagenomic data from 102 gout patients (77 in the discovery cohort and 25 in the validation cohort) and 86 healthy controls (HCs) (63 and 23 in each cohort). A subset of gout patients in the discovery cohort provided longitudinal samples at Weeks 2, 4, and 24. Our analysis revealed significant alterations in the gut virome of gout patients, including reduced viral richness and shifts in viral family composition. Notably, Siphoviridae, Myoviridae, and Podoviridae were depleted, while Quimbyviridae, Retroviridae, and Schitoviridae were enriched in gout patients. We identified 359 viral operational taxonomic units (vOTUs) associated with gout. Enriched vOTUs in gout patients predominantly consisted of Fusobacteriaceae, Bacteroidaceae, and Selenomonadaceae phages, while control-enriched vOTUs included Ruminococcaceae, Oscillospiraceae, and Enterobacteriaceae phages. Longitudinal analysis revealed that a substantial proportion of these virome signatures remained stable over 6 months. Functional profiling highlighted the enrichment of viral auxiliary metabolic genes, suggesting potential metabolic interactions between viruses and host bacteria. Notably, gut virome signatures effectively discriminated gout patients from HCs, with high classification performance in the validation cohort. This study provides the first comprehensive characterization of the gut virome in gout, revealing its potential role in disease pathogenesis and highlighting virome-based signatures as promising biomarkers for gout diagnosis and future therapeutic strategies.}, }
@article {pmid40207279, year = {2025}, author = {Teng, NM and Malfettone, A and Dalby, MJ and Kiu, R and Seki, D and Robinson, T and Gion, M and Bermejo, B and Pérez-García, JM and Prat, A and Vázquez, RM and Llombart-Cussac, A and Curigliano, G and Schmid, P and Barroso-Sousa, R and Mancino, M and Shimizu, E and Rodríguez-Morató, J and Mina, L and Hall, LJ and Robinson, SD and Cortés, J}, title = {Profiling the gut and oral microbiota of hormone receptor-positive, HER2-negative metastatic breast cancer patients receiving pembrolizumab and eribulin.}, journal = {Microbiome research reports}, volume = {4}, number = {1}, pages = {4}, pmid = {40207279}, issn = {2771-5965}, abstract = {Aim: Changes in host-associated microbial communities (i.e., the microbiota) may modulate responses to checkpoint blockade immunotherapy. In the KELLY phase II study (NCT03222856), we previously demonstrated that pembrolizumab [anti-programmed cell death protein 1 (PD-1)] combined with eribulin (plus microtubule-targeting chemotherapy) showed encouraging antitumor activity in patients with hormone receptor (HR)-positive/human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (mBC) who had received prior treatments. Methods: A total of 58 fecal and 67 saliva samples were prospectively collected from a subset of 28 patients at baseline (BL), after three treatment cycles, and end of treatment. Shotgun metagenomics, 16S rRNA gene amplicon sequencing, and bioinformatics and statistical approaches were used to characterize fecal and oral microbiota profiles. Results: Treatment caused no substantial perturbations in gut or oral microbiota, suggesting minimal drug-related microbial toxicity. Bacteroides and Faecalibacterium were the dominant gut microbiota genera, while Prevotella and Streptococcus were present in both oral and gut samples, highlighting potential gut-oral microbial interactions. Additionally, clinical benefit (CB) appeared to be associated with gut-associated Bacteroides fragilis (B. fragilis) and a BL oral abundance of Streptococcus ≥ 30%. Notably, B. fragilis NCTC 9343 supernatant induced dose-dependent lactate dehydrogenase (LDH) release from the MCF-7 (HR-positive/HER2-negative) BC cell line. Conclusion: These findings suggest that specific gut and oral microbiota may modulate the effectiveness of combinatory anti-BC therapies, potentially through the action of microbial metabolites.}, }
@article {pmid40207161, year = {2025}, author = {Helmi, NR}, title = {Exploring the diversity and antimicrobial potential of actinomycetes isolated from different environments in Saudi Arabia: a systematic review.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1568899}, pmid = {40207161}, issn = {1664-302X}, abstract = {The increasing prevalence of antimicrobial resistance (AMR) presents a significant global health challenge, underscoring the urgent need for novel antimicrobial agents. Actinomycetes, particularly Streptomyces species, are well known for synthesizing bioactive compounds with antibacterial, antifungal, and antiviral properties. This review explores the diversity and antimicrobial potential of actinomycetes from Saudi Arabia's unique ecosystems, including terrestrial (soil, rhizosphere), aquatic (marine, freshwater), extreme (deserts, caves, hot springs, mountains, and mangroves), and other unique environments. The adaptation of these microorganisms to harsh environmental conditions has driven the evolution of unique strains with enhanced biosynthetic capacities. Several studies have demonstrated their antimicrobial efficacy against multidrug-resistant pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, Pseudomonas aeruginosa, and Candida albicans. However, challenges in actinomycete research persist, including difficulties in culturing rare strains, limited genomic characterization, and high production costs. Recent advancements, such as genome mining, metagenomics, AI-driven bioinformatics, and CRISPR-based gene activation, offer promising avenues for unlocking novel antimicrobial compounds. Additionally, synthetic biology, advanced fermentation technologies, and nanotechnology-based drug delivery systems are enhancing the industrial scalability of actinomycete-derived antibiotics. Beyond antimicrobials, actinomycete-derived compounds show potential applications in oncology, immunotherapy, and agriculture. Alternative therapeutic strategies, including quorum sensing inhibitors, phage therapy, and combination therapies, are being explored to combat AMR. Cutting-edge analytical techniques, such as mass spectrometry, liquid chromatography, and nuclear magnetic resonance spectroscopy (NMR), are essential for structural elucidation and mechanism characterization of new bioactive compounds. To harness Saudi Arabia's microbial biodiversity effectively, interdisciplinary collaborations between microbiologists, biotechnologists, and pharmaceutical industries are crucial. Sustainable bioprospecting and advanced bioprocessing strategies will facilitate the translation of actinomycete-derived bioactive compounds into clinically viable therapeutics. Expanding research efforts into underexplored Saudi ecosystems can lead to groundbreaking discoveries in antibiotic development and beyond.}, }
@article {pmid40207154, year = {2025}, author = {Ahn, JS and Han, EJ and Chung, HJ}, title = {Comparison of metagenomic analysis of fecal and gastrointestinal tract samples for identifying beneficial gut microorganisms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1533580}, pmid = {40207154}, issn = {1664-302X}, abstract = {INTRODUCTION: Previous research on the gut microbiome has primarily focused on fecal microbiota, raising concerns about whether fecal samples accurately represent the entire intestinal microbiota. Studies have shown that microbial communities across the gastrointestinal (GI) tract are more diverse than those in feces, suggesting that microbial composition may vary depending on the sampling method. Additionally, analyzing the broader diversity of microbial communities in the GI tract may enhance the identification of potentially beneficial microbiota.<br><br>METHODS: In this study, we compare gut microbiome datasets obtained from fecal samples and GI samples (collected by pooling luminal contents and mucosal scrapings from the stomach to the end of the colon) of 6-month-old mice using 16S rRNA sequencing. We further investigate the associations between gut microbiota and motor, cognitive, and emotional functions in mice, examining differences between the two sample types. To assess these variations, we apply DESeq2 analysis to identify microbial species enriched in high-functioning groups and evaluate how their selection may differ depending on the sampling approach.<br><br>RESULTS: Our findings reveal notable differences in microbial composition between fecal and GI samples, suggesting that sampling methods may influence the identification of beneficial bacteria.<br><br>DISCUSSION: These results highlight the importance of selecting an appropriate sampling approach in microbiome research to ensure a comprehensive understanding of gut microbiota-host interactions.}, }
@article {pmid40207150, year = {2025}, author = {Zhao, C and Yang, Y and Zhao, P and Bai, L}, title = {Comparative analysis of the fecal microbiota in Père David's deer and five other captive deer species.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1547348}, pmid = {40207150}, issn = {1664-302X}, abstract = {INTRODUCTION: Gut microbes are essential for host nutrition, immunity, and development. Various factors influence the composition and function of the gut microbial community. However, there is limited knowledge regarding the comparison of gut microbiota across different deer species, particularly those in the World Deer Park of Baotou (Inner Mongolia, China).<br><br>METHODS: This study utilized 16S rRNA gene amplicon sequencing to analyze the fecal microbiota and potential microbial function in P&#xe8;re David's Deer (Elaphurus davidianus), Sika deer (Cervus nippon), American Wapiti (Cervus canadensis), Red Deer (Cervuselaphus), Fallow Deer (Dama dama), and Reindeer (Rangifer tarandus).<br><br>RESULTS AND DISCUSSION: The findings indicated no significant differences in alpha diversity, yet there was a noteworthy distinction in beta diversity among the six deer groups. At the phylum level, the predominant bacteria in the deer populations were Firmicutes, Bacteroidetes, and Proteobacteria. At the genus level, 54 core bacterial microbiota were identified. The top four genera in AW, FD, PD, and SD were Ruminococcaceae UCG-005, Rikenellaceae RC9 gut group, RuminococcaceaeUCG-010 and Christensenellaceae R-7 group. The results of the neutral model revealed that neutral processes predominantly governed the gut microbiota community assembly in different deer species, particularly in P&#xe8;re David's deer. PICRUSt2 predictions showed significant enrichment of fecal bacterial functions related to fatty acid, lipid, metabolic regulator, and amino acid biosynthesis. This comparative analysis sheds light on the microbial community structure, community assembly, and potential functions, offering improved insights into the management and conservation of deer species, especially P&#xe8;re David's deer. Future research might focus on exploring metagenomic functions and dynamics in wild settings or across different seasons using metagenomics or metatranscriptomics.}, }
@article {pmid40206877, year = {2025}, author = {Shi, M and Qin, T and Pu, Z and Yang, Z and Lim, KJ and Yang, M and Wang, Z}, title = {Salt stress alters the selectivity of mature pecan for the rhizosphere community and its associated functional traits.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1473473}, pmid = {40206877}, issn = {1664-462X}, abstract = {INTRODUCTION: Salt stress is a major global environmental factor limiting plant growth. Rhizosphere bacteria, recruited from bulk soil, play a pivotal role in enhancing salt stress resistance in herbaceous and crop species. However, whether the rhizosphere bacterial community of a mature tree can respond to salt stress, particularly in saline-alkalitolerant trees, remains unexplored. Pecan (Carya illinoinensis), an important commercially cultivated nut tree, is considered saline-alkali tolerant.<br><br>METHODS: Pecan trees (12 years) were subjected to different NaCl concentrations for 12 weeks. Collected samples included bulk soil, rhizosphere soil, roots, leaves, and fruit. Amplicon sequencing data and shotgun metagenomic sequencing data obtained from the samples were investigated: 1) microbial communities in various ecological niches of mature pecan trees; 2) the characteristic of the rhizosphere bacteria community and the associated functional traits when pecan suffered from salt stress.<br><br>RESULTS AND DISCUSSION: We characterized the mature pecan-associated microbiome (i.e., fruit, leaf, root, and rhizosphere soil) for the first time. These findings suggest that niche-based processes, such as habitat selection, drive bacterial and fungal community assembly in pecan tissues. Salt stress reduced bacterial diversity, altered community composition, and shifted pecan's selective pressure on Proteobacteria and Actinobacteria. Shotgun metagenomic sequencing further revealed functional traits of the rhizosphere microbiome in response to salt stress. This study enhances our understanding of mature tree-associated microbiomes and supports the theory that shaping the rhizosphere microbiome may be a strategy for saline-alkali-tolerant mature trees to resist salt stress. These findings provide insights into salt tolerance in mature trees and suggest potential applications, such as the development of bio-inoculants, for managing saline environments in agricultural and ecological contexts.}, }
@article {pmid40206699, year = {2025}, author = {Connors, E and Gallagher, KL and Dutta, A and Oliver, M and Bowman, JS}, title = {Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot.}, journal = {Polar biology}, volume = {48}, number = {2}, pages = {62}, pmid = {40206699}, issn = {0722-4060}, abstract = {UNLABELLED: The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00300-025-03380-y.}, }
@article {pmid40206488, year = {2025}, author = {He, J and Chen, Y and Jiang, Z and Li, F and Zhu, M and Xu, Z and Wang, M and Tang, M and Wu, Y and Li, Y}, title = {Diagnostic value of metagenomic next-generation sequencing in detecting Pneumocystis jirovecii pneumonia in HIV-infected patients.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1567484}, pmid = {40206488}, issn = {2296-858X}, abstract = {INTRODUCTION: Accurate diagnosis of Pneumocystis jirovecii pneumonia (PJP) in HIV patients remains challenging. This study compares metagenomic next-generation sequencing (mNGS) with PCR, GMS staining, and serum β-D-glucan (BG) assays for PJP detection and co-infection identification.<br><br>METHODS: BALF samples from 34 HIV-positive PJP patients and 50 non-PJP controls were analyzed. Diagnostic performance metrics (sensitivity, specificity, NPV, AUC) and co-pathogen profiles were evaluated for mNGS versus conventional methods.<br><br>RESULTS: mNGS and PCR both achieved 100% sensitivity. mNGS showed higher specificity (91.3% vs. 88%) and AUC (0.898 vs. 0.940 for PCR). Co-infections were detected in 67.6% of PJP cases by mNGS, including cytomegalovirus (41.2%), Epstein-Barr virus (29.4%), and non-tuberculous mycobacteria (14.7%). GMS and BG assays exhibited lower sensitivity (64.7% and 76.5%, respectively).<br><br>DISCUSSION: mNGS offers superior specificity, accuracy, and co-infection detection compared to traditional methods. Its high NPV (100%) supports clinical utility in ruling out PJP. While resource-intensive, mNGS is a promising first-line diagnostic tool for HIV-associated PJP, particularly in polymicrobial infection settings.}, }
@article {pmid40206430, year = {2025}, author = {Zhou, Z and Sun, L and Zhou, W and Gao, W and Yuan, X and Zhou, H and Ren, Y and Li, B and Wu, Y and She, J}, title = {Probiotic Bifidobacterium reduces serum TMAO in unstable angina patients via the gut to liver to heart axis.}, journal = {Liver research (Beijing, China)}, volume = {9}, number = {1}, pages = {57-65}, pmid = {40206430}, issn = {2542-5684}, abstract = {BACKGROUND AND AIMS: Studies indicate that the gut microbiota and its metabolites are involved in the progression of cardiovascular diseases, and enterohepatic circulation plays an important role in this progression. This study aims to identify potential probiotics for the treatment of unstable angina (UA) and elucidate their mechanisms of action.<br><br>METHODS: Initially, the gut microbiota from patients with UA and control was analyzed. To directly assess the effects of Bifidobacterium supplementation, 10 patients with UA were enrolled and administered Bifidobacterium (630&#xa0;mg per intake twice a day for 1 month). The fecal metagenome, serum trimethylamine N-oxide (TMAO) levels, and other laboratory parameters were evaluated before and after Bifidobacterium supplementation.<br><br>RESULTS: After supplementing with Bifidobacterium for 1&#xa0;month, there were statistically significant differences (P&#xa0;<&#xa0;0.05) in TMAO, aspartate aminotransferase, total cholesterol, and low-density lipoprotein compared to before. Additionally, the abundance of Bifidobacterium longum increased significantly, although the overall abundance of Bifidobacterium did not reach statistical significance. The gut microbiota, metabolites, and gut-liver axis are involved in the progression of UA, and potential mechanisms should be further studied.<br><br>CONCLUSIONS: Metagenomic analysis demonstrated a reduced abundance of Bifidobacterium in patients with UA. Supplementation with Bifidobacterium restored gut dysbiosis and decreased circulating TMAO levels in patients with UA. This study provides evidence that Bifidobacterium may exert cardiovascular-protective effects through the gut-liver-heart axis.<br><br>CLINICAL TRIAL NUMBER: ChiCTR2400093946.}, }
@article {pmid40205852, year = {2025}, author = {Nowicki, M and Mroczek, M and Mukhedkar, D and Bała, P and Nikolai Pimenoff, V and Arroyo Mühr, LS}, title = {HPV-KITE: sequence analysis software for rapid HPV genotype detection.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf155}, pmid = {40205852}, issn = {1477-4054}, mesh = {Humans ; Genotype ; Algorithms ; *Software ; *Papillomaviridae/genetics/classification ; *Papillomavirus Infections/virology/diagnosis ; High-Throughput Nucleotide Sequencing ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Human papillomaviruses (HPVs) are among the most diverse viral families that infect humans. Fortunately, only a small number of closely related HPV types affect human health, most notably by causing nearly all cervical cancers, as well as some oral and other anogenital cancers, particularly when infections with high-risk HPV types become persistent. Numerous viral polymerase chain reaction-based diagnostic methods as well as sequencing protocols have been developed for accurate, rapid, and efficient HPV genotyping. However, due to the large number of closely related HPV genotypes and the abundance of nonviral DNA in human derived biological samples, it can be challenging to correctly detect HPV genotypes using high throughput deep sequencing. Here, we introduce a novel HPV detection algorithm, HPV-KITE (HPV K-mer Index Tversky Estimator), which leverages k-mer data analysis and utilizes Tversky indexing for DNA and RNA sequence data. This method offers a rapid and sensitive alternative for detecting HPV from both metagenomic and transcriptomic datasets. We assessed HPV-KITE using three previously analyzed HPV infection-related datasets, comprising a total of 1430 sequenced human samples. For benchmarking, we compared our method's performance with standard HPV sequencing analysis algorithms, including general sequence-based mapping, and k-mer-based classification methods. Parallelization demonstrated fast processing times achieved through shingling, and scalability analysis revealed optimal performance when employing multiple nodes. Our results showed that HPV-KITE is one of the fastest, most accurate, and easiest ways to detect HPV genotypes from virtually any next-generation sequencing data. Moreover, the method is also highly scalable and available to be optimized for any microorganism other than HPV.}, }
@article {pmid40205718, year = {2025}, author = {Zhang, H and Yang, M and Ying, W and Hou, J and Zhou, Q and Sun, B and Wang, Y and Hui, X and Liu, L and Yao, H and Sun, J and Wang, W and Wang, X}, title = {Invasive fungal disease in a large cohort of hospitalized children with inborn errors of immunity in China.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {36}, number = {4}, pages = {e70074}, doi = {10.1111/pai.70074}, pmid = {40205718}, issn = {1399-3038}, support = {ZD2021CY001//the Shanghai Municipal Science and Technology Major Project/ ; }, mesh = {Humans ; China/epidemiology ; Male ; Female ; Retrospective Studies ; *Invasive Fungal Infections/epidemiology/drug therapy ; Child, Preschool ; Child ; Infant ; Prevalence ; *Immunologic Deficiency Syndromes/epidemiology/complications ; Adolescent ; Hospitalization ; Infant, Newborn ; }, abstract = {BACKGROUND: Invasive fungal disease (IFD) is a common complication observed in inborn errors of immunodeficiency (IEI) patients, and little is known about the overall prevalence of IFD in IEI patients. We aimed to summarize the fungal spectrum and outcomes of IFDs in a Chinese cohort of hospitalized patients with IEI.<br><br>METHODS: In this retrospective study, 607 IEI patients hospitalized from January 2018 to June 2022 were included. Demographic, clinical, and fungal infection data and IEI patient characteristics were collected and analyzed according to the IEI classification.<br><br>RESULTS: One hundred and two IEI patients were diagnosed with proven or probable IFD. The overall prevalence of IFD was 17% (102/607). There were 29 different genotypes, among which CYBB (25%), CD40LG (9%), and RAG1 (7%) mutations were the most common. Most IFD infections (87/102) were caused by one fungus. Invasive Aspergillus, Pneumocystis jirovecii pneumonia, and Penicillium infections were more commonly observed in patients with congenital defects in phagocytes, immunodeficiencies affecting cellular and humoral immunity, and defects in innate immunity, respectively. Most IFDs observed in IEI patients were single-site infections, most of which were lung infections (74%). Seventeen patients were diagnosed with disseminated IFDs, nine of which were caused by Penicillium. All patients received antifungal treatments. Eight patients (8%) died within 3&#x2009;months of IFD diagnosis.<br><br>CONCLUSIONS: IFD occurrence suggests the presence of immunity impairment. The IFD fungal profile may indicate different types of IEI. Early recognition of immunodeficiency and optimal timing of antifungal therapy can reduce fatality in IEI patients.}, }
@article {pmid40205678, year = {2025}, author = {He, Y and Zhao, G and Ouyang, X and Wang, S and Chen, Y and Li, C and He, Y and Gao, J and Han, S and Zhao, J and Wang, J and Wang, C}, title = {Creatine-mediated ferroptosis inhibition is involved in the intestinal radioprotection of daytime-restricted feeding.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2489072}, doi = {10.1080/19490976.2025.2489072}, pmid = {40205678}, issn = {1949-0984}, mesh = {Animals ; Mice ; Gastrointestinal Microbiome/drug effects/radiation effects ; *Creatine/metabolism/pharmacology/administration &amp; dosage ; *Ferroptosis/drug effects/radiation effects ; Mice, Inbred C57BL ; Male ; *Intestines/radiation effects/microbiology ; *Radiation-Protective Agents/metabolism/administration &amp; dosage ; Radiation, Ionizing ; Feces/microbiology ; Enterocytes/radiation effects/metabolism ; }, abstract = {Ionizing radiation-induced intestinal injury (IRIII) is a catastrophic disease lack of sufficient medical countermeasures currently. Regulation of the gut microbiota through dietary adjustments is a potential strategy to mitigate IRIII. Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention with pleiotropic health benefits. Whether this dietary pattern influences the pathogenesis of IRIII remains vague. We evaluated the impact of TRF on intestinal radiosensitivity in this study and discovered that only daytime TRF (DTRF), not nighttime TRF, could ameliorate intestinal damage in mice that received a high dose of IR. Faecal metagenomic and metabolomic studies revealed that the intestinal creatine level was increased by approximate 9 times by DTRF, to which the Bifidobacterium pseudolongum enrichment contribute. Further investigations showed that creatine could activate the energy sensor AMP-activated protein kinase in irradiated enterocytes and induce phosphorylation of acetyl-CoA carboxylase, resulting in reduced production of polyunsaturated fatty acids and reduced ferroptosis after IR. The administration of creatine mitigated IRIII and reduced bacteremia and proinflammatory responses. Blockade of creatine import compromised the ferroptosis inhibition and mitigation of DTRF on IRIII. Our study demonstrates a radioprotective dietary mode that can reshape the gut microbiota and increase intestinal creatine, which can suppress IR-induced ferroptosis, thereby providing effective countermeasures for IRIII prevention.}, }
@article {pmid40205588, year = {2025}, author = {Li, M and Wang, Z and Ma, Z and Wang, Y and Jia, H and Zhang, L and Chen, P and Mao, Y and Yang, Z}, title = {Metagenomic analysis reveals microbial drivers of heat resistance in dairy cattle.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {35}, pmid = {40205588}, issn = {2524-4671}, support = {2022YFF1001200//National Key Research and Development Program of China/ ; }, abstract = {Heat stress poses a significant challenge to dairy cattle, leading to adverse physiological effects, reduced milk yield, impaired reproduction performance and economic losses. This study investigates the role of the rumen microbiome in mediating heat resistance in dairy cows. Using the entropy-weighted TOPSIS method, we classified 120 dairy cows into heat-resistant (HR) and heat-sensitive (HS) groups based on physiological and biochemical markers, including rectal temperature (RT), respiratory rate (RR), salivation index (SI) and serum levels of potassium ion (K[+]), heat shock protein 70 (HSP70) and cortisol. Metagenomic sequencing of rumen fluid samples revealed distinct microbial compositions and functional profiles between the two groups. HR cows exhibited a more cohesive and functionally stable microbiome, dominated by taxa such as Ruminococcus flavefaciens and Succiniclasticum, which are key players in fiber degradation and short-chain fatty acid production. Functional analysis highlighted the enrichment of the pentose phosphate pathway (PPP) in HR cows, suggesting a metabolic adaptation that enhances oxidative stress management. In contrast, HS cows showed increased activity in the tricarboxylic acid (TCA) cycle, pyruvate metabolism and other energy-intensive pathways, indicating a higher metabolic burden under heat stress. These findings underscore the critical role of the rumen microbiome in modulating heat resistance and suggest potential microbiome-based strategies for improving dairy cattle resilience to climate change.}, }
@article {pmid40205543, year = {2025}, author = {Zou, Z and Zhao, W and Chen, Y and Liu, Z and He, G and Zhang, H}, title = {Extracorporeal membrane oxygenation in the treatment of critical Pneumocystis jirovecii pneumonia in a child with Langerhans cell histiocytosis: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {492}, pmid = {40205543}, issn = {1471-2334}, mesh = {Humans ; *Extracorporeal Membrane Oxygenation/methods ; Female ; *Pneumonia, Pneumocystis/therapy/complications/microbiology ; Child, Preschool ; *Pneumocystis carinii/genetics/isolation &amp; purification ; *Histiocytosis, Langerhans-Cell/complications/drug therapy ; Treatment Outcome ; }, abstract = {BACKGROUND: Children with Langerhans cell histiocytosis (LCH) are particularly susceptible to infections such as Pneumocystis jirovecii pneumonia (PJP) due to the immunosuppressive effects of chemotherapy, which can progress to acute respiratory distress syndrome (ARDS) and respiratory failure. The use of Extracorporeal Membrane Oxygenation (ECMO) to manage hypoxemia secondary to PJP in LCH presents unique challenges, including the prevention of catheter-related bloodstream infections associated with arterial and venous access. This study explores a case wherein ECMO was crucial in treating severe PJP-induced respiratory failure in a pediatric patient with LCH.<br><br>CASE PRESENTATION: A 3-year-old female with a history of LCH, undergoing long-term chemotherapy and corticosteroid treatment, was admitted with fever, dyspnea, and lethargy. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid confirmed Pneumocystis jirovecii (PJ). Despite aggressive management with invasive high-frequency ventilation, inhaled nitric oxide, and prone positioning, the patient's oxygenation remained critically low, with severe hypercapnia and resultant severe respiratory acidosis, necessitating vasopressor support for hemodynamic stability and venoarterial (VA) ECMO intervention. Early initiation of VA ECMO facilitated ultraprotective lung ventilation and circulatory support, effectively preventing hemodynamic collapse. The patient was successfully decannulated after 13 days of ECMO support.<br><br>CONCLUSION: While PJP is a rare and extremely serious opportunistic infection, the VA ECMO support in this pediatric case effectively managed severe PJP without ECMO-related complications. This highlights ECMO as a potentially viable, relatively effective, and safe adjunctive therapy in the management of severe PJP infections in children.}, }
@article {pmid40205497, year = {2025}, author = {Grønbæk, IMB and Halkjær, SI and Mollerup, S and Hansen, EH and Paulsen, SJ and Engel, S and Theede, K and Wilkens, R and Boysen, T and Petersen, AM}, title = {The effects of probiotic treatment with Bifidobacterium breve, Bif195 for small intestinal Crohn's disease and the gut microbiome: results from a randomised, double-blind, placebo-controlled trial.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {19}, pmid = {40205497}, issn = {1757-4749}, support = {A6876//The Capital Region's Research Foundation for Health Research/ ; }, abstract = {BACKGROUND: The aetiology of Crohn's disease, a chronic inflammatory bowel disease, is multifactorial and not completely understood. However, the association with gut dysbiosis is well-established, and manipulation of the gut microbiota has gained interest as a treatment strategy. This study aimed to investigate the effects of the probiotic strain Bifidobacterium breve, Bif195™ (Bif195) on intestinal inflammation, symptoms, and the gut microbiome composition in patients with small intestinal Crohn's disease.<br><br>METHODS: This was a randomised, double-blind, placebo-controlled trial. Thirty-three patients with small intestinal Crohn's disease were assigned to eight weeks of treatment with Bif195 or placebo (1:1). The primary outcome was changes in bowel wall thickness measured by intestinal ultrasonography. Other outcomes were changes in symptom severity, quality of life, faecal calprotectin, fatigue, and specific inflammatory parameters on ultrasonography. Changes in the microbiome composition were also examined.<br><br>RESULTS: Bif195 did not affect the bowel wall thickness in the small intestine compared to placebo. Nor did we observe effects on secondary or clinical explorative outcomes. Analysis of the gut microbiome showed that the relative abundance of B. breve rose during the intervention in the Bif195 group, but the result was statistically non-significant. Surprisingly, we observed a clustering of baseline microbiome data into two groups that differed in several aspects including a statistically significant difference in the incidence of previous bowel resections among the participants. Furthermore, changes in symptom scores after eight weeks of intervention were significantly different across the two microbiome groups, with an interaction effect of p&#x2009;=&#x2009;0.04.<br><br>CONCLUSIONS: Eight weeks of treatment with Bif195 did not affect clinical outcomes for Crohn's disease. However, variations in baseline microbiome data influenced the results. This underscores the importance of assessing baseline microbiome data in intervention studies in Crohn's disease.<br><br>CLINICALTRIALS: gov NCT04842149.}, }
@article {pmid40205473, year = {2025}, author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Eguiarte, LE and Souza, V}, title = {Running against the clock: Exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf033}, pmid = {40205473}, issn = {1574-6941}, abstract = {The Cuatro Ciénegas Basin is a biodiversity hotspot known for its unique biodiversity. However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas and Archean Domes. Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from Pozas Rojas and Archean Domes: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and Archean Domes: Halanaerobium sp. (63%) and Desulfovermiculus halophilus (60%). Furthermore, metagenome assembled genomes from Ectothiorhodospira genus were found in both Archean Domes and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the Archean Domes system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin's biodiversity.}, }
@article {pmid40205381, year = {2025}, author = {Chen, G and Yin, L and Zhang, H}, title = {Isolation and characterization of goose astrovirus genotype 1 causing enteritis in goslings from Sichuan Province, China.}, journal = {BMC veterinary research}, volume = {21}, number = {1}, pages = {259}, pmid = {40205381}, issn = {1746-6148}, support = {ZYN2024087//Central University Basic Scientific Research Business Expenses Special Funds/ ; }, abstract = {Since 2017, goose astrovirus (GoAstV) has been widely prevalent in various provinces of China, causing economic losses in the goose industry, with outbreak mortality rates ranging from 10 to 60%. Notably, a goose farm in Sichuan Province has faced an outbreak of infectious disease in 1-3 weeks old goslings, with a mortality rate of approximately 30%. Viral metagenomic analysis of fecal samples identified Goose astrovirus genotype 1 (GoAstV-1), and PCR analysis confirmed the presence of GoAstV-1. Furthermore, we successfully isolated a GoAstV-C1 strain using goose embryos named AAstV/Goose/CHN/2023/C1 (GenBank No. PP108251), and its viral titer was calculated as 10^4.834 ELD50/0.5 mL using the Reed-Muench method. The genome size of GoAstV-C1 was about 7,261 nucleotides through amplifying with Sanger sequencing and assembling with SeqMan software. Phylogenetic analysis revealed that GoAstV-1 strains are classified into three major subtypes: A, B, and C, with the GoAstV-C1 strain identified as a unique variant within subtype B, characterized by distinct genetic divergence features. Experimental inoculation of one-day-old goslings with the virus resulted in a mortality rate of 5 out of 15 (p-value = 0.0421) and a significant reduction in weight gain compared to controls (p-value = 0.005). Pathological examination revealed that GoAstV-C1 infection caused severe damage to the liver, spleen, and kidneys. Interestingly, unlike most GoAstV, which leads to characteristic gout symptoms, our isolates GoAstV-C1 caused obvious intestinal damage characterized by necrosis, inflammatory infiltration, and crypt architectural disruption. We indicated that GoAstV-C1 displays a unique intestinal tropism rather than characteristic gout symptoms and elucidated genomic features and evolutionary relationships of GoAstV strains. These findings help advance our knowledge of the epidemiology and pathogenicity of GoAstV-1, and the predicted structure of capsid protein could serve as a potential target for designing novel antiviral drugs or vaccines against GoAstV-1.}, }
@article {pmid40204977, year = {2025}, author = {Deng, Z and Poulsen, JS and Nielsen, JL and Weissbrodt, DG and Spanjers, H and van Lier, JB}, title = {Identification of protein-degraders in an anaerobic digester by protein stable isotope probing and metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {87}, pmid = {40204977}, issn = {1432-0614}, support = {201708450043//China Scholarship Council/ ; }, mesh = {Anaerobiosis ; *Metagenomics ; *Acinetobacter/metabolism/genetics ; Carbon Isotopes/metabolism ; Bacterial Proteins/metabolism/genetics ; Isotope Labeling ; Metabolic Networks and Pathways ; Proteomics ; *Bioreactors/microbiology ; Proteolysis ; Glucose/metabolism ; *Proteins/metabolism ; }, abstract = {Presence of carbohydrates hampers protein degradation in anaerobic digesters. To understand this phenomenon, we used proteogenomics to identify the active protein-degraders in the presence of low and high carbohydrates concentrations. Active metabolic pathways of the identified protein-degraders were investigated using proteomics with [13]C-protein substrates (protein stable isotope probing). Results showed that 1) Acinetobacter was the active protein-degraders under both protein-fed and protein-glucose mixture-fed conditions, 2) the relative abundance of Acinetobacter was not affected by the presence of carbohydrates, 3) the incorporation of the [13]C-labelled protein substrate was predominantly observed in outer membrane-bound proteins and porin proteins, which are associated with proteinases or the transportation of amino acids across the cell wall. The Acinetobacter metabolic model and the incubation conditions suggested that glucose and proteins were degraded through anaerobic respiration. The negative impact of carbohydrates on protein biodegradation was attributed to Acinetobacter's preference for carbohydrates. This work highlights that efficient degradation of protein and carbohydrate mixtures in anaerobic digesters requires a staged or time-phased approach and enrichment of active protein-degraders, offering a new direction for process optimization in anaerobic digestion systems. KEY POINTS: • Acinetobacter identified for the first time as main anaerobic protein-degrader • Metabolic model revealed protein degradation via anaerobic respiration • Metabolic pathway analysis indicated SO4[2-] or Fe[3+] as terminal electron acceptors.}, }
@article {pmid40204761, year = {2025}, author = {Li, F and Hooi, SL and Choo, YM and Teh, CSJ and Toh, KY and Lim, LWZ and Lee, YQ and Chong, CW and Ahmad Kamar, A}, title = {Progression of gut microbiome in preterm infants during the first three months.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12104}, pmid = {40204761}, issn = {2045-2322}, support = {IF047-2021//International Funding/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Female ; Male ; Prospective Studies ; *Bacteria/genetics/classification ; Infant ; Gestational Age ; Bifidobacterium/genetics/isolation &amp; purification ; Meconium/microbiology ; Metagenomics ; }, abstract = {The colonization and evolution of gut microbiota early in life play a vital role in shaping a healthy, robust immune system for infant health, whether in combating short-term illness or improving long-term health outcomes. Early-life clinical practices may interrupt or disrupt the normal colonization process of the infant gut microbiota, thereby increasing disease susceptibility. In this prospective cohort study, we analyzed the gut microbiota of 46 term and 23 preterm infants using 16S rRNA gene metagenomic sequencing. Fecal samples were collected at six timepoints during the first three months of life. Notably, gestational age was the main factor contributing to differences in the meconium microbial composition. Intriguingly, our study unveiled a more homogeneous microbial composition in preterm infants with more abundant Bifidobacterium from the postnatal age (PNA) of one month. Concurrently, the beneficial bacteria Bifidobacterium and Lactobacillus gradually increased, and the potentially pathogenic bacteria Clostridium, Enterobacter, Enterococcus, Klebsiella, and Pseudomonas gradually decreased. Furthermore, our study underscored a link between decreased microbial diversity of preterm infants and exclusive breastfeeding and antibiotic exposure. Moreover, preterm infants with patent ductus arteriosus (PDA) exhibited reduced microbial diversity but higher abundances of Streptococcus oralis and Streptococcus mitis.}, }
@article {pmid40204742, year = {2025}, author = {Napit, R and Gurung, A and Poudel, A and Chaudhary, A and Manandhar, P and Sharma, AN and Raut, S and Pradhan, SM and Joshi, J and Poyet, M and Groussin, M and Rajbhandari, RM and Karmacharya, DB}, title = {Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12156}, pmid = {40204742}, issn = {2045-2322}, mesh = {*Gene Transfer, Horizontal ; Animals ; Humans ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/drug effects ; Nepal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Birds/microbiology ; Metagenome ; }, abstract = {Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably, Prevotella spp. was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing E. coli (STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.}, }
@article {pmid40204671, year = {2025}, author = {Luo, G and Fan, L and Liang, B and Guo, J and Gao, SH}, title = {Determining Antimicrobial Resistance in the Plastisphere: Lower Risks of Nonbiodegradable vs Higher Risks of Biodegradable Microplastics.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c00246}, pmid = {40204671}, issn = {1520-5851}, abstract = {The plastisphere is a potential contributor to global antimicrobial resistance (AMR), posing potential threats to public and environmental health. However, comprehensively quantifying the contribution of microplastics with different biodegradability to AMR is lacking. In this study, we systematically quantified AMR risk mediated by biodegradable and nonbiodegradable microplastics using abundance-based methods and a custom AMR risk ranking framework that includes antimicrobial resistance genes (ARGs) abundance, mobility, and host pathogenicity. Our results demonstrated that biodegradable microplastics exhibited higher AMR risk compared to that of nonbiodegradable plastics. Key resistance genes, including those for multidrug, bacitracin, and aminoglycoside resistance, were predominant. Machine learning analysis identified cell motility as the most significant signature associated with AMR risk, highlighting its potential role in promoting ARGs dissemination. In addition, biodegradable microplastics promoted oxidative stress and SOS responses, which likely enhanced horizontal gene transfer (HGT) and AMR. Metagenome-assembled genomes (MAGs) analysis uncovered the colocalization of microplastic degradation genes, ARGs, and virulence factors (VFs), further supporting the elevated risk in biodegradable plastisphere. The proximity of ARGs to mobile genetic elements (MGEs) suggests that microplastic degradation processes might favor ARGs mobility. These findings would contribute critical insights into AMR dissemination in the plastisphere, emphasizing the need for integrated environmental and public health strategies under the context of One Health.}, }
@article {pmid40204030, year = {2025}, author = {Bao, Y and Feng, S and Yu, F and Ye, W and Xing, H and Zhu, X and Bao, W and Huang, M}, title = {Self-Regulating pH Pyrite-Construction waste Biofilter: Denitrification Performance, metabolic Pathways, and clogging Alleviation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132500}, doi = {10.1016/j.biortech.2025.132500}, pmid = {40204030}, issn = {1873-2976}, abstract = {Waste-based denitrification filters face challenges like alkalinity accumulation, low efficiency, and clogging. This study proposes a novel denitrification filter using construction waste and pyrite (WPDF) to address these issues. WPDF's performance, safety, and mechanisms were evaluated by measuring effluent, filler characteristics and metagenomics. Results demonstrated a high total nitrogen removal load (88.65 g N m[-3]d[-1]) with minimal biofilm (13 %) and filler accumulation (39 %), effectively mitigating clogging. Phosphorus removal relied on chemical precipitation in construction waste. WPDF was pH self-regulating and promoted the formation and release of fulvic acid. Pyrite promotes bio-metabolism, making WPDF enriched in energy metabolism (6 %) and transporter capacity (6 %). Functional prediction indicated that WPDF was more abundant in genes related to denitrification, glycolysis, and electron transport, which promoted the heterotrophic denitrification process. This study provides a novel, efficient, and eco-friendly possible solution for wastewater and offers new insights into the molecular mechanisms of carbon and nitrogen metabolism.}, }
@article {pmid40203979, year = {2025}, author = {Genitsaris, S and Stefanidou, N and Kourkoutmani, P and Michaloudi, E and Gros, M and García-Gómez, E and Petrović, M and Ntziachristos, L and Moustaka-Gouni, M}, title = {Do coastal bacterioplankton communities hold the molecular key to the rapid biodegradation of Polycyclic Aromatic Hydrocarbons (PAHs) from shipping scrubber effluent?.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121563}, doi = {10.1016/j.envres.2025.121563}, pmid = {40203979}, issn = {1096-0953}, abstract = {Shipping scrubber effluents, containing a cocktail of Polycyclic Aromatic Hydrocarbons (PAHs), show undisputed effects at single-species experiments while PAHs fate in the marine environment after effluent discharge is still investigated. Bacterioplankton, composed of abundant diverse taxa with xenobiotic-degrading capabilities, are the first responders to scrubber emissions and can affect PAHs impacts on marine life. This work aims to examine the fate of scrubber effluent PAHs and alkyl-PAHs in mesocosms of coastal bacterioplankton communities from a pristine (phytoplankton carbon biomass was 8.16 μg C L[-1]) and a eutrophic (105.35 μg C L[-1]) coastal site. High-throughput 16S rRNA metabarcoding revealed differential responses of the bacterioplankton linked to their initial community structure and population abundances. Taxa known for their PAHs-degrading capacity were retrieved, including the genera Roseobacter, Porticoccus, Marinomonas, Arcobacter, Lentibacter, Lacinutrix, Pseudospirillum, Glaciecola, Vibrio, Marivita, and Mycobacterium, and were found to have increased roles in shifted communities by increasing their relative abundances at least 5-fold in treatments with high scrubber effluent additions. Additionally, metagenomic analysis of shotgun sequencing, indicated an increase on the number of Clusters of Orthologous Genes (COGs) associated with pathways involved in PAHs degradation. Up to 198 more COGs involved in signal transduction were retrieved in scrubber effluent enriched mesocosms compared to controls, while 15, 86, and 136 more COGs associated with naphthalene, aromatic compound, and benzoate degradation, respectively, were detected in the pristine mesocosms after effluent additions. In both experiments, bacterioplankton responses towards xenobiotic degradation under increased PAHs and alkyl-PAHs were coupled with a drop in their concentrations, below the limit of detection by Day 3 of the experiment in the eutrophic community, and by half in Day 6 in the pristine environment's community. Our findings indicate that PAHs and alkyl-PAHs impacts can be rapidly reduced in natural systems of high bacterial activity.}, }
@article {pmid40203710, year = {2025}, author = {Qv, M and Wu, Q and Wang, W and Wang, H and Zhu, L}, title = {Metagenomic insights into the response of microbial metabolic function and extracellular polymeric substances from microalgae-bacteria consortia to fluoroquinolone antibiotics.}, journal = {Journal of environmental management}, volume = {381}, number = {}, pages = {125283}, doi = {10.1016/j.jenvman.2025.125283}, pmid = {40203710}, issn = {1095-8630}, abstract = {Microalgae-bacteria consortia (MBC) are considered a promising bioremediation technology for removing pollutants from swine wastewater. However, the overuse of antibiotics poses challenges to the effective functioning of MBC. In this study, the removal efficiency of nutrients in wastewater by MBC under different antibiotic concentrations (0, 1, 5, 10 and 50 mg/L) was evaluated. The changes of functional microbial abundance were elucidated and the response mechanism of MBC against antibiotics was investigated. Antibiotics inhibited the accumulation of MBC biomass and reduced the removal efficiency of ammonia nitrogen and total phosphorus in wastewater by 8.39 % and 8.74 % respectively. In addition, antibiotics affected the relative abundance of microorganisms (Raineyella, from 30.72 % to 15.96 %) and functional genes (glnA, gudB, NirK, NirBD, NarB, NapAB, NorBC and NosZEPS) involved in N metabolism. MBC could defend against the adverse effects of antibiotics by regulating the content of proteins in the extracellular polymeric substances.}, }
@article {pmid40203094, year = {2025}, author = {Isobe, N and Tanaka, K and Ishii, S and Shimane, Y and Okada, S and Daicho, K and Sakuma, W and Uetani, K and Yoshimura, T and Kimoto, K and Kimura, S and Saito, T and Nakajima, R and Tsuchiya, M and Ikuta, T and Kawagucci, S and Iwata, T and Nomaki, H}, title = {Fully circular shapable transparent paperboard with closed-loop recyclability and marine biodegradability across shallow to deep sea.}, journal = {Science advances}, volume = {11}, number = {15}, pages = {eads2426}, doi = {10.1126/sciadv.ads2426}, pmid = {40203094}, issn = {2375-2548}, abstract = {To mitigate marine pollution from single-use plastics, it is crucial to transition to next-generation commodity materials that are derived from biomass and are recyclable and marine biodegradable even at abyssal depths in case of the accidental release to the ocean. Here, we develop an optically transparent millimeter-thick paperboard called transparent paperboard (tPB) through dissolution and coagulation of cellulose. The tPB is made entirely of pristine cellulose and compositionally identical to paper. A cup-shaped tPB can hold just-boiled water without an internal film coating because of its high wet tensile properties and anisotropic thermal properties. In addition, the spent tPB is material recyclable in a closed system, where all chemicals and water are also recyclable. Furthermore, the marine biodegradability of tPB across shallow to abyssal depths is confirmed by on-site degradation tests and metagenomic analyses. Hence, tPB is expected to serve as a key fully circular commodity material in sustainable societies of the future.}, }
@article {pmid40202861, year = {2025}, author = {Singh, AK and Sathaye, SB and Rai, AK and Singh, SP}, title = {Novel Cellobiose 2-Epimerase from Thermal Aquatic Metagenome for the Production of Epilactose.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c09753}, pmid = {40202861}, issn = {1520-5118}, abstract = {Epilactose is a prebiotic molecule that exerts a bifidogenic effect and increases calcium and iron absorption in the small intestine. This study identifies a novel cellobiose 2-epimerase gene (ceM) by investigating metagenomic data generated from a thermal aquatic habitat. The computation of secondary and tertiary structure analysis, molecular docking, and MD simulation analysis indicated the protein CEM to be a novel cellobiose 2-epimerase. The gene was expressed in Escherichia coli, followed by biochemical characterization of the purified protein. CEM is capable of transforming lactose into the high-value rare sugar, epilactose, in a wide range of temperatures (4-70 °C) and pH (6.0-10.0). The enzyme was exposed to 50 °C, and hardly a 10% loss in activity was recorded after 32 h of heat treatment, suggesting that CEM is a thermostable protein. CEM is a kinetically highly efficient enzyme, with a turnover number of 9832 ± 490 s[-1] for lactose to epilactose epimerization. The maximum conversion yield of 26% epilactose was obtained in 15 min of catalytic reaction. Further, the enzyme was successfully tested to transform lactose in milk and whey samples.}, }
@article {pmid40202719, year = {2025}, author = {Huang, Z and Liu, C and Zhao, X and Guo, Y}, title = {The effect of elevated levels of the gut metabolite TMAO on glucose metabolism after sleeve gastrectomy.}, journal = {Archives of physiology and biochemistry}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/13813455.2025.2489721}, pmid = {40202719}, issn = {1744-4160}, abstract = {Purpose：Bariatric surgery can effectively alleviate obesity and diabetes by regulation of the gut microbiota. This study aimed to investigate the change in the gut microbiota metabolite TMAO and to explore its effect on glucose metabolism after sleeve gastrectomy (SG). Materials and methods：Diet-induced obesity mouse models were established, and the mice were randomly divided into four groups: an SG group, a sham-operated group pair-fed with the SG group (PF), a sham-operated group fed ad libitum (AL), and a lean control group (C). At 10 weeks post-surgery, the changes in glycogen content of liver, gut microbiota and the level of FMO3 in the liver were evaluated, and their correlation with TMAO production was analysed. The expression levels of the TMAO/PERK/FOXO1 pathway and the gluconeogenic genes G6PC and PCK1 were measured. Results：At 10 weeks post-surgery, hepatocyte glycogen levels were restored, and serum TMA and TMAO levels were significantly increased. Faecal metagenomic sequencing results showed that the abundances of Ruminococcaceae and Lachnospiraceae, which were positively correlated with TMAO production, were significantly increased after surgery. While the changes in FMO3, the key enzyme producing TMAO in the liver was found decreased significantly after SG. The expression levels of the TMAO/PERK/FOXO1 pathway and the gluconeogenic genes G6PC and PCK1 were measured. Inconsistent with the changing trend of TMAO, the expression of PERK, FOXO1, PCK, and G6PC significantly decreased after SG. Conclusions：SG can significantly reduce obesity and restore glucose metabolism. After surgery, TMAO metabolites increased in a microbiota-dependent manner.}, }
@article {pmid40202375, year = {2025}, author = {Pan, C and Xu, P and Yuan, M and Wei, S and Lu, Y and Lu, H and Zhang, W}, title = {Effects of Different Feeding Patterns on the Gut Virome of 6-Month-Old Infants.}, journal = {Journal of medical virology}, volume = {97}, number = {4}, pages = {e70344}, doi = {10.1002/jmv.70344}, pmid = {40202375}, issn = {1096-9071}, support = {//This study was supported by the Zhenjiang Science and Technology Innovation Funds-Clinical Medicine Key Laboratory and Scientific Research Project of Health Commission of Jiangsu Province./ ; }, mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; *Virome ; Feces/virology ; *Breast Feeding ; Female ; Male ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; *Feeding Behavior ; Bacteriophages/genetics/classification/isolation &amp; purification ; Milk, Human/virology ; *Gastrointestinal Tract/virology ; }, abstract = {The gut microbiome is essential for infant health, and in recent years, the impact of enteroviruses on infant health and disease has received increasing attention. The transmission of breast milk phages to the infant gastrointestinal tract contributes to the shaping of the infant gut virome, while breastfeeding regulates the colonization of the infant gut virome. In this study, we collected fecal samples from healthy infants and analyzed the distribution characteristics of infant viral communities by viral metagenomic analysis, and analyzed the differences in infant viral communities under different feeding practices. Our results indicate that the infant intestinal virome consists of phages and eukaryotic viruses. Caudovirales and Microviridae dominated the phage composition, and except for Siphoviridae, which was more predominant in the intestines of formula-fed infants, there were no significant differences in the overall abundance of other Caudovirales and Microviridae in the intestines of infants with different feeding patterns. Breastfeeding can lead to a higher diversity of infant gut viruses through vertical transmission, and a highly diverse gut virome helps maintain the maturation of the gut microbiome. This study informs the shaping of gut virome in healthy infants by breastfeeding and contributes to further research on infant gut virome characteristics and formation processes.}, }
@article {pmid40202358, year = {2025}, author = {Alexandre, A and Gerard, &#xc0; and Sergio, I and Whim, T and Isabelle, L and Maria José, C and Lorena, I and Enrique, H and Gerardo, MA and Carolina, M and José, N and Vanessa, B and Rubén, L}, title = {Geographic Influence on Subgingival Microbiota in Health and Periodontitis: A Multinational Shotgun Metagenomic Study.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.13406}, pmid = {40202358}, issn = {1600-0765}, abstract = {AIMS: To assess the differences in the taxonomical and functional profile of the subgingival microbiota isolated from healthy subjects (HS) and patients with periodontitis (PP) from four different countries.<br><br>METHODS: In this study, 80 subgingival samples from HS and PP from four different countries (Belgium, Chile, Peru, and Spain) were analyzed using shotgun metagenomic sequencing.<br><br>RESULTS: The results indicated significant variation in &#x3b1;-diversity between HS and PP, segregated by country, with PP from Peru clearly standing out from the rest. In terms of composition, &#x3b2;-diversity was explained more by the country of origin (6.8%) than by the diagnosis (4.1%). In addition, more than 75 different taxa, 63 of which were identified at the species level, showed significantly different relative abundances when comparing the country of origin, diagnosis, and both variables combined. Moreover, 85 metabolic pathways showed significantly different relative abundances between HS and PP, with species commonly associated with periodontitis, such as Porphyromonas gingivalis and Tannerella forsythia, strongly contributing to the reinforcement of periodontitis-associated pathways. On the other hand, differences in functional profiles based on the country of origin were almost nonexistent, suggesting that variability in taxonomic profiles does not have a direct impact on healthy or periodontitis-associated functional profiles.<br><br>CONCLUSION: These findings suggest that microbial analysis should take into account the geographic origin of samples in order to provide a more accurate description of the subgingival microbiota. Moreover, they lay the groundwork for larger and more comprehensive studies that might analyze this phenomenon in the future.}, }
@article {pmid40202322, year = {2025}, author = {Scheffer, G and Chakraborty, A and Amundson, KK and Khan, R and Wilkins, MJ and Evans, P and Hubert, CRJ}, title = {Polymer biodegradation by Halanaerobium promotes reservoir souring during hydraulic fracturing.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0225324}, doi = {10.1128/aem.02253-24}, pmid = {40202322}, issn = {1098-5336}, abstract = {UNLABELLED: Hydraulically fractured shale reservoirs have facilitated studies of unexplored niches in the continental deep biosphere. In high-salinity North American shale systems, members of the genus Halanaerobium seem to be ubiquitous. Polymers like guar gum used as gelling agents in hydraulic fracturing fluids are known to be fermentable substrates, but metabolic pathways encoding these processes have not been characterized. To explore this, produced water samples from the Permian Basin were incubated both at 30°C to simulate above-ground storage conditions and at 60°C to simulate subsurface reservoir conditions. Guar metabolism coincided with Halanaerobium growing only at 30°C, revealing genes for polymer biodegradation through the mixed-acid fermentation pathway in different metagenome-assembled genomes (MAGs). Whereas thiosulfate reduction to sulfide is often invoked to explain the dominance of Halanaerobium in these settings, genes for thiosulfate metabolism were lacking in Halanaerobium genomes with high estimated completeness. Sulfide production was observed in 60°C incubations, with corresponding enrichment of Desulfohalobium and Desulfovibrionaceae that possess complete pathways for coupling mannose and acetate oxidation to sulfate reduction. These findings outline how production of fermentation intermediates (mannose and acetate) by Halanaerobium in topside settings can result in reservoir souring when these metabolites are introduced into the subsurface through produced water reuse.<br><br>IMPORTANCE: Hydraulically fractured shale oil reservoirs are ideal for studying extremophiles such as thermohalophiles. During hydraulic fracturing, reservoir production water is stored in surface ponds prior to reuse. Microorganisms in these systems therefore need to withstand various environmental changes such as the swing between warm downhole oil reservoir temperatures and cooler surface conditions. While most studies on hydraulically fractured oil reservoirs mimic the environmental conditions found in oil wells, this study follows this water cycle during fracking and the associated microbial metabolic potential during topside-produced water storage and subsurface oil reservoir conditions. Of particular interest are members of the genus Halanaerobium that have been reported to reduce thiosulfate contributing to souring of oil reservoirs. Here, we show that some Halanaerobium strains were unable to grow at hotter temperatures reflective of oil reservoir conditions and lack genes for thiosulfate reduction, despite the proposed importance of this metabolism in other studies. Rather, it is likely that these organisms metabolize complex organics in fracking fluids at lower temperatures, thereby generating substrates that support reservoir souring by thermophilic sulfate-reducing bacteria at higher temperatures. In this way, Halanaerobium promotes souring indirectly by feeding sulfate-reducing microorganisms fermentation products (e.g., acetate and hydrogen) rather than via direct sulfidogenesis via thiosulfate reduction. Therefore, the novelty of this research is not within the detection of known oil reservoir colonizing bacteria but rather in the relationship between bacteria and the indirect involvement of Halanaerobium, promoting souring throughout the produced water reuse cycle.}, }
@article {pmid40202301, year = {2025}, author = {Mahillon, M and Debonneville, C and Groux, R and Roquis, D and Brodard, J and Faoro, F and Foissac, X and Schumpp, O and Dittmer, J}, title = {From insect endosymbiont to phloem colonizer: comparative genomics unveils the lifestyle transition of phytopathogenic Arsenophonus strains.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0149624}, doi = {10.1128/msystems.01496-24}, pmid = {40202301}, issn = {2379-5077}, abstract = {UNLABELLED: Bacteria infecting the plant phloem represent a growing threat worldwide. While these organisms often resist in vitro culture, they multiply both in plant sieve elements and hemipteran vectors. Such cross-kingdom parasitic lifestyle has emerged in diverse taxa via distinct ecological routes. In the genus Arsenophonus, the phloem pathogens "Candidatus Arsenophonus phytopathogenicus" (Ap) and "Ca. Phlomobacter fragariae" (Pf) have evolved from insect endosymbionts, but the genetic mechanisms underlying this transition have not been explored. To fill this gap, we obtained the genomes of both strains from insect host metagenomes. The resulting assemblies are highly similar in size and functional repertoire, rich in viral sequences, and closely resemble the genomes of several facultative endosymbiotic Arsenophonus strains of sap-sucking hemipterans. However, a phylogenomic analysis demonstrated distinct origins, as Ap belongs to the "Triatominarum" clade, whereas Pf represents a distant species. We identified a set of orthologs encoded only by Ap and Pf in the genus, including hydrolytic enzymes likely targeting plant substrates. In particular, both bacteria encode putative plant cell wall-degrading enzymes and cysteine peptidases related to xylellain, a papain-like peptidase from Xylella fastidiosa, for which close homologs are found in diverse Pseudomonadota infecting the plant vasculature. In silico predictions and gene expression analyses further support a role during phloem colonization for several of the shared orthologs. We conclude that the double emergence of phytopathogenicity in Arsenophonus may have been mediated by a few horizontal gene transfer events, involving genes acquired from other Pseudomonadota, including phytopathogens.<br><br>IMPORTANCE: We investigate the genetic mechanisms of a transition in bacterial lifestyle. We focus on two phloem pathogens belonging to the genus Arsenophonus: "Candidatus Arsenophonus phytopathogenicus" and "Ca. Phlomobacter fragariae." Both bacteria cause economically significant pathologies, and they have likely emerged among facultative insect endosymbionts. Our genomic analyses show that both strains are highly similar to other strains of the genus associated with sap-sucking hemipterans, suggesting a recent lifestyle shift. Importantly, although the phytopathogenic Arsenophonus strains belong to distant clades, they share a small set of orthologs unique in the genus pangenome. We provide evidence that several of these genes produce hydrolytic enzymes that are secreted and may target plant substrates. The acquisition and exchange of these genes may thus have played a pivotal role in the lifestyle transition of the phytopathogenic Arsenophonus strains.}, }
@article {pmid40201781, year = {2025}, author = {Belkina, D and Stepanov, I and Makarkina, M and Porotikova, E and Lifanov, I and Kozhevnikov, E and Gorislavets, S and Vinogradova, S}, title = {In-depth population genetic study of Vitis vinifera ssp. sylvestris from the Black Sea region and its virome.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1536862}, pmid = {40201781}, issn = {1664-462X}, abstract = {The spread of cultivated grapevine from primary centers of origin is inevitably accompanied by the range expansion of its pathogens, including viruses. A limited number of wild Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi populations have survived in the centers of grapevine domestication and can be used for comprehensive studies. We analyzed 50 grapevines collected in protected areas of the Black Sea region, which belong to the Caucasian domestication center. Based on genotyping of grapevines using simple sequence repeats as DNA markers, we determined the phylogenetic placement of V. vinifera ssp. sylvestris from the Black Sea region compared to cultivated and wild grapevines of the world. Using high-throughput sequencing of total RNA, we obtained the viromes of these grapevines. Ten viruses and one viroid were identified. The most common viruses detected were Vitis cryptic virus, grapevine rupestris stem pitting-associated virus, grapevine Pinot gris virus, and grapevine virus T. Among the economically significant viruses, we identified grapevine leafroll-associated virus 1 and grapevine virus A. A total of 91 complete or nearly complete virus genomes and one viroid genome were assembled, and phylogenetic analysis was performed. Two novel (+) ssRNA viruses were discovered, tentatively named Abrau grapevine-associated virus in the order Hepelivirales and Taurida grapevine-associated virus in the order Picornavirales. It is important to comprehensively consider the phylogeography of both viruses and their plant hosts. This is the first study that simultaneously addresses the population genetics of V. vinifera ssp. sylvestris from the Caucasian domestication center and its viruses.}, }
@article {pmid40201723, year = {2025}, author = {Luo, H and Jiang, Y and He, Y and Zhou, H}, title = {Clinical Value of Metagenomic Next-Generation Sequencing From Blood Samples to Identify Pneumocystis jirovecii Pneumonia in Patients With Human Immunodeficiency Virus.}, journal = {Open forum infectious diseases}, volume = {12}, number = {4}, pages = {ofaf170}, pmid = {40201723}, issn = {2328-8957}, abstract = {BACKGROUND: The aim of this study was to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) of blood samples for identifying Pneumocystis jirovecii pneumonia (PJP) in patients with human immunodeficiency virus (HIV).<br><br>METHODS: A total of 76 people with HIV (PWH) with suspected lung infections were enrolled in the study. The patients were divided into two groups: the PJP group and the non-PJP group.All patients underwent pulmonary computed tomography scans, and blood or respiratory tract specimens were subjected to mNGS and conventional microbiological tests. Patient characteristics were collected from their medical records.<br><br>RESULTS: Thirty patients were diagnosed with PJP and 46 were confirmed to have non-P jirovecii (Pj) infectious pneumonia. mNGS was conducted on bronchoalveolar lavage fluid samples from 25 patients and on blood samples from 59 patients. Twenty-one of 22 (95.5%) blood samples from the PIP group contained sequences of Pi, with the number of specific reads for circulating Pj sequences ranging from 2 to 2035. In the non-PJP group, 4 blood samples exhibited low Pj sequences, ranging from 1 to 2 reads. The sensitivity and specificity for blood samples were 95.5% (95% confidence interval [CI], 91.2%-98.4%) and 90.0% (95% Cl, 89.5%-100%), respectively.<br><br>CONCLUSIONS: Our study indicates that mNGS of blood samples exhibits high sensitivity and specificity for diagnosing PJP in PWH. Caution should be exercised when interpreting low Pj mNGS read counts in blood samples; the definitive diagnosis of PJP relies on the synthesis of clinical data with Pj mNGS results. Further studies are necessary to validate this finding.}, }
@article {pmid40201438, year = {2025}, author = {Lu, W and Yi, X and Ge, Y and Zhang, X and Shen, K and Zhuang, H and Deng, Z and Liu, D and Cao, J and Ma, C}, title = {Effects of dietary fiber on the composition, function, and symbiotic interactions of intestinal microbiota in pre-weaned calves.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1554484}, pmid = {40201438}, issn = {1664-302X}, abstract = {INTRODUCTION: Dietary fiber plays a crucial role in maintaining gastrointestinal health. However, its protective effects on the intestinal health of calves remain to be fully elucidated. This study aimed to investigate the impact of dietary fiber supplementation on the intestinal microbiota of pre-weaned calves and its potential role in modulating microbial metabolic pathways.<br><br>METHODS: A randomized controlled trial was conducted, enrolling 135 calves that were randomly assigned into three groups: (1) inulin supplementation, (2) psyllium husk powder (PHP) supplementation, and (3) a control group receiving no dietary fiber. Fecal microbiota samples were collected from calves without diarrhea at five time points (0, 7, 14, 28, and 56 days of age). Metagenomic sequencing was performed to analyze microbial composition and functional pathways. Additionally, a differential analysis of carbohydrate-active enzymes (CAZymes) was performed to evaluate the effect of dietary fiber on carbohydrate metabolism enzyme activity within the intestinal microbiota.<br><br>RESULTS: Calves supplemented with dietary fiber exhibited a significant increase in the abundance of Bifidobacterium and Prevotella compared to the control group. These bacterial genera contributed to intestinal protection by modulating secondary bile acid metabolism and flavonoid metabolism pathways. CAZymes differential analysis revealed an increased abundance of carbohydrate metabolism enzymes in response to dietary fiber supplementation, with distinct microbial community compositions observed among different fiber treatments. Notably, at 56 days of age, calves fed PHP harbored intergeneric symbiotic clusters comprising Clostridium, Prevotella, and Bacteroides, suggesting a cooperative microbial network that may contribute to intestinal homeostasis.<br><br>DISCUSSION: The findings of this study highlight the beneficial effects of dietary fiber on calf intestinal microbiota, particularly in enhancing microbial diversity and enzymatic activity related to carbohydrate metabolism. The observed microbial symbiosis in PHP-fed calves suggests a potential role in maintaining intestinal homeostasis. These insights provide a theoretical foundation for optimizing dietary interventions to promote gut health in calves during the transition period. Further research is warranted to explore the mechanistic interactions between dietary fiber, gut microbiota, and host health outcomes.}, }
@article {pmid40201435, year = {2025}, author = {Tang, J and Li, P and Xu, H and Han, J}, title = {Clinical application of metagenomic next-generation sequencing in rapid diagnosis and prognostic assessment of herpes simplex encephalitis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1534513}, pmid = {40201435}, issn = {1664-302X}, abstract = {PURPOSE: Herpes simplex encephalitis (HSE) ranks among the most common causes of severe viral encephalitis. It leads to meningitis or encephalitis, with patients frequently encountering adverse outcomes. In this study, we utilized metagenomic next-generation sequencing (mNGS) to rapidly and accurately detect and identify the HSV pathogen directly from cerebrospinal fluid (CSF) samples, aiming to achieve a definitive diagnosis for encephalitis patients.<br><br>METHODS: From 2018 to 2023, we prospectively identified and enrolled 28 patients diagnosed with HSE at Hengshui People's Hospital. CSF samples were subjected to mNGS to facilitate the diagnosis and characterization of HSE in this cohort. We compiled the clinical characteristics, supplementary examinations, and outcomes of HSE patients, with prognosis assessed using the Glasgow Outcome Scale (GOS) scores at discharge, 1&#x202f;month post-discharge, and 3&#x202f;months thereafter.<br><br>RESULTS: In this cohort of 28 patients, 12 were females and 16 males, with a mean age of 41.82&#x202f;&#xb1;&#x202f;18.23. HSE manifested with a variety of clinical symptoms, the most prevalent being headaches (67.9%), fever exceeding 38&#xb0;C (60.7%), and altered consciousness (60.7%). Seizures (42.9%), vomiting (35.7%), and speech deficits (35.7%) were frequently observed, with a minority of patients displaying personality changes (28.6%). CSF analysis revealed pleocytosis and a mild increase in protein levels. Magnetic resonance imaging (MRI) abnormalities (28.6%) were primarily confined to the frontal and temporal lobes as well as limbic regions, with no indications of cerebral hemorrhage. Half of the patients exhibited Electroencephalogram (EEG) changes suggestive of encephalitis. HSE was confirmed through mNGS analysis of CSF within 3&#x202f;days of admission. All patients received empirical treatment with ganciclovir, with 46.4% undergoing hormonotherapy and 32.1% receiving immunoglobulin therapy. At the three-month follow-up, 32.1% had GOS scores <5.<br><br>CONCLUSION: HSE often presents with nonspecific signs of encephalitis, and it's not easy for traditional CNS examinations to confirm the diagnosis. mNGS serves as a cutting-edge diagnostic tool for the rapid and precise identification of HSE, facilitating timely clinical diagnosis and intervention to prevent the progression of the disease.}, }
@article {pmid40201423, year = {2025}, author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Boenigk, J}, title = {The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf049}, pmid = {40201423}, issn = {2730-6151}, abstract = {Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence in situ hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against Microbacterium lacusdiani (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.}, }
@article {pmid40201367, year = {2025}, author = {Wen, Y and Zhang, W and Li, Y and Liao, X and Xu, J and Zhen, R and Qin, P}, title = {Epidemiological characteristics of human psittacosis in Guangzhou, China, January 2021 to June 2024.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1526990}, pmid = {40201367}, issn = {2296-2565}, mesh = {Humans ; China/epidemiology ; Male ; Middle Aged ; Adult ; *Psittacosis/epidemiology ; Female ; Aged ; Animals ; Seasons ; Zoonoses/epidemiology ; Adolescent ; Young Adult ; Prevalence ; Child ; }, abstract = {BACKGROUND: Psittacosis is a global and underappreciated zoonosis, with increasing reported cases in many countries. There have been several outbreaks and even deaths of psittacosis reported in China. Understanding its epidemiological characteristics and dimensions is crucial for formulating precise prevention and control strategies. This study aimed to analyze the epidemiological characteristics of human psittacosis in Guangzhou, China.<br><br>METHODS: The demographic characteristics, clinical manifestations, temporal patterns, geographic distribution and potential exposures of psittacosis in Guangzhou were analyzed based on the surveillance data and epidemiological investigation conducted between January 2021 and June 2024. Seasonal and trend decomposition using LOESS was applied to decompose the number of psittacosis cases into trend, seasonal and remainder component.<br><br>RESULTS: A total of 148 cases were reported, with a significant increase in the number of psittacosis cases over the study period. Most of cases were sporadic and detected by metagenomic next-generation sequencing (mNGS). Psittacosis was predominant males aged 40-79&#x202f;years. Fever and pneumonia were the most commonly observed clinical manifestations. A seasonal trend was observed in the number of psittacosis cases with a high prevalence of cases in December and March. A total of 108 local cases (87%) occurred in rural regions. Among local cases, 67.7% reported a history of contact with birds or poultry, and 17.7% had been exposed to a related environment. The suspected source of infection differed between urban and rural areas, with parrots being the primary source in urban areas and poultry in rural areas.<br><br>CONCLUSION: Increasing clinicians' awareness, enhancing epidemiological surveillance, paying close attention to the epidemic in rural areas, and implementing measures against avian influenza, will be conducive to preventing and controlling psittacosis.}, }
@article {pmid40200351, year = {2025}, author = {Zhang, Z and Huang, Z and Fang, X and Bai, G and Li, W and Zhang, W and Zhang, C}, title = {Diagnosis and surgical treatment of chronic destructive septic hip arthritis.}, journal = {Arthroplasty (London, England)}, volume = {7}, number = {1}, pages = {19}, pmid = {40200351}, issn = {2524-7948}, support = {2023Y9092//Joint Funds for the Innovation of Science and Technology, Fujian province/ ; 2022Y4003//University-Industry Research Cooperation Project of Science and Technology, Fujian province/ ; YXRQN-ZCF2023//The First Affiliated Hospital of Fujian Medical University Excellent Talent Program/ ; YJCRC-B-ZWM2024//The First Affiliated Hospital of Fujian Medical University Excellent Talent Program/ ; }, abstract = {Septic hip arthritis (SHA) is a relatively rare but hazardous disease. Much controversy exists regarding the definition, diagnosis and treatment of chronic destructive SHAs. This review aims to provide an overview of the diagnostic and therapeutic approaches for chronic, destructive SHA and suggest possible research directions for this disease's future diagnosis and treatment. There is no unified naming or classification standard for SHAs. Chronic destructive SHA still requires a comprehensive diagnosis combining history, signs, bacterial culture, histopathological examination, inflammation and other indicators, of which metagenomic next-generation sequencing is a promising diagnostic tool. Previous treatment options for this disease include debridement, debridement + Girdlestone femoral head and neck resection, and debridement + Girdlestone femoral head and neck resection + two-stage arthroplasty. Among them, one-stage spacer implantation + two-stage arthroplasty is the current standard surgical option with a high success rate and low reinfection rate, while one-stage arthroplasty is a new treatment option proposed in recent years with unique advantages but limitations in terms of surgical indications. In the future, more high-quality studies are needed to provide the latest evidence to support clinical decision-making.}, }
@article {pmid40200155, year = {2025}, author = {Zhou, Z and Hu, X and Wang, J and Wang, N}, title = {Invasive cerebral aspergillosis in a pregnant woman: a rare case of intracranial giant granuloma.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {478}, pmid = {40200155}, issn = {1471-2334}, mesh = {Humans ; Female ; Pregnancy ; Adult ; Antifungal Agents/therapeutic use ; *Neuroaspergillosis/diagnosis/drug therapy/pathology/surgery/microbiology ; *Granuloma/microbiology/pathology/diagnosis/surgery ; *Pregnancy Complications, Infectious/diagnosis/microbiology/drug therapy/pathology ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; Brain/pathology/diagnostic imaging/microbiology ; }, abstract = {BACKGROUND: Invasive Cerebral Aspergillosis (ICA) is a rare fungal infection affecting the brain, primarily seen in individuals with compromised immune systems. Despite various treatment options, substantial cerebral granulomas caused by ICA still result in high mortality and recurrence rates.<br><br>CASE PRESENTATION: We report a rare instance of ICA in a 30-year-old pregnant woman. The infection initiated in the nasal cavity and progressed to form a large intracranial granuloma, leading to brain herniation. Diagnosis was confirmed through histopathology, Polymerase Chain Reaction (PCR), and metagenomic next-generation sequencing (mNGS) following decompressive craniotomy and sinus window drainage surgery. Prompt administration of antifungal medication resulted in a favorable prognosis.<br><br>CONCLUSION: This case highlights the critical roles of mNGS and PCR in the early diagnosis of ICA, as well as the pivotal importance of surgical interventions and prompt initiation of antifungal therapy in enhancing patient outcomes.}, }
@article {pmid40199830, year = {2025}, author = {Singh, P and Haldhar, P and Das, T and Chaubey, G and Gupta, MK and Kumar, B}, title = {Thermal Stress and Its Effects on the Gut Microbiome of Parthenium Beetles.}, journal = {Archives of insect biochemistry and physiology}, volume = {118}, number = {4}, pages = {e70058}, doi = {10.1002/arch.70058}, pmid = {40199830}, issn = {1520-6327}, support = {//The authors received no specific funding for this work./ ; }, mesh = {Animals ; *Coleoptera/microbiology/physiology ; *Gastrointestinal Microbiome ; *Stress, Physiological ; Bacteria/classification/isolation &amp; purification/genetics ; Hot Temperature ; RNA, Ribosomal, 16S/analysis ; }, abstract = {The gut microbiota plays a vital role in nutrient and energy utilization, as well as in the host's ability to adapt its immune system to environmental changes. As a biological control agent for the invasive Parthenium weed, the Parthenium beetle Zygogramma bicolorata (Z. bicolorata) Pallister is often exposed to fluctuating temperatures, which may induce stress in its natural habitat. This study utilized 16S amplicon sequencing to explore the impact of temperature stress on the gut microbiome of Z. bicolorata under cold (15°C), control (27°C), and hot (35°C) conditions. A total of 11 bacterial phyla and 149 genera were identified, with Firmicutes, Proteobacteria, and Cyanobacteria being the most abundant. Temperature treatments significantly influenced the diversity of the gut microbiota, as evidenced by alpha diversity measures. Principal coordinate analysis further revealed substantial variations in microbiome composition across the different temperature conditions. Additionally, PICRUSt2 analysis suggested that the gut microbiota is linked to metagenomic functions related to amino acid and carbohydrate transport, inorganic ion metabolism, and cellular processes. Our findings suggest that thermal stress alters the gut microbiome of Parthenium beetles, offering new insights into how these beetles may have ecologically adapted to temperature fluctuations, while also highlighting the potential role of gut microbes in maintaining beetle health under environmental stress.}, }
@article {pmid40199391, year = {2025}, author = {Tan, Y and Li, L and Zhao, Z and Li, Y and Li, T and Li, Y and Sheng, X and Shen, L and Xu, Z and Song, S and Zhang, P}, title = {Simultaneous pollutant removal and organic matter sequestration by coral sand-pyrite-based electroactive constructed wetlands.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132498}, doi = {10.1016/j.biortech.2025.132498}, pmid = {40199391}, issn = {1873-2976}, abstract = {The development of integrated solutions for sewage treatment and soil restoration in remote regions remains a challenge. This study innovatively designed coral sand-pyrite-based electroactive constructed wetlands (E-CWs) to synchronize wastewater purification and organic matter (OM) enrichment. Metagenomic analyses revealed that the addition of pyrite increased the abundance of iron redox-related genes, whereas coral sand salinity promoted the enrichment of functional bacteria for OM decomposition. Furthermore, the combined substrate comprising coral sand and pyrite facilitated the adsorption and sequestration of OM, while providing a stable environment for microorganisms. This achieved dual objectives: efficient chemical oxygen demand removal (90.6 ± 2.4 %) from sewage and substantial OM sequestration in substrates (total organic carbon: 2.9-4.8 %). This study achieved sewage treatment through the combination of coral sand and pyrite as substrates of E-CWs and enhanced the OM content of the substrates, contributing to the improvement of local soil infertility.}, }
@article {pmid40198556, year = {2025}, author = {Holden, S and Kim, SH and Chen, W and Li, X and Bakkeren, G and Brar, GS}, title = {Identification of Rust Fungi Using High-Throughput Sequencing Data from Environmental Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2898}, number = {}, pages = {151-188}, pmid = {40198556}, issn = {1940-6029}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Basidiomycota/genetics/isolation &amp; purification/classification ; *Plant Diseases/microbiology ; *Fungi/genetics ; DNA, Fungal/genetics ; }, abstract = {Working with any plant-associated microbe comes with the inherent challenge that no environment is sterile, and a plant's metabiome is teeming with life. When collecting field samples outside of the laboratory, this issue is compounded further. Rust fungi, being obligate plant pathogens, are challenging to maintain, and strict protocols must be adhered to in the laboratory to prevent cross-contamination. In this era of big data and easy access to next generation sequencing (NGS), it is increasingly common for scientists to work with large sequencing datasets, which must first be evaluated for quality and filtered for potentially nontarget reads. Sequencing data files from environmental samples often contain genetic material from organisms not targeted by the experimental design. This situation can lead to issues if researchers assume the presence of only their intended subjects. Additionally, the origin of some samples may be inherently unknown, making the main objective of certain sequencing experiments to identify all organisms present, not just the expected ones.This chapter details common in silico approaches for identifying and classifying samples from sequencing data, drawing on experiences with cereal rust samples collected in the field. While the concepts are broadly applicable, they may require some tailoring for your species of interest. The chapter does not cover population-genomics level approaches to sample classification; instead, it describes essential quality control steps that researchers should implement before conducting downstream analyses to ensure that their data is appropriate for the intended tests.}, }
@article {pmid40198136, year = {2025}, author = {Fishman, JA and Denner, J and Scobie, L}, title = {International Xenotransplantation Association (IXA) Position Paper on Infectious Disease Considerations in Xenotransplantation.}, journal = {Transplantation}, volume = {}, number = {}, pages = {}, pmid = {40198136}, issn = {1534-6080}, abstract = {Clinical xenotransplantation has the potential to address shortages of human organs for patients with end-stage organ failure. Advances in genetic engineering, immunosuppressive regimens, and infectious disease diagnostics have improved prospects for clinical xenotransplantation. Management of the infectious risks posed by clinical xenotransplantation requires biosecure breeding and validated methods for microbiological surveillance of source animals and recipients. Novel infection control protocols may complement biosafety requirements. Infectious risks in xenotransplantation include both known human pathogens common to immunosuppressed organ recipients and from porcine organisms or xenozoonoses for which the clinical manifestations are less well defined and for which microbial assays and therapies are more limited. Some pig-specific organisms do not infect human cells but have systemic manifestations when active within the xenograft. The human risk posed by porcine endogenous retroviruses (PERV) is uncertain. There are no documented transmissions of PERV in humans and swine are available with inactivated genomic PERV loci. Metagenomic sequencing will complement more traditional diagnostic tools in the detection of any unknown pathogens in xenotransplantation recipients. Such data are required for the development of protocols for donor and recipient microbiological surveillance, infection control, and antimicrobial therapies that will enhance the safety of clinical xenotransplantation.}, }
@article {pmid40197807, year = {2025}, author = {Fishman, JA and Denner, J and Scobie, L}, title = {International Xenotransplantation Association (IXA) Position Paper on Infectious Disease Considerations in Xenotransplantation.}, journal = {Xenotransplantation}, volume = {32}, number = {2}, pages = {e70001}, doi = {10.1111/xen.70001}, pmid = {40197807}, issn = {1399-3089}, mesh = {*Transplantation, Heterologous/adverse effects/methods ; Animals ; Humans ; Swine ; *Heterografts/microbiology/virology ; Endogenous Retroviruses ; *Communicable Diseases/transmission ; }, abstract = {Clinical xenotransplantation has the potential to address shortages of human organs for patients with end-stage organ failure. Advances in genetic engineering, immunosuppressive regimens, and infectious disease diagnostics have improved prospects for clinical xenotransplantation. Management of the infectious risks posed by clinical xenotransplantation requires biosecure breeding and validated methods for microbiological surveillance of source animals and recipients. Novel infection control protocols may complement biosafety requirements. Infectious risks in xenotransplantation include both known human pathogens common to immunosuppressed organ recipients and from porcine organisms or xenozoonoses for which the clinical manifestations are less well defined and for which microbial assays and therapies are more limited. Some pig-specific organisms do not infect human cells but have systemic manifestations when active within the xenograft. The human risk posed by porcine endogenous retroviruses (PERV) is uncertain. There are no documented transmissions of PERV in humans and swine are available with inactivated genomic PERV loci. Metagenomic sequencing will complement more traditional diagnostic tools in the detection of any unknown pathogens in xenotransplantation recipients. Such data are required for the development of protocols for donor and recipient microbiological surveillance, infection control, and antimicrobial therapies that will enhance the safety of clinical xenotransplantation.}, }
@article {pmid40197788, year = {2025}, author = {Arenas-Montes, J and Alcala-Diaz, JF and Garcia-Fernandez, H and Gutierrez-Mariscal, FM and Lopez-Moreno, A and Luque-Cordoba, D and Arenas-de Larriva, AP and Torres-Peña, JD and Luque, RM and Prodam, F and Priego-Capote, F and Delgado-Lista, J and Lopez-Miranda, J and Camargo, A}, title = {A microbiota pattern associated with cardiovascular events in secondary prevention: the CORDIOPREV study.}, journal = {European heart journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/eurheartj/ehaf181}, pmid = {40197788}, issn = {1522-9645}, support = {//Fundacion Patrimonio Comunal Olivarero/ ; //CEAS/ ; //Centro de Excelencia en Investigacion sobre Aceite de Oliva/ ; CVI-7450//Junta de Andalucia/ ; //Diputaciones de Jaen y C&#xf3;rdoba/ ; //Ministerio de Medio Ambiente, Medio Rural y Marino/ ; //Spanish Government/ ; AGL2012/39615//Ministerio de Ciencia e Innovaci&#xf3;n, Spain/ ; //MCIN/AEI/10.13039/501100011033/ ; CP14/00114//Instituto de Salud Carlos III/ ; PI-0055-2021//Consejer&#xed;a de Salud y Familias, Junta de Andaluc&#xed;a/ ; //Consejeria de Innovaci&#xf3;n, Ciencia y Empresa, Proyectos de Investigaci&#xf3;n de Excelencia/ ; //European Union/ ; CP14/00114//Programa Miguel-Servet/ ; //Servicio Andaluz de Salud-Junta de Andalucia/ ; C1-0001-2022//Nicolas Monardes Programme Contract/ ; }, abstract = {BACKGROUND AND AIMS: Preventing new cardiovascular events in patients with established cardiovascular disease (CVD) is a daunting task for clinicians. Intestinal microbiota may help identify patients at risk, thus improving the strategies of secondary prevention. The aim of this study was to evaluate the baseline differences between the gut microbiota from coronary heart disease (CHD) patients suffering new major adverse cardiovascular events (MACEs) in the following 7 years, compared with CHD patients who did not undergo new MACE in this period, and to build a score associated with the risk of suffering new MACE.<br><br>METHODS: Within the framework of the CORDIOPREV study, a clinical trial that involved 1002 patients with CHD, intestinal microbiota was examined in patients with available faecal samples (n = 679, 132 MACE), through 16S metagenomics on the Illumina MiSeq and Quiime2 software. Lipopolysaccharide (LPS) was measured using limulus amoebocyte lysate test.<br><br>RESULTS: Random survival forest identified 10 bacterial taxa with a higher predictive power for MACE incidence. Receiver operating characteristic curves yielded an area under the curve of 65.2% (59.1%-71.3%) in the training set and 68.6% (59.3%-77.9%) in the validation set. The intestinal microbiota risk score was associated with a MACE incidence hazard ratio of 2.01 (95% confidence interval 1.37-3.22). Lipopolysaccharide analysis showed a greater LPS post-prandial fold change in the MACE group (P = .005).<br><br>CONCLUSIONS: These results reinforce the relationship between intestinal microbiota and CVD and suggest that a microbiota profile is associated with MACE in CHD patients, in addition to higher endotoxaemia.}, }
@article {pmid40197742, year = {2025}, author = {He, C and Gonsior, M and Liu, J and Jiao, N and Chen, F}, title = {Genome-streamlined SAR202 bacteria are widely present and active in the euphotic ocean.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf049}, pmid = {40197742}, issn = {1751-7370}, abstract = {SAR202 bacteria are a diverse group of bacteria in the ocean. The SAR202 lineages dominate the bacterial community and evolve specialized metabolisms for oxidizing recalcitrant organic compounds in the dark ocean. SAR202 bacteria are also present in the euphotic oceans; however, their ecological roles and metabolic potential remain poorly understood. In this study, we collected 392 non-redundant metagenome-assembled genomes from different oceans, with 18% of these SAR202 genomes characterized by small genome sizes (< 2 Mbp), low GC content (< 40%), and high gene density. The 70 genome-streamlined SAR202 bacteria constitute more than an average of 90% of SAR202 in the euphotic zone and exhibit streamlined metabolic features compared to the dark ocean SAR202. Genome-streamlined SAR202 are distributed in many major SAR202 lineages (i.e. I, II, III, and VI). Phylogenomic analysis shows that the genome-streamlined SAR202 clades diverged from the non-genome-streamlined SAR202 lineages and evolved independently within the same clades. Certain genes are enriched in genome-streamlined SAR202, such as proteorhodopsin genes and the coding genes of major facilitator superfamily transporters, nucleoside transporters, and deoxyribodipyrimidine photo-lyase, indicating their adaptation to sunlit oligotrophic water. A detailed comparison between genome-streamlined SAR202 and non-genome-streamlined SAR202 was made to illustrate their distinct niche distribution and metabolic buildup. In addition, the metatranscriptomic analysis supports that genome-streamlined SAR202 bacteria are active in the upper ocean. This study represents a systematic study of streamlined SAR202 bacteria that occupy the euphotic ocean and provides a comprehensive view of the ecological roles of SAR202 bacteria in the ocean.}, }
@article {pmid40197145, year = {2025}, author = {Feng, KH and Qi, YH and Ye, ZX and Li, T and Jiao, GY and Zhang, CX and Chen, JP and Lu, G and Li, JM}, title = {Diversity and evolution analysis of RNA viruses in three wheat aphid species.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {353}, doi = {10.1186/s12864-025-11512-1}, pmid = {40197145}, issn = {1471-2164}, support = {2024YFD1400400//National Key Research and Development Program of China/ ; LY24C140001//Natural Science Foundation of Zhejiang Province/ ; 2024J016//Ningbo Natural Science Foundation/ ; 2023S029//Ningbo Commonweal Project/ ; }, mesh = {*Aphids/virology/genetics ; Animals ; }, abstract = {BACKGROUND: Although advances in metagenomics, viral diversity and non-retroviral endogenous viral elements (EVEs) in wheat aphids remain underexplored. By analyzing 470 publicly available datasets and one laboratory-generated transcriptome, the RNA virome and EVEs in the genomes of Sitobion avenae, Schizaphis graminum, and Rhopalosiphum padi were systematically investigated.<br><br>RESULTS: We identified 43 RNA viruses, including 12 novel and 31 known RNA viruses. These viruses were widely distributed and abundant in different geographic populations of three wheat aphid species. +ssRNA viruses were the dominant type of aphid viruses. Besides, 90 EVEs were discovered in the genomes of three aphid species. In addition, the EVEs exhibit potential domestication and novel functional roles within aphid genomes.<br><br>CONCLUSIONS: This study expands the understanding of RNA virus diversity in aphids and provides valuable insights into the potential functions of EVEs in virus-host coevolution.}, }
@article {pmid40197113, year = {2025}, author = {Karabekmez, ME}, title = {Harnessing Human Holobiome and Meta-Multi-Omics Analyses for Medical Applications.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/omi.2025.0024}, pmid = {40197113}, issn = {1557-8100}, abstract = {Next-generation sequencing technology has revolutionized all fields of living systems, and its applications almost reinvented some research areas including metagenomics. The microbiotas in our body, including those of the oral, nasal, ocular, alveolar, skin regions, and particularly gut microbiota, have close linkages with our health status. Maturation of experimental techniques for metagenomics has been followed by other related omics platforms, for example, metatranscriptomics, metaproteomics, and all possible metacounterparts of multiomics studies. Now, we are on the eve of a meta-multi-omics era for the analysis of human holobiome in medical research. This era will help buttress the current efforts for systems medicine by illuminating the relationships between human holobiome and health or all human diseases including not only cancers but also infectious diseases, autoimmune diseases, obesity, aging, genetic disorders, and psychiatric conditions. Equally important, meta-multi-omics era is also poised to inform the determinants of human health and, by extension, help build individually tailored precision medicine interventions.}, }
@article {pmid40197060, year = {2025}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of the Neisseriaceae family in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0327524}, doi = {10.1128/spectrum.03275-24}, pmid = {40197060}, issn = {2165-0497}, abstract = {The human oral microbiome is a diverse ecosystem in which bacterial species have evolved to occupy specific niches within the oral cavity. The Neisseriaceae family, which includes human oral species in the genera Neisseria, Eikenella, Kingella, and Simonsiella, plays a significant role in both commensal and pathogenic relationships. In this study, we investigate the distribution and functional adaptations of Neisseriaceae species across oral habitats, focusing on their site tropisms and ecological roles. We employed a metapangenomic approach in which a curated set of reference genomes representing Neisseriaceae diversity was used for competitive mapping of metagenomic reads. Our analysis revealed distinct habitat preferences among Neisseriaceae species, with Kingella oralis, Neisseria elongata, and Neisseria mucosa primarily found in dental plaque; Neisseria subflava on the tongue dorsum; and Neisseria cinerea in the keratinized gingiva. Functional enrichment analyses identified genes and pathways underpinning habitat-specific adaptations. Plaque specialists showed metabolic versatility, with adaptations in nitrogen metabolism, including nitrate reduction and denitrification, lysine degradation, and galactose metabolism. Tongue dorsum specialists exhibited adaptations including enhanced capabilities for amino acid biosynthesis, short-chain fatty acid and glycerol transport, as well as lipopolysaccharide glycosylation, which may aid in resisting antimicrobial peptides and maintaining membrane integrity. These findings provide insights into the ecological roles and adaptive strategies of Neisseriaceae species within the human oral microbiome and establish a foundation for exploring functional specialization and microbial interactions in these niches.IMPORTANCEUnraveling the distribution and functional adaptations of Neisseriaceae within the human oral microbiome is essential for understanding the roles of these abundant and prevalent commensals in both health and disease. Through a metapangenomic approach, we uncovered distinct habitat preferences of various Neisseriaceae taxa across the oral cavity and identified key genetic traits that may drive their habitat specialization and role in host-microbe interactions. These insights enhance our understanding of the microbial dynamics that shape oral microbial ecology, offering potential pathways for advancing oral health research.}, }
@article {pmid40197053, year = {2025}, author = {Langsiri, N and Meyer, W and Irinyi, L and Worasilchai, N and Pombubpa, N and Wongsurawat, T and Jenjaroenpun, P and Luangsa-Ard, JJ and Chindamporn, A}, title = {Optimizing fungal DNA extraction and purification for Oxford Nanopore untargeted shotgun metagenomic sequencing from simulated hemoculture specimens.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0116624}, doi = {10.1128/msystems.01166-24}, pmid = {40197053}, issn = {2379-5077}, abstract = {UNLABELLED: Long-read metagenomics provides a promising alternative approach to fungal identification, circumventing methodological biases, associated with DNA amplification, which is a prerequisite for DNA barcoding/metabarcoding based on the primary fungal DNA barcode (Internal Transcribed Spacer (ITS) region). However, DNA extraction for long-read sequencing-based fungal identification poses a significant challenge, as obtaining long and intact fungal DNA is imperative. Comparing different lysis methods showed that chemical lysis with CTAB/SDS generated DNA from pure fungal cultures with high yields (ranging from 11.20 ± 0.17 µg to 22.99 ± 2.22 µg depending on the species) while preserving integrity. Evaluating the efficacy of human DNA depletion protocols demonstrated an 88.73% reduction in human reads and a 99.53% increase in fungal reads compared to the untreated yeast-spiked human blood control. Evaluation of the developed DNA extraction protocol on simulated clinical hemocultures revealed that the obtained DNA sequences exceed 10 kb in length, enabling a highly efficient sequencing run with over 80% active pores. The quality of the DNA, as indicated by the 260/280 and 260/230 ratios obtained from NanoDrop spectrophotometer readings, exceeded 1.8 and 2.0, respectively. This demonstrated the great potential of the herein optimized protocol to extract high-quality fungal DNA from clinical specimens enabling long-read metagenomics sequencing.<br><br>IMPORTANCE: A novel streamlined DNA extraction protocol was developed to efficiently isolate high molecular weight fungal DNA from hemoculture samples, which is crucial for long-read sequencing applications. By eliminating the need for labor-intensive and shear-force-inducing steps, such as liquid nitrogen grinding or bead beating, the protocol is more user-friendly and better suited for clinical laboratory settings. The automation of cleanup and extraction steps further shortens the overall turnaround time to under 6 hours. Although not specifically designed for ultra-long DNA extraction, this protocol effectively supports fungal identification through Oxford Nanopore Technology (ONT) sequencing. It yields high molecular weight DNA, resulting in longer sequence fragments that improve the number of fungal reads over human reads. Future improvements, including adaptive sampling technology, could further simplify the process by reducing the need for human DNA depletion, paving the way for more automated, bioinformatics-driven workflows.}, }
@article {pmid40197051, year = {2025}, author = {Shamash, M and Sinha, A and Maurice, CF}, title = {Improving gut virome comparisons using predicted phage host information.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0136424}, doi = {10.1128/msystems.01364-24}, pmid = {40197051}, issn = {2379-5077}, abstract = {UNLABELLED: The human gut virome is predominantly made up of bacteriophages (phages), viruses that infect bacteria. Metagenomic studies have revealed that phages in the gut are highly individual specific and dynamic. These features make it challenging to perform meaningful cross-study comparisons. While several taxonomy frameworks exist to group phages and improve these comparisons, these strategies provide little insight into the potential effects phages have on their bacterial hosts. Here, we propose the use of predicted phage host families (PHFs) as a functionally relevant, qualitative unit of phage classification to improve these cross-study analyses. We first show that bioinformatic predictions of phage hosts are accurate at the host family level by measuring their concordance to Hi-C sequencing-based predictions in human and mouse fecal samples. Next, using phage host family predictions, we determined that PHFs reduce intra- and interindividual ecological distances compared to viral contigs in a previously published cohort of 10 healthy individuals, while simultaneously improving longitudinal virome stability. Lastly, by reanalyzing a previously published metagenomics data set with >1,000 samples, we determined that PHFs are prevalent across individuals and can aid in the detection of inflammatory bowel disease-specific virome signatures. Overall, our analyses support the use of predicted phage hosts in reducing between-sample distances and providing a biologically relevant framework for making between-sample virome comparisons.<br><br>IMPORTANCE: The human gut virome consists mainly of bacteriophages (phages), which infect bacteria and show high individual specificity and variability, complicating cross-study comparisons. Furthermore, existing taxonomic frameworks offer limited insight into their interactions with bacterial hosts. In this study, we propose using predicted phage host families (PHFs) as a higher-level classification unit to enhance functional cross-study comparisons. We demonstrate that bioinformatic predictions of phage hosts align with Hi-C sequencing results at the host family level in human and mouse fecal samples. We further show that PHFs reduce ecological distances and improve virome stability over time. Additionally, reanalysis of a large metagenomics data set revealed that PHFs are widespread and can help identify disease-specific virome patterns, such as those linked to inflammatory bowel disease.}, }
@article {pmid40196042, year = {2025}, author = {Wang, H and Zhu, W and Lei, J and Liu, Z and Cai, Y and Wang, S and Li, A}, title = {Gut microbiome differences and disease risk in colorectal cancer relatives and healthy individuals.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1573216}, pmid = {40196042}, issn = {2235-2988}, mesh = {Humans ; Feces/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Family ; }, abstract = {Given the heightened focus on high-risk populations, this study aimed to provide insights into early susceptibility and preventive strategies for colorectal cancer (CRC) by focusing on high-risk populations. In this research, fecal samples from 1,647 individuals across three discovery cohorts and nine external validation cohorts were sequenced using whole-genome metagenomic sequencing. A prediction model based on random forest was constructed using the nine external cohorts and independently validated with the three discovery cohorts. A disease probability (POD) model based on microbial biomarkers was developed to assess CRC risk. We found that the gut microbiome composition of CRC relatives differed from that of controls, with enrichment of species such as Fusobacterium and Bacteroides and a reduction in beneficial genera like Coprococcus and Roseburia. Additionally, dietary red meat intake emerged as a risk factor. The POD model indicated an elevated risk of CRC in unaffected relatives. The findings suggest that the POD for CRC may be increased in unaffected relatives or individuals living in shared environments, although this difference did not reach statistical significance. Our study introduces a novel framework for assessing the risk of colorectal cancer in ostensibly healthy individuals.}, }
@article {pmid40196035, year = {2025}, author = {Decadt, H and Díaz-Muñoz, C and Vermote, L and Pradal, I and De Vuyst, L and Weckx, S}, title = {Long-read metagenomics gives a more accurate insight into the microbiota of long-ripened gouda cheeses.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1543079}, pmid = {40196035}, issn = {1664-302X}, abstract = {Metagenomic studies of the Gouda cheese microbiota and starter cultures are scarce. During the present study, short-read metagenomic sequencing (Illumina) was applied on 89 Gouda cheese and processed milk samples, which have been investigated before concerning their metabolite and taxonomic composition, the latter applying amplicon-based, high-throughput sequencing (HTS) of the full-length 16S rRNA gene. Selected samples were additionally investigated using long-read metagenomic sequencing (Oxford Nanopore Technologies, ONT). Whereas the species identified by amplicon-based HTS and metagenomic sequencing were identical, the relative abundances of the major species differed significantly. Lactococcus cremoris was more abundant in the metagenomics-based taxonomic analysis compared to the amplicon-based one, whereas the opposite was true for the non-starter lactic acid bacteria (NSLAB). This discrepancy was related to a higher fragmentation of the lactococcal DNA compared with the DNA of other species when applying ONT. Possibly, a higher fragmentation was linked with a higher percentage of dead or metabolically inactive cells, suggesting that full-length 16S rRNA gene amplicon-based HTS might give a more accurate view on active cells. Further, fungi were not abundantly present in the Gouda cheeses examined, whereas about 2% of the metagenomic sequence reads was related to phages, with higher relative abundances in the cheese rinds and long-ripened cheeses. Intraspecies differences found by short-read metagenomic sequencing were in agreement with the amplicon sequence variants obtained previously, confirming the ability of full-length 16S rRNA gene amplicon-based HTS to reach a taxonomic assignment below species level. Metagenome-assembled genomes (MAGs) were retrieved for 15 species, among which the starter cultures Lc. cremoris and Lactococcus lactis and the NSLAB Lacticaseibacillus paracasei, Loigolactobacillus rennini, and Tetragenococcus halophilus, although obtaining MAGs from Lc. cremoris and Lc. lactis was more challenging because of a high intraspecies diversity and high similarity between these species. Long-read metagenomic sequencing could not improve the retrieval of lactococcal MAGs, but, overall, MAGs obtained by long-read metagenomic sequencing solely were superior compared with those obtained by short-read metagenomic sequencing solely, reaching a high-quality draft status of the genomes.}, }
@article {pmid40195635, year = {2025}, author = {Lv, H and Zhou, J and Guo, Y and Liao, S and Chen, H and Luo, F and Xu, J and Zhang, Z and Zhang, Z}, title = {Uniportal endoscopic decompression and debridement for infectious diseases of spine with neurological deficits: a retrospective study in China.}, journal = {Asian spine journal}, volume = {}, number = {}, pages = {}, doi = {10.31616/asj.2025.0020}, pmid = {40195635}, issn = {1976-1902}, abstract = {STUDY DESIGN: A retrospective study.<br><br>PURPOSE: To evaluate the clinical efficacy of uniportal endoscopic decompression and debridement (UEDD) in treating infectious diseases of the spine (IDS) with neurological deficits.<br><br>OVERVIEW OF LITERATURE: IDS patients with neurological deficits often require urgent surgical decompression. However, the efficacy of UEDD in this complex patient population is not well-characterized.<br><br>METHODS: This retrospective study analyzed 32 consecutive IDS patients who underwent UEDD surgery. Clinical features, laboratory data (erythrocyte sedimentation rate and C-reactive protein), and treatment outcomes were analyzed.<br><br>RESULTS: Definite microorganisms were identified in 27 patients (84.3%), with 24 (88.9%) meeting cure criteria. The cure rate was significantly higher in the detected pathogen group compared to the undetected pathogen group (88.9% vs. 80%; &#x3c7;&#xb2;=19.36, p<0.0001). Metagenomic next generation sequencing (mNGS) provided faster diagnosis (41.72&#xb1;6.81 hours) compared to tissue culture (95.74&#xb1;35.47 hours, p<0.05). The predominant causative pathogen was Mycobacterium tuberculosis, followed by Staphylococcus aureus. Significant improvements were observed in Visual Analog Scale pain scores, from a mean of 7.9 preoperatively to 1.06 at 1 year postoperatively. The Oswestry Disability Index revealed a similar trend, showing significant improvement (p<0.05).<br><br>CONCLUSIONS: UEDD is a viable alternative to traditional open surgery for managing IDS in high-risk patients. UEDD offers a dual therapeutic-diagnostic advantage during the initial admission phase, enabling simultaneous debridement, neurological decompression, and targeted biopsy in a single intervention. Compared with traditional tissue culture, mNGS enables rapid microbiological diagnosis and extensive pathogen coverage.}, }
@article {pmid40195460, year = {2025}, author = {Bhagat, NR and Bharti, VK and Shukla, G and Rishi, P and Chaurasia, OP}, title = {Gut bacteriome dynamics in high altitude-adapted chicken lines: a key to future poultry therapeutics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11910}, pmid = {40195460}, issn = {2045-2322}, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome ; *Altitude ; Metagenomics/methods ; *Bacteria/genetics/classification ; *Adaptation, Physiological ; Metagenome ; }, abstract = {High-altitude-adapted chickens harbor a unique gut bacteriome essential for their survival under extremely cold and hypoxic environment, however, little is known about their population and functional dynamics, limiting their application in poultry production. Hence, this study employed amplicon-based metagenomics to examine the gut bacterial diversity and their functional profile in two high-altitude-adapted chicken lines, e.g. LEHBRO-1 and LEHBRO-3. The results revealed significant variations in taxonomic abundance at the phylum level, with Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria predominating in LEHBRO-1, whereas Firmicutes, Proteobacteria, Bacteroidetes, Planctomycetes, and Actinobacteria predominated in LEHBRO-3. Genus-level diversity and Linear Discriminant Analysis Effect Size (LEfSe) biomarker analysis also substantiated the differences in the gut bacterial communities between the two chicken lines. Furthermore, functional profiling revealed enrichment of carbohydrate, nucleotide, lipid, amino acid, fatty acid, energy, and glycan metabolic pathways in the gut bacteriomes of these high-altitude chicken lines. The Statistical Analysis of Metagenomic Profiles (STAMP) for metabolic profiling identified a significant difference in purine and protein metabolism between these two chicken lines. These findings indicate the unique gut bacteriome and their functional diversity in high-altitude-adapted chickens, which would provide a foundation for future research on gut therapeutics to improve chicken health and productivity in high-altitude areas.}, }
@article {pmid40195156, year = {2025}, author = {Sefrji, FO and Abulfaraj, AA and Alshehrei, FM and Al-Andal, A and Alnahari, AA and Tashkandi, M and Baz, L and Barqawi, AA and Almutrafy, AM and Alshareef, SA and Alkhatib, SN and Abuauf, HW and Jalal, RS and Aloufi, AS}, title = {Comprehensive analysis of orthologous genes reveals functional dynamics and energy metabolism in the rhizospheric microbiome of Moringa oleifera.}, journal = {Functional &amp; integrative genomics}, volume = {25}, number = {1}, pages = {82}, pmid = {40195156}, issn = {1438-7948}, mesh = {*Moringa oleifera/microbiology/genetics/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Energy Metabolism/genetics ; Soil Microbiology ; Bacteria/genetics/classification ; Adenosine Triphosphate/metabolism ; Metagenome ; }, abstract = {Moringa oleifera, known for its nutritional and therapeutic properties, exhibits a complex relationship with its rhizospheric soil microbiome. This study aimed to elucidate the microbiome's structural composition, molecular functions, and its role in plant growth by integrating Clusters of Orthologous Genes (COG) analysis with enzymatic functions previously identified through KEGG, CAZy, and CARD databases. Metagenomic sequencing and bioinformatics analysis were performed from the rhizospheric soil microbiome of M. oleifera collected from the Mecca district in Saudi Arabia. The analysis revealed a role for the rhizospheric microbiome in energy production, storage, and regulation, with glucose serving as a crucial precursor for NADH synthesis and subsequent ATP production via oxidative phosphorylation. Key orthologous genes (OGs) implicated in this process include NuoD, NuoH, NuoM, NuoN, NuoL, atpA, QcrB/PetB, and AccC. Additionally, OGs involved in ATP hydrolysis, such as ClpP, EntF, YopO, and AtoC, were identified. Taxonomic analysis highlighted Actinobacteria and Proteobacteria as the predominant phyla, with enriched genera including Blastococcus, Nocardioides, Streptomyces, Microvirga, Sphingomonas, and Massilia, correlating with specific OGs involved in ATP hydrolysis. This study provides insights into the molecular mechanisms underpinning plant-microbe interactions and highlights the multifaceted roles of ATP-dependent processes in the rhizosphere. Further research is recommended to explore the potential applications of these findings in sustainable agriculture and ecosystem management.}, }
@article {pmid40194944, year = {2025}, author = {Wilson, I and Perry, T and Eisenhofer, R and Rismiller, P and Shaw, M and Grutzner, F}, title = {Microbiota changes in lactation in the short-beaked echidna (Tachyglossus aculeatus).}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf036}, pmid = {40194944}, issn = {1574-6941}, abstract = {Monotreme and marsupial development is characterised by a short gestation, with young exposed to the environment at an early developmental stage and supported by a long lactation in the pouch, pseudo-pouch, or burrow. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich environment. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation, but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiota (n = 22) during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Metataxonomic profiling using 16S rRNA gene sequencing revealed that pseudo-pouch microbial communities undergo dramatic changes during lactation, with significant differences in taxonomic composition compared with samples taken outside of breeding season or during courtship and mating. This suggests that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. Furthermore, captivity was not found to have a significant effect on pseudo-pouch microbiota. This study pioneers pouch microbiota research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programs in the future.}, }
@article {pmid40194477, year = {2025}, author = {Zhang, H and Zhang, X and Sun, H and Ling, H and Xie, R and Fang, L and Guo, M and Wu, X}, title = {Polyvinyl chloride microplastic triggers bidirectional transmission of antibiotic resistance genes in soil-earthworm systems.}, journal = {Environment international}, volume = {198}, number = {}, pages = {109414}, doi = {10.1016/j.envint.2025.109414}, pmid = {40194477}, issn = {1873-6750}, abstract = {The diffusion and distribution of ubiquitous microplastics and antibiotic resistance genes (ARGs) in soil ecosystems are easily influenced by earthworm activity. However, minimal research exists on the bidirectional dissemination of ARGs in the soil-earthworm ecosystems under microplastic stress. Focusing on the typical microplastic polyvinyl chloride (PVC) microspheres in simulated soil-earthworm (Eisenia fetida) systems, we characterized the PVC-triggered interactive transmission of ARGs between earthworm guts and their dwelling soils using shotgun metagenomics and qPCR methodologies. PVC exposure did not alter the diversity and relative abundance of ARGs in earthworm-uninoculated soils but significantly increased those in earthworm-inoculated soils. Meanwhile, the abundance of ARGs increased in the earthworm gut under PVC stress. Source tracking analysis showed a higher source proportion of soil-borne ARGs into earthworm gut under PVC treatments. Mechanistically, PVC-triggered increasing prevalence of ARGs was significantly related to both the bacterial community and mobile genetic elements-mediated horizontal transfer in the soils, whereas the bacterial community predominated the process in the earthworm guts. Overall, our findings reveal a PVC-triggered bidirectional transmission pattern of ARGs between earthworm guts and their dwelling soils and highlight the overlooked ecotoxicological risk of microplastics in soil-earthworm systems.}, }
@article {pmid40193404, year = {2025}, author = {Aroney, STN and Newell, RJP and Nissen, JN and Camargo, AP and Tyson, GW and Woodcroft, BJ}, title = {CoverM: Read alignment statistics for metagenomics.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf147}, pmid = {40193404}, issn = {1367-4811}, abstract = {SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses 'Mosdepth arrays' for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results.<br><br>CoverM is free software available at https://github.com/wwood/coverm. CoverM is implemented in Rust, with Python (https://github.com/apcamargo/pycoverm) and Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.}, }
@article {pmid40193328, year = {2025}, author = {Jagadesan, S and Guda, C}, title = {MetaDAVis: An R shiny application for metagenomic data analysis and visualization.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0319949}, doi = {10.1371/journal.pone.0319949}, pmid = {40193328}, issn = {1932-6203}, mesh = {*Metagenomics/methods ; Humans ; RNA, Ribosomal, 16S/genetics ; *Software ; *Metagenome ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {The human microbiome exerts tremendous influence on maintaining a balance between human health and disease. High-throughput sequencing has enabled the study of microbial communities at an unprecedented resolution. Generation of massive amounts of sequencing data has also presented novel challenges to analyzing and visualizing data to make biologically relevant interpretations. We have developed an interactive Metagenome Data Analysis and Visualization (MetaDAVis) tool for 16S rRNA as well as the whole genome sequencing data analysis and visualization to address these challenges using an R Shiny application. MetaDAVis can perform six different types of analyses that include: i) Taxonomic abundance distribution; ii) Alpha and beta diversity analyses; iii) Dimension reduction tasks using PCA, t-SNE, and UMAP; iv) Correlation analysis using taxa- or sample-based data; v) Heatmap generation; and vi) Differential abundance analysis. MetaDAVis creates interactive and dynamic figures and tables from multiple methods enabling users to easily understand their data using different variables. Our program is user-friendly and easily customizable allowing those without any programming background to perform comprehensive data analyses using a standalone or web-based interface.}, }
@article {pmid40193099, year = {2025}, author = {Chiu, CY and López-Labrador, FX and Wilson, MR and de Vries, JJC}, title = {The Regulatory Landscape for Clinical Metagenomic Testing.}, journal = {JAMA neurology}, volume = {}, number = {}, pages = {}, doi = {10.1001/jamaneurol.2025.0461}, pmid = {40193099}, issn = {2168-6157}, }
@article {pmid40193036, year = {2025}, author = {Kim, SY and Seol, D and Jung, M and Kwak, W and Kim, H and Cho, S and Kim, TH}, title = {Assessing the Efficacy of Ligilactobacillus salivarius CLS0420 and Lacticaseibacillus paracasei CLPC0603 on Vaginal Well-Being in Healthy Women: A Pilot, Randomized, Double-Blind, Placebo-Controlled Trial.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40193036}, issn = {1867-1314}, abstract = {Despite the growing development of probiotics for preventing bacterial vaginosis (BV), their effectiveness in women without BV has not been thoroughly investigated. This pilot, randomized, double-blind, placebo-controlled study aims to assess the impact of orally administered probiotic strains, exhibiting in vitro antimicrobial activity against Gardnerella vaginalis and Candida albicans, on vaginal well-being in women without preexisting health conditions. Healthy women (n = 30, aged 19-50) were enrolled and randomly assigned using simple randomization to receive either probiotic or placebo capsules. After excluding dropouts, 26 participants (15 in the probiotic group, 11 in the placebo group) completed the study, undergoing a 3-week intervention. Vaginal well-being was assessed before and after the intervention using self-assessed health on a 5-point Likert scale, along with analysis of the vaginal microbiome by targeting the 16S-ITS-23S rRNA operon region with the Nanopore sequencing platform and MIrROR database. Notably, only the probiotic group exhibited a significant improvement in self-assessed overall gut and vaginal health following the intervention (p = 0.009 and p = 0.003, respectively). Nevertheless, no significant changes were observed in the vaginal bacterial community following the intervention and confirming the vaginal colonization of orally ingested probiotic strains through metagenome sequencing proved challenging. In summary, these findings suggest that while oral probiotics may improve perceived vaginal well-being, their role in modulating the vaginal microbiome in healthy women remains inconclusive. Additional research with a larger sample size is necessary to substantiate the endorsement of oral probiotic consumption for preventing BV or maintaining vaginal health in healthy women. This study was retrospectively registered at Clinical Research Information Service (CRIS) (KCT0008957, November 15, 2023).}, }
@article {pmid40192235, year = {2025}, author = {Jiao, Y and Ren, J and Xie, S and Yuan, N and Shen, J and Yin, H and Wang, J and Guo, H and Cao, J and Wang, X and Wu, D and Zhou, Z and Qi, X}, title = {Raffinose-metabolizing bacteria impair radiation-associated hematopoietic recovery via the bile acid/FXR/NF-κB signaling pathway.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2488105}, doi = {10.1080/19490976.2025.2488105}, pmid = {40192235}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/radiation effects ; *Bile Acids and Salts/metabolism ; Mice ; *NF-kappa B/metabolism/genetics ; Signal Transduction/radiation effects ; *Raffinose/metabolism ; Mice, Inbred C57BL ; Whole-Body Irradiation/adverse effects ; *Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Fecal Microbiota Transplantation ; Male ; *Acute Radiation Syndrome/microbiology/metabolism ; *Hematopoiesis/radiation effects ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Dysbiosis/microbiology ; }, abstract = {Radiation-associated hematopoietic recovery (RAHR) is critical for mitigating lethal complications of acute radiation syndrome (ARS), yet therapeutic strategies remain limited. Through integrated multi-omics analysis of a total body irradiation (TBI) mouse model, we identify Bacteroides acidifaciens-dominated gut microbiota as key mediators of RAHR impairment. 16S ribosomal rRNA sequencing revealed TBI-induced dysbiosis characterized by Bacteroidaceae enrichment, while functional metagenomics identified raffinose metabolism as the most significantly perturbed pathway. Notably, raffinose supplementation (10% w/v) recapitulated radiation-induced microbiota shifts and delayed bone marrow recovery. Fecal microbiota transplantation (FMT) revealed a causative role for raffinose-metabolizing microbiota, particularly Bacteroides acidifaciens, in delaying RAHR progression. Mechanistically, B. acidifaciens-mediated bile acid deconjugation activated FXR, subsequently suppressing NF-κB-dependent hematopoietic recovery. Therapeutic FXR inhibition via ursodeoxycholic acid (UDCA) had been shown to be a viable method for rescuing RAHR. Our results delineated a microbiome-bile acid-FXR axis as a master regulator of post-irradiation hematopoiesis. Targeting B. acidifaciens or its metabolic derivatives could represent a translatable strategy to mitigate radiation-induced hematopoietic injury.}, }
@article {pmid40191975, year = {2025}, author = {Okechukwu Paul-Chima, U and Chinyere Nkemjika, A and Melvin Nnaemeka, U and Onohuean, H}, title = {Harnessing plant metabolic pathways for innovative diabetes management: unlocking the therapeutic potential of medicinal plants.}, journal = {Plant signaling &amp; behavior}, volume = {20}, number = {1}, pages = {2486076}, doi = {10.1080/15592324.2025.2486076}, pmid = {40191975}, issn = {1559-2324}, mesh = {*Plants, Medicinal/metabolism ; Humans ; *Diabetes Mellitus/drug therapy/metabolism ; *Metabolic Networks and Pathways ; }, abstract = {The exploration of plant signaling pathways is transforming the way diabetes is managed, providing new, multi-target strategies for controlling this complex metabolic disorder. Medicinal plants are rich in bioactive compounds like phytohormones, flavonoids and polyphenols, which regulate key pathways including oxidative stress, inflammation, insulin resistance, and gut microbiota modulation. Research is emerging on the therapeutic potential of Momordica charantia, Cinnamomum verum and Trigonella foenum-graecum, which enhance insulin secretion, sensitivity and glucose homeostasis. These plant derived compounds, resveratrol and plant based insulin mimetics, not only address metabolic dysfunction but also offer holistic treatment for long term complications such as neuropathy and retinopathy. The development of precision medicine advances the tailoring of plant based therapies to individual metabolic responses, increasing efficacy and decreasing reliance on synthetic drugs with adverse side effects. Despite challenges of standardization, regulatory barriers, and limited clinical trials, incorporating medicinal plants into national diabetes management guidelines represents a cost effective and accessible option, particularly in resource limited settings. In this review, we highlight the importance of collaborative work across disciplines and the use of technologies such as artificial intelligence to speed research and optimize patient specific applications. The therapeutic power of plant signaling pathways is harnessed to develop sustainable, inclusive, and effective diabetes management strategies.}, }
@article {pmid40191290, year = {2025}, author = {Kurt, H and Sever Kaya, D and Akçok, &#x130; and Sarı, C and Albayrak, E and Velioğlu, HM and Şamlı, HE and Özdüven, ML and Sürmeli, Y}, title = {Discovery and In Silico Characterization of Anatolian Water Buffalo Rumen-Derived Bacterial Thermostable Xylanases: A Sequence-Based Metagenomic Approach.}, journal = {ACS omega}, volume = {10}, number = {12}, pages = {12679-12698}, pmid = {40191290}, issn = {2470-1343}, abstract = {This study involved shotgun sequencing of rumen metagenomes from three Anatolian water buffalos, an exploration of the relationship between microbial flora and xylanases, and in silico analyses of thermostable xylanases, focusing on their sequence, structure, and dynamic properties. For this purpose, the rumen metagenome of three Anatolian water buffalos was sequenced and bioinformatically analyzed to determine microbial diversity and full-length xylanases. Analyses of BLAST, biophysicochemical characteristics, phylogenetic tree, and multiple sequence alignment were performed with Blastp, ProtParam, MEGA11 software, and Clustal Omega, respectively. Three-dimensional homology models of three xylanases (AWBRMetXyn5, AWBRMetXyn10, and AWBRMetXyn19) were constructed by SWISS-MODEL and validated by ProSA, ProCheck, and Verify3D. Also, their 3D models were structurally analyzed by PyMOL, BANΔIT, thermostability predictor, What If, and Protein Interaction Calculator (PIC) software. Protein-ligand interactions were examined by docking and MD simulation. Shotgun sequence and Blastp analyses showed that Clostridium (Clostridiales bacterial order), Ruminococcus (Oscillospiraceae bacterial family), Prevotella (Bacteroidales bacterial order), and Butyrivibrio (Lachnospiraceae bacterial family) were found as dominant potential xylanase-producer genera in three rumen samples. Furthermore, the biophysicochemical analysis indicated that three xylanases exhibited an aliphatic index above 80, an instability index below 40, and melting temperatures (T m) surpassing 65 °C. Phylogenetic analysis placed three xylanases within the GH10 family, clustering them with thermophilic xylanases, while homology modeling identified the optimal template as a xylanase from a thermophilic bacterium. The structural analysis indicated that three xylanases possessed the number of salt bridges, hydrophobic interactions, and T m score higher than 50, 165, and 70 °C, respectively; however, the reference thermophilic XynAS9 had 43, 145, and 54.41 °C, respectively. BANΔIT analysis revealed that three xylanases exhibited lower B'-factor values in the β3-α1 loop/short-helix at the N-terminal site compared to the reference thermophilic XynAS9. In contrast, six residues (G79, M123, D150, T199, A329, and G377) possessed higher B'-factor values in AWBRMetXyn5 and their aligned positions in AWBRMetXyn10 and AWBRMetXyn19, relative to XynAS9 including Gln, Glu, Ile, Lys, Ser, and Val at these positions, respectively. MD simulation results showed that the β9-η5 loop including catalytic nucleophile glutamic acid in the RMSF plot of three xylanases had a higher fluctuation than the aligned region in XynAS9. The distance analysis from the MD simulation showed that the nucleophile residue in AWBRMetXyn5 and AWBRMetXyn10 remained closer to the ligand throughout the simulation compared with XynAS9 and AWBRMetXyn19. The most notable difference between AWBRMetXyn5 and AWBRMetXyn10 was the increased amino acid fluctuations in two specific regions, the η3 short-helix and the η3-α3 loop, despite a minimal sequence difference of only 1.24%, which included three key amino acid variations (N345, N396, and T397 in AWBRMetXyn5; D345, K396, and A397 in AWBRMetXyn10). Thus, this study provided computational insights into xylanase function and thermostability, which could inform future protein engineering efforts. Additionally, three xylanases, especially AWBRMetXyn5, are promising candidates for various high-temperature industrial applications. In a forthcoming study, three xylanases will be experimentally characterized and considered for potential industrial applications. In addition, the amino acid substitutions (G79Q, M123E, D150I, T199K, A329S, and G377V) and the residues in the β3-α1 loop will be targeted for thermostability improvement of AWBRMetXyn5. The amino acids (N345, N396, and T397) and the residues on the β9-η5 loop, η3 short-helix, and η3-α3 loop will also be focused on development of the catalytic efficiency.}, }
@article {pmid40190795, year = {2025}, author = {Zhang, Y and Dai, Y and Li, J and Cong, W and Zhang, Y and Nie, X and Wu, Q and Xue, Y}, title = {Climate Change and Human Pressure: Assessing the Vulnerability of Snow Leopard (Panthera uncia) Habitat Integrated With Prey Distribution on the Qinghai-Tibet Plateau.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71232}, pmid = {40190795}, issn = {2045-7758}, abstract = {Climate change is significantly altering the distribution of large carnivores and their primary prey species, with particular emphasis on the changing prey distribution in high-altitude regions. The Qinghai-Tibet Plateau, known for its rich biodiversity, is highly sensitive to climate change, affecting the habitats of snow leopards (Panthera uncia) and blue sheep (Pseudois nayaur). Our study identified blue sheep as the primary prey of snow leopards through metagenomic analysis and used bioclimatic data and Land Use/Cover Change (LUCC) information to model habitat suitability under three climate scenarios (RCP 2.6, RCP 4.5, and RCP 8.5). Projections showed that under RCP 4.5 and RCP 8.5, snow leopard habitats will decrease by 13.0% and 23.4%, while blue sheep habitats will decrease by 38.3% and 49.7%, respectively. These habitats are expected to shift to higher altitudes, with snow leopards experiencing a more significant shift. Based on these findings, we recommend adjusting protected area boundaries for S1 (Ideal distribution range), establishing ecological corridors for S2 (stepping stone), and implementing targeted measures to mitigate human-wildlife conflicts in S3 (potential conflict area). To protect these species, international efforts to reduce carbon emissions, cross-administrative cooperation, and community-based conservation strategies are essential.}, }
@article {pmid40190731, year = {2025}, author = {Atencio, B and Malavin, S and Rubin-Blum, M and Ram, R and Adar, E and Ronen, Z}, title = {Site-specific incubations reveal biofilm diversity and functional adaptations in deep, ancient desert aquifers.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1533115}, pmid = {40190731}, issn = {1664-302X}, abstract = {Deep pristine aquifers are ecological hotspots with diverse microbial life, where microorganisms exist either attached (sessile) to solid substrates or suspended in groundwater (planktonic). Characterizing the attached microbial communities is of paramount importance, especially in the context of biofouling. However, obtaining samples of attached microbes that thrive under natural (undisturbed) conditions is challenging. Our study addresses this by retrieving sessile microbes on-site. We installed columns filled with site-specific rock cuttings at the wellhead, allowing fresh groundwater to flow continuously for approximately 60 days. We hypothesized that the attached microbial communities would differ structurally from planktonic microbes due to the aquifer's lithological and mineralogical composition. This study involved an exploratory examination of the microbial communities in different aquifers with distinct mineralogies, including quartzitic sandstone, calcareous, chert, and highly heterogeneous (clastic) aquifers in Israel's Negev Desert. Metagenomic analysis revealed both shared and distinct microbial communities among attached and planktonic forms in the various environments, likely shaped by the aquifers' physical, lithological, and mineralogical properties. A wealth of carbon-fixation pathways and energy-conservation strategies in the attached microbiome provide evidence for the potential productivity of these biofilms. We identified widespread genetic potential for biofilm formation (e.g., via pili, flagella, and extracellular polymeric substance production) and the interactome (e.g., quorum-sensing genes). Our assessment of these functions provides a genomic framework for groundwater management and biofouling treatment.}, }
@article {pmid40190171, year = {2025}, author = {Milev, M and Roglev, B and Kondeva Rogleva, M and Georgieva, M and Miloshev, G and Ruskovska, T}, title = {Impact of (poly)phenol-rich dietary sources on DNA damage: Insights from human intervention studies using the Comet assay - a review and perspective.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-40}, doi = {10.1017/S000711452500073X}, pmid = {40190171}, issn = {1475-2662}, abstract = {(Poly)phenols are plant-derived food bioactives abundantly present in human diet. They exert positive effects on various aspects of human health, and in particular in reducing the risk of chronic non-communicable diseases. Dietary (poly)phenols have been reported to improve vascular function, blood lipids, insulin sensitivity, and to decrease systemic inflammation. Evidence also suggests that (poly)phenols may exert protective effects on DNA, by reducing the extent of its damage. In recent years, advanced analytical methods, including transcriptomics, metabolomics, proteomics, and metagenomics, have been employed to unravel the complex impact of (poly)phenols in health and disease. Advances in bioinformatics enable an integrated multi-omics approach to data analysis, opening avenues for discovering new, previously unknown molecular mechanisms of action. Innovative solutions and automation of the Comet assay offer new opportunities for more in-depth analysis of the impact of (poly)phenols on DNA damage and its inclusion in integrative bioinformatic models. Such an approach has the potential to uncover new multi-level interactions and to reveal previously unknown factors underlying inter-individual variabilities in health-promoting effects of (poly)phenols. This review provides an insight into the application of the Comet assay in human intervention studies using (poly)phenol-rich dietary sources. Recent advancements in the Comet assay technology, and the prospects for more extensive use of this method in future human intervention studies with (poly)phenols could contribute to the development of personalized dietary recommendations for these plant-derived food bioactives.}, }
@article {pmid40190120, year = {2025}, author = {Aboulalazm, FA and Kazen, AB and deLeon, O and Müller, S and Saravia, FL and Lozada-Fernandez, V and Hadiono, MA and Keyes, RF and Smith, BC and Kellogg, SL and Grobe, JL and Kindel, TL and Kirby, JR}, title = {Reutericyclin, a specialized metabolite of Limosilactobacillus reuteri, mitigates risperidone-induced weight gain in mice.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2477819}, doi = {10.1080/19490976.2025.2477819}, pmid = {40190120}, issn = {1949-0984}, mesh = {Animals ; *Risperidone/adverse effects ; *Limosilactobacillus reuteri/metabolism ; *Weight Gain/drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Antipsychotic Agents/adverse effects ; Probiotics/administration &amp; dosage ; Feces/microbiology ; Energy Metabolism/drug effects ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {The role of xenobiotic disruption of microbiota, corresponding dysbiosis, and potential links to host metabolic diseases are of critical importance. In this study, we used a widely prescribed antipsychotic drug, risperidone, known to influence weight gain in humans, to induce weight gain in C57BL/6J female mice. We hypothesized that microbes essential for maintaining gut homeostasis and energy balance would be depleted following treatment with risperidone, leading to enhanced weight gain relative to controls. Thus, we performed metagenomic analyses on stool samples to identify microbes that were excluded in risperidone-treated animals but remained present in controls. We identified multiple taxa including Limosilactobacillus reuteri as a candidate for further study. Oral supplementation with L. reuteri protected against risperidone-induced weight gain (RIWG) and was dependent on cellular production of a specialized metabolite, reutericyclin. Further, synthetic reutericyclin was sufficient to mitigate RIWG. Both synthetic reutericyclin and L. reuteri restored energy balance in the presence of risperidone to mitigate excess weight gain and induce shifts in the microbiome associated with leanness. In total, our results identify reutericyclin production by L. reuteri as a potential probiotic to restore energy balance induced by risperidone and to promote leanness.}, }
@article {pmid40189999, year = {2025}, author = {Peng, K and Gao, Y and Li, C and Wang, Q and Yin, Y and Hameed, MF and Feil, E and Chen, S and Wang, Z and Liu, YX and Li, R}, title = {Benchmarking of analysis tools and pipeline development for nanopore long-read metagenomics.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2025.03.044}, pmid = {40189999}, issn = {2095-9281}, }
@article {pmid40189749, year = {2025}, author = {Birebent, R and Drubay, D and Alves Costa Silva, C and Marmorino, F and Vitali, G and Piccinno, G and Hurtado, Y and Bonato, A and Belluomini, L and Messaoudene, M and Routy, B and Fidelle, M and Zalcman, G and Mazieres, J and Audigier-Valette, C and Moro-Sibilot, D and Goldwasser, F and Scherpereel, A and Pegliasco, H and Ghiringhelli, F and Reni, A and Barlesi, F and Albiges, L and Planchard, D and Martinez, S and Besse, B and Segata, N and Cremolini, C and Zitvogel, L and Iebba, V and Derosa, L}, title = {Surrogate markers of intestinal dysfunction associated with survival in advanced cancers.}, journal = {Oncoimmunology}, volume = {14}, number = {1}, pages = {2484880}, doi = {10.1080/2162402X.2025.2484880}, pmid = {40189749}, issn = {2162-402X}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Dysbiosis/microbiology ; Middle Aged ; *Colorectal Neoplasms/mortality/microbiology/pathology ; Aged ; Prognosis ; *Carcinoma, Non-Small-Cell Lung/mortality/microbiology/pathology ; *Lung Neoplasms/mortality/microbiology/pathology ; Akkermansia/isolation &amp; purification ; *Urogenital Neoplasms/mortality/microbiology/pathology ; }, abstract = {Deviations in the diversity and composition of the gut microbiota are called "gut dysbiosis". They have been linked to various chronic diseases including cancers and resistance to immunotherapy. Stool shotgun based-metagenomics informs on the ecological composition of the gut microbiota and the prevalence of homeostatic bacteria such as Akkermansia muciniphila (Akk), while determination of the serum addressin MAdCAM-1 instructs on endothelial gut barrier dysfunction. Here we examined patient survival during chemo-immuno-therapy in 955 cancer patients across four independent cohorts of non-small cell lung (NSCLC), genitourinary (GU) and colorectal (CRC) cancers, according to hallmarks of gut dysbiosis. We show that Akk prevalence represents a stable and favorable phenotype in NSCLC and CRC cancer patients. Over-dominance of Akk above the healthy threshold was observed in dismal prognosis in NSCLC and GU and mirrored an immunosuppressive gut ecosystem and excessive intestinal epithelial exfoliation in NSCLC. In CRC, the combination of a lack of Akk and low sMAdCAM-1 levels identified a subset comprising 28% of patients with reduced survival, independent of the immunoscore. We conclude that gut dysbiosis hallmarks deserve integration within the diagnosis toolbox in oncological practice.}, }
@article {pmid40189708, year = {2025}, author = {Gen-Jiménez, A and Flores-Félix, JD and Rincón-Molina, CI and Manzano-Gómez, LA and Villalobos-Maldonado, JJ and Ruiz-Lau, N and Roca-Couso, R and Ruíz-Valdiviezo, VM and Rincón-Rosales, R}, title = {Native Rhizobium biofertilization enhances yield and quality in Solanum lycopersicum under field conditions.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {4}, pages = {126}, pmid = {40189708}, issn = {1573-0972}, support = {19337.24-P//Tecnol&#xf3;gico Nacional de M&#xe9;xico/ ; }, mesh = {*Solanum lycopersicum/growth &amp; development/microbiology ; *Rhizobium/physiology ; Soil Microbiology ; *Fertilizers ; Soil/chemistry ; Fruit/growth &amp; development ; Nitrogen/analysis/metabolism ; Microbiota ; Agriculture/methods ; }, abstract = {In response to growing concerns about the environmental and economic impacts of chemical fertilizers, this study explores the potential of biofertilization using native Rhizobium strains to enhance the growth, yield, and quality of Solanum lycopersicum (tomato) under field conditions. The experiment assessed the effects of Rhizobium biofertilization on plant performance and soil microbial communities by applying R. calliandrae, R. jaguaris, R. mayense, and a bacterial consortium, in comparison to conventional chemical fertilization. Key parameters such as plant height, fruit yield, macronutrient and micronutrient content, and fruit quality (lycopene and β-carotene levels) were measured. Results showed that R. calliandrae and R. jaguaris significantly enhanced fruit yield, nitrogen, potassium, manganese, and boron levels, while also improving fruit quality compared to the control. The impact of strain inoculation on the structure of the microbial community was also examined. Metataxonomic analysis of rhizospheric soils revealed no significant changes in microbial diversity, indicating that biofertilization with Rhizobium strains promotes plant growth without disrupting the composition of the soil microbiome. These findings suggest that Rhizobium biofertilization is a viable and sustainable alternative to chemical fertilizers, providing benefits to both crop productivity and soil health while minimizing the environmental footprint associated with conventional agricultural practices. The study underscores the importance of carefully selecting bacterial species with complementary functions to maximize the effectiveness of biofertilization strategies.}, }
@article {pmid40189564, year = {2025}, author = {He, Y and Zhuo, S and Li, M and Pan, J and Jiang, Y and Hu, Y and Sanford, RA and Lin, Q and Sun, W and Wei, N and Peng, S and Jiang, Z and Li, S and Li, Y and Dong, Y and Shi, L}, title = {Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {94}, pmid = {40189564}, issn = {2049-2618}, support = {42472366, 92051111 and 42272353//National Natural Science Foundation of China/ ; 122-G1323522144//Fundamental Research Funds for the Chinese Central Government via China University of Geosciences (Wuhan)/ ; }, mesh = {*Symbiosis ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics/methods ; Metagenome ; Folic Acid/biosynthesis ; Ecosystem ; Phylogeny ; Genome, Bacterial ; *Microbiota ; }, abstract = {BACKGROUND: Candidate Phyla Radiation (CPR) represents a unique superphylum characterized by ultra-small cell size and symbiotic lifestyle. Although CPR bacteria have been identified in varied environments, their broader distribution, associations with hosts, and ecological roles remain largely unexplored. To address these knowledge gaps, a serpentinite-like environment was selected as a simplified model system to investigate the CPR communities in hyperalkaline environments and their association with hosts in extreme conditions. Additionally, the enzymatic activity, global distribution, and evolution of the CPR-derived genes encoding essential metabolites (e.g., folate or vitamin B9) were analyzed and assessed.<br><br>RESULTS: In the highly alkaline serpentinite-like ecosystem (pH&#x2009;=&#x2009;10.9-12.4), metagenomic analyses of the water and sediment samples revealed that CPR bacteria constituted 1.93-34.8% of the microbial communities. Metabolic reconstruction of 12 high-quality CPR metagenome-assembled genomes (MAGs) affiliated to the novel taxa from orders UBA6257, UBA9973, and Paceibacterales suggests that these bacteria lack the complete biosynthetic pathways for amino acids, lipids, and nucleotides. Notably, the CPR bacteria commonly harbored the genes associated with essential folate cofactor biosynthesis and metabolism, including dihydrofolate reductase (folA), serine hydroxymethyltransferase (glyA), and methylenetetrahydrofolate reductase (folD). Additionally, two presumed auxotrophic hosts, incapable of forming tetrahydrofolate (THF) due to the absence of folA, were identified as potential hosts for some CPR bacteria harboring folA genes. The functionality of these CPR-derived folA genes was experimentally verified by heterologous expression in the folA-deletion mutant Escherichia coli MG1655 &#x394;folA. Further assessment of the available CPR genomes (n&#x2009;=&#x2009;4,581) revealed that the genes encoding the proteins for the synthesis of bioactive folate derivatives (e.g., folA, glyA, and/or folD genes) were present in 90.8% of the genomes examined. It suggests potential widespread metabolic complementarity in folate biosynthesis between CPR and their hosts.<br><br>CONCLUSIONS: This finding deepens our understanding of the mechanisms of CPR-host symbiosis, providing novel insight into essential cofactor-dependent mutualistic CPR-host interactions. Our observations suggest that CPR bacteria may contribute to auxotrophic organisms and indirectly influence biogeochemical processes. Video Abstract.}, }
@article {pmid40189545, year = {2025}, author = {Serrana, JM and Nascimento, FJA and Dessirier, B and Broman, E and Posselt, M}, title = {Environmental drivers of the resistome across the Baltic Sea.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {92}, pmid = {40189545}, issn = {2049-2618}, mesh = {*Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Microbiota/genetics ; *Seawater/microbiology ; Oceans and Seas ; *Geologic Sediments/microbiology ; Metagenome ; Salinity ; Anti-Bacterial Agents/pharmacology ; Temperature ; }, abstract = {BACKGROUND: Antimicrobial resistance is a major global health concern, with the environment playing a key role in its emergence and spread. Understanding the relationships between environmental factors, microbial communities, and resistance mechanisms is vital for elucidating environmental resistome dynamics. In this study, we characterized the environmental resistome of the Baltic Sea and evaluated how environmental gradients and spatial variability, alongside its microbial communities and associated functional genes, influence resistome diversity and composition across geographic regions.<br><br>RESULTS: We analyzed the metagenomes of benthic sediments from 59 monitoring stations across a 1,150&#xa0;km distance of the Baltic Sea, revealing an environmental resistome comprised of predicted antimicrobial resistance genes (ARGs) associated with resistance against 26 antibiotic classes. We observed spatial variation in its resistance profile, with higher resistome diversity in the northern regions and a decline in the dead zones and the southern areas. The combined effects of salinity and temperature gradients, alongside nutrient availability, created a complex environmental landscape that shaped the diversity and distribution of the predicted ARGs. Salinity predominantly influenced microbial communities and predicted ARG composition, leading to clear distinctions between high-saline regions and those with lower to mid-level salinity. Furthermore, our analysis suggests that microbial community composition and mobile genetic elements might be crucial in shaping ARG diversity and composition.<br><br>CONCLUSIONS: We presented that salinity and temperature were identified as the primary environmental factors influencing resistome diversity and distribution across geographic regions, with nutrient availability further shaping these patterns in the Baltic Sea. Our study also highlighted the interplay between microbial communities, resistance, and associated functional genes in the benthic ecosystem, underscoring the potential role of microbial and mobile genetic element composition in ARG distribution. Understanding how environmental factors and microbial communities modulate environmental resistomes will help predict the impact of future environmental changes on resistance mechanisms in complex aquatic ecosystems. Video Abstract.}, }
@article {pmid40189243, year = {2025}, author = {Chitcharoen, S and Sawaswong, V and Klomkliew, P and Chanchaem, P and Payungporn, S}, title = {Comparative analysis of human gut bacterial microbiota between shallow shotgun metagenomic sequencing and full-length 16S rDNA amplicon sequencing.}, journal = {Bioscience trends}, volume = {}, number = {}, pages = {}, doi = {10.5582/bst.2024.01393}, pmid = {40189243}, issn = {1881-7823}, abstract = {The human gut microbiome is increasingly recognized as important to health and disease, influencing immune function, metabolism, mental health, and chronic illnesses. Two widely used, cost-effective, and fast approaches for analyzing gut microbial communities are shallow shotgun metagenomic sequencing (SSMS) and full-length 16S rDNA sequencing. This study compares these methods across 43 stool samples, revealing notable differences in taxonomic and species-level detection. At the genus level, Bacteroides was most abundant in both methods, with Faecalibacterium showing similar trends but Prevotella was more abundant in full-length 16S rDNA. Genera such as Alistipes and Akkermansia were more frequently detected by full-length 16S rDNA, whereas Eubacterium and Roseburia were more prevalent in SSMS. At the species level, Faecalibacterium prausnitzii, a key indicator of gut health, was abundant across both datasets, while Bacteroides vulgatus was more frequently detected by SSMS. Species within Parabacteroides and Bacteroides were primarily detected by 16S rDNA, contrasting with higher SSMS detection of Prevotella copri and Oscillibacter valericigenes. LEfSe analysis identified 18 species (9 species in each method) with significantly different detection between methods, underscoring the impact of methodological choice on microbial diversity and abundance. Differences in classification databases, such as Ribosomal Database Project (RDP) for 16S rDNA and Kraken2 for SSMS, further highlight the influence of database selection on outcomes. These findings emphasize the importance of carefully selecting sequencing methods and bioinformatics tools in microbiome research, as each approach demonstrates unique strengths and limitations in capturing microbial diversity and relative abundances.}, }
@article {pmid40188788, year = {2025}, author = {Lu, H and Miao, J and Zhang, N and Ji, J and Zhang, R and Zhu, S and Wei, X}, title = {Targeting regulation of nitrate removal and chlorophenol degradation through hydrogen/oxygen switching.}, journal = {Water research}, volume = {281}, number = {}, pages = {123581}, doi = {10.1016/j.watres.2025.123581}, pmid = {40188788}, issn = {1879-2448}, abstract = {Nitrate is a common co-contaminant with 2,4-dichlorophenol (2,4-DCP) in water, presenting a challenge for environmental remediation. Under anaerobic conditions, the ring cleavage of chlorophenol is inefficient, while under aerobic conditions, nitrate removal is hindered. In this study, a microbial consortium capable of hydrogenotrophic denitrification and 2,4-DCP degradation was cultured, aiming to achieve efficient nitrate removal and 2,4-DCP degradation by alternately switching between hydrogen (H2) and oxygen (O2). Under H2 conditions, nitrate removal exceeded 90 %, while under O2 conditions, 2,4-DCP degradation reached 100 %. Under H2 conditions, the abundance of the Nar gene which was involved in nitrate reduction was higher than that under O2 conditions, promoting hydrogenotrophic denitrification. In contrast, under O2 conditions, 2,4-DCP degradation occurred via hydroxylation, ring-cleavage, dechlorination, and mineralization through the TCA cycle. Metagenomic and metabolomic analysis was performed to explore microbial metabolic pathways and potential synergistic mechanisms involved in hydrogenotrophic denitrification and 2,4-DCP biodegradation. In the H2-atmosphere, microbes (Methylobacillus and Chromobacterium), genes (E3.1.1.45 and speG), and metabolites (Cytosine and Uridine) may play a crucial role in hydrogenotrophic denitrification. In the O2-atmosphere, the functional genus of Paracoccus and Aquamicrobium associated with genes (tfdB and tfdC) may contribute to 2,4-DCP and its metabolites 2-Chloromaleylacetate degradation. These findings confirmed the role of functional microbial communities through H2/O2 regulation. This work provides a promising technological reference for treating industrial wastewater containing phenols and nitrogen.}, }
@article {pmid40188743, year = {2025}, author = {Deng, K and Wang, L and Nguyen, SM and Shrubsole, MJ and Cai, Q and Lipworth, L and Gupta, DK and Zheng, W and Shu, XO and Yu, D}, title = {A dietary pattern promoting gut sulfur metabolism is associated with increased mortality and altered circulating metabolites in low-income American adults.}, journal = {EBioMedicine}, volume = {115}, number = {}, pages = {105690}, doi = {10.1016/j.ebiom.2025.105690}, pmid = {40188743}, issn = {2352-3964}, abstract = {BACKGROUND: Excessive hydrogen sulfide in the gut, generated by sulfur-metabolising bacteria from foods, has been linked to intestinal inflammation and human diseases. We aim to investigate the interplay between diet and sulphur-metabolising bacteria in relation to mortality and circulating metabolites in understudied populations.<br><br>METHODS: In the Southern Community Cohort Study (SCCS), a prospective cohort of primarily low-income American adults, habitual diets were assessed using a food frequency questionnaire at baseline (2002-2009). A sulfur microbial diet score (SMDS) was developed among 514 Black/African American participants by linking habitual dietary intakes with the abundance of sulfur-metabolising bacteria profiled by faecal shotgun metagenomics. The SMDS was then constructed among all eligible SCCS participants (50,114 Black/African American and 23,923 non-Hispanic White adults), and its associations with mortality outcomes were examined by Cox proportional hazards model and Fine-Grey subdistribution hazard model. The association between SMDS and 1110 circulating metabolites was examined by linear regression among 1688 SCCS participants with untargeted metabolomic profiling of baseline plasma samples.<br><br>FINDINGS: Over an average 13.9-year follow-up, SMDS was associated with increased all-cause mortality (HR [95% CI] for the highest vs. lowest quartiles: 1.21 [1.15-1.27]) and cardiovascular disease (1.18 [1.08-1.29]), cancer (1.13&#xa0;[1.02-1.25]), and gastrointestinal cancer-specific (1.22 [1.00-1.49]) mortality among Black/African American participants (all P-trend<0.05). The associations were largely consistent across participant subgroups. Similar results were observed among non-Hispanic White participants. The SMDS was associated with 112 circulating metabolites, which mediated 36.15% of the SMDS-mortality association (P&#xa0;=&#xa0;0.002).<br><br>INTERPRETATION: A dietary pattern promoting sulfur-metabolising gut bacteria may contribute to increased total and disease mortality in low-income American adults.<br><br>FUNDING: This study was funded by the National Institutes of Health, United States, to Vanderbilt University Medical Center, United States, and Anne Potter Wilson Chair endowment to Vanderbilt University, United States.}, }
@article {pmid40188549, year = {2025}, author = {Sun, J and Yang, W and Li, M and Zhang, S and Sun, Y and Wang, F}, title = {Metagenomic analysis reveals soil microbiome responses to microplastics and ZnO nanoparticles in an agricultural soil.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138164}, doi = {10.1016/j.jhazmat.2025.138164}, pmid = {40188549}, issn = {1873-3336}, abstract = {Both microplastics (MPs) and engineered nanoparticles are pervasive emerging contaminants that can produce combined toxicity to terrestrial ecosystems, yet their effects on soil microbiomes remain inadequately understood. Here, metagenomic analysis was employed to investigate the impacts of three common MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and zinc oxide nanoparticles (nZnO) on soil microbiomes. Both MPs and nZnO significantly altered the taxonomic, genetic, and functional diversity of soil microbes, with distinct effects depending on dosage or type. Archaea, fungi, and viruses exhibited more pronounced responses compared to bacteria. Higher doses of MPs and nZnO reduced gene abundance for nutrient cycles like C degradation and N cycling, but enhanced CO2 fixation and S metabolism. nZnO consistently decreased the complexity, connectivity, and modularity of microbial networks; however, these negative effects could be mitigated by co-existing MPs, particularly at elevated doses. Notably, PLA (10 %, w/w) exhibited greater harm to fungal communities and increased negative interactions between microbes and nutrient-cycling genes, posing unique risks compared to PE and PS. These findings demonstrate that MPs and nZnO interact synergistically, complicating ecological predictions and emphasizing the need to consider pollutant interactions in ecological risk assessments, particularly for biodegradable MPs.}, }
@article {pmid40188455, year = {2025}, author = {Li, Z and Xu, H and Zhang, L and Zhou, Y}, title = {Genome-Resolved Metagenomic and Metatranscriptomics Reveal Feammox Metabolism of Anaerobic Ammonia Oxidation Bacteria in Microaerobic Granular Sludge.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c13580}, pmid = {40188455}, issn = {1520-5851}, abstract = {Anammox is an energy-efficient nitrogen removal process in which anammox bacteria (AnAOB) oxidize NH4[+]-N to N2 using NO2[-]-N as the electron acceptor. Recent evidence suggests that AnAOB can perform extracellular electron transfer (EET), potentially coupling Fe(III) reduction with NH4[+]-N oxidation (Feammox). However, whether AnAOB directly participate in Feammox within complex wastewater treatment systems remains unclear. Here, we investigated the iron-mediated nitrogen metabolism pathways in a microaerobic granular sludge (MGS) reactor by integrating enzyme inhibition assays with analyses of gene dynamics and co-occurrence patterns of nitrogen- and iron-cycling genes. Results demonstrate that AnAOB contributed to Feammox activity. The iron reduction gene CT573071, coding a porin-cytochrome c protein complex associated with EET, co-occurred with hao, hzsABC, and hdh genes in Candidatus Kuenenia, suggesting its role in Feammox. Furthermore, four high-quality metagenome-assembled genomes (MAGs) affiliated with Kuenenia stuttgartiensis_A harbored CT573071, hao-like, hzsABC, and hdh genes, along with the hao-cluster, which catalyzes the oxidation of NH4[+]-N to hydroxylamine. This genomic evidence further supports their dual metabolic capacity. Metatranscriptomic analysis confirmed CT573071 upregulation and its coexpression with the hao, hzsABC, and hdh genes. These findings establish the potential role of K. stuttgartiensis_A in Feammox, providing novel insights into nitrogen removal in low-strength wastewater treatment systems.}, }
@article {pmid40187695, year = {2025}, author = {Palumbo, S and Lucarelli, G and Lasorsa, F and Damiano, R and Autorino, R and Aveta, A and Spena, G and Perdonà, S and Russo, P and Giulioni, C and Cafarelli, A and Finati, M and Siracusano, S and Pandolfo, SD}, title = {Urobiome and Inflammation: A Systematic Review on Microbial Imbalances and Diagnostic Tools for Urinary Disorders.}, journal = {Urology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.urology.2025.03.050}, pmid = {40187695}, issn = {1527-9995}, abstract = {OBJECTIVE: To synthesize current knowledge on urobiome alterations, innovative diagnostic advancements, and emerging therapeutic strategies targeting urobiome dysbiosis in inflammatory urinary tract disorders, including urinary tract infections (UTIs), non-gonococcal urethritis (NGU), and interstitial cystitis.<br><br>METHODS: A systematic review was conducted by screening the most important scientific databases. The search included the keywords: (microbiome) OR (microbial) OR (bacteria) OR (bacterial profile) AND (urine) OR (urinary) AND (first-morning sample) OR (first void). Only original studies in English involving human specimens were considered.<br><br>RESULTS: Of the 760 articles initially identified, a final sample of 20 original studies met the inclusion criteria. Disruptions in the urobiome composition were associated with increased colonization by pathogens such as Escherichia coli and Mycoplasma genitalium, resulting in inflammation and recurrent urinary conditions. Advanced diagnostic techniques, including metaproteomics, metagenomics, and point-of-care assays like NG-LFA, demonstrated enhanced capabilities for rapid pathogen detection and differentiation of inflammatory conditions. Therapeutic interventions targeting urobiome dysbiosis, particularly probiotics (Lactobacillus rhamnosus, L. reuteri, L. crispatus), showed promising efficacy in reducing recurrence and inflammation in clinical trials.<br><br>CONCLUSIONS: Urobiome dysbiosis plays a critical role in inflammatory urinary tract disorders. Innovative diagnostic methods and targeted therapeutic approaches, especially probiotics, offer substantial potential to improve patient outcomes. Further research is warranted to refine these strategies and validate their clinical applicability.}, }
@article {pmid40187301, year = {2025}, author = {Peng, Q and Wu, Z and Qian, D and Ren, H and Xie, G}, title = {Comprehensive multi-omics analysis of secondary distillate from fermented Huangjiu residue: Insights into flavor formation and microbial dynamics.}, journal = {Food chemistry}, volume = {482}, number = {}, pages = {144145}, doi = {10.1016/j.foodchem.2025.144145}, pmid = {40187301}, issn = {1873-7072}, abstract = {Huangjiu residue distillate, or Zaoshao, is a traditional Chinese liquor produced from the fermentation and distillation of Huangjiu lees. This study investigates the fermentation mechanisms and flavor formation of secondary Zaoshao, derived from the second round of Huangjiu lees fermentation, using flavoromics, amino acid and organic acid profiling, and metagenomics. Flavoromics identified ethyl octanoate, ethyl decanoate, ethyl dodecanoate, ethyl hexadecanoate, and ethyl (Z)-octadec-9-enoate as key flavor compounds. Amino acid and organic acid profiling showed continuous increases in amino acid content and significant changes in organic acids during fermentation. Metagenomics identified 9 dominant genera and 10 key species, with Saccharomyces, Saccharopolyspora, Aspergillus, Streptomyces, and Bacillus playing crucial roles in fermentation and flavor formation. These findings provide insights into microbial community functions and offer a foundation for regulating microbial consortia to enhance the flavor quality of secondary Zaoshao.}, }
@article {pmid40187295, year = {2025}, author = {Coskuner-Weber, O and Alpsoy, S and Yolcu, O and Teber, E and de Marco, A and Shumka, S}, title = {Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing.}, journal = {Computational biology and chemistry}, volume = {118}, number = {}, pages = {108444}, doi = {10.1016/j.compbiolchem.2025.108444}, pmid = {40187295}, issn = {1476-928X}, abstract = {The burgeoning field of aquaculture has become a pivotal contributor to global food security and economic growth, presently surpassing capture fisheries in aquatic animal production as evidenced by recent statistics. However, the dense fish populations inherent in aquaculture systems exacerbate abiotic stressors and promote pathogenic spread, posing a risk to sustainability and yield. This study delves into the transformative potential of metagenomics, a method that directly retrieves genetic material from environmental samples, in elucidating microbial dynamics within aquaculture ecosystems. Our findings affirm that metagenomics, bolstered by tools in big data analytics, bioinformatics, and machine learning, can significantly enhance the precision of microbial assessment and pathogen detection. Furthermore, we explore quantum computing's emergent role, which promises unparalleled efficiency in data processing and model construction, poised to address the limitations of conventional computational techniques. Distinct from metabarcoding, metagenomics offers an expansive, unbiased profile of microbial biodiversity, revolutionizing our capacity to monitor, predict, and manage aquaculture systems with high accuracy and adaptability. Despite the challenges of computational demands and variability in data standardization, this study advocates for continued technological integration, thereby fostering resilient and sustainable aquaculture practices in a climate of escalating global food requirements.}, }
@article {pmid40187264, year = {2025}, author = {Kwon, H and Li, B and Xu, M and Wang, Q and Maqbool, T and Lu, H and Winkler, M and Jiang, D}, title = {Minimizing byproduct formation in bioelectrochemical denitrification with anammox bacteria.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138110}, doi = {10.1016/j.jhazmat.2025.138110}, pmid = {40187264}, issn = {1873-3336}, abstract = {Autotrophic bioelectrochemical denitrification (BED) holds promise for nitrate remediation. However, the accumulation of byproducts such as NO2[-], N2O, and NH4[+], poses a significant challenge to effluent quality and climate adaptation. This study hypothesized that introducing anaerobic ammonium oxidation bacteria (anammox) to BED could alleviate this issue through synergy: a) anammox can utilize NH4[+] and NO2[-] from BED without producing N2O, as seen in canonical denitrification, and b) BED can recycle NO3[-] from the anammox anabolic pathway. Results showed that Anammox_BED reduced NO2[-] accumulation by two-thirds, lowered the relative abundance of N2O by 80 %, and eliminated NO. Metagenomic analysis revealed that the anammox species Ca. Brocadia sapporoensis tripled in abundance in the bulk sludge. Meanwhile, Pseudomonas stutzeri and Bosea robiniae, species capable of reducing nitrate via extracellular electron transfer (EET) and supplying NO2[-] to anammox, halved in relative abundance, while the abundance of Stenotrophomonas acidaminiphila, a non-EET, ammonia assimilation species, doubled following anammox introduction. Metatranscriptomic analysis found upregulation of denitrification-related functional genes in Anammox_BED biofilm and survival- and motility- related genes in bulk sludge, possibly due to insufficient substrate. Overall, BED-Anammox successfully diverted the rate-limiting EET nitrite reduction towards anammox-driven nitrite utilization thereby mitigating the generation of unwanted intermediates.}, }
@article {pmid40187012, year = {2025}, author = {Khan, MM and Mushtaq, MA and Suleman, M and Ahmed, U and Ashraf, MF and Aslam, R and Mohsin, M and Rödiger, S and Sarwar, Y and Schierack, P and Ali, A}, title = {Fecal microbiota landscape of commercial poultry farms in Faisalabad, Pakistan: A 16S rRNA gene-based metagenomics study.}, journal = {Poultry science}, volume = {104}, number = {6}, pages = {105089}, doi = {10.1016/j.psj.2025.105089}, pmid = {40187012}, issn = {1525-3171}, abstract = {This study explores the microbiota of broiler and layer farms, aiming to understand how genetic breed, age, and farm type influence microbial communities in commercial settings. Fecal samples from 18 poultry farms (twelve layers and six broilers) in Faisalabad, Pakistan were analyzed using 16S rRNA gene sequencing of the V3-V4 region to evaluate bacterial composition. The dominant phylum, Firmicutes, accounted for 58.72 % of the microbial population, with Lactobacillus being the most abundant genus in both broilers and layers. The total abundance of potentially pathogenic genera was also assessed with Enterococcus and Corynebacterium being the most prevalent across all farms, regardless of bird type. Layers exhibited greater microbial richness and diversity than broilers, while the Karachi cage system (KCS) farm type showed higher richness than Floor system (FS). Although the breed significantly influenced microbial diversity, age was not a determining factor. Co-occurrence analyses revealed close interactions among phyla (Actinobacteriota, Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota) and genera (Lactobacillus, Brevibacterium, Enterococcus), suggesting their pivotal roles within the microbial community. Additionally, functional analysis detected important metabolic pathways and traced microbial signatures of key pathogenic bacteria, enhancing our understanding of microbial contributions to poultry health. Despite limitations such as the need for broader geographic sampling and accounting for diet and medication, this study advances microbiome research in Pakistan's poultry sector, emphasizing consistent taxa and opening avenues for future investigations into microbiome manipulations for improved food safety and achieve better sustainable practices.}, }
@article {pmid40186063, year = {2025}, author = {Saveetha, K and Somala, CS and Anand, T and Balamurugan, D and Vasudevan, V and Saravanan, KM and Senthil, R}, title = {Impact of Soil Microbiomes on Mung Bean Cultivation: Insights from 16S rRNA Metagenomics.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40186063}, issn = {1559-0305}, abstract = {Cyclic nutrient processes, soil health maintenance, and plant development are contingent upon soil microbiomes. The microbial makeup of the soil of Maruthupandiyar College, Thanjavur, is assessed using 16S rRNA gene sequencing. QIIME2, in conjunction with the SILVA database, analyzed the sequencing data to examine microbial diversity and composition. The experimental results revealed a diverse array of bacteria in soil physicochemical properties. The alpha and beta diversity assessment revealed significant microbial community complexity and distribution patterns disparities. The research revealed bacterial groups associated with biological nitrogen fixing, suggesting their potential to enhance mung bean growth. The current study illustrates the significance of microbial interactions in soil for sustaining soil fertility and enhancing crop output. Research findings provide essential insights into improving the sustainability of tropical agriculture through intentional microbial management to create sustainable soil health systems.}, }
@article {pmid40185904, year = {2025}, author = {Wang, D and Gui, S and Pu, J and Zhong, X and Yan, L and Li, Z and Tao, X and Yang, D and Zhou, H and Qiao, R and Zhang, H and Cheng, X and Ren, Y and Chen, W and Chen, X and Tao, W and Chen, Y and Chen, X and Liu, Y and Xie, P}, title = {PsycGM: a comprehensive database for associations between gut microbiota and psychiatric disorders.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {40185904}, issn = {1476-5578}, support = {CSTB2024NSCQ-MSX1027//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; CSTB2024NSCQ-QCXMX0033//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; 82371526//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Psychiatric disorders pose substantial global burdens on public health, yet therapeutic options remain limited. Recently, gut microbiota is in the spotlight of new research on psychiatric disorders, as emerging discoveries have highlighted the importance of gut microbiome in the regulation of central nervous system via mediating the gut-brain-axis bidirectional communication. While metagenomics studies have accumulated for psychiatric disorders, few systematic efforts were dedicated to integrating these high-throughput data across diverse phenotypes, interventions, geographical regions, and biological species. To present a panoramic view of global data and provide a comprehensive resource for investigating the gut microbiota dysbiosis in psychiatric disorders, we developed the PsycGM, a manually curated and well-annotated database that provides the literature-supported associations between gut microbiota and psychiatric disorders or intervention measures. In total, PsycGM incorporated 559 studies from 31 countries worldwide, encompassing research involving humans, rats, mice, and non-human primates. PsycGM documented 8907 curated associations between 1514 gut microbial taxa and 11 psychiatric disorders, as well as 4050 associations between 869 taxa and 232 microbiota-based and non-microbiota-based interventions. Moreover, PsycGM provided a user-friendly web interface with comprehensive information, enabling browsing, retrieving and downloading of all entries. In the application of PsycGM, we panoramically depicted the intestinal microecological imbalance in depression. Additionally, we identified 9 microbial taxa consistently altered in patients with depression, with the most common dysregulations observed for Parabacteroides, Alistipes, and Faecalibacterium; in animal models of depression, consistent changes were observed in 21 microbial taxa, most frequently reported as Helicobacter, Lactobacillus, Roseburia, and the ratio of Firmicutes/Bacteroidetes. PsycGM is a comprehensive resource for future investigations on the role of gut microbiota in mental and brain health, and for therapeutic target innovations based on modifications of gut microbiota. PsycGM is freely accessed at http://psycgmomics.info .}, }
@article {pmid40185827, year = {2025}, author = {Chornchoem, P and Tandhavanant, S and Saiprom, N and Preechanukul, A and Thongchompoo, N and Sensorn, I and Chantratita, W and Chantratita, N}, title = {Metagenomic evaluation, antimicrobial activities, and immune stimulation of probiotics from dietary supplements and dairy products.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11537}, pmid = {40185827}, issn = {2045-2322}, support = {220211/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Probiotics/pharmacology ; *Dietary Supplements/microbiology ; *Dairy Products/microbiology ; *Metagenomics/methods ; Humans ; Lactobacillus/genetics ; Killer Cells, Natural/immunology/drug effects ; Bifidobacterium/genetics ; Animals ; Macrophages/immunology/drug effects ; Anti-Bacterial Agents/pharmacology ; Cytokines/metabolism ; Mice ; }, abstract = {Probiotics are widely marketed as dietary supplements and dairy products for their purported antimicrobial and immunomodulatory activities, often with limited supporting evidence. We identified and isolated probiotics from commercial dietary supplements and dairy products using metagenomics and cultured-based methods. We assessed their anti-bacterial activity against diverse pathogens and investigated their immunomodulatory effects on phagocytes and natural killer (NK) cells. Metagenomic analysis revealed that Lactobacillus and Bifidobacterium were the predominant genera in dietary supplements, while Streptococcus spp. was dominated in dairy products. However, only 37% of the predominant microorganisms identified by metagenomics were accurately listed on product labels. Among 70 representative probiotic strains, 4.3-17.1% probiotic strains demonstrated strong antibacterial-effects against pathogenic bacteria. Notably, specific strains of Bifidobacterium longum and Lactobacillus plantarum exhibited strong antagonistic activity against extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli. Some strains of Lactobacillus spp. significantly enhanced phagocytic activity in monocytes and increased IFN-γ production in NK cells, while members of Lactobacillus rhamnosus significantly suppressed TNF-α, IL-6, and IL-8 production in lipopolysaccharide-stimulated macrophages. In contrast, Bifidobacterium animalis stimulated the production of anti-inflammatory cytokines. This study highlights discrepancies in probiotic labeling and demonstrates the antimicrobial and immunomodulatory potential of specific probiotic strains, suggesting their utility in enhancing health and wellness.}, }
@article {pmid40185819, year = {2025}, author = {Manzoor, M and Leskelä, J and Pietiäinen, M and Martinez-Majander, N and Könönen, E and Sinisalo, J and Putaala, J and Pussinen, PJ and Paju, S}, title = {Oral microbiome dysbiosis in cryptogenic ischemic stroke patients with high-risk patent foramen ovale.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11535}, pmid = {40185819}, issn = {2045-2322}, support = {286246//Research Council of Finland/ ; 340750//Research Council of Finland/ ; 355532//Research Council of Finland/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; }, mesh = {Humans ; *Foramen Ovale, Patent/complications/microbiology ; Female ; Male ; *Ischemic Stroke/microbiology/etiology/complications ; *Dysbiosis/microbiology/complications ; *Microbiota ; Adult ; Middle Aged ; Saliva/microbiology ; Case-Control Studies ; *Mouth/microbiology ; Risk Factors ; }, abstract = {Patent foramen ovale (PFO) is the most common congenital heart abnormality of foetal origin and has been associated with cryptogenic ischemic stroke (CIS) through several mechanisms, with most theories supporting paradoxical embolism. Other possible but unknown contributing factors, such as the role of the microbiome in PFO-associated strokes, remain unclear. We analysed saliva metagenomes to study the differences in the oral microbiome between young-onset CIS patients with clinically relevant high-risk PFO (n = 52) and those without PFO (n = 52). Age- and sex-matched stroke-free controls (n = 16) with high-risk PFO were included for the comparison. Beta diversity was significantly different between patients and controls with high-risk PFO, but not between patients with and without high-risk PFO. The phylum Ascomycota and class Saccharomycetes were significantly more abundant in patients with high-risk PFO than in those without high-risk PFO. Additionally, the abundance of Lactococcus, including Lactococcus raffinolactis and L. cremoris, was higher in controls with high-risk PFO than in patients with high-risk PFO. These findings highlight that oral dysbiosis and high-risk PFO may form a critical but under-recognized combination in the aetiology of CIS. Future research should focus on elucidating the precise mechanisms of these interactions and developing targeted interventions.}, }
@article {pmid40185271, year = {2025}, author = {Guajardo-Leiva, S and Díez, B and Rojas-Fuentes, C and Chnaiderman, J and Castro-Nallar, E and Catril, V and Ampuero, M and Gaggero, A}, title = {From sewage to genomes: expanding our understanding of the urban and semi-urban wastewater RNA virome.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121509}, doi = {10.1016/j.envres.2025.121509}, pmid = {40185271}, issn = {1096-0953}, abstract = {Wastewater is a hotspot for viral diversity, harboring various microbial, plant, and animal viruses, including those that infect humans. However, the dynamics, resilience, and ecological roles of viral communities during treatment are largely unknown. In this study, we explored RNA virus ecogenomics using metagenomics from influent and effluent samples across three wastewater catchment areas in Chile, with a population of 7.05 million equivalent inhabitants. We identified 14,212 RNA-dependent RNA polymerase (RdRP)-coding sequences from the Orthornavirae kingdom, clustering into 4,989 viral species. Using extensive databases of 14,150 family-level representative sequences, we classified 90% of our sequences at the family level. Our analysis revealed that treatment reduced viral richness and evenness (Shannon index), but phylogenetic diversity remained unchanged. Effluents showed lower richness and evenness than influents with similar phylogenetic diversity. Species turnover, influenced by catchment area and treatment, accounted for 54% of sample dissimilarities (Weighted Unifrac). Biomarker analysis indicated that families like Astroviridae and Fiersviridae were more abundant in influents, while Reoviridae and Virgaviridae dominated effluents. This suggests that viral resistance to treatment varies and cannot be solely attributed to genome type, size, or morphology. We traced viral genomes through time and space, identifying sequences like the Pepper Mild Mottle Virus (PMMoV) from the Virgaviridae family over large distances and periods, highlighting its wastewater marker potential. High concentrations of human pathogens, such as Rotavirus (Reoviridae) and Human Astrovirus (Astroviridae), were found in both influents and effluents, stressing the need for continuous monitoring, especially for treated wastewater reuse.}, }
@article {pmid40185197, year = {2025}, author = {Jiang, Y and Yang, J and Liu, Y and Liu, Y and Zhou, W and Yang, B and Hu, B and Wu, H}, title = {A Neonate with Meningitis Caused by probiotic-related Clostridium butyricum.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {107900}, doi = {10.1016/j.ijid.2025.107900}, pmid = {40185197}, issn = {1878-3511}, abstract = {Clostridium butyricum (C. butyricum), a normal gut bacterium in humans, is commonly used as a probiotic. We described a 26-day-old premature neonate who was diagnosed with probiotic-related C. butyricum meningitis. Upon the admission, suppurative meningitis was considered based on cerebrospinal fluid (CSF) biochemical test and neuroimaging examination, and C. butyricum was subsequently identified by CSF metagenomic next-generation sequencing. Given the history of administrating living C. butyricum products before admission, probiotics-associated suppurative meningitis was considered a high possibility, leading to the confirmation of anti-infection treatment including vancomycin and meropenem. Following this therapy, the infant's CSF profiles demonstrated improvement. Additionally, further phylogenetic analysis confirmed the high homologous of C. butyricum from CSF with probiotics. This is the first report of C. butyricum infection in neonates, highlighting the importance for prudence in administrating probiotics for neonates, particularly in high-risk groups such as preterm infants, those with central venous catheters and intestinal diseases.}, }
@article {pmid40185186, year = {2025}, author = {Liu, Y and Pei, Y and Wang, H and Yang, Z}, title = {Lead promoted bile acid deconjugation by modulating gut bacteria encoding bile salt hydrolase (BSH) in Rana chensinensis tadpoles.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126187}, doi = {10.1016/j.envpol.2025.126187}, pmid = {40185186}, issn = {1873-6424}, abstract = {Bile salt hydrolase (BSH) is produced by gut bacteria and is responsible for deconjugating amino acids from the aliphatic side chains of conjugated bile acids (BAs), initiating the critical first step in BAs metabolism. Lead (Pb) is known to cause gut microbial dysbiosis, but whether it affects BAs profiles by reshaping the gut microbiota remains elusive. Here, using targeted BAs metabolomics and metagenomics sequencing, we found that 200 μg/L Pb treatment led to a significant increase in the abundance of BSH-producing microbiota (e.g., Eubacterium and Yersinia), thus promoting the deconjugation of taurocholic acid (TCA) and taurochenodeoxycholic acid (TCDCA). Consequently, the accumulation of relatively hydrophobic BAs cholic acid (CA) and chenodeoxycholic acid (CDCA) may cause damage to enterocytes (e.g., reduced microvilli and enterocyte heights), which attenuated tadpole digestion and ultimately led to significant reductions in morphological parameters. The inhibition of tadpole growth by Pb toxicity may negatively affect their survival and even increase their risk of death. Overall, these results revealed for the first time the toxicological mechanism by which Pb reshapes the gut microbiota and thus disrupts the BAs profile, shedding new insights into the detrimental effects of Pb toxicity on amphibian growth.}, }
@article {pmid40185016, year = {2025}, author = {Yang, M and Yang, H and Wang, W and Fang, H and Huang, L and Li, D and Fu, L and Ding, S and Li, XD and Liu, CQ and Wei, G and Li, D and Cui, G and Fan, Z and Zeng, F}, title = {Impact of particle-attached microbial denitrification on N2O production in an agricultural-urban watershed.}, journal = {Journal of environmental management}, volume = {381}, number = {}, pages = {125223}, doi = {10.1016/j.jenvman.2025.125223}, pmid = {40185016}, issn = {1095-8630}, abstract = {Anthropogenically influenced rivers are key hotspots for nitrous oxide (N2O) emissions. However, the seasonal and spatial heterogeneity of N2O emissions in subtropical riverine systems, particularly the role of particle-attached microbes (PAM) in regulating N2O production, remains poorly understood, contributing to uncertainties in global N2O estimates. This study investigates the potential impacts of PAM-driven nitrogen transformations on N2O production in the Dongjiang River under agricultural and urban influences. Water samples collected during the wet and dry seasons were analyzed for N2O concentrations, dual nitrogen-oxygen isotopes (δ[15]N-NO3[-], δ[18]O-NO3[-]), and metagenomic sequencing of PAM. All samples exhibited N2O supersaturation, with emissions significantly higher in the dry season than in the wet season. A linearly positive δ[15]N-δ[18]O correlation, accompanied by lower NO3[-] in the bottom layers than the surface layers in the dry season indicates active denitrification, leading to elevated N2O concentrations. PAM-driven denitrification was identified as the dominant nitrogen transformation process, supported by higher abundances of denitrification genes (nirKS, norBC, nosZ) relative to nitrification genes (amoABC). Despite aerobic water column conditions, low-oxygen microhabitats around suspended particles facilitated N2O production. A significantly positive correlation (p < 0.05, R[2] = 0.42) between N2O concentrations and the nirK/nosZ gene ratio suggests that gene expression imbalances contributed to net N2O accumulation. Additionally, the downstream urban area exhibited lower DO and higher DOC levels, enhancing denitrification and increasing N2O production by 4.7 % compared to the upstream agricultural region. Seasonal differences further influenced N2O dynamics: higher DOC/NO3[-] ratios in the dry season promoted heterotrophic denitrification, while elevated temperatures in the wet season favored complete denitrification, reducing N2O emissions. These findings provide critical insights into PAM-driven nitrogen cycling, informing strategies for mitigating N2O emissions and managing nitrogen pollution in subtropical riverine systems.}, }
@article {pmid40184966, year = {2025}, author = {Tu, M and Lin, H and Zhang, X and Zhang, X and Yan, J}, title = {Elemental sulfur facilitates co-metabolism of Cr(VI) and nitrate by autotrophic denitrifiers in constructed wetlands.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138153}, doi = {10.1016/j.jhazmat.2025.138153}, pmid = {40184966}, issn = {1873-3336}, abstract = {The antagonistic microbial reduction of chromate and nitrate poses significant challenges for their simultaneous removal in autotrophic denitrifying systems. This study explored the treatment performance and mechanisms for the simultaneous removal of chromate (0, 2, and 10 mg·L[-1]) and nitrate (20 mg·L[-1]) in constructed wetland (CW) microcosms with elemental sulfur additions at 0-, 5-, and 25-times background levels. Results showed that sulfur-amended microcosms achieved chromate and nitrate removal up to 76.46 % and 28.12 % higher, respectively, than 0S groups. Notably, the nitrate removal rate constant was higher in the presence of chromate than its absence, exclusively in the 25S groups. In a sediment core assay, the 25S groups also exhibited substantially facilitating effect of chromate removal potential in the presence of nitrate. Metagenomic analyses revealed upregulations of denitrification and sulfur oxidation-related functional genes along with sulfur supplementation. Autotrophic denitrifiers including Dechloromonas, Thiobacillus, Sulfuricella, and Sulfuritalea made significant contributions to chromate and nitrate removal rates, as well as functional genes encoding sulfur, nitrogen, and chromium transformation, in response to sulfur addition. These findings shed first light on the co-metabolism of chromate and nitrate by sulfur-based autotrophic denitrifiers, emphasizing their pivotal role in denitrification systems, e.g., CWs, with chromate inputs.}, }
@article {pmid40184824, year = {2025}, author = {Zhu, H and Mao, X and Sajnani, S and Yang, H and Li, T and Tan, S}, title = {Psychrophilic insights into petroleum degradation: Gene abundance dynamics.}, journal = {Enzyme and microbial technology}, volume = {188}, number = {}, pages = {110642}, doi = {10.1016/j.enzmictec.2025.110642}, pmid = {40184824}, issn = {1879-0909}, abstract = {Petroleum degradation by psychrophiles can be enhanced on the basis of omics analyses, which offer better sensitivity than traditional biochemical methods do. A metagenomic analysis focusing on gene abundance comparisons may provide new guidance to optimize soil decontamination under cold environmental conditions. The soil used in this study was sampled from Dalian, from which an indigenous consortium was isolated. The degradative soil systems, initially categorized into control (DLC) and experimental (DLD) groups, were kept at room temperature (20 ± 5 °C) for six weeks. The DLD group was subsequently transferred to a low-temperature environment (5-10 °C) for 90 days and renamed DDL. A petroleum removal rate of 74.59 % was achieved in the process from DLD to DDL groups. Each soil sample was subjected to analysis and metagenomic sequencing. The abundance of genes of interest was compared between pathways to determine trends. The findings demonstrate that psychrophilic degradation is more effective than natural remediation is. The soil microbial community structure displayed site specificity, with 802 genes in DDL associated with 249 pathways, indicating greater abundance of psychrophilic genes in DDL than in DLC. The abundance of key genes was at different orders of magnitude but showed similar trends. The abundance of genes associated with hydrocarbon-related metabolism surpassed that of genes associated with sphingolipid, fatty acid, or benzene metabolism. This study provides valuable insights into psychrophilic microbe-driven petroleum degradation and indicates the need for precise supplementation of biosurfactants to improve remediation efficiency.}, }
@article {pmid40184708, year = {2025}, author = {He, D and Nong, Y and He, Y and Luo, Y and Li, C and Gao, J and Dang, C and Fu, J}, title = {Effect of pre-chlorination on bioelectricity production and stabilization of excess sludge by microbial fuel cell.}, journal = {Water research}, volume = {281}, number = {}, pages = {123564}, doi = {10.1016/j.watres.2025.123564}, pmid = {40184708}, issn = {1879-2448}, abstract = {Microbial fuel cell (MFC) is a technology that can generate electricity while degrading excess sludge. However, the complex components, intricate biological structures, and inhibitory compounds in sludge limit the application of MFC. Therefore, this study utilized chlorination as a sludge pretreatment method to improve the comprehensive performance of MFC in sludge treatment. Results showed that pre-chlorination at a dose of 0.2 mg/L increased output voltage of MFC by 500 % from approximately 100 mV to around 600 mV, and power density by 15.60 % from 3.15 W/m[3] to 3.64 W/m[3], and simultaneously increased the degradation of sludge MLSS (mixed liquor suspended solids), MLVSS (mixed liquor volatile suspended solids), EPS (extracellular polymeric substances) polysaccharide and protein by 9.64 %, 47.07 %, 18.63 % and 16.26 %, respectively. Molecular composition analysis of EPS in sludge by three-dimensional excitation emission matrix fluorescence spectroscopy (3D-EEM), Fourier transform infrared spectroscopy (FTIR) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) indicated pre-chlorination significantly promoted the molecular transformation in MFC. The microbiome analysis of anode biofilm in MFC by scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), metagenomics and metametabolomics revealed that pre-chlorination facilitated the development of biomass, enrichment of electricity-producing bacteria (EPB), enhancement of electricity-producing activity and metabolic activity. Moreover, the sludge EPS was the importance source for the microbial metabolites in MFC was validated by the joint analysis of FT-ICR-MS and metametabolomics.}, }
@article {pmid40184705, year = {2025}, author = {Barrantes-Jiménez, K and Lejzerowicz, F and Tran, T and Calderón-Osorno, M and Rivera-Montero, L and Rodríguez-Sánchez, C and Wikmark, OG and Eiler, A and Grossart, HP and Arias-Andrés, M and Rojas-Jiménez, K}, title = {Anthropogenic imprint on riverine plasmidome diversity and proliferation of antibiotic resistance genes following pollution and urbanization.}, journal = {Water research}, volume = {281}, number = {}, pages = {123553}, doi = {10.1016/j.watres.2025.123553}, pmid = {40184705}, issn = {1879-2448}, abstract = {Plasmids are key determinants in microbial ecology and evolution, facilitating the dissemination of adaptive traits and antibiotic resistance genes (ARGs). Although the molecular mechanisms governing plasmid replication, maintenance, and transfer have been extensively studied, the specific impacts of urbanization-induced pollution on plasmid ecology, diversity, and associated ARGs in tropical regions remain underexplored. This study investigates these dynamics in a tropical aquatic ecosystem, providing novel insights into how pollution shapes plasmid composition and function. In contrast to the observed decrease in chromosomal diversity, we demonstrate that pollution associated with urbanization increases the diversity and taxonomic composition of plasmids within a bacterial community (plasmidome). We analyzed eighteen water and sediment metagenomes, capturing a gradient of pollution and ARG contamination along a tropical urban river. Plasmid and chromosomal diversity profiles were found to be anti-correlated. Plasmid species enrichment along the pollution gradient led to significant compositional differences in water samples, where differentially abundant species suggest plasmid maintenance within specific taxonomic classes. Additionally, the diversity and abundance of ARGs related to the plasmidome increased concomitantly with the intensity of fecal and chemical pollution. These findings highlight the critical need for targeted plasmidome studies to better understand plasmids' environmental spread, as their dynamics are independent of chromosomal patterns. This research is crucial for understanding the consequences of bacterial evolution, particularly in the context of environmental and public health.}, }
@article {pmid40184632, year = {2025}, author = {Huang, Y and Mao, X and Zheng, X and Zhao, Y and Wang, D and Wang, M and Chen, Y and Liu, L and Wang, Y and Polz, MF and Zhang, T}, title = {Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf058}, pmid = {40184632}, issn = {1751-7370}, abstract = {Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analyzed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.}, }
@article {pmid40184383, year = {2025}, author = {Shen, C and Wedell, E and Pop, M and Warnow, T}, title = {TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012593}, doi = {10.1371/journal.pcbi.1012593}, pmid = {40184383}, issn = {1553-7358}, mesh = {*Metagenomics/methods ; Algorithms ; *Software ; Computational Biology/methods ; Databases, Genetic ; Likelihood Functions ; Sequence Analysis, DNA/methods ; }, abstract = {We present TIPP3 and TIPP3-fast, new tools for abundance profiling in metagenomic datasets. Like its predecessor, TIPP2, the TIPP3 pipeline uses a maximum likelihood approach to place reads into labeled taxonomies using marker genes, but it achieves superior accuracy to TIPP2 by enabling the use of much larger taxonomies through improved algorithmic techniques. We show that TIPP3 is generally more accurate than leading methods for abundance profiling in two important contexts: when reads come from genomes not already in a public database (i.e., novel genomes) and when reads contain sequencing errors. We also show that TIPP3-fast has slightly lower accuracy than TIPP3, but is also generally more accurate than other leading methods and uses a small fraction of TIPP3's runtime. Additionally, we highlight the potential benefits of restricting abundance profiling methods to those reads that map to marker genes (i.e., using a filtered marker-gene based analysis), which we show typically improves accuracy. TIPP3 is freely available at https://github.com/c5shen/TIPP3.}, }
@article {pmid40183829, year = {2025}, author = {Moscona, R and Wagner, T and Geva, M and Bucris, E and Erster, O and Zuckerman, NS and Mor, O}, title = {Newly designed amplicons-based method for near-full-length genome (NFLG) sequencing of HIV-1 group M recombinant forms.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {362}, pmid = {40183829}, issn = {1573-4978}, mesh = {*HIV-1/genetics ; Humans ; *Genome, Viral/genetics ; Phylogeny ; HIV Infections/virology/genetics ; Recombination, Genetic/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; Genotype ; }, abstract = {BACKGROUND: Over the years the spread of HIV-1 across the globe resulted in the creation of multiple subtypes and new recombinant forms (RFs). While the pol gene region of the HIV-1 genome is used for resistance mutations analysis and initial detection of RFs, whole genome sequencing analysis is required to determine recombination events across the viral genome. Here, we present a newly designed robust near-full length genome (NFLG) sequencing approach for the sequencing of HIV-1 genomes, out of clinical whole blood samples. This method has been successfully tested for various HIV-1 subtypes and RFs.<br><br>METHODS AND RESULTS: The method is based on an in-house developed set of 32 pan-genotypic primer pairs, divided into two pools, each containing 16 primer pairs covering the entire HIV-1 genome. Two parallel multiplex PCR reactions were used to generate 32 overlapping DNA fragments spanning the HIV-1 genome. Nextera XT protocol was used to obtain barcoded DNA libraries, which were sequenced with the Illumina Miseq platform using a V3 kit. A consensus sequence was determined for each sample and was used to define recombination events across the genome. For this aim, a combined analysis of several computational tools including HIV BLAST, phylogenetic analysis, RIP, SimPlot&#x2009;+&#x2009;&#x2009;+&#x2009;and jpHMM were employed. Overall, plasma samples from 33 patients suspected to carry RFs and 2 different, known pure subtypes controls, were included in this study. Genome coverage varied between RFs, while the gag and pol genes were nearly fully covered, the highly variable env gene region was not. Yet, these NFLG analyses enabled the identification of recombination events genome wide.<br><br>CONCLUSIONS: In summary, we describe a methodology for HIV-1 NFLG sequencing, which is based on partially overlapping, multiple PCR fragments, spanning the HIV-1 genome. Additionally, this newly refined method was compared to HIV-1 NFLG results of PCR-free metagenomic sequencing and proved to obtain greater coverage of the HXB2 reference genome. Yet, further testing and validation on a larger cohort is required. Still, this method enables sequencing of 20 different patient samples in a single MiSeq sequencing run and was used for the characterization of different HIV-1 RFs and pure subtypes circulating in Israel.}, }
@article {pmid40183042, year = {2025}, author = {Li, T and Shafiul Alam, M and Yang, Y and Mohammad Al-Amin, H and Rahman, M and Islam, F and Conte, MA and Price, DC and Hang, J}, title = {Metagenome analysis of viruses associated with Anopheles mosquitoes from Ramu Upazila, Cox's Bazar District, Bangladesh.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19180}, pmid = {40183042}, issn = {2167-8359}, mesh = {*Anopheles/virology ; Animals ; Bangladesh ; Phylogeny ; *Mosquito Vectors/virology ; *Metagenome ; Male ; Female ; High-Throughput Nucleotide Sequencing ; }, abstract = {Bangladesh has a warm climate and landscapes favourable for the proliferation of mosquitoes. Mosquito-borne pathogens including malaria and arthropod-borne viruses (arboviruses) remain a serious threat to the public health requiring constant vector control and disease surveillance. From November 2018 to April 2019, Anopheles mosquitoes were collected in three unions in the Ramu Upazila (sub-district) of Cox's Bazar District, Bangladesh. The mosquito specimens were combined into pools based on date of collection, household ID, and sex. Metagenome next-generation sequencing was conducted to elucidate diversity of virus sequences in each pool. Homology-based taxonomic classification and phylogenetic analyses identified a broad diversity of putative viruses from 12 known families, with additional unclassified viruses also likely present. Analysis of male mosquitoes showed some of these viruses are likely capable of being vertically transmitted. Moreover, many of the assembled virus sequences share homology and phylogenetic affinity with segments in sequenced Anopheles genomes, and may represent endogenous viral elements derived from a past evolutionary relationship between these putative viruses and their mosquito hosts.}, }
@article {pmid40182804, year = {2025}, author = {Sarwar, A and Aslam, B and Mahmood, S and Muzammil, S and Siddique, AB and Sarwar, F and Khurshid, M and Rasool, MH and Sasanya, J and Aljasir, SF}, title = {Distribution of multidrug-resistant Proteus mirabilis in poultry, livestock, fish, and the related environment: One Health heed.}, journal = {Veterinary world}, volume = {18}, number = {2}, pages = {446-454}, doi = {10.14202/vetworld.2025.446-454}, pmid = {40182804}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The emergence of multidrug-resistant (MDR) Proteus mirabilis in food-producing animals and their associated environments is a growing public health concern. The indiscriminate use of antimicrobials in animal husbandry exacerbates resistance development, posing significant threats to food safety and sustainability. This study investigates the distribution, antibiotic resistance patterns, and virulence-associated genes (VAGs) of P. mirabilis isolated from poultry, livestock, fish, and their environments in Pakistan under a One Health perspective.<br><br>MATERIALS AND METHODS: A total of 225 samples were collected from poultry (n = 100), livestock (n = 75), and aquatic sources (n = 50) from March 2023 to September 2024. Standard microbiological methods were employed for the isolation and identification of P. mirabilis. Polymerase chain reaction (PCR)-based detection of antibiotic resistance genes and VAGs was performed using specific primers. Antibiotic susceptibility was assessed through the disk diffusion method following Clinical and Laboratory Standards Institute 2022 guidelines. Statistical analyses, including analysis of variance and correlation models, were applied to assess the relationships between variables.<br><br>RESULTS: P. mirabilis was detected in 28.44% (64/225) of the total samples, with the highest occurrence observed in poultry (38%), followed by livestock (22.67%) and aquatic sources (18%). Resistance to ampicillin (100%), chloramphenicol (82%), cefepime (75%), and ciprofloxacin (75%) was widespread. PCR analysis revealed a high occurrence of extended-spectrum beta-lactamase-producing P. mirabilis carrying bla CTX-M (49%), bla OXA (54%), and bla TEM (25.67%) genes. In addition, VAGs such as zapA (39.53%), ucaA (34.88%), and hpmA (32.55%) were frequently identified. The presence of MDR P. mirabilis in fish and related environments (18%) is alarming, highlighting potential zoonotic and foodborne transmission risks.<br><br>CONCLUSION: The study underscores the widespread distribution of MDR P. mirabilis in animal-based food sources, raising significant concerns regarding food safety and antimicrobial resistance. The findings reinforce the need for stringent monitoring and regulatory policies to mitigate MDR bacterial dissemination across the food supply chain. Future research should employ metagenomic approaches for comprehensive surveillance and risk assessment.}, }
@article {pmid40182766, year = {2025}, author = {Lazarevic, V and Gaïa, N and Pham, TT and de Lorenzi-Tognon, M and Girard, M and Mauffrey, F and Charretier, Y and Renzi, G and Huber, C and Schrenzel, J}, title = {Identification of causative agents of infective endocarditis by metagenomic next-generation sequencing of resected valves.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1532257}, doi = {10.3389/fcimb.2025.1532257}, pmid = {40182766}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Middle Aged ; Female ; *Heart Valves/microbiology/surgery ; Sensitivity and Specificity ; Aged ; *Endocarditis/microbiology/diagnosis/surgery ; Prospective Studies ; *Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Adult ; Aged, 80 and over ; }, abstract = {BACKGROUND: Infective endocarditis (IE) is a rare and life-threatening condition with considerable mortality rates. Diagnosis is often complicated by negative blood culture results, limiting the accurate identification of causative pathogens. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) of cardiac valve specimens compared to conventional clinical laboratory methods for identifying pathogens in IE.<br><br>METHODS: Nineteen patients with suspected IE who were scheduled for surgical valve removal were prospectively enrolled. The metagenomic workflow included bacterial DNA enrichment from resected valves using the Molzym Ultra-Deep Microbiome Prep, sequencing of metagenomic libraries using the Illumina MiSeq platform, and Kraken 2 taxonomic assignments based on read data.<br><br>RESULTS: Valve mNGS achieved a sensitivity of 82.4% and a specificity of 100% relative to the final adjudicated pathogen diagnosis. Blood culture, considered the reference standard, exhibited slightly higher sensitivity (88.2%) with comparable specificity (100%). In comparison, valve culture (sensitivity: 29.4%, specificity: 50.0%) and microscopy (sensitivity: 35.3%, specificity: 100%) showed lower diagnostic performance. Delays between blood culture negativization and valve resection impacted mNGS sensitivity, likely due to pathogen clearance. Notably, valves resected within 12 days from blood culture negativization achieved 100% diagnostic accuracy, emphasizing the importance of timing for optimal mNGS results.<br><br>CONCLUSION: This study underscores mNGS as a valuable diagnostic tool for detecting IE pathogens, complementing traditional diagnostic methods. The detection of antibiotic resistance genes and multi-locus sequence typing profiles in some samples further demonstrated its utility.}, }
@article {pmid40182295, year = {2025}, author = {Hou, J and Yin, H and Wang, D and Luo, J and Yang, W and Kang, T}, title = {The influence of rhizosphere soil microorganisms and environmental factors on gentiopicroside content in the roots and rhizomes of Gentiana scabra Bunge from Liaoning Province.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1554981}, doi = {10.3389/fmicb.2025.1554981}, pmid = {40182295}, issn = {1664-302X}, abstract = {BACKGROUND: Rhizosphere soil microorganisms, as the second genome of plants, play an important role in the formation of secondary metabolites of medicinal plants and are one of the key factors in the formation of the authenticity of medicinal materials.<br><br>METHODS: In this paper, the rhizosphere soils of Gentiana scabra Bunge from six producing areas in Liaoning Province were taken as the research objects. Through high-throughput sequencing technology, and with the help of PLS-DA and RDA, the impacts of rhizosphere soil microorganisms and environmental factors on the quality of G. scabra were explored in depth.<br><br>RESULTS: Alpha diversity shows that the diversity of bacterial communities varies significantly, while the regularity of fungi is weak; beta diversity shows that samples from different producing areas can be effectively grouped according to community structure. LDA effect shows that the differential species of bacteria and fungi vary among different producing areas. Indicator and random forest analysis show that Sphingomonas and Subgroup_2 are the main indicator species of the bacterial communities in the high-content group, which can increase the evenness of microbial communities and maintain or enhance species diversity. The regularity of fungal communities is relatively weak. Functional metagenomic analysis shows that the functions of soil microorganisms in the six producing areas are similar but the relative abundances are different. The main functions of bacteria are closely related to microbial metabolism in diverse environments, biosynthesis of secondary metabolites, metabolic pathways, etc.; fungi are mainly lichen parasite, plant saprotroph, and ericoid mycorrhizal. PLS-DA and RDA analysis show that properly adjusting the key environmental factors of Ca, pH, and rapidly available potassium, which have a great influence on G. scabra, can affect the abundances of microorganisms such as Subgroup_2, Burkholderia-Caballeronia-Paraburkholderia, Metarhizium, Bryobacter, Fusarium, Rhodanobacter, Cladophialophora, Sphingomonas and Trichoderma, and then regulate the content of gentiopicroside.<br><br>DISCUSSION: This study provides practical microbial approaches and strategies for improving gentiopicroside content in the roots and rhizomes of G. scabra, and lays a solid scientific foundation for ensuring the quality and safety of genuine medicinal materials and the stable and sustainable development of the G. scabra planting industry.}, }
@article {pmid40182288, year = {2025}, author = {Lin, TS and Zhu, Z and Lin, X and Huang, HY and Li, LP and Li, J and Ni, J and Li, P and Chen, L and Tang, W and Liu, H and Se, X and Xie, M and Long, C and Chiu, CM and Fang, SH and Zhao, J and Lin, YC and Yu, X and Huang, HD}, title = {Enhancing bloodstream infection diagnostics: a novel filtration and targeted next-generation sequencing approach for precise pathogen identification.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1538265}, doi = {10.3389/fmicb.2025.1538265}, pmid = {40182288}, issn = {1664-302X}, abstract = {Bloodstream infections (BSIs) pose a significant diagnostic challenge, largely due to the limitations of traditional methods such as blood cultures. These methods often yield low positive rates, have lengthy processing times that delay treatment, and are limited in detecting only a narrow range of pathogens. Such delays and inaccuracies can critically impede timely clinical interventions, potentially compromising patient outcomes. Next-generation sequencing (NGS) is a powerful tool for rapid, precise pathogen identification. While metagenomic NGS (mNGS) offers broad pathogen coverage, it is often costly and complex. Targeted NGS (tNGS), however, focuses on key regions of clinically relevant pathogens, reducing costs and simplifying workflows while maintaining high sensitivity, making it more practical for routine diagnostics. In this study, we introduce a novel approach combining a human cell-specific filtration membrane with a multiplex tNGS panel to overcome these challenges. The filtration membrane, designed with surface charge properties to be electrostatically attractive to leukocytes for the selective capture of specific cells, demonstrated high efficiency in removing host cells and nucleic acids, achieving over a 98% reduction in host DNA and thereby minimizing background interference in pathogen detection. Additionally, we developed an effective multiplex tNGS panel targeting over 330 clinically relevant pathogens and verified its consistency with mNGS and blood culture results, demonstrating a significant improvement in detection sensitivity. By integrating these two methods, we achieved a synergistic enhancement in diagnostic capability, boosting pathogen reads by 6- to 8-fold, which enabled reliable identification even in cases of low-abundance pathogens. This approach provides faster, more accurate, and more sensitive detection of BSIs, enabling earlier identification of infections. This facilitates timely and targeted treatment, ultimately improving patient outcomes in critical care settings. Given the unique properties of the filtration membrane and the strengths of the tNGS panel, this approach shows promising applications in prenatal and genetic health support, as well as in advancing early cancer screening strategies.}, }
@article {pmid40182062, year = {2025}, author = {Simon, SA and Soares, AR and Bornemann, TLV and Lange, A and Griesdorn, L and Fuentes, A and Dieckmann, M and Krok, BA and Ruff, SE and Hügler, M and Moraru, C and Probst, AJ}, title = {Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf041}, doi = {10.1093/ismeco/ycaf041}, pmid = {40182062}, issn = {2730-6151}, abstract = {Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes in enrichment cultures, no single technique can render simultaneous data on both metabolic capacities and mobile genetic elements. Here, we apply long-read sequencing to monitor the incorporation of non-canonical bases in genome-resolved metagenomic datasets and elucidate the replication patterns of both bacteria and phages. This technology enables the simultaneous reconstruction of both prokaryotic and viral genomes (alongside genomics downstream analyses like metabolic predictions), in addition to providing information regarding their replication in enrichment cultures. By spiking the base analog 5-bromo-2'-deoxyuridine (BrdU) into activated sludge microcosms, we determined that 114 of the 118 high-quality genomes recovered were actively replicating in enrichment cultures from activated sludge and identified both slow (low BrdU incorporation and change in abundance) and rapidly replicating organisms (high BrdU incorporation and change in abundance). Some of the genomes detected exhibited regions rich in BrdU that were predicted to represent prophages in their lytic cycle. Ultimately, this novel means of monitoring the replication responses of microbes, and deciphering their genomes and active mobile genetic elements will advance and empower strategies aimed at isolating previously uncultivated microbes in pure culture.}, }
@article {pmid40182061, year = {2025}, author = {Cheung, S and Morando, M and Magasin, J and Cornejo-Castillo, FM and Zehr, JP and Turk-Kubo, KA}, title = {NifH gene amplicon sequencing and metagenomic approaches are complementary in assessing diazotroph diversity.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf038}, doi = {10.1093/ismeco/ycaf038}, pmid = {40182061}, issn = {2730-6151}, abstract = {Exploring the diversity of diazotrophs is key to understanding their role in supplying fixed nitrogen that supports marine productivity. A nested PCR assay using the universal primer set nifH1-nifH4, which targets the nitrogenase (nifH) gene, is a widely used approach for studying marine diazotrophs by amplicon sequencing. Metagenomics, direct sequencing of DNA without PCR, has provided complementary views of the diversity of marine diazotrophs. A significant fraction of the metagenome-derived nifH sequences (e.g. Planctomycete- and Proteobacteria-affiliated) were reported to have nucleotide mismatches with the nifH1-nifH4 primers, leading to the suggestion that nifH amplicon sequencing does not detect specific diazotrophic taxa and underrepresents diazotroph diversity. Here, we report that these mismatches are mostly located in a single-base at the 5'-end of the nifH4 primer, which does not impact detection of the nifH genes. This is demonstrated by the presence of nifH genes that contain the nucleotide mismatches in a recent compilation of global ocean nifH amplicon datasets, with high relative abundances detected in a variety of samples. While the metagenome- and metatranscriptome-derived nifH genes accounted for 4.4% of the total amplicon sequence variants from the global ocean nifH amplicon database, the corresponding amplicon sequence variants can have high relative abundances (accounting for 47% of the reads in the database). These analyses underscore that nifH amplicon sequencing using the nifH1-nifH4 primers is an important tool for studying diversity of marine diazotrophs, particularly as a complement to metagenomics which can provide taxonomic and metabolic information for some dominant groups.}, }
@article {pmid40181528, year = {2025}, author = {Sun, Q and Teng, R and Shi, Q and Liu, Y and Cai, X and Yang, B and Cao, Q and Shu, C and Mei, X and Zeng, W and Hu, B and Zhang, J and Qiu, H and Liu, L}, title = {Clinical implement of Probe-Capture Metagenomics in sepsis patients: A multicentre and prospective study.}, journal = {Clinical and translational medicine}, volume = {15}, number = {4}, pages = {e70297}, doi = {10.1002/ctm2.70297}, pmid = {40181528}, issn = {2001-1326}, support = {2022YFC2504405//National Key Research and Development Program of China/ ; 82341032//National Natural Science Foundation of China/ ; 81930058//National Natural Science Foundation of China/ ; 82270083//National Natural Science Foundation of China/ ; LGY2022025//Second Level Talents of the '333 High Level Talents Training Project' in the sixth phase in Jiangsu/ ; ZDXYS202205//Jiangsu Provincial Medical Key Laboratory/ ; HMJH-2020-0005//Hongmian Plan' Project of Guangzhou/ ; }, mesh = {Humans ; *Sepsis/diagnosis/microbiology/blood/drug therapy ; *Metagenomics/methods ; Male ; Female ; Prospective Studies ; Aged ; Middle Aged ; Blood Culture/methods ; }, abstract = {BACKGROUND: Accurate pathogen identification is critical for managing sepsis. However, traditional microbiological methods are time-consuming and exhibit limited sensitivity, particularly with blood samples. Metagenomic sequencing of plasma or whole blood was highly affected by the proportion of host nucleic acid.<br><br>METHODS: We developed a Probe-Capture Metagenomic assay and established a multicentre prospective cohort to assess its clinical utility. In this study, 184 blood samples from patients suspected of sepsis were sent for blood culture and Probe-Capture Metagenomic sequencing before using antibiotics. The pathogen-positive rate and auxiliary abilities in diagnosis were compared among Probe-Capture Metagenomics, blood culture and real-time PCR (RT-PCR). Antibiotic therapy adjustments were based on the identification of pathogens, and changes in the Sequential Organ Failure Assessment (SOFA) score were monitored on days 0, 3 and 7 of admission.<br><br>RESULTS: A total of 184 sepsis patients were enrolled, with a mean age of 66 years (range 56-74). The Probe-Capture Metagenomics method, confirmed by RT-PCR, demonstrated a significantly higher pathogen detection rate than blood culture alone (51.6%&#xa0;vs. 17.4%, p&#xa0;<&#xa0;.001). When combining the results of blood culture and RT-PCR, Probe-Capture Metagenomics achieved a concordance rate of 91.8% (169/184), with a sensitivity of 100% and specificity of 87.1%. In terms of clinical impact, antibiotic therapy was adjusted for 64 patients (34.8%) based on the results from Probe-Capture Metagenomics, and 41 patients (22.3%) showed a&#xa0;>&#xa0;2-point decrease in SOFA score following antibiotic adjustments.<br><br>CONCLUSION: Probe-Capture Metagenomics significantly enhances the ability of pathogen detection compared with traditional metagenomics. Compared to blood culture and RT-PCR in sepsis patients, it leads to improved antibiotic treatment and better patient outcomes. This study, for the first time, evaluates the clinical impact of metagenomic sequencing by integrating antibiotic adjustments and SOFA score changes, indicating that approximately one-fifth of sepsis patients benefit from this advanced diagnostic approach.<br><br>TRIAL REGISTRATION: This study has been registered in clinical trials (clinicaltrials.gov) on 30 November 2018, and the registration number is NCT03760315.<br><br>KEY POINTS: Probe-Capture Metagenome had a significantly higher positive rate than blood culture (51.6%&#xa0;vs. 17.4%, p&#xa0;<&#xa0;.001). Combining blood culture and RT-PCR results, Probe-Capture Metagenome achieved a consistency rate of 91.8%. Antibiotics were adjusted in 34.8% of patients based on Probe-Capture Metagenome results, and 22.3% of patients experienced a more than 2-point decrease in SOFA score.}, }
@article {pmid40181443, year = {2025}, author = {Xu, F and Chen, C and Lu, S and Xue, M and Ding, H and Song, Y and Zhang, Y and Sun, K and Tang, L and Wang, W and Wang, M and Tang, Y and Tan, D and Yao, C and Shi, D and Mao, E and Shao, M and Ying, Y and Zhou, C and Huang, L and Peng, H and Kuang, Z and Wang, S and Ma, Q and Sun, S and Guo, D and Gu, T and Yang, B and Ma, L and Gao, C and Lu, X and Zhang, H and Wang, R and Tong, C and Song, Z}, title = {Impact of metagenomics next-generation sequencing on etiological diagnosis and early outcomes in sepsis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {394}, pmid = {40181443}, issn = {1479-5876}, support = {2021YFC2501800//Key Technologies Research and Development Program/ ; 2023YFC0872500//Key Technologies Research and Development Program/ ; 2023YFC3043507//Key Technologies Research and Development Program/ ; 82072214//National Natural Science Foundation of China/ ; 23Y31900100//Science and Technology Commission of Shanghai Municipality/ ; 21MC1930400//Science and Technology Commission of Shanghai Municipality/ ; PWYts2021-17//Shanghai Pudong New Area Health Commission/ ; }, mesh = {Humans ; *Sepsis/diagnosis/microbiology/etiology/mortality ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; Aged ; Treatment Outcome ; Prognosis ; Prospective Studies ; Adult ; }, abstract = {BACKGROUND: Clinical implications of metagenomics next-generation sequencing (mNGS) in sepsis have not been fully evaluated. This study aimed to determine the diagnostic, therapeutic, and prognostic impacts of mNGS in sepsis.<br><br>METHODS: This multicenter prospective study was conducted at 19 sites in China from 2020 to 2021, and 859 adult patients hospitalized with sepsis were enrolled. The advantages, challenges, knowledge gaps and privacy risks of mNGS were carefully introduced to all participants, and participants chose on their own to either receive conventional microbiological test (CMT) alone (conventional-test-only group, n&#x2009;=&#x2009;394) or receive mNGS test along with CMT (combined test group, n&#x2009;=&#x2009;465). For prognostic analysis, the primary endpoint was 28-day mortality. Secondary endpoints included 7-day mortality and average per-day hospital cost. Inverse probability of treatment weighting was used to balance covariates between groups. Concurrent CMT and mNGS results from patients in the combined test group were used for diagnostic analyses. Therapeutic impact of mNGS was evaluated based on subsequent antibiotic adjustment.<br><br>RESULTS: Compared with composite reference standard, the positive percent agreement of mNGS among infected site samples was significantly higher than that of CMT (92.0% [95% CI, 88.7 to 94.5] vs. 51.1% [95% CI, 45.9 to 56.2], p&#x2009;<&#x2009;0.001), while the negative percent agreement of mNGS was inferior to that of CMT (39.6% [95% CI, 29.5 to 50.4] vs. 69.2% [95% CI, 58.7 to 78.5], p&#x2009;<&#x2009;0.001). The mNGS test identified causal microbes in 344 (74.0%) patients, and concomitant antibiotic changes occurred in 136 patients (29.2%). Death by day 7 occurred in 24 of 465 (5.2%) patients in the combined test group and in 34 of 394 (8.6%) patients in the conventional-test-only group (hazard ratio, 0.44 [95% CI, 0.26 to 0.77], p&#x2009;=&#x2009;0.004). However, no significant difference in 28-day mortality was observed between two study groups (hazard ratio, 0.82 [0.56 to 1.20], p&#x2009;=&#x2009;0.300).<br><br>CONCLUSIONS: The mNGS test of infected site samples exhibited 40% higher pathogen detection rate than CMT in patients with sepsis, which led to improved etiological diagnosis and tailored antibiotic therapy. Additional use of mNGS halved the risk of early death in 7 days, but did not improve 28-day survival in patients with sepsis.<br><br>TRIAL REGISTRATION: chictr.org.cn Identifier: ChiCTR2000031113. Registered 22 March 2020.}, }
@article {pmid40181255, year = {2025}, author = {Mohammadzadeh, R and Mahnert, A and Shinde, T and Kumpitsch, C and Weinberger, V and Schmidt, H and Moissl-Eichinger, C}, title = {Age-related dynamics of predominant methanogenic archaea in the human gut microbiome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {193}, pmid = {40181255}, issn = {1471-2180}, support = {P 32697//Austrian Science Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Aged ; *Archaea/classification/genetics/metabolism/isolation &amp; purification ; *Methane/metabolism ; Feces/microbiology ; Aged, 80 and over ; Young Adult ; Female ; Male ; *Aging ; Age Factors ; Methanobrevibacter/genetics ; Metagenomics ; Phylogeny ; Bacteria/classification/genetics/metabolism ; }, abstract = {BACKGROUND: The reciprocal relationship between aging and alterations in the gut microbiota is a subject of ongoing research. While the role of bacteria in the gut microbiome is well-documented, specific changes in the composition of methanogens during extreme aging and the impact of high methane production in general on health remain unclear. This study was designed to explore the association of predominant methanogenic archaea within the human gut and aging.<br><br>METHODS: Shotgun metagenomic data from the stool samples of young adults (n&#x2009;=&#x2009;127, Age: 19-59 y), older adults (n&#x2009;=&#x2009;86, Age: 60-99 y), and centenarians (n&#x2009;=&#x2009;34, age: 100-109 years) were analyzed.<br><br>RESULTS: Our findings reveal a compelling link between age and the prevalence of high methanogen phenotype, while overall archaeal diversity diminishes. Surprisingly, the archaeal composition of methanogens in the microbiome of centenarians appears more akin to that of younger adults, showing an increase in Methanobrevibacter smithii, rather than Candidatus Methanobrevibacter intestini. Remarkably, Ca. M. intestini emerged as a central player in the stability of the archaea-bacteria network in adults, paving the way for M. smithii in older adults and centenarians. Notably, centenarians exhibit a highly complex and stable network of these two methanogens with other bacteria. The mutual exclusion between Lachnospiraceae and these methanogens throughout all age groups suggests that these archaeal communities may compensate for the age-related drop in Lachnospiraceae by co-occurring with Oscillospiraceae.<br><br>CONCLUSIONS: This study underscores the dynamics of archaeal microbiome in human physiology and aging. It highlights age-related shifts in methanogen composition, emphasizing the significance of both M. smithii and Ca. M. intestini and their partnership with butyrate-producing bacteria for potential enhanced health.}, }
@article {pmid40180917, year = {2025}, author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA}, title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3204}, pmid = {40180917}, issn = {2041-1723}, support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; }, abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.}, }
@article {pmid40180909, year = {2025}, author = {Bedarf, JR and Romano, S and Heinzmann, SS and Duncan, A and Traka, MH and Ng, D and Segovia-Lizano, D and Simon, MC and Narbad, A and Wüllner, U and Hildebrand, F}, title = {A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease.}, journal = {NPJ Parkinson's disease}, volume = {11}, number = {1}, pages = {66}, pmid = {40180909}, issn = {2373-8057}, support = {BB/CCG2260/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, abstract = {Current treatment of Parkinson's Disease (PD) remains symptomatic, and disease-modifying approaches are urgently required. A promising approach is to modify intestinal microbiota and key metabolites of bacterial fermentation: short-chain fatty acids (SCFA), which are decreased in PD. A prospective, controlled pilot study (DRKS00034528) was conducted on 11 couples (PD patient plus healthy spouse as control (CO)). Participants followed a 4-week diet rich in dietary fibre, including intake of the prebiotic Lactulose. Gut metagenomes, faecal and urinary metabolites, and clinical characteristics were assessed. The dietary intervention significantly augmented faecal SCFA and increased Bifidobacteria spp., reducing PD-related gastrointestinal symptoms. The pre-existing bacterial dysbiosis in PD (depletion of Blautia, Dorea, Erysipelatoclostridium) persisted. Bacterial metabolite composition in faeces and urine positively changed with the intervention: Brain-relevant gut metabolic functions involved in neuroprotective and antioxidant pathways, including S-adenosyl methionine, glutathione, and inositol, improved in PD. These promising results warrant further investigation in larger cohorts.}, }
@article {pmid40180580, year = {2025}, author = {Chiu, CY and Servellita, V and de Lorenzi-Tognon, M and Benoit, P and Sumimoto, N and Foresythe, A and Cerqueira, FM and Williams-Bouyer, N and Ren, P and Herrera, LNS and Gaston, DC and Sayyad, L and Whitmer, SL and Klena, J and Vikram, HR and Gold, JAW and Gade, L and Parnell, L and Misas, E and Chiller, TM and Griffin, IS and Basavaraju, SV and Smith, DJ and Litvintseva, AP and Chow, NA}, title = {Metagenomic Identification of Fusarium solani Strain as Cause of US Fungal Meningitis Outbreak Associated with Surgical Procedures in Mexico, 2023.}, journal = {Emerging infectious diseases}, volume = {31}, number = {5}, pages = {}, doi = {10.3201/eid3105.241657}, pmid = {40180580}, issn = {1080-6059}, abstract = {We used metagenomic next-generation sequencing (mNGS) to investigate an outbreak of Fusarium solani meningitis in US patients who had surgical procedures under spinal anesthesia in Matamoros, Mexico, during 2023. Using a novel method called metaMELT (metagenomic multiple extended locus typing), we performed phylogenetic analysis of concatenated mNGS reads from 4 patients (P1-P4) in parallel with reads from 28 fungal reference genomes. Fungal strains from the 4 patients were most closely related to each other and to 2 cultured isolates from P1 and an additional case (P5), suggesting that all cases arose from a point source exposure. Our findings support epidemiologic data implicating a contaminated drug or device used for epidural anesthesia as the likely cause of the outbreak. In addition, our findings show that the benefits of mNGS extend beyond diagnosis of infections to public health outbreak investigation.}, }
@article {pmid40180222, year = {2025}, author = {Yang, Y and Wang, D and Li, L and Song, J and Yang, X and Li, J}, title = {Evolution of enteric viruses in the progression of colorectal cancer via the adenoma-carcinoma sequence pathway.}, journal = {Virus research}, volume = {}, number = {}, pages = {199569}, doi = {10.1016/j.virusres.2025.199569}, pmid = {40180222}, issn = {1872-7492}, abstract = {The global incidence of colorectal cancer (CRC) is increasing. In the majority of CRC cases, colon cancer develops from alterations in the adenoma-carcinoma sequence pathway. Currently, there are few studies regarding the effects of enteric viruses on the adenoma-carcinoma sequence pathway, and subsequently, the progression and development of the CRC. Here, fecal and tissue samples from a normal control group, an adenomatous polyp group, and a colorectal adenocarcinoma group were collected to gain a deeper understanding of the variations in enteric viruses in CRC patients and to analyze their significance. With the progression of CRC from adenoma to adenocarcinoma, the number of DNA viruses in the virus-like particles (VLPs) of fecal and tissue samples gradually increased, and there were distinct differences in the composition of enteric viruses among the different groups. Multiple species correlation analysis revealed extensive interactions among viruses, bacteria, and fungi in fecal and tissue samples. Functional analysis also revealed that the functional pathways in fecal and tissue samples also underwent significant changes. In conclusion, the changes in the composition and function of enteric viruses in the progression of CRC via adenoma-carcinoma sequence pathway were analyzed in this study, and these changes hold certain importance for exploring the role of enteric viruses in the occurrence of this disease; however, their mode of action and specific mechanisms require further investigation.}, }
@article {pmid39930907, year = {2025}, author = {Doorenspleet, K and Jansen, L and Oosterbroek, S and Kamermans, P and Bos, O and Wurz, E and Murk, A and Nijland, R}, title = {The Long and the Short of It: Nanopore-Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species-Level Assignment Depend on Amplicon Lengths.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14079}, doi = {10.1111/1755-0998.14079}, pmid = {39930907}, issn = {1755-0998}, support = {//European Regional Development Fund Interreg North Sea region GEANS/ ; TEWZ118017//Rijksdienst voor Ondernemend Nederland/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; North Sea ; *Vertebrates/classification/genetics ; *Aquatic Organisms/classification/genetics ; DNA Primers/genetics ; Biodiversity ; *Nanopore Sequencing/methods ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Fishes/genetics/classification ; Sequence Analysis, DNA ; DNA, Mitochondrial/genetics ; }, abstract = {To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA-based techniques and especially environmental (e)DNA metabarcoding is becoming a powerful monitoring tool. However, current approaches rely on genetic target regions under 500 bp, offering limited taxonomic resolution. We developed a method for long-read eDNA metabarcoding, using Nanopore sequencing of a longer amplicon and present DECONA, a read processing pipeline to enable improved identification of marine vertebrate species. We designed a universal primer pair targeting a 2 kb region of fish mitochondrial DNA and compared it to the commonly used MiFish primer pair targeting a ~ 170 bp region. In silico testing showed that 2 kb fragments improved accurate identification of closely related species. Analysing eDNA from a North Sea aquarium showed that sequences from both primer pairs could be assigned to most species, and additional species level assignments could be made through the 2 kb primer pair. Interestingly, this difference was opposite in eDNA from the North Sea, where not the 2 kb but the MiFish primer pair detected more species. This study demonstrates the feasibility of using long-read metabarcoding for eDNA vertebrate biodiversity assessments. However, our findings suggests that longer fragments are less abundant in environmental settings, but not in aquarium settings, suggesting that longer fragments may provide a more recent snapshot of the community. Thus, long-read metabarcoding can expand the molecular toolbox for biodiversity assessments by improving species-level identification and may be especially useful when the temporal origin of the eDNA signal is better understood.}, }
@article {pmid40180172, year = {2025}, author = {Li, VW and Dong, TS and Funes, D and Hernandez, L and Kushnir, NR and Nair, D and Jacobs, JP and Reddy, ST and Mayer, EA and Chang, L and Meriwether, D}, title = {Mass spectrometric profiling of primary estrogens and estrogen metabolites in human stool and plasma partially elucidates the role of the gut microbiome in estrogen recycling.}, journal = {Molecular and cellular endocrinology}, volume = {}, number = {}, pages = {112534}, doi = {10.1016/j.mce.2025.112534}, pmid = {40180172}, issn = {1872-8057}, abstract = {Primary estrogens and estrogen metabolites are commonly measured in human plasma and serum, but there exist almost no recent reports for human stool. This knowledge gap limits our understanding of the relationships between systemic and gut estrogens. We developed a highly sensitive liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) method to determine, in human plasma and stool, the free and conjugated levels of estrone, estradiol, and estriol together with their additional hydroxyestrogen and methoxyestrogen metabolites. We investigated human stool and plasma estrogens in healthy control men; in follicular and luteal phase premenopausal women; and in postmenopausal women. Most estrogens were present in plasma and stool of all groups, while the plasma and stool levels of hydroxyestrogen and methoxyestrogen metabolites but not estrone were correlated. In stool, estrogens were higher in premenopausal women, with estrogens increasing across the menstrual cycle. We combined these LC-MS/MS measures with shotgun metagenomic sequencing of the stool microbiomes. Estrogen deconjugation enzyme gene copy numbers (β-glucuronidase and arylsulfatase) were higher in premenopausal women; while the gene copy number of β-glucuronidase + arylsulfatase, but not β-glucuronidase alone, correlated with deconjugated stool estrogens in all groups. Moreover, β-glucuronidase + arylsulfatase gene copy numbers correlated with combined plasma estrogens in men and with individual plasma estrogen metabolites in men and premenopausal women. These results support the hypothesis that gut microbial β-glucuronidase and arylsulfatase control the deconjugation of gut estrogens while modulating systemic levels through the uptake and recirculation of these deconjugated estrogens. The intestine may thus constitute an important additional compartment in estrogen physiology.}, }
@article {pmid40179782, year = {2025}, author = {Chen, S and Xin, X and Wang, Z and Wang, H and Yan, W}, title = {Enhancing tetramethylammonium hydroxide degradation in anaerobic digestion: Neglected role of iron-based conductive materials in regulating degradation pathway.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138115}, doi = {10.1016/j.jhazmat.2025.138115}, pmid = {40179782}, issn = {1873-3336}, abstract = {The rapid expansion of TFT-LCD industry led to significant environmental challenges due to the highly corrosive and ecotoxic tetramethylammonium hydroxide (TMAH). This study explores a previously unrecognized role of iron-based conductive materials - nano magnetite (Fe3O4) and nano zero-valent iron (ZVI) - in enhancing TMAH degradation and regulating degradation pathways in anaerobic digestion systems. Results show these materials significantly enhance degradation efficiency as TMAH concentration increases. At the highest TMAH level (10 g/L), while the control group achieved only 78.41 % degradation efficiency, Fe3O4 and ZVI groups reached efficiencies of 97.36 % and 94.96 %, with methane yields increased by 89.00 % and 97.21 %. Mechanistic exploration revealed these materials promoted secretion of charged functional groups into extracellular polymeric substances that effectively shielded microbes from TMAH toxicity. Additionally, they stimulated flavin and riboflavin production, enhancing interspecies electron transfer rates by up to 46.14-fold for Fe3O4 and 9.00-fold for ZVI. Microbial and metagenomic analyses further uncovered these materials induced a shift in TMAH degradation from methylotrophic methanogenesis to syntrophic metabolism, facilitating a more efficient breakdown of TMAH through direct interspecies electron transfer. These findings unravel the effects of iron-based conductive materials in regulating degradation pathways, offering a promising approach to addressing environmental challenges posed by TFT-LCD industry.}, }
@article {pmid40179570, year = {2025}, author = {Zhang, P and Liu, Y and Xu, M and Zhang, J and Xia, J and Shi, Y and Wang, J and Han, B and Feng, G}, title = {Gut microbiota characteristics and prognostic value in patients with aneurysmal subarachnoid hemorrhage: A clinical study.}, journal = {Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia}, volume = {136}, number = {}, pages = {111200}, doi = {10.1016/j.jocn.2025.111200}, pmid = {40179570}, issn = {1532-2653}, abstract = {BACKGROUND: This study aims to explore the characteristics of gut microbiota in the aneurysmal subarachnoid hemorrhage (aSAH) group and the healthy control group, as well as in the good prognosis group and the poor prognosis group. It also investigates the relationship between the severity of aSAH and gut microbiota, and the predictive value of gut microbiota for the prognosis outcome of patients with aSAH.<br><br>METHODS: Stool samples from 22 patients with aSAH and 11 healthy controls were subjected to metagenomic sequencing, and species annotations were obtained through the taxonomic information database corresponding to the NR database. The characteristics of the gut microbiota in the aSAH group versus the healthy control group, and the good prognosis group versus the poor prognosis group were analyzed.The correlations between differential microbiota and clinical hematology markers between the aSAH and control groups and between gut microbiota and aSAH severity were analyzed. The prognosis of patients with aSAH after three months was assessed. Finally, gut microbiota with significant effects were screened for potential as biomarkers, and the predictive value of gut microbiota for different prognostic outcomes in patients with aSAH was explored.<br><br>RESULTS: Gut microbiota composition, diversity, and abundance differed significantly between patients in the aSAH group and the control group. Additionally, the composition, diversity, and abundance differed between patients with good and poor prognosis. Five dominant genera--Bacillus, Eggerthia, Hominisplanchenecus, Carnobacterium, and Bifidobacterium were identified as potential biomarkers for predicting aSAH outcomes.<br><br>CONCLUSION: Patients with aSAH have altered gut microbiota composition, structure, and diversity compared with the healthy population. These alterations may be potential biomarkers for aSAH diagnosis and outcome prediction.}, }
@article {pmid40178790, year = {2025}, author = {Yuan, J and Yang, J and Sun, Y and Meng, Y and He, Z and Zhang, W and Dang, L and Song, Y and Xu, K and Lv, N and Zhang, Z and Guo, P and Yin, H and Shi, W}, title = {An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP).}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {40178790}, issn = {1869-1889}, abstract = {China's progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station's microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.}, }
@article {pmid40178526, year = {2025}, author = {Contreras-de la Rosa, PA and De la Torre-Zavala, S and O Connor-Sánchez, A and Prieto-Davó, A and Góngora-Castillo, EB}, title = {Exploring the microbial communities in coastal cenote and their hidden biotechnological potential.}, journal = {Microbial genomics}, volume = {11}, number = {4}, pages = {}, doi = {10.1099/mgen.0.001382}, pmid = {40178526}, issn = {2057-5858}, mesh = {*Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Bacteria/genetics/classification/metabolism ; Biotechnology ; Secondary Metabolism/genetics ; Metagenomics/methods ; *Geologic Sediments/microbiology ; Multigene Family ; Polyketide Synthases/genetics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Bacterial secondary metabolites are crucial bioactive compounds with significant therapeutic potential, playing key roles in ecological processes and the discovery of novel antimicrobial agents and natural products. Cenotes, as extreme environments, harbour untapped microbial diversity and hold an interesting potential as sources of novel secondary metabolites. While research has focused on the fauna and flora of cenotes, the study of their microbial communities and their biosynthetic capabilities remains limited. Advances in metagenomics and genome sequencing have greatly improved the capacity to explore these communities and their metabolites. In this study, we analysed the microbial diversity and biotechnological potential of micro-organisms inhabiting sediments from a coastal cenote. Metagenomic analyses revealed a rich diversity of bacterial and archaeal communities, containing several novel biosynthetic gene clusters (BGCs) linked to secondary metabolite production. Notably, polyketide synthase BGCs, including those encoding ladderanes and aryl-polyenes, were identified. Bioinformatics analyses of these pathways suggest the presence of compounds with potential industrial and pharmaceutical applications. These findings highlight the biotechnological value of cenotes as reservoirs of secondary metabolites. The study and conservation of these ecosystems are essential to facilitate the discovery of new bioactive compounds that could benefit various industries.}, }
@article {pmid40178319, year = {2025}, author = {Herzog, E and Ishida, K and Scherlach, K and Chen, X and Bartels, B and Niehs, SP and Cheaib, B and Panagiotou, G and Hertweck, C}, title = {Antibacterial Siderophores of Pandoraea Pathogens and their Impact on the Diseased Lung Microbiota.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e202505714}, doi = {10.1002/anie.202505714}, pmid = {40178319}, issn = {1521-3773}, abstract = {Antibiotic-resistant bacteria of the genus Pandoraea, frequently acquired from the environment, are an emerging cause of opportunistic respiratory infections, especially in cystic fibrosis (CF) patients. However, their specialized metabolites, including niche and virulence factors, remained unknown. Through genome mining of environmental and clinical isolates of diverse Pandoraea species, we identified a highly conserved biosynthesis gene cluster (pan) that codes for a non-ribosomal peptide synthetase (NRPS) assembling a new siderophore. Using bioinformatics-guided metabolic profiling of wild type and a targeted null mutant, we discovered the corresponding metabolites, pandorabactin A and B. Their structures and chelate (gallium) complexes were elucidated by a combination of chemical degradation, derivatization, NMR, and MS analysis. Metagenomics and bioinformatics of sputum samples of CF patients indicated that the presence of the pan gene locus correlates with the prevalence of specific bacteria in the lung microbiome. Bioassays and mass spectrometry imaging showed that pandorabactins have antibacterial activities against various lung pathogens (Pseudomonas, Mycobacterium, and Stenotrophomonas) through depleting iron in the competitors. Taken together, these findings offer first insight into niche factors of Pandoraea and indicate that pandorabactins shape the diseased lung microbiota through the competition for iron.}, }
@article {pmid40177842, year = {2025}, author = {Larnder, AH and Manges, AR and Murphy, RA}, title = {The estrobolome: Estrogen-metabolizing pathways of the gut microbiome and their relation to breast cancer.}, journal = {International journal of cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/ijc.35427}, pmid = {40177842}, issn = {1097-0215}, support = {/CAPMC/CIHR/Canada ; //Weston Family Foundation/ ; }, abstract = {Increasing evidence links the gut microbiome to carcinogenesis. Disruptions in estrogen regulation by the estrobolome-gut microbiota with estrogen-related functions-may promote breast cancer. However, precise information on estrobolome targets and their underlying mechanisms is limited. This review identifies relevant targets for measuring the estrobolome, focusing on enzymes and microbial taxa involved in processing estrogens, precursors, metabolites, and phytoestrogens, to facilitate the exploration of potential links to breast cancer. Evidence from breast cancer case-control studies is synthesized to assess alignment with these targets, highlight gaps in the evidence, and suggest new paths forward. Findings from case-control studies were heterogeneous and showed limited alignment with estrobolome targets, with only Escherichia coli and Roseburia inulinivorans identified as differentially abundant and functionally relevant between cases and controls. The lack of compelling evidence for estrobolome-specific mechanisms may reflect measurement challenges or may suggest that broader ecological changes in the microbiome, which influence a network of interacting mechanisms, are more influential for carcinogenesis. To clarify the estrobolome's role in breast cancer, future research should use advanced sequencing techniques and methods such as metabolomics and transcriptomics, while considering clinical and behavioral factors that may modify estrobolome mechanisms.}, }
@article {pmid40177486, year = {2025}, author = {Yang, S and Chen, J and Zheng, J and Mao, H and Deng, F and Wu, D and Chai, J}, title = {Feeding systems influence the rumen resistome in yaks by changing the microbiome.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1505938}, doi = {10.3389/fmicb.2025.1505938}, pmid = {40177486}, issn = {1664-302X}, abstract = {The rumen microbiome serves as a reservoir of antibiotic-resistance genes (ARGs) with significant implications for public health. This study aimed to investigate the effects of different feeding systems on the rumen resistome in yaks. Yaks that grazed naturally on pasture were used as controls, while the experimental yaks were housed in a high-density pen environment and fed a specially designed diet to optimally meet their nutritional requirements, with increased interactions with farm workers. Metagenomic analysis was performed to assess changes in the rumen microbiome and resistome. Dietary factors influencing changes in the rumen microbiome and resistome were identified. A greater variety of microbiomes associated with carbohydrate digestion was found in yaks under a house-feeding system, such as Stomatobaculum longum and Succiniclasticum ruminis. Although grazing yaks exhibited various dominant antibiotic resistance genes (ARGs) at the class level, house-fed yaks were mainly enriched with tetracycline-resistant genes. A random forest model identified specific ARG signatures for each group, such as Sent_cmlA and Sliv_cmlR (Phenicol) and vanHD (Glycopeptide) prevalent in grazing yaks, while tet44, tetW, tetW/N/W, and tet40 were abundant in house-fed yaks. ARG interactions varied by feeding system, with signature ARGs in each group showing distinct correlations. Nevertheless, strong correlations among ARGs existed regardless of the treatments, such as the positive correlation between tetW and tetW/N/W in both groups. The rumen microbiome was strongly associated with the resistome, especially regarding abundant microbiomes and ARGs. Proteobacteria carrying ARGs were observed in grazing yaks, while Firmicutes served as hosts for ARGs in yaks under a housed feeding system. The specific bacteria contributing to the distinct ARGs in each group were identified. For instance, members of Firmicutes (Clostridium tepidiprofundi) carried their ARG signatures, such as tet44. These findings emphasized that diet, along with environmental factors and farmworker interactions, contributed to changes in the rumen resistome of yaks. This study is the first to discuss how multiple factors within a feeding regime influence the gut resistome, highlighting the drawbacks of intensive feedings with respect to the gut resistome.}, }
@article {pmid40177475, year = {2025}, author = {Tenea, GN and Reyes, P and Flores, C}, title = {Crosslinking bacterial postbiotics for microbial and quality control of strawberries postharvest: bacteriological and 16S amplicon metagenome evidence.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570312}, doi = {10.3389/fmicb.2025.1570312}, pmid = {40177475}, issn = {1664-302X}, abstract = {INTRODUCTION: Strawberries are renowned for their exceptional flavor and nutritional properties but have a short shelf life due to rapid ripening and a high vulnerability to postharvest microbial decay. Postbiotic formulations (PBFs) derived from lactic acid bacteria (LAB) can be developed into effective preservation products, extending postharvest shelf life while maintaining fruit quality.<br><br>METHODS: This study aimed to assess the effects of postbiotic-based formulations (PBFs) consisting of two key components: (1) a precipitated peptide-protein extract (PP) from Weissella cibaria UTNGt21O, serving as the antimicrobial agent, and (2) an exopolysaccharide (EPS) from W. confusa UTNCys2-2, functioning as the biopolymer carrier. These formulations were tested against a multidrug-resistant Serratia liquefaciens P4StpC1 strain, isolated from ready-to-eat strawberries, and their potential mode of action was analyzed in vitro. Time-kill assays and electron microscopy were used to evaluate their impact on the target cells. Furthermore, the performance of PBFs was compared to a commercial disinfectant (C1) in terms of their effects on strawberry microbiota and fruit quality, employing bacteriological techniques and 16S amplicon metagenomic analysis.<br><br>RESULTS: The selected PBFs showed bacteriolytic effect on Serratia in vitro. The target cell viability was significantly reduced upon 1&#x202f;h co-cultivation by inducing several morphological and ultrastructural modifications. Dipping strawberries at the ripe stage four in PBFs indicated no increase in total cell counts, thus the microorganisms colonization was retained during storage with refrigeration. The 16S metagenome analysis showed that the treatment impacted the fruit microbiota, significantly increasing Lactobacillus abundance (p&#x202f;<&#x202f;0.001) by day eight compared to the disinfectant control. This suggests the formulation supports beneficial microbes, enhancing antimicrobial effects. Additionally, the postbiotic coating improved shelf-life, preserved fruit quality, and delayed deterioration in strawberries. The strawberries quality attributes were not affected by the treatment. Principal Component Analysis (PCA) revealed clear sample separation based on maturity stage, independent of the treatment.<br><br>CONCLUSION: The results highlight the potential of crosslinking of a peptide-protein fraction with EPS to prevent the colonization of undesirable microorganisms on postharvest strawberries while enhancing their safety and quality.}, }
@article {pmid40177465, year = {2025}, author = {Krause, SMB and van den Berg, NI and Brenzinger, K and Zweers, H and Bodelier, PLE}, title = {Beyond methane consumption: exploring the potential of methanotrophic bacteria to produce secondary metabolites.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf030}, doi = {10.1093/ismeco/ycaf030}, pmid = {40177465}, issn = {2730-6151}, abstract = {Microbial methane-consuming communities significantly impact biogeochemical processes and greenhouse gas emissions. In this study, we explored secondary metabolites produced by methane-oxidizing bacteria (MOB) and their ecological roles. We analyzed the volatile profiles of four MOB strains under controlled conditions and conducted a meta-analysis using high-quality genomes from 62 cultured MOB strains and 289 metagenome-assembled genomes to investigate their potential for producing secondary metabolites. Results show species-specific volatile production, such as germacrene by Methylobacter luteus, which may play a role in the regulation of environmental methane consumption. The meta-analysis revealed that biosynthetic gene clusters (BGCs) for terpenes and β-lactones were more prevalent in the Methylocystaceae and/or Beijerinckiaceae families, while aryl polyene BGCs were dominant in the Methylococcaceae family, reflecting habitat-specific adaptations. These findings advance our understanding of the metabolic capabilities of MOB and underscore the importance of integrating experimental data with genomic and metabolomic analyses to elucidate their ecology, environmental interactions, and contributions to methane cycling.}, }
@article {pmid40177421, year = {2025}, author = {Tian, Y and Yang, X and Yang, Y and Lin, T and Wang, G and Zhang, Y and Wu, H and Wang, J}, title = {Aeromonas veronii-induced septic arthritis of the hip in a child with acute lymphoblastic leukemia.}, journal = {Open life sciences}, volume = {20}, number = {1}, pages = {20221042}, doi = {10.1515/biol-2022-1042}, pmid = {40177421}, issn = {2391-5412}, abstract = {Septic arthritis of the hip (SAH) is a prevalent form of infectious arthritis in children that can lead to serious complications if not promptly diagnosed and treated. A 6-year 4-month-old female child with a 1-year history of acute lymphoblastic leukemia chemotherapy was admitted to our hospital due to a 1-day fever. After 1 week, the child experienced right inguinal pain and exhibited severe restriction in the flexion of the right lower limb and hip. Consequently, edema was observed in the right lower extremity and foot. SAH was initially diagnosed using computed tomography and magnetic resonance imaging examinations of both hip joints. Subsequently, incision and irrigation procedure were performed on the hip joint. Following the surgery, pus metagenomic next-generation sequencing (mNGS) were conducted promptly, and the mNGS analysis indicated an Aeromonas veronii infection. The diagnosis of A. veronii SAH was subsequently confirmed through polymerase chain reaction. The child's condition was successfully treated with a combination of amikacin and imipenem-cilastatin, leading to improvement and subsequent discharge in a satisfactory state. SAH caused by A. veronii is a rare occurrence, and the utilization of mNGS holds significant potential for the early detection of uncommon infections in immunosuppressed children.}, }
@article {pmid40177267, year = {2025}, author = {Yan, Z and Sun, C and Tang, W and Cao, W and Lv, J and Liang, Z and Wei, S and Zhong, W and Zhao, Z and Zhao, Z and Li, Y}, title = {Application of the metagenomic next-generation sequencing technology to identify the causes of pleural effusion.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1525100}, doi = {10.3389/fmed.2025.1525100}, pmid = {40177267}, issn = {2296-858X}, abstract = {BACKGROUND: Pleural effusion (PE), frequently encountered in clinical practice, can arise from a variety of underlying conditions. Accurate differential diagnosis of PE is crucial, as treatment and prognosis are heavily dependent on the underlying etiology. However, diagnosing the cause of PE remains challenging, relying on mycobacteriological methods that lack sensitivity and are time-consuming, or on histological examinations that require invasive biopsies. The recent advancements in metagenomic next-generation sequencing (mNGS) have shown promising applications in the diagnosis of infectious diseases. Despite this, there is limited research on the utility of mNGS as a comprehensive diagnostic tool for simultaneously identifying the causes of PE, particularly in cases of tuberculosis or malignancy.<br><br>METHODS: This study aimed to assess the efficacy of mNGS in detecting tuberculous pleural effusion (TPE) and malignant pleural effusion (MPE). A total of 35 patients with PE were included, and their PE samples were analyzed using mNGS.<br><br>RESULTS: Among the participants, 8 were ultimately diagnosed with TPE, and 10 were diagnosed with MPE, with lung adenocarcinoma being the most prevalent pathological type (50%, 5/10), according to established diagnostic criteria. Additionally, 7 patients were diagnosed with non-infectious PE. However, mNGS identified only 2 cases of TPE and 8 cases of MPE. The sensitivity of mNGS for detecting Mycobacterium tuberculosis was 25% (2/8), while the specificity was 100%. For tumor detection, mNGS demonstrated a sensitivity of 80%, a specificity of 92.6%, and an AUC of 0.882.<br><br>CONCLUSION: mNGS is effective in distinguishing MPE from non-MPE, but is not suitable for diagnosing TPE.}, }
@article {pmid40177264, year = {2025}, author = {Kananen, K and Veseli, I and Quiles Pérez, CJ and Miller, SE and Eren, AM and Bradley, PH}, title = {Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf039}, doi = {10.1093/bioadv/vbaf039}, pmid = {40177264}, issn = {2635-0041}, abstract = {MOTIVATION: Gene function annotation in microbial genomes and metagenomes is a fundamental in silico first step toward understanding metabolic potential and determinants of fitness. The Kyoto Encyclopedia of Genes and Genomes publishes a curated list of profile hidden Markov models to identify orthologous gene families (KOfams) with roles in metabolism. However, the computational tools that rely upon KOfams yield different annotations for the same set of genomes, leading to different downstream biological inferences.<br><br>RESULTS: Here, we apply three open-source software tools that can annotate KOfams to genomes of phylogenetically diverse bacterial families from host-associated and free-living biomes. We use multiple computational approaches to benchmark these methods and investigate individual case studies where they differ. Our results show that despite their fundamental similarities, these methods have different annotation rates and quality. In particular, a method that adaptively tunes sequence similarity thresholds substantially improves sensitivity while maintaining high accuracy. We observe particularly large improvements for protein families with few reference sequences, or when annotating genomes from nonmodel organisms (such as gut-dwelling Lachnospiraceae). Our findings show that small improvements in annotation workflows can maximize the utility of existing databases and meaningfully improve in silico characterizations of microbial metabolism.<br><br>Anvi'o is available at https://anvio.org under the GNU GPL license. Scripts and workflow are available at https://github.com/pbradleylab/2023-anvio-comparison under the MIT license.}, }
@article {pmid40176261, year = {2025}, author = {Sim, BZ and Mah, JK and Heldman, MR and Stanly, KL and Hanson, KE and Caliendo, AM and Andes, D and Ostroskly-Zeichner, L and Wingard, JR and Alexander, BD}, title = {Plasma microbial cell-free DNA Metagenomic Sequencing for Diagnosis of Invasive Fungal Diseases Among High Risk Outpatient and Inpatient Immunocompromised Hosts.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf170}, pmid = {40176261}, issn = {1537-6591}, abstract = {BACKGROUND: New and minimally-invasive tools to aid the diagnosis of invasive fungal diseases (IFD) are urgently needed as the immunocompromised population at highest risk increases. Advancements in molecular technology have rendered new diagnostics more readily available for clinical use.<br><br>METHODS: This case-control study utilized prospectively collected, archived plasma specimens and data from the Aspergillus Technology Consortium (AsTeC) Repository to investigate the diagnostic performance of microbial cell free DNA (mcfDNA) sequencing as a minimally-invasive diagnostic for IFDs in a population of high-risk immunocompromised hosts including hematologic malignancy, stem cell and solid organ transplants patients. The 2008 Mycoses Study Group/European Organization for the Research and Treatment of Cancer diagnostic criteria served as the gold standard for test performance.<br><br>RESULTS: Sixty-five adult subjects with proven or probable IFD and 65 controls without IFD were included. Among IFD episodes Aspergillus was the most common pathogen (70.8%, 46/65), followed by Mucorales (10.8%, 7/65). Overall, sensitivity was 47.7% and specificity was 100%. Sensitivity varied based on disease certainty and pathogen; sensitivity was higher in proven versus probable IFD (60.0% vs 37.1%, respectively) and higher for subjects with invasive mucormycosis (100%) compared with aspergillosis (45.7%).<br><br>CONCLUSIONS: A positive result by mcfDNA sequencing may reduce the need for invasive sampling in patients with suspected IFD. In this exploratory analysis, its high sensitivity and specificity for invasive mucormycosis suggests it could be useful for early treatment and intervention of this IFD. Future studies should focus on understanding how specific factors impact the sensitivity of mcfDNA sequencing for invasive aspergillosis.}, }
@article {pmid40176190, year = {2025}, author = {Xing, J and Niu, T and Yu, T and Zou, B and Shi, C and Wang, Y and Fan, S and Li, M and Bao, M and Sun, Y and Gao, K and Qiu, J and Zhang, D and Wang, N and Jiang, Y and Huang, H and Cao, X and Zeng, Y and Wang, J and Zhang, S and Hu, J and Zhang, D and Sun, W and Yang, G and Yang, W and Wang, C}, title = {Faecalibacterium prausnitzii-derived outer membrane vesicles reprogram gut microbiota metabolism to alleviate Porcine Epidemic Diarrhea Virus infection.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {90}, pmid = {40176190}, issn = {2049-2618}, support = {U21A20261//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Swine ; *Porcine epidemic diarrhea virus/physiology ; *Gastrointestinal Microbiome ; *Swine Diseases/virology/microbiology ; *Faecalibacterium prausnitzii/metabolism/physiology ; *Coronavirus Infections/veterinary/virology/microbiology ; Probiotics/administration &amp; dosage ; Feces/microbiology ; *Bacterial Outer Membrane/metabolism ; }, abstract = {BACKGROUND: The Porcine Epidemic Diarrhea Virus (PEDV) is one of the major challenges facing the global pig farming industry, and vaccines and treatments have proven difficult in controlling its spread. Faecalibacterium prausnitzii (F.prausnitzii), a key commensal bacterium in the gut, has been recognized as a promising candidate for next-generation probiotics due to its potential wide-ranging health benefits. A decrease in F.prausnitzii abundance has been associated with certain viral infections, suggesting its potential application in preventing intestinal viral infections. In this study, we utilized a piglet model to examine the potential role of F.prausnitzii in PEDV infections.<br><br>RESULTS: A piglet model of PEDV infection was established and supplemented with F.prausnitzii, revealing that F.prausnitzii mitigated PEDV infection. Further studies found that outer membrane vesicles (OMVs) are the main functional components of F.prausnitzii, and proteomics, untargeted metabolomics, and small RNA-seq were used to analyze the composition of OMVs. Exhaustion of the gut microbiota demonstrated that the function of Fp. OMVs relies on the presence of the gut microbiota. Additionally, metagenomic analysis indicated that Fp. OMVs altered the gut microbiota composition, enhancing the abundance of Faecalibacterium prausnitzii, Prevotellamassilia timonensis, and Limosilactobacillus reuteri. Untargeted metabolomics analysis showed that Fp. OMVs increased phosphatidylcholine (PC) levels, with PC identified as a key metabolite in alleviating PEDV infection. Single-cell sequencing revealed that PC altered the relative abundance of intestinal cells, increased the number of intestinal epithelial cells, and reduced necroptosis in target cells. PC treatment in infected IPEC-J2 and Vero cells alleviated necroptosis and reduced the activation of the RIPK1-RIPK3-MLKL signaling axis, thereby improving PEDV infection.<br><br>CONCLUSION: F.prausnitzii and its OMVs play a critical role in mitigating PEDV infections. These findings provide a promising strategy to ameliorate PEDV infection in piglets. Video Abstract.}, }
@article {pmid40176137, year = {2025}, author = {Sommer, F and Bernardes, JP and Best, L and Sommer, N and Hamm, J and Messner, B and López-Agudelo, VA and Fazio, A and Marinos, G and Kadibalban, AS and Ito, G and Falk-Paulsen, M and Kaleta, C and Rosenstiel, P}, title = {Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {91}, pmid = {40176137}, issn = {2049-2618}, support = {SO1141/10-1//Deutsche Forschungsgemeinschaft/ ; CRC1182//Deutsche Forschungsgemeinschaft/ ; miTARGET//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; RNA, Ribosomal, 16S/genetics ; *Fecal Microbiota Transplantation ; *Aging/physiology ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; *Intestinal Mucosa/microbiology/metabolism ; *Inflammation/microbiology ; Mice, Inbred C57BL ; *Rejuvenation ; Permeability ; *Intestines/microbiology ; Metagenomics ; Intestinal Barrier Function ; }, abstract = {BACKGROUND: Alterations in the composition and function of the intestinal microbiota have been observed in organismal aging across a broad spectrum of animal phyla. Recent findings, which have been derived mostly in simple animal models, have even established a causal relationship between age-related microbial shifts and lifespan, suggesting microbiota-directed interventions as a potential tool to decelerate aging processes. To test whether a life-long microbiome rejuvenation strategy could delay or even prevent aging in non-ruminant mammals, we performed recurrent fecal microbial transfer (FMT) in mice throughout life. Transfer material was either derived from 8-week-old mice (young microbiome, yMB) or from animals of the same age as the recipients (isochronic microbiome, iMB) as control. Motor coordination and strength were analyzed by rotarod and grip strength tests, intestinal barrier function by serum LAL assay, transcriptional responses by single-cell RNA sequencing, and fecal microbial community properties by 16S rRNA gene profiling and metagenomics.<br><br>RESULTS: Colonization with yMB improved coordination and intestinal permeability compared to iMB. yMB encoded fewer pro-inflammatory factors and altered metabolic pathways favoring oxidative phosphorylation. Ecological interactions among bacteria in yMB were more antagonistic than in iMB implying more stable microbiome communities. Single-cell RNA sequencing analysis of intestinal mucosa revealed a salient shift of cellular phenotypes in the yMB group with markedly increased ATP synthesis and mitochondrial pathways as well as a decrease of age-dependent mesenchymal hallmark transcripts in enterocytes and TA cells, but reduced inflammatory signaling in macrophages.<br><br>CONCLUSIONS: Taken together, we demonstrate that life-long and repeated transfer of microbiota material from young mice improved age-related processes including coordinative ability (rotarod), intestinal permeability, and both metabolic and inflammatory profiles mainly of macrophages but also of other immune cells. Video Abstract.}, }
@article {pmid40175903, year = {2025}, author = {Cao, L and Sun, H and Xu, Z and Xu, X and Shi, G and Zhang, J and Liang, C and Li, T and Liu, C and Wang, M and Tian, S and Li, E}, title = {Metagenomic and physicochemical profiling reveal microbial functions in pit mud for Jiang-Nong Jianxiang Baijiu fermentation.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {190}, pmid = {40175903}, issn = {1471-2180}, mesh = {*Fermentation ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; China ; Food Microbiology ; *Metagenome ; Microbiota ; *Alcoholic Beverages/microbiology ; }, abstract = {BACKGROUND: The unique flavour and quality of Baijiu, a treasure of traditional Chinese culture, has attracted increasing attention. The pit mud is a key component for forming the unique flavour styles of different Baijiu brands. Hence, conducting in-depth research on the microbial colonies present in pit mud is paramount for enhancing the intricate bouquets of Baijiu flavours.<br><br>RESULTS: This study conducts a comprehensive metagenomic examination of the microbial ecosystem within Chinese&#xa0;Jiang-Nong Jianxiang Baijiu fermentation pit mud. Within the pit mud walls, six prominent species, each accounting for more than 1% of the average relative abundance, emerged as key contributors: Lentilactobacillus buchneri, Secundilactobacillus silagincola, Clostridium tyrobutyricum, Lentilactobacillus parafarraginis, Ligilactobacillus acidipiscis, and Lactobacillus acetotolerans. Conversely, at the pit mud bases, four species surpassed this threshold: Petrimonas sp. IBARAKI, Methanosarcina barkeri, Methanofollis ethanolicus, and Proteiniphilum propionicum. Notably, the abundance of Clostridium in the pit mud walls impart superior saccharifying capabilities compared with those at the bases. The consistently high relative abundance of enzymes belonging to the glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) across both the pit mud walls and the bases highlight their importance in fermentation.<br><br>CONCLUSIONS: The microbial composition analysis results underscore the important role of pit mud microorganisms in facilitating starch saccharification, ethyl caproate and ethyl butyrate production, among other aromatic compounds. Microbes residing in the pit mud walls may be exhibited a heightened propensity for lactic acid generation, whereas those inhabiting the bases may be displayed a stronger inclination towards caproic acid production. This research serves as a valuable reference for future endeavours aimed at harnessing microbial resources to refine and optimize Baijiu fermentation methodologies.}, }
@article {pmid40175854, year = {2025}, author = {Abuzahrah, SS}, title = {Exploring the microorganisms biodiversity associated with sponge species in the red sea through 18S ribosomal RNA gene sequencing.}, journal = {AMB Express}, volume = {15}, number = {1}, pages = {60}, pmid = {40175854}, issn = {2191-0855}, abstract = {Around the world, sponges play a significant role in marine ecosystems, and a wide variety of sponge species can be found in the coast of Red Sea of Saudi Arabia. The unique environmental conditions of the Red Sea, including warm, oligotrophic water and high salinity, have encouraged the growth of abundant sponge fauna. Our study aims to investigate the biodiversity, taxonomic composition, and phylogenetic relationships of eukaryotic organisms linked with sponges in the Red Sea off the coast of Saudi Arabia and infer the possible ecological roles and functional contributions of the identified eukaryotic taxa to sponge health and ecosystem functioning. The study investigated the microbial diversity, focusing on the genera Hyalosynedra sp., Navicula sp., Papiliocellulus sp., Psammodictyon sp., Pynococcus sp., Ostreococcus sp., Micromonas sp., and other unclassified species. Our metagenomic analysis and phylogenetic evaluation revealed a deep and diverse microbial community, with each genus performing significant ecological roles, including nutrient cycling, primary production, and contributing to marine food networks. Moreover, these genera display promising biotechnological prospects, including uses in bioremediation, biofuel production, and the synthesis of high-value biomolecules. Comparative analysis with other marine regions has focused on both the similarities and unique aspects of the Red Sea microbial community, which are influenced by its distinct environmental conditions. The gained findings contribute to a deeper understanding of the ecological dynamics in the Red Sea and open new avenues for biotechnological exploration in marine ecosystems.}, }
@article {pmid40175821, year = {2025}, author = {Takagi, K and Tamura, Y and Narita, N and Komatsu, S and Yamazaki, S and Matsumura, A and Kubota, K and Matsumiya, T and Sawada, K and Nakaji, S and Mikami, T and Kobayashi, W}, title = {Involvement of Megasphaera in the oral microbiome and dyslipidemia onset: evidence from a community-based study in Japan.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {40175821}, issn = {1874-9356}, support = {21K10202//Japan Society for the Promotion of Science/ ; 22K17281//Japan Society for the Promotion of Science/ ; 24K13233//Japan Society for the Promotion of Science/ ; JPMJCE 1302//Japan Science and Technology Agency/ ; JPMJCA&#x3000;2201//Japan Science and Technology Agency/ ; JPMJPE 2210//Japan Science and Technology Agency/ ; }, abstract = {Dyslipidemia is a major risk factor for cardiovascular diseases and is influenced by genetic and environmental factors, including diet. Emerging research suggests a link between the gut microbiome and metabolic disorders. While the connection between the gut microbiota and dyslipidemia is well documented, the specific relationship between oral bacteria and dyslipidemia has not been thoroughly investigated. This study aimed to identify oral bacterial species associated with dyslipidemia in a community-based Japanese population. We conducted a metagenomic analysis on tongue coating samples from 763 participants in the Iwaki Health Promotion Project, which were collected during health checkups in 2017 and 2019. Dyslipidemia was diagnosed using standard lipid level criteria. The oral microbiome was analyzed via 16S rDNA amplicon sequencing. Statistical analyses included multiple regression and β diversity assessments. Our analysis revealed that the abundances of several bacterial genera, including Veillonella, Atopobium, Stomatobaculum, Tanneralla, and Megasphaera, are significantly associated with dyslipidemia. A higher relative abundance of Megasphaera was specifically observed in individuals with dyslipidemia. Moreover, Megasphaera abundance was closely associated with the onset of dyslipidemia (P = 0.038, odds ratio: 1.005, 95% confidence interval: 1.000-1.009), suggesting its role in metabolic regulation. This study revealed a significant association between the abundance of specific oral bacteria and dyslipidemia, suggesting the potential of using the oral microbiota as a biomarker for the early detection and management of dyslipidemia. Future research should explore the mechanisms through which oral bacteria influence lipid metabolism and the potential for microbioma-based therapies.}, }
@article {pmid40175737, year = {2025}, author = {Sawhney, SS and Thänert, R and Thänert, A and Hall-Moore, C and Ndao, IM and Mahmud, B and Warner, BB and Tarr, PI and Dantas, G}, title = {Gut microbiome evolution from infancy to 8 years of age.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {40175737}, issn = {1546-170X}, support = {R01AI155893//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01HD092414//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD092414//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; T32GM007067//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; MD-FR-2013-292//Children's Discovery Institute (CDI)/ ; 5P30 DK052574//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; }, abstract = {The human gut microbiome is most dynamic in early life. Although sweeping changes in taxonomic architecture are well described, it remains unknown how, and to what extent, individual strains colonize and persist and how selective pressures define their genomic architecture. In this study, we combined shotgun sequencing of 1,203 stool samples from 26 mothers and their twins (52 infants), sampled from childbirth to 8 years after birth, with culture-enhanced, deep short-read and long-read stool sequencing from a subset of 10 twins (20 infants) to define transmission, persistence and evolutionary trajectories of gut species from infancy to middle childhood. We constructed 3,995 strain-resolved metagenome-assembled genomes across 399 taxa, and we found that 27.4% persist within individuals. We identified 726 strains shared within families, with Bacteroidales, Oscillospiraceae and Lachnospiraceae, but not Bifidobacteriaceae, vertically transferred. Lastly, we identified weaning as a critical inflection point that accelerates bacterial mutation rates and separates functional profiles of genes accruing mutations.}, }
@article {pmid40175647, year = {2025}, author = {Ahn, JS and Kim, S and Han, EJ and Hong, ST and Chung, HJ}, title = {Increasing spatial working memory in mice with Akkermansia muciniphila.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {546}, pmid = {40175647}, issn = {2399-3642}, support = {C512230//Korea Basic Science Institute (KBSI)/ ; RS-2023-00224099//National Research Foundation of Korea (NRF)/ ; }, abstract = {Recent research has shown the gut microbiome's impact on memory, yet limitations hinder the identification of specific microbes linked to cognitive function. We measured spatial working memory in individual mice before and after fecal microbiota transplantation (FMT) to develop a targeted analysis that identifies memory-associated strains while minimizing host genetic effects. Transplantation of human fecal into C57BL/6 mice yielded varied outcomes: some mice showed significant improvements while others had negligible changes, indicating that these changes are due to differences in FMT colonization. Metagenomic analysis, stratified by memory performance, revealed a positive correlation between the abundance of Akkermansia muciniphila and improved memory. Moreover, administering two A. muciniphila strains, GMB 0476 and GMB 2066, to wild-type mice elevated spatial working memory via BDNF activation. Our findings indicate that specific gut microbes, particularly A. muciniphila, may modulate memory and represent potential targets for therapeutic intervention in cognitive enhancement.}, }
@article {pmid40175554, year = {2025}, author = {Ryan, FJ and Clarke, M and Lynn, MA and Benson, SC and McAlister, S and Giles, LC and Choo, JM and Rossouw, C and Ng, YY and Semchenko, EA and Richard, A and Leong, LEX and Taylor, SL and Blake, SJ and Mugabushaka, JI and Walker, M and Wesselingh, SL and Licciardi, PV and Seib, KL and Tumes, DJ and Richmond, P and Rogers, GB and Marshall, HS and Lynn, DJ}, title = {Bifidobacteria support optimal infant vaccine responses.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40175554}, issn = {1476-4687}, abstract = {Accumulating evidence indicates that antibiotic exposure may lead to impaired vaccine responses[1-4]; however, the mechanisms underlying this association remain poorly understood. Here we prospectively followed 191 healthy, vaginally born, term infants from birth to 15 months, using a systems vaccinology approach to assess the effects of antibiotic exposure on immune responses to vaccination. Exposure to direct neonatal but not intrapartum antibiotics was associated with significantly lower antibody titres against various polysaccharides in the 13-valent pneumococcal conjugate vaccine and the Haemophilus influenzae type b polyribosylribitol phosphate and diphtheria toxoid antigens in the combined 6-in-1 Infanrix Hexa vaccine at 7 months of age. Blood from infants exposed to neonatal antibiotics had an inflammatory transcriptional profile before vaccination; in addition, faecal metagenomics showed reduced abundance of Bifidobacterium species in these infants at the time of vaccination, which was correlated with reduced vaccine antibody titres 6 months later. In preclinical models, responses to the 13-valent pneumococcal conjugate vaccine were strongly dependent on an intact microbiota but could be restored in germ-free mice by administering a consortium of Bifidobacterium species or a probiotic already widely used in neonatal units. Our data suggest that microbiota-targeted interventions could mitigate the detrimental effects of early-life antibiotics on vaccine immunogenicity.}, }
@article {pmid40175522, year = {2025}, author = {Gichuki, BM and Van Camp, AG and Shao, Y}, title = {A new strain of thought in gut metagenomics.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40175522}, issn = {1740-1534}, }
@article {pmid40175313, year = {2025}, author = {Fortin, SG and Uhlig, K and Hale, RC and Song, B}, title = {Microplastic biofilms as potential hotspots for plastic biodegradation and nitrogen cycling: A metagenomic perspective.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf035}, pmid = {40175313}, issn = {1574-6941}, abstract = {Microplastics are an emerging contaminant worldwide, with the potential to impact organisms and facilitate the sorption and release of chemicals. Additionally, they create a novel habitat for microbial communities, forming biofilms known as the plastisphere. While the plastisphere has been studied in select aquatic environments, those in estuarine ecosystems merit additional attention due to their proximity to plastic debris sources. Additionally, the role plastisphere communities play in nutrient cycling has rarely been examined. This study used metagenomic analysis to investigate the taxonomic composition and functional genes of developing plastisphere communities living on petroleum-based (polyethylene and polyvinyl chloride) and biopolymer-based (polylactic acid) substrates. Isolated metagenome assembled genomes (MAGs) showed plastisphere communities have the genes necessary to perform nitrification and denitrification and degrade petroleum and biopolymer-based plastics. The functions of these plastispheres have implications for estuarine nitrogen cycling and provide a possible explanation for the plastisphere microbes' competitiveness in biofilm environments. Overall, microplastics in the estuarine system provide a novel habitat for microbial communities and associated nitrogen cycling, facilitating the growth of microbes with plastic degrading capabilities.}, }
@article {pmid40174744, year = {2025}, author = {Liu, M and Wang, S and Zhou, H and Liu, H and Huang, D and Liu, L and Li, Q and Chen, H and Lei, Y and Jin, LN and Zhang, W}, title = {Thermal Environment Driving Specific Microbial Species to Form the Visible Biofilms on the UNESCO World Heritage Dazu Rock Carvings.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121510}, doi = {10.1016/j.envres.2025.121510}, pmid = {40174744}, issn = {1096-0953}, abstract = {The Dazu Rock Carvings, a UNESCO World Heritage site with over a millennium of history, are facing significant deterioration from microbial biofilms. However, the key microbial species responsible and the environmental factors driving their growth remain unclear. To address this gap, we conducted metagenomic sequencing to characterize the microbial community on the carvings, followed by correlation analyses with a variety of environmental factors in the surrounding air and within the rocks. Bacterial communities exhibited significantly higher richness and diversity than eukaryotic communities, though diversity metrics showed no significant differences between visibly colonized and uncolonized surfaces. We identified a distinctive consortium of 64 bacterial species, 35 fungal species, and 1 algal species specifically associated with visible biofilms, occurring at 9.56-fold higher relative abundance in colonized areas. These microorganisms contribute to characteristic green, brown-black, and white coloration on the carvings. Statistical analysis revealed absolute humidity and dew point temperature as key environmental factors influencing biofilm visibility, with thresholds of 21.00 g/m[3] and 23.4°C respectively, above which biofilms became visible. This study provides precise targets for conservation efforts and establishes critical environmental parameters to guide preservation strategies for this irreplaceable cultural heritage.}, }
@article {pmid40174653, year = {2025}, author = {Balasundaram, G and Gahlot, P and Hafyan, RH and Tyagi, VK and Gadkari, S and Sahu, A and Barber, B and Mutiyar, PK and Kazmi, AA and Kleiven, H}, title = {Anaerobic digestion of thermal hydrolysis pretreated sludge: Process performance, metagenomic analysis, techno-economic and life cycle assessment.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132470}, doi = {10.1016/j.biortech.2025.132470}, pmid = {40174653}, issn = {1873-2976}, abstract = {This study assessed the potential of thermal hydrolysis process (THP) combined with anaerobic digestion (AD) for high solids sewage sludge treatment across various hydraulic retention times (HRTs). Optimal performance was achieved at a 10-day HRT (6 kg VS/m[3]·day), yielding 408 L CH4/kg VS added and 54 % volatile solids (VS) removal under THP conditions of 160 °C, 30 min, and 6 bar pressure. Microbial analysis revealed predominant acetoclastic and hydrogenotrophic methanogens. Four scenarios were designed and analyzed for environmental and economic performance: Scenario 1 (conventional AD-CHP), Scenario 2 (conventional AD-BioCNG), Scenario 3 (THP AD-BioCNG), and Scenario 4 (THP AD-CHP). The results showed that scenarios with CHP integration achieved better environmental performance by generating sufficient energy to meet demand, with energy consumption as a key factor. Notably, scenario 4 had the lowest global warming potential (GWP) at -0.0185 kg CO2-eq, outperforming conventional AD (Scenario 1) with CHP, which had a GWP of -0.00232 kg CO2-eq. However, profitability analysis showed that Scenario 3 was the most economically viable, with a net present value (NPV) of $4.3 million, an internal rate of return (IRR) of 10.21 %, and a 17-year payback period. Although it had higher capital ($58 million) and operational costs ($12.5 million/year) than Scenario 4 ($45 million and $8.6 million/year), its greater biomethane yield resulted in higher revenue ($20.7 million/year), making it the most profitable option. While Scenario 4 offered the best environmental benefits, Scenario 3 emerged as the most financially sustainable choice. These findings highlight the environmental and economic advantage of utilizing THP-AD process over conventional AD, suggesting that THP-AD optimizes methane production, solids reduction, and environmental impact, making the Bio CNG pathway a sustainable and economically viable option.}, }
@article {pmid40174641, year = {2025}, author = {He, T and Zhang, X and Zhang, X}, title = {Thousands-years-old deep-sea DNA viruses reveal the evolution of human pathogenic viruses.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.03.057}, pmid = {40174641}, issn = {2090-1224}, abstract = {INTRODUCTION: In the last two decades, outbreaks of pathogenic viruses have led to significant human mortality and economic repercussions. Despite extensive investigations into tracing these viruses in terrestrial environments, their origins remain enigmatic.<br><br>OBJECTIVES: The Earth's biosphere encompasses both sunlight-dependent terrestrial and surface ocean ecosystems, as well as the sunlight-independent deep-sea ecosystem. However, the traceability of human pathogenic viruses in the deep sea has not been thoroughly explored. This study aimed to investigate the presence of human pathogenic viruses in the deep sea.<br><br>METHODS: In this study, we performed a viral metagenomic analysis using a global deep-sea sediment virome 2.0 dataset which contained 159 deep-sea sediment samples with geologic ages from 2,500 to 7,750 years.<br><br>RESULTS: A total of 554,664 viral operational taxonomic units (vOTUs) were identified and further obtained 2,254 potential pathogenic viruses of vertebrates. Among them, 23 vOTUs exhibited high homology with 12 species of human pathogenic viruses which belonged to 4 viral families. Notably, variola virus, the first human pathogenic virus eradicated from humans and now only found in laboratories, was discovered in the ancient deep-sea sediments. The evolution analysis showed that these DNA viruses might represent the ancestors or variants of human pathogenic viruses, suggesting that the deep sea could be a crucial reservoir for human pathogenic viruses.<br><br>CONCLUSION: Our findings present all the ancient pathogenic DNA viruses of humans found in the deep sea for the first time, highlighting the source of the future epidemics. It is imperative to implement the stringent virus monitoring and management measures for human activities in marine environments to address the emerging challenges of marine biosecurity and promote sustainable use of oceans.}, }
@article {pmid40174574, year = {2025}, author = {Zeng, S and Almeida, A and Mu, D and Wang, S}, title = {Embracing the unknown: Proteomic insights into the human microbiome.}, journal = {Cell metabolism}, volume = {37}, number = {4}, pages = {799-801}, doi = {10.1016/j.cmet.2025.02.003}, pmid = {40174574}, issn = {1932-7420}, abstract = {Protein-level investigations into the human microbiome provide insights into active microbial functions. Recently, Valdés-Mas et al.[1] introduced a metagenome-informed metaproteomics approach to functionally explore species-level microbiome-host interactions and quantify the dietary exposome. Its potential has been implemented in mice and humans to uncover proteomic signatures of health and inflammatory bowel disease.}, }
@article {pmid40174565, year = {2025}, author = {Krohn, C and Khudur, L and Biek, SK and Elliott, JA and Tabatabaei, S and Jiang, C and Wood, JL and Dias, DA and Dueholm, MKD and Rees, CA and O'Carroll, D and Stuetz, R and Batstone, DJ and Surapaneni, A and Ball, AS}, title = {Microbial population shifts during disturbance induced foaming in anaerobic digestion of primary and activated sludge.}, journal = {Water research}, volume = {281}, number = {}, pages = {123548}, doi = {10.1016/j.watres.2025.123548}, pmid = {40174565}, issn = {1879-2448}, abstract = {Foaming during anaerobic digestion (AD) of sewage sludge is poorly understood and remains an uncontrollable operational obstacle for sewage treatment systems globally, causing mechanical damage, increased hazards and reduced biogas recovery. Foams during AD commonly occur after process disturbances, such as organic loading shocks. However, it is still unclear whether these foam events are biologically driven and linked to the abundance of organisms like filamentous or hydrophobic bacteria. A time-series study was conducted, comparing digestion performance, microbial community succession, metagenomes, and metabolomes in six anaerobic continuous stirred-tank reactors (CSTRs): a control group fed normally (n = 3), and one treated group inhibited through organic shock loading of more than twice the steady state loading rate with glycerol (treatment, n = 3). As soon as microbial activity and methanogenesis recovered after inhibition, significant volumes of foam accumulated simultaneously in the reactor headspace of the three treated CSTRs. Microbial abundance profiles (16S rRNA, V3-V4) from 165 days of operation showed that filamentous or mycolic acid-producing organisms were not associated with this foam event. Shock loading led to acidification, biomass decline and microbial imbalance, contributing indirectly to the foam event. During that period, metabolomes and functional pathway abundances indicated that the stressed microbial biomass was enriched in long-chain fatty acids prior to foaming. This biomass, combined with pH changes, may have modified the physicochemical properties of sludge, leading to the fractionation of organic mass once gas production resumed. More research is needed to understand how abiotic and biotic interactions contribute to foam formation.}, }
@article {pmid40174457, year = {2025}, author = {Han, Q and Wang, Y and Shi, C and Qian, Y and Wang, X and Wang, S and Sun, X and Yu, Q and Li, H}, title = {Urban landscape lakes with backwater hide higher antibiotic resistance risk than living water.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138101}, doi = {10.1016/j.jhazmat.2025.138101}, pmid = {40174457}, issn = {1873-3336}, abstract = {The pollution of antibiotic resistance genes (ARGs) in urban landscape lakes threatens the aquatic ecosystems and public health. However, a comprehensive understanding of the fate of ARGs in different types of park landscape lakes (i.e., backwater and living water) remains deficient. Here, we profiled the distribution, diversity, origin and potential spread risk to human of ARGs in backwater and living water using metagenomics and 16S rRNA gene sequencing. Our results showed higher antibiotic resistance risk presented in backwater due to higher ARG diversity, while higher resistance transfer risk occurred in living water due to higher mobile genetic elements (MGEs) diversity. Source tracking analysis revealed Yellow River water was the main the dominant source of ARGs in both backwater and living water, with an average contribution of 41.06 % and 65.82 %, respectively. Notably, nine high-risk ARGs (such as mdtM and msrA) significantly enriched in human feces, implying possible spread risk from environment to human. Metagenomics binning revealed that MAGs carrying ARGs mainly belong to Actinobacteria, while MAGs carrying MGEs belong to Proteobacteria. Our study highlights the significance of healthy management of park landscape lakes to prevent the spread of resistomes to the public.}, }
@article {pmid40174456, year = {2025}, author = {Long, M and Zheng, CW and Zhou, C and Rittmann, BE}, title = {Mitigating chromate toxicity through concurrent denitrification in the H2-based membrane biofilm reactor.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138073}, doi = {10.1016/j.jhazmat.2025.138073}, pmid = {40174456}, issn = {1873-3336}, abstract = {High concentrations of hexavalent chromium (Cr(VI)) in industrial wastewaters pose significant environmental and health hazards. Biotranformation is a viable means to lower Cr(VI) toxicity, but research to date has focused on wastewaters with low concentrations (e.g., 2-5 mg/L Cr(VI)). This study evaluated the dynamics of biosorption and biotransformation of higher-concentration Cr(VI) by biofilms in the H2-based membrane biofilm reactor (MBfR). While the biofilm in an MBfR receiving Cr(VI) alone had limited capacity to remove Cr(VI) and Cr(VI) removal ceased in 30 days, an autotrophic denitrifying biofilms achieved 99 % reduction of over 20 mg/L Cr(VI) to less-toxic trivalent chromium (Cr(III)) in continuous long-term operation system over 4 months. Increasing the H2 pressure from 3 psig to 10 psig improved Cr(VI) removal from 87 % to 99 %, which occurred in parallel with over 95 % NO3[-] reduction to N2. Metagenomic analyses revealed the mechanisms of Cr(VI) bioreduction and highlighted the beneficial role of nitrate (NO3[-]) as the primary electron acceptor. For example, nitrite reductase NrfA could reduce Cr(VI), which lowered Cr(VI) caused oxidative stress. This research demonstrates the MBfR's effectiveness in reducing elevated levels of Cr(VI) and provides mechanistic understanding of the roles of denitrification in accelerating Cr(VI) reduction and detoxification.}, }
@article {pmid40174424, year = {2025}, author = {Dai, Z and Li, Y and Zhang, Y and Xiang, T and Peng, J and Mao, X and Fan, Y and Wang, F and Yang, S and Cao, W}, title = {Nutrient enrichment by high aquaculture effluent input exacerbates imbalances between methane production and oxidation in mangrove sediments.}, journal = {Water research}, volume = {280}, number = {}, pages = {123552}, doi = {10.1016/j.watres.2025.123552}, pmid = {40174424}, issn = {1879-2448}, abstract = {Frequent aquaculture activities introduce substantial nutrients into mangrove ecosystems; however, the impact of this nutrient enrichment on methane (CH4) emissions and the associated microbial communities remains largely unexplored. In this study, we used the static chamber method, combined with 16S rRNA-based, metagenomic sequencing and binning techniques, to investigate the emission patterns of greenhouse gases (GHGs), with a particular focus on CH4, in mangroves subjected to different levels of effluents. The results showed that the effluent input decreased the mineral protection of sediment carbon (C) pools and increased C loss by more than double. In particular, high effluent input increased CH4 emissions by 243.3 %. Random forest analysis revealed that changes in methanogens were an important factor in explaining the variation of CH4 emissions. Amplicon data showed that the proportion of methylotrophic methanogens increased after effluent input, and metagenomic binning further attributed this change to the adaptability of methylotrophic methanogens to the substances transporting by the effluent. The enhanced hypoxia in sediments resulting from effluent input promoted the transition of methanotrophic communities from aerobic to anaerobic types and made anaerobic oxidation of CH4 more reliant on sulfur reduction rather than nitrate reduction. The PLS model further revealed that the nutrients brought by effluent input stimulated an increase in DOC content which induced an imbalance between CH4 production and oxidation in sediments by facilitating methanogens but inhibiting methanotrophs, ultimately resulting in an increase in CH4 fluxes. These findings underscore the significance of mangroves receiving effluent input as critical consequent reactors, highlighting the necessity to consider effects of high nutrient enrichment by aquaculture effluent input on GHG emissions and blue C potential in mangroves.}, }
@article {pmid40172536, year = {2025}, author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR}, title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0056924}, doi = {10.1128/iai.00569-24}, pmid = {40172536}, issn = {1098-5522}, abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.}, }
@article {pmid40172519, year = {2025}, author = {Chaves-Sierra, C and Botero-Rozo, D and Rodriguez-Cruz, MC and Montoya, C and Romero, HM}, title = {Detection and molecular characterization of 'Candidatus Liberibacter' in Colombian oil palms affected by Lethal Wilt Disease.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-10-24-2079-RE}, pmid = {40172519}, issn = {0191-2917}, abstract = {Lethal wilt (LW), also known as "Marchitez Letal (ML)" in Colombia, is an endemic disease affecting oil palms (Elaeis guineensis Jacq.) and is a leading cause of crop loss. The disease is characterized by the drying of leaflets from the tip to the base, primarily impacting the lower third of the plant and progressively moving upward. This progression leads to physiological disturbances, including necrosis at the tips of immature inflorescence bracts (spines) and the detachment of bunch fruits, ultimately causing wilting. As a phytosanitary measure, infected palms are eradicated to prevent further spread of the disease. The primary goal of this research was to identify the bacteria associated with LW and to validate a molecular detection method. A 16S amplicon-based analysis was employed to identify and compare the microbial diversity in LW-affected palm tissues with those of healthy plants. Among the 16 OTUs corresponding to different bacterial genera found in all LW samples, taxonomic classification and symptomatology suggested that the bacteria closely associated with LW belong to the genus Candidatus Liberibacter. Further phylogenetic analysis indicated that these bacteria are part of the Rhizobiaceae family, grouping closely with other species of the genus Candidatus. Liberibacter. The concentration of the pathogen in different oil palm tissues was determined using droplet digital PCR (ddPCR) and quantitative PCR (qPCR), expressed in copies/µL in the LW samples. This study represents the first report of 'Candidatus Liberibacter sp'. being associated with lethal wilt in oil palms of the Arecaceae family in Colombia. The findings from this research have the potential to contribute significantly to the development of effective management strategies to prevent crop losses.}, }
@article {pmid40172478, year = {2025}, author = {Wang, H and Zhao, X and Li, D and Meng, L and Liu, S and Zhang, Y and Huo, L}, title = {Marine Metagenome Mining Reveals Lanthipeptides Colwesin A-C, Exhibiting Novel Ring Topology and Anti-inflammatory Activity.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00057}, pmid = {40172478}, issn = {2161-5063}, abstract = {Marine natural products are promising sources for drug discovery due to their unique structures and diverse biological activities. The establishment of the Global Marine Microbiome Genome Catalogue (GOMC) has significantly expanded the repository of natural products derived from marine-associated bacteria. In this study, we identified the Class I lanthipeptide biosynthetic gene cluster col from Colwellia_A sp. based on the GOMC database. Through heterologous expression in Escherichia coli and subsequent structural analysis, we characterized three novel lanthipeptides, colwesins A-C, which possess unique cyclic structures characterized by an exceptionally large number of thioether rings. To the best of our knowledge, colwesin C is the first lanthipeptide simultaneously containing locked, nonoverlapped, and nested ring topologies. These findings highlight the robust ring-forming capacity of Class I lanthipeptide synthetases. Colwesins A-C were found to exhibit anti-inflammatory activity in lipopolysaccharide-induced mouse macrophage RAW264.7 cell lines without detectable cytotoxicity. Overall, our results broaden our understanding of the structural diversity of marine-derived lanthipeptides.}, }
@article {pmid40172215, year = {2025}, author = {Brito Rodrigues, P and de Rezende Rodovalho, V and Sencio, V and Benech, N and Creskey, M and Silva Angulo, F and Delval, L and Robil, C and Gosset, P and Machelart, A and Haas, J and Descat, A and Goosens, JF and Beury, D and Maurier, F and Hot, D and Wolowczuk, I and Sokol, H and Zhang, X and Ramirez Vinolo, MA and Trottein, F}, title = {Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2486511}, doi = {10.1080/19490976.2025.2486511}, pmid = {40172215}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/virology/metabolism ; *Metagenomics ; *Metabolomics ; *Disease Models, Animal ; Cricetinae ; *SARS-CoV-2/genetics ; Aging ; Age Factors ; Dysbiosis/microbiology ; Male ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Mesocricetus ; Metabolome ; }, abstract = {Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium, Oscillospiraceae, Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.}, }
@article {pmid40172109, year = {2025}, author = {Tarracchini, C and Lordan, C and Milani, C and Moreira, LPD and Alabedallat, QM and de Moreno de LeBlanc, A and Turroni, F and Lugli, GA and Mancabelli, L and Longhi, G and Brennan, L and Mahony, J and LeBlanc, JG and Nilaweera, KN and Cotter, PD and van Sinderen, D and Ventura, M}, title = {Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {}, number = {}, pages = {e0018423}, doi = {10.1128/mmbr.00184-23}, pmid = {40172109}, issn = {1098-5557}, abstract = {SUMMARYIn recent years, exhaustive efforts have been made to dissect the composition of gut-associated microbial communities and associated interactions with their human host, which are thought to play a crucial role in host development, physiology, and metabolic functions. Although such studies were initially focused on the description of the compositional shifts in the microbiota that occur between different health conditions, more recently, they have provided key insights into the functional and metabolic contributions of the gut microbiota to overall host physiology. In this context, an important metabolic activity of the human gut microbiota is believed to be represented by the synthesis of various vitamins that may elicit considerable benefits to human health. A growing body of scientific literature is now available relating to (predicted) bacterial vitamin biosynthetic abilities, with ever-growing information concerning the prevalence of these biosynthetic abilities among members of the human microbiota. This review is aimed at disentangling if and how cooperative trophic interactions of human microbiota members contribute to vitamin production, and if such, gut microbiota-mediated vitamin production varies according to different life stages. Moreover, it offers a brief exploration of how different diets may influence vitamin production by shaping the overall composition and metabolic activity of the human gut microbiota while also providing preliminary insights into potential correlations between human microbiota-associated vitamin production and the occurrence of human diseases and/or metabolic disorders.}, }
@article {pmid40171165, year = {2025}, author = {Shi, H and Li, J}, title = {MAGs-based genomic comparison of gut significantly enriched microbes in obese individuals pre- and post-bariatric surgery across diverse locations.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1485048}, pmid = {40171165}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; *Bariatric Surgery ; Metagenome ; Metagenomics/methods ; Genomics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Gastric Bypass ; Computational Biology/methods ; Adult ; }, abstract = {INTRODUCTION: Obesity, a pressing global health issue, is intricately associated with distinct gut microbiota profiles. Bariatric surgeries, such as Laparoscopic Sleeve Gastrectomy (LSG), Sleeve Gastrectomy (SG), and Roux-en-Y Gastric Bypass (RYGB), induce substantial weight loss and reshape gut microbiota composition and functionality, yet their comparative impacts remain underexplored.<br><br>METHODS: This study integrated four published metagenomic datasets, encompassing 500 samples, and employed a unified bioinformatics workflow for analysis. We assessed gut microbiota &#x3b1;-diversity, identified species biomarkers using three differential analysis approaches, and constructed high-quality Metagenome-Assembled Genomes (MAGs). Comparative genomic, functional profiling&#xa0;and KEGG pathway analyses were performed, alongside estimation of microbial growth rates via Peak-to-Trough Ratios (PTRs).<br><br>RESULTS: RYGB exhibited the most pronounced enhancement of gut microbiota &#x3b1;-diversity compared to LSG and SG. Cross-cohort analysis identified 39 species biomarkers: 27 enriched in the non-obesity group (NonOB_Enrich) and 12 in the obesity group (OB_Enrich). Among the MAGs, 177 were NonOB_Enrich and 14 were OB_Enrich. NonOB_Enrich MAGs displayed enriched carbohydrate degradation profiles (e.g., GH105, GH2, GH23, GH43, and GT0 families) and higher gene diversity in fatty acid biosynthesis and secondary metabolite pathways, alongside significant enrichment in amino acid metabolism (KEGG analysis). Post-surgery, Akkermansia muciniphila and Bacteroides uniformis showed elevated growth rates based on PTRs.<br><br>DISCUSSION: These findings underscore RYGB's superior impact on gut microbiota diversity and highlight distinct microbial functional adaptations linked to weight loss, offering insights for targeted therapeutic strategies.}, }
@article {pmid40170926, year = {2025}, author = {Zhai, R and Zhao, C and Chang, L and Liu, J and Zhao, T and Jiang, J and Zhu, W}, title = {Diets shape thermal responses in Chinese giant salamanders by altering liver metabolism.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1546912}, pmid = {40170926}, issn = {1664-302X}, abstract = {Diet can influence the thermal performance of ectotherms, providing potential strategies for biological conservation in the context of global warming. The endangered Andrias davidianus is susceptible to heat stress due to energy deficiency in the liver when fed a worm-based diet rich in carbohydrates. A fish-based diet, rich in protein and lipids, improves their thermal performance, but the underlying physiological mechanisms remain unclear. In this study, we used metabolomics and metagenomics to examine the combined effects of temperature (15, 20, and 25°C) and diet (fish-based and worm-based) on liver metabolism and gut microbiota. Our results show that both temperature and diet shape liver metabolism, with several vital metabolic pathways (e.g., TCA cycle and sulfate metabolism) regulated by their combined effects. Notably, diet-dependent thermal responses in energy metabolism were observed, with fish-fed salamanders exhibiting a marked upregulation of the TCA cycle intermediates under heat stress, a response absent in worm-fed individuals. Given the role of TCA cycle in heat susceptibility of A. davidianus, these findings suggest that the TCA cycle likely mediates the interactive effects of temperature and diet on thermal performance. We then examined whether the gut microbiota is also a target of interactive effects or a mediator of the diet's influence on liver metabolism. While both temperature and diet shape microbiota composition, functional shifts occur only in response to temperature, indicating that the microbiota is not a major link between diet and liver metabolism. However, several bacterial groups (e.g., Thiosulfatimonas and Alcanivorax), jointly regulated by temperature and diet, correlate with liver metabolites, suggesting alternative, function-independent pathways through which dietary-related microbial changes may influence liver metabolism and even thermal tolerance. Overall, this study provides molecular insights into the dietary modulation of thermal performance in A. davidianus and highlight the potential of dietary microbial management strategies for amphibian conservation.}, }
@article {pmid40170918, year = {2025}, author = {Hager, K and Luo, ZH and Montserrat-Diez, M and Ponce-Toledo, RI and Baur, P and Dahlke, S and Andrei, AS and Bulzu, PA and Ghai, R and Urich, T and Glatzel, S and Schleper, C and Rodrigues-Oliveira, T}, title = {Diversity and environmental distribution of Asgard archaea in shallow saline sediments.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1549128}, pmid = {40170918}, issn = {1664-302X}, abstract = {In recent years, our understanding of archaeal diversity has greatly expanded, especially with the discovery of new groups like the Asgard archaea. These archaea show diverse phylogenetic and genomic traits, enabling them to thrive in various environments. Due to their close relationship to eukaryotes, a large number of metagenomic studies have been performed on Asgard archaea. Research on the fine scale distribution, diversity and quantification in saline aquatic sediments where they mostly occur, has, however, remained scarce. In this study, we investigated depths of shallow saline sediment cores from three distinct European environments: the Baltic Sea near Hiddensee, the coastal Lake Techirghiol in Romania, and an estuarine canal in Piran, Slovenia. Based on 16S rDNA amplicon sequencing, we observe variation in the relative abundance and occurrence of at least seven different Asgard groups that are distinct between the three environments and in their depth distribution. Lokiarchaeia and Thorarchaeia emerge as dominant Asgard groups across all sites, reaching maximal relative abundances of 2.28 and 2.68% of the total microbial communities respectively, with a maximal abundance of all Asgard reaching approx. 5.21% in Hiddensee. Quantitative PCR assays provide insights into the absolute abundance of Lokiarchaeia, supporting distinct patterns of distribution across depths in different sediments. Co-occurrence network analysis indicates distinct potential microbial partners across different Asgard groups. Overall, our study shows that Asgard archaea are found as a stable component in shallow sediment layers and have considerably diversified on macro- and microscales.}, }
@article {pmid40170844, year = {2025}, author = {Zhou, Y and Han, W and Feng, Y and Wang, Y and Liu, X and Sun, T and Xu, J}, title = {Revealing gut microbiota biomarkers associated with melanoma immunotherapy response and key bacteria-fungi interaction relationships: evidence from metagenomics, machine learning, and SHAP methodology.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1539653}, pmid = {40170844}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Melanoma/therapy/immunology/microbiology ; *Metagenomics/methods ; *Immunotherapy/methods ; *Machine Learning ; Male ; *Bacteria/genetics/classification/immunology ; Female ; Fungi/immunology ; Middle Aged ; Skin Neoplasms/immunology/therapy/microbiology ; Biomarkers ; Aged ; Adult ; Treatment Outcome ; }, abstract = {INTRODUCTION: The gut microbiota is associated with the response to immunotherapy in cutaneous melanoma (CM). However, gut fungal biomarkers and bacterial-fungal interactions have yet to be determined.<br><br>METHODS: Metagenomic sequencing data of stool samples collected before immunotherapy from three independent groups of European ancestry CM patients were collected. After characterizing the relative abundances of bacteria and fungi, Linear Discriminant Analysis Effect Size (LEfSe) analysis, Random Forest (RF) model construction, and SHapley Additive exPlanations (SHAP) methodology were applied to identify biomarkers and key bacterial-fungal interactions associated with immunotherapy responders in CM.<br><br>RESULTS: Diversity analysis revealed significant differences in the bacterial and fungal composition between CM immunotherapy responders and non-responders. LEfSe analysis identified 45 bacterial and 4 fungal taxa as potential biomarkers. After constructing the RF model, the AUC of models built using bacterial and fungal data separately were 0.64 and 0.65, respectively. However, when bacterial and fungal data were combined, the AUC of the merged model increased to 0.71. In the merged model, the following taxa were identified as important biomarkers: Romboutsia, Endomicrobium, Aggregatilinea, Candidatus Moduliflexus, Colwellia, Akkermansia, Mucispirillum, and Rutstroemia, which were associated with responders, whereas Zancudomyces was associated with non-responders. Moreover, the positive correlation interaction between Akkermansia and Rutstroemia is considered a key bacterial-fungal interaction associated with CM immunotherapy response.<br><br>CONCLUSION: Our results provide valuable insights for the enrichment of responders to immunotherapy in CM patients. Moreover, this study highlights the critical role of bacterial-fungal interactions in CM immunotherapy.}, }
@article {pmid40170341, year = {2025}, author = {Sorn, S and Matsuura, N and Honda, R}, title = {Metagenome-Assembled Genomes and Metatranscriptome Analysis of Perfluorooctane Sulfonate-Reducing Bacteria Enriched From Activated Sludge.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70087}, doi = {10.1111/1462-2920.70087}, pmid = {40170341}, issn = {1462-2920}, support = {19K22925//Japan Society for the Promotion of Science/ ; 22K19865//Japan Society for the Promotion of Science/ ; //Steel Foundation for&#xa0;Environmental&#xa0;Protection&#xa0;Technology/ ; }, mesh = {*Fluorocarbons/metabolism ; *Alkanesulfonic Acids/metabolism ; *Sewage/microbiology ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Biodegradation, Environmental ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; Transcriptome ; Biotransformation ; Phylogeny ; }, abstract = {Per- and polyfluoroalkyl substances (PFAS) exhibit a widespread distribution across diverse global ecosystems throughout their lifecycle, posing substantial risks to human health. The persistence of PFAS makes biodegradation a challenging yet environmentally friendly solution for their treatment. In the authors' previous study, a bacterial consortium capable of reducing perfluorooctane sulfonate (PFOS) was successfully enriched from activated sludge. This study aimed to investigate the array of genes associated with PFOS reduction via biosorption and biotransformation to elucidate the metabolic pathways. Two metagenome-assembled genomes (MAGs) based on 16S rRNA sequences that share 99.86% and 97.88% similarity with Hyphomicrobium denitrificans and Paracoccus yeei, respectively were obtained. They were found to contain several genes encoding enzymes that potentially regulate biofilm formation of biosorption and facilitate the desulfonation and defluorination processes of biotransformation. Transcriptomic analysis demonstrated the high expression levels of these genes, including alkanesulfonate monooxygenase, catechol dioxygenase, (S)-2-haloacid dehalogenase and putative cytochrome P450, suggesting their involvement in PFOS biotransformation. The expression of these genes supports the presence of candidate metabolites of PFOS biotransformation detected in the previous study. These findings emphasise the significant potential of bacterial consortia and the crucial role played by genes encoding enzymes in facilitating the remediation of PFOS contaminants.}, }
@article {pmid40170118, year = {2025}, author = {Li, J and Sun, W and Cao, Y and Wu, J and Duan, L and Zhang, M and Luo, X and Deng, Q and Peng, Z and Mou, X and Li, W and Wang, P}, title = {Increased temperature enhances microbial-mediated lignin decomposition in river sediment.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {89}, pmid = {40170118}, issn = {2049-2618}, support = {32200090//National Natural Science Foundation of China/ ; 91951205//National Natural Science Foundation of China/ ; 2023A1515012270//Guangdong Basic and Applied Basic Research Foundation, China/ ; }, mesh = {*Lignin/metabolism ; *Geologic Sediments/microbiology ; *Rivers/microbiology/chemistry ; *Temperature ; *RNA, Ribosomal, 16S/genetics ; Bacteria/metabolism/classification/genetics ; Carbon Dioxide/metabolism ; Carbon Cycle ; Metagenomics ; }, abstract = {BACKGROUND: Lignin, as the most abundant recalcitrant organic carbon in terrestrial ecosystems, plays a crucial role in the Earth's carbon cycle. After lignin entering aquatic environments, portion of it tends to accumulate in sediments, forming a stable carbon relatively reservoir. However, the increasing temperature caused by human activities may impact microbial-mediated lignin decomposition, thereby affecting sedimentary carbon reservoirs. Therefore, revealing how temperature affects microbial-mediated lignin decomposition in river sediment, a topic that remains elusive, is essential for comprehending the feedbacks between river carbon reservoirs and climate. To address this, we conducted stable isotope probing of river surface sediment using [13]C-lignin and [13]C-vanillin, and utilized a series of techniques, including CO2 production analysis, 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics, to identify the lignin-decomposing microbes and the effects of temperature on microbial-mediated lignin decomposition.<br><br>RESULTS: We found that elevated temperatures not only increased the total sediment respiration (total CO2) and the CO2 emissions from lignin/vanillin decomposition, but also enhanced priming effects. The [13]C-labled taxa, including Burkholderiales, Sphingomonadales, and Pseudomonadales, were identified as the main potential lignin/vanillin decomposers, and their abundances and activity significantly increased as temperature increased. Furthermore, we observed that increasing temperature significantly increased the activity of lignin decomposing pathways, including &#x3b2;-aryl ether fragments and 4,5-PDOG pathway. Additionally, as temperature increases, the transcriptional abundances of other carbon cycling related genes, such as pulA (starch decomposition) and xyla (hemicellulose decomposition), also exhibited increasing trends. Overall, our study elucidated the potential lignin-decomposing microbes and pathways in river sediment and their responses to temperature increasing.<br><br>CONCLUSIONS: Our study demonstrated that the temperature increasing can increase the rate of lignin/vanillin decomposition via affecting the activity of lignin-decomposing microbes. This finding indicates that the ongoing intensification of global warming may enhance the decomposition of recalcitrant organic carbon in river sediment, thereby impacting global carbon cycling. Video Abstract.}, }
@article {pmid40169660, year = {2025}, author = {Legrand, TPRA and Alexandre, PA and Wilson, A and Farr, RJ and Reverter, A and Denman, SE}, title = {Genome-centric metagenomics reveals uncharacterised microbiomes in Angus cattle.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {547}, pmid = {40169660}, issn = {2052-4463}, mesh = {Animals ; Cattle/microbiology ; *Metagenomics ; *Microbiota ; *Feces/microbiology ; Metagenome ; Saliva/microbiology ; Mouth/microbiology ; }, abstract = {Understanding the intricate nexus between cattle health and microbiome dynamics holds profound implications for enhancing animal productivity and welfare. However, our understanding of the role of these microbial communities is limited in beef cattle, especially in understudied body sites such as the oral and nasal microbiome. Here, using a genome-centric metagenomics approach, we recovered substantial metagenome-assembled genomes (MAGs) from the faecal, oral and nasal microbiome of Australian Angus cattle from different herds and life stages. The MAGs recovered from faecal samples were dominated by Bacillota and Bacteroidota, while the MAGs from saliva and nasal mucus samples were mainly associated with Pseudomonadota, Actinomycetota and Bacteroidota. Functional annotation of the MAGs revealed enriched pathways involved in the production of some amino acids, nucleic acids and short chain fatty acids (SCFA). The metabolic capacities of the MAGs were correlated with their taxonomy, notably at the phylum level. Overall, this study provides a comprehensive catalogue of MAGs to further our understanding of their role in the health and fitness of beef cattle.}, }
@article {pmid40169555, year = {2025}, author = {Li, H and Liu, P and Sun, T and Li, Y and Wu, J and Huang, Y and Yang, J and Yuan, M and Zhang, J and Yang, J and Wong, ML and Licinio, J and Zheng, P}, title = {Dynamic alterations of depressive-like behaviors, gut microbiome, and fecal metabolome in social defeat stress mice.}, journal = {Translational psychiatry}, volume = {15}, number = {1}, pages = {115}, pmid = {40169555}, issn = {2158-3188}, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Stress, Psychological/metabolism/microbiology ; *Feces/microbiology/chemistry ; Male ; *Social Defeat ; *Metabolome ; *Disease Models, Animal ; *Depressive Disorder, Major/metabolism/microbiology ; *Behavior, Animal ; *Anhedonia ; Humans ; Mice, Inbred C57BL ; Female ; RNA, Ribosomal, 16S/genetics ; Depression/metabolism/microbiology ; }, abstract = {Gut microbiome is implicated in the onset and progression of major depressive disorder (MDD), but the dynamic alterations of depressive symptoms, gut microbiome, and fecal metabolome across different stages of stress exposure remain unclear. Here, we modified the chronic social defeat stress (CSDS) model to evaluate mice subjected to social defeat stress for 1, 4, 7, and 10 days. Behavioral tests, 16S rRNA, metagenomics, and fecal metabolomics were conducted to investigate the impact of stress exposure on behaviors, gut microbiota and fecal metabolites. We observed that depressive-like behaviors, such as anhedonia and social avoidance, worsened significantly as stress exposure increased. The microbial composition, function, and fecal metabolites exhibited distinct separations across the different social defeat stress groups. Mediation analysis identified key bacteria, such as Lachnospiraceae_UCG-001 and Bacteroidetes, and fecal metabolites like valeric acid and N-acetylaspartate. In our clinical depression cohort, we confirmed that fecal valeric acid levels, were significantly lower in depressive-like mice and MDD patients, correlating closely with stress exposure and anhedonia in mice. Further analysis of serum and brain metabolites in mice revealed sustained changes of N-acetylaspartate abundance in fecal, serum, and cortical samples following increasing stress exposure. Together, this study elucidated the characteristics of depressive-like behaviors, gut microbiome, and fecal metabolome across various social defeat stress exposure, and identified key bacteria and fecal metabolites potentially involved in modulating social defeat stress response and depressive-like behaviors, providing new insights into the pathogenesis and intervention of depression.}, }
@article {pmid40169141, year = {2025}, author = {Zhang, J and Ying, X and Hu, R and Huang, Y and Wang, R and Wu, L and Han, D and Ma, R and He, K}, title = {Metagenomic and metabolomic analysis of gut microbiome's role in spinal cord injury recovery in rats.}, journal = {Biomolecules &amp; biomedicine}, volume = {}, number = {}, pages = {}, doi = {10.17305/bb.2025.12164}, pmid = {40169141}, issn = {2831-090X}, abstract = {Spinal cord injury (SCI) induces profound systemic changes, including disruptions in gut microbiome composition and host metabolism. This study aimed to investigate the impact of SCI on gut microbial diversity and serum metabolites in rats, and to explore potential microbiome-metabolite interactions that may influence recovery. Male Sprague-Dawley (SD) rats were assigned to either SCI or sham-operated groups. Fecal samples were collected for whole-genome metagenomic sequencing, and serum samples were analyzed using untargeted metabolomics. Gut microbial composition and diversity were assessed using α- and β-diversity indices, while Linear discriminant analysis effect size (LEfSe) identified differentially abundant taxa. Metabolomic pathway analysis was performed to detect significant changes in serum metabolites, and Spearman's correlation was used to evaluate associations between gut microbes and metabolites. SCI significantly altered gut microbiota composition, with increased proportions of Ligilactobacillus and Staphylococcus, and decreased proportions of Lactobacillus and Limosilactobacillus. Metabolomic analysis revealed disrupted energy metabolism and elevated oxidative stress in SCI rats, as indicated by increased serum levels of pyruvate and lactic acid. Correlation analysis further identified significant associations between specific gut bacteria and key metabolites, suggesting microbiome-driven metabolic dysregulation following SCI. These findings highlight significant interactions between the gut microbiota and host metabolism after SCI and suggest that microbiome-targeted interventions may hold therapeutic potential for improving recovery by modulating metabolic function and oxidative stress responses.}, }
@article {pmid40156868, year = {2025}, author = {Yang, W and Luyten, Y and Reister, E and Mangelson, H and Sisson, Z and Auch, B and Liachko, I and Roberts, RJ and Ettwiller, L}, title = {Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.}, journal = {Nucleic acids research}, volume = {53}, number = {6}, pages = {}, pmid = {40156868}, issn = {1362-4962}, support = {//New England Biolabs, Inc./ ; R44AI172703/GF/NIH HHS/United States ; //Bill &amp; Melinda Gates Foundation/ ; }, mesh = {*Methyltransferases/metabolism/genetics ; *Microbiota/genetics ; DNA Methylation ; Bacteriophages/genetics/enzymology ; High-Throughput Nucleotide Sequencing ; Bacteria/genetics/enzymology ; Substrate Specificity ; Bacterial Proteins/metabolism/genetics ; Sequence Analysis, DNA/methods ; DNA, Viral/genetics/metabolism ; }, abstract = {Methylation patterns in bacteria can be used to study restriction-modification or other defense systems with novel properties. While m4C and m6A methylation are well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 (rapid identification of methyltransferase specificity sequencing) on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on bacteriophage DNA and compared with host DNA, strengthening evidence for phage-host interactions. Applied to three different microbiomes, the method unveiled over 1900 motifs that were deposited in REBASE. The motifs include a novel eight-base recognition site (CATm5CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5C methyltransferase specificities, providing insights into bacterial biology and biotechnological applications.}, }
@article {pmid40169073, year = {2025}, author = {Sun, L and Yin, Y and Guo, Y and Chen, H and Wang, H}, title = {Metagenomic Next-Generation Sequencing Enhances the Diagnosis of Q Fever: A Retrospective Observational Study.}, journal = {Travel medicine and infectious disease}, volume = {}, number = {}, pages = {102845}, doi = {10.1016/j.tmaid.2025.102845}, pmid = {40169073}, issn = {1873-0442}, abstract = {BACKGROUND: Q fever, a global zoonosis, poses a significant challenge for public health due to its varied and nonspecific clinical presentations, making diagnosis difficult. Metagenomic next-generation sequencing (mNGS) is a potential tool for diagnosing Q fever.<br><br>METHODS: This retrospective observational study was conducted on patients with Q fever admitted to Peking University People's Hospital, from May 2023 to November 2024. mNGS was performed using the patient's peripheral blood, and the qPCR of Coxiella burnetii was also adopted. Subsequently, the clinical data of patients diagnosed with Q fever were systematically evaluated.<br><br>RESULTS: Twelve peripheral blood samples of 12 patients were detected Coxiella burnetii positive by mNGS. Most patients were male (10, 83.33%). Fever (12, 100%), muscle soreness (8, 66.7%), and headache (4, 33.3%) were the most common clinical manifestations. Specific qPCR of Coxiella burnetii was detected positive in 8 patients. Chronic Q fever was diagnosed in two patients, who had aortic valve replacement, and their immunological markers, like anti-nuclear were elevated. Once the diagnosis was clear, proper antibiotics were used, and all patients were discharged in better health.<br><br>CONCLUSION: Metagenomic next-generation sequencing enhances the diagnosis of Q fever, especially for patients displaying atypical and various clinical symptoms and having unclear epidemiological data or histories of antibiotic use.}, }
@article {pmid40169018, year = {2025}, author = {Wallace, MA and Wille, M and Geoghegan, J and Imrie, RM and Holmes, EC and Harrison, XA and Longdon, B}, title = {Making sense of the virome in light of evolution and ecology.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2044}, pages = {20250389}, doi = {10.1098/rspb.2025.0389}, pmid = {40169018}, issn = {1471-2954}, support = {//Leverhulme Trust/ ; //National Health and Medical Research Council (NHMRC)/ ; //Royal Society/ ; /WT_/Wellcome Trust/United Kingdom ; //Webster Family Chair in Viral Pathogenesis/ ; //New Zealand Royal Society Rutherford Discovery Fellowship/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; }, mesh = {*Virome ; *Viruses/genetics ; Biological Evolution ; Metagenomics ; Ecology ; Ecosystem ; Phylogeny ; }, abstract = {Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.}, }
@article {pmid40168930, year = {2025}, author = {Tang, GX and Huang, YH and Feng, LW and Hu, YC and Wei, JL and Lü, H and Liu, LH and Zhao, HM and Xiang, L and Li, H and Mo, CH and Li, YW and Cai, QY}, title = {New insights into rhizosphere bacterial community shaped by lettuce genotypes for divergent degradation efficiencies of phthalates.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138077}, doi = {10.1016/j.jhazmat.2025.138077}, pmid = {40168930}, issn = {1873-3336}, abstract = {Rhizosphere dissipation of organic pollutants benefits safe utilization of the polluted agricultural soil. Nevertheless, dissipation variation of phthalates (PAEs) in rhizosphere among different vegetable genotypes and the related microbial mechanisms remain unknown. Here, twelve lettuce cultivars with different genetic relationships identified by 18S rRNA gene sequencing were cultivated in soil spiked with di-(2-ethylhexyl) phthalate (DEHP). Bacterial communities and function genes in rhizosphere of lettuce were analyzed by 16S rRNA gene and metagenomic sequencing. Results showed significant variations in DEHP concentrations of roots (2.8-15.3 mg/kg) and shoots (0.70-1.8 mg/kg) among 12 cultivars. Notably, cultivars L11 and L12 showed the lowest DEHP accumulation in roots and shoots, being lower by 82 % and 58 % than the highest accumulators (cultivars L5 and L6), respectively. This accumulation variation was closely connected with their genetic relationships and exhibited genotype-dependent trait. The significantly different bacterial community diversities and structures were recorded in rhizosphere among 12 cultivars. Especially, bacterial communities in rhizosphere of cultivars L11 and L12 (low-DEHP accumulators with high DEHP dissipation) strengthened their adaptation by enriching pollutant-resistant taxa, increasing extracellular polymeric substance contents and biofilm formation, as well as constructing complex ecological networks under DEHP pollution. Moreover, PAE-degrading bacteria and genes (e.g., hydrolase65, phtAb, and pcaI) in rhizosphere were enriched by low-DEHP accumulators, which benefited DEHP removal and subsequently safe agricultural products. This study provides new insights into microbial mechanisms on rhizosphere DEHP degradation and its correlation with accumulation variation among different crop genotypes.}, }
@article {pmid40168814, year = {2025}, author = {Harish, J and Prasannakumar, MK and Venkateshbabu, G and Karan, R and Mahesh, HB and Devanna, P and Sarangi, AN and Patil, SS and Tejashwini, V and Lohithaswa, HC and Kagale, S}, title = {Molecular and genomic insights into the pathogenicity of Sarocladium zeae causing maize stalk rot disease.}, journal = {Microbiological research}, volume = {296}, number = {}, pages = {128146}, doi = {10.1016/j.micres.2025.128146}, pmid = {40168814}, issn = {1618-0623}, abstract = {Post-flowering stalk rot (PFSR) of maize has been traditionally associated with Fusarium verticillioides. Conversely, this study reveals Sarocladium zeae as a new phytopathogen responsible for the disease. This research was conducted to gain a comprehensive understanding of S. zeae by investigating its pathogenic mechanisms, profiling its metabolome, and deciphering its genomic characteristics. Maize stalks displaying stalk rot symptoms were collected from various regions of India. S. zeae was isolated and characterized using ITS and TEF-1α sequencing. Cultures of S. zeae exhibited slower growth on PDA medium compared to F. verticillioides, which dominated due to its rapid growth rate. Pathogenicity was confirmed through a toothpick inoculation assay. The symptoms induced by S. zeae was characterized by powdery, dry, pale brown-black discoloration, were distinct from the typical dark-brown lesions of Fusarium stalk rot. Enzymatic assays revealed increased activity of β-glucosidase, cellulase, and pectate lyase in infected stalks, while qPCR analysis showed the upregulation of endoglucanase and β-glucosidase genes in infected stalks underscored the critical roles of cellulase and β-glucosidase in pathogenicity Metagenomic analysis identified S. zeae as the predominant species in infected stalk samples. Genome assembly revealed the pathogen's complete genetic repertoire, including genes encoding effector proteins and CAZymes involved in cell wall degradation. Moreover, we have demonstrated that the S. zeae as a causal agent of maize stalk rot and further shedding light on its transition from an endophytic to a pathogenic lifestyle. Taken together, this research represents the first report to attribute maize stalk rot to S. zeae and to present its complete genome assembly, significantly advancing the understanding of its biology and pathogenic potential.}, }
@article {pmid40168753, year = {2025}, author = {Ji, X and Yu, X and Xu, Y and Wu, Q and Madadi, M and Khaneghah, AM}, title = {Initial acidity regulates microbial sulfur metabolism in the spontaneous fermentation of sesame flavor-type baijiu.}, journal = {International journal of food microbiology}, volume = {435}, number = {}, pages = {111182}, doi = {10.1016/j.ijfoodmicro.2025.111182}, pmid = {40168753}, issn = {1879-3460}, abstract = {Volatile sulfur compounds play a crucial role in fermented foods, however, their metabolism during spontaneous food fermentation remains underexplored. With 3-(methylthio)-1-propanal as a case, we revealed the effect of initial acidity on the sulfur metabolism during sesame flavor-type baijiu fermentation. Results showed that the content of 3-(methylthio)-1-propanal reached 383.29 μg/kg with 1.8 mmol/10 g of the initial acidity, and it decreased to 320.54 μg/kg when the initial acidity increased to 2.4 mmol/10 g. Metagenomic analysis identified 11 core microbes associated with sulfur metabolism, characterized by gene abundance (> 0.5 %) and catalytic enzyme distribution frequency (> 10 %). Saccharomyces was the main producer of sulfur compounds. Lactobacillus was an important player in the methyl cycle pathway of sulfur metabolism. Low initial acidity increased the abundance of Lactobacillus and the content of genes associated with the methyl cycle pathway (P < 0.05). This resulted in a significant increase of methionine (253.26 mg/kg) (P < 0.05) and 3-(methylthio)-1-propanal contents (383.29 μg/kg) (P < 0.05). In simulated fermentation, the content of 3-(methylthio)-1-propanal significantly increased by 2.91 folds when Saccharomyces cerevisiae was cocultured with Lactobacillus acetotolerans (P < 0.05), and the transcription of genes related to sulfur metabolism significantly increased by 33.71 folds (P < 0.05). Results indicated that low initial acidity increased the abundance of Lactobacillus, which mediates the methyl cycle pathway in the sulfur metabolism, thereby increasing the contents of methionine and volatile sulfur compounds. This work provided insight into the regulation of metabolic mechanisms of volatile sulfur compounds in baijiu fermentation.}, }
@article {pmid40168325, year = {2025}, author = {Yun, H and Seo, JH and Kim, YK and Yang, J}, title = {Examining the bacterial diversity including extracellular vesicles in air and soil: implications for human health.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0320916}, doi = {10.1371/journal.pone.0320916}, pmid = {40168325}, issn = {1932-6203}, mesh = {*Extracellular Vesicles/metabolism ; *Soil Microbiology ; Humans ; *Bacteria/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Air Microbiology ; Microbiota ; Biodiversity ; Metagenomics/methods ; }, abstract = {As the significance of human health continues to rise, the microbiome has shifted its focus from microbial composition to the functional roles it plays. In parallel, interest in ultrafine particles associated with clinically important impact has been increasing. Bacterial extracellular vesicles (BEVs), involved in systemic microbiome activity, are nano-sized spherical vesicles (20 - 100 nm in diameter) containing DNA, RNA, proteins, and lipids. They are known to be absorbed into the body potentially through air and soil, circulate in the blood, and directly impact diseases by affecting organs. Therefore, the aim of this study is to examine the biodiversity of bacteria and BEVs and predicted functional pathways. We sampled air and soil samples in Seoul, Korea and analyzed metagenomics based on 16S rRNA sequencing. At the phylum levels, Firmicutes in BEVs from soil and air were significantly higher than in bacteria, and Acidobacteria in both bacteria and BEVs from soil were significantly higher than from air (p < 0.05). The most dominant genera were Pseudomonas in bacteria from air and soil; and Escherichia-Shigella in BEVs from air and soil. In addition, Two-component system (ko02020) and ATP-binding cassette transporters (ko02010) were dominant functional pathways in both air and soil. The most functional pathways and orthologous groups were significantly different between air and soil (p < 0.05). In conclusion, human health can be affected differently depending on type of environment. Future study is necessary to have a better understanding of human health effects from environmental microbiota.}, }
@article {pmid40167463, year = {2025}, author = {Sun, C and Liu, H and Teng, J and Feng, W and Wang, D and Wang, X and Zhao, J and Wang, Q}, title = {Impact of Microplastic Exposure on Sand Crab Scopimera globosa Behavior: Implications for Microplastic Transport and Sulfur Cycling through Bioturbation.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c01192}, pmid = {40167463}, issn = {1520-5851}, abstract = {The accumulation of microplastics (MPs) in estuarine regions and their ecological consequences have become global environmental concerns. Estuarine sediments function as major sinks for MPs and hotspots for critical biogeochemical processes, which are significantly influenced by benthic bioturbation. However, the impacts of MPs on the behavior of highly mobile benthic organisms and the ecological effects of bioturbation activities remain poorly understood. This study utilized laboratory simulation experiments, AI-based behavioral tracking, and metagenomic sequencing to systematically examine the effects of sand crab bioturbation on MPs migration, sediment physicochemical properties and sulfur cycling processes. Results demonstrated that sand crab bioturbation substantially enhanced the vertical migration of MPs, with fluxes to surface layers and the overlying water increasing by 27-fold compared to undisturbed conditions. Exposure to PE-MPs reduced sand crabs' surface foraging intensity and induced behavioral abnormalities. The crabs actively avoided MPs, exhibiting a preference for burrowing and residing in deeper sediment layers. This behavioral shift significantly altered microbial community distributions, with an increase of Pseudomonadota abundance and a decline of sulfate-reducing bacteria Thermodesulfobacteriota abundance. Furthermore, bioturbation accelerated sulfate oxidation in deeper sediments while inhibited dissimilatory sulfate reduction. This study is the first to identify the role of bioturbation in promoting the upward migration of MPs in sediments. Altered sand crab bioturbation will impact sediment biogeochemistry, estuarine function, and coastal resilience.}, }
@article {pmid40167332, year = {2025}, author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF}, title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14105}, doi = {10.1111/1755-0998.14105}, pmid = {40167332}, issn = {1755-0998}, support = {CEEC/0482/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0069/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/BIA/00329/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/50027/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0048/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; }, abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.}, }
@article {pmid40166061, year = {2025}, author = {Zhang, L and Guo, Y and Wang, X and Gai, W and Liu, L}, title = {Severe adenovirus pneumonia complicated by acute respiratory distress syndrome in immunocompetent patients: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1524783}, pmid = {40166061}, issn = {2296-858X}, abstract = {BACKGROUND: Human adenovirus (HAdV) is one of the most important pathogens detected in acute respiratory illness in pediatric and immunocompromised patients, but it is relatively rare to develop severe pneumonia in immunocompetent patients. We analyzed the clinical features, as well as the diagnosis and treatment processes, to provide a reference for clinical practice.<br><br>CASE PRESENTATION: We report a case of severe pneumonia caused by HAdV, complicated by acute respiratory distress syndrome (ARDS), in an immunocompetent patient with no underlying conditions. Chest computed tomography (CT) revealed consolidation in the right lower lung. Conventional microbial tests were negative, but metagenomic next-generation sequencing (mNGS) identified a large number of HAdV sequences in blood and sputum. Together with the clinical symptoms, this confirmed the diagnosis of severe pneumonia caused by HAdV. The patient was discharged after timely treatment with cidofovir.<br><br>CONCLUSION: In our study, we described a rare case of severe pneumonia caused by HAdV, complicated by ARDS, in an immunocompetent patient. mNGS proves to be an effective diagnostic tool for guiding treatment decisions.}, }
@article {pmid40165946, year = {2025}, author = {Guo, Z and Wang, X and Li, Y and Zhang, Y and Guo, P and Zhang, J and Zhang, Z and Ma, X}, title = {Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1563225}, pmid = {40165946}, issn = {1664-3224}, mesh = {Animals ; Mice ; *Pomegranate/chemistry ; *Zingiber officinale ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Enteritis/drug therapy/microbiology/veterinary ; *Aquaporins/metabolism/genetics ; Cytokines/metabolism ; Chronic Disease ; Disease Models, Animal ; Powders ; Plant Extracts/pharmacology/administration &amp; dosage ; Aquaporin 3 ; Aquaporin 4 ; }, abstract = {To explore the efficacy and mechanism of Pomegranate peel Ginger ultrafine powder (PG) in treating chronic enteritis in mice. Sixty SPF-grade mice were randomly divided into a blank group, a model group, loperamide hydrochloride group (5 mg/kg), a high-dose PG group (100 mg/kg), a medium-dose group (50 mg/kg), and a low-dose group (25 mg/kg), with 10 mice in each group and an equal number of males and females. A chronic enteritis mouse model was established using a multifactorial method of low temperature + ice water + castor oil. The blank group was given an equal amount of physiological saline intragastrically, while the other groups were intervened with corresponding drugs for 7 consecutive days. After 7 days, samples were collected, and Enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of interleuckin 1β (IL-1β), IL-6, and Tumor necrosis factorα(TNF-α) in mouse serum. HE staining was used to examine the pathological changes in the small intestine. oxidative reagent kits were used to detect the content of total superoxide dismutase(T-SOD) and Malondialdehyde (MDA) in the small intestine. Western blot was used to detect the expression of Aquaporin 8(AQP8) proteins in the small intestine. Real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to detect the expression of AQP3, AQP4, AQP8, and Sodium/hydrogen exchanger 8 (NHE8) genes in the small intestine. metagenomics was used to detect the gut microbiota in mouse feces. Compared with the model group, all doses of PG groups reduced the levels of IL-1β, IL-6, and TNF-α in mouse serum (P<0.05), improved pathological changes in the small intestine, increased the content of T-SOD in the small intestine tissue, reduced the content of MDA, increased the expression of AQP4 and AQP8 mRNA, and decreased the expression of AQP3 and NHE8 mRNA (P<0.05), increased the expression of AQP8 protein. PG could improve the pathological changes of chronic enteritis in mice, enhance antioxidant capacity, and alleviate diarrhea caused by chronic enteritis by downregulating the expression of intestinal epithelial transport proteins and acute-phase proteins, and altering gut microbiota.}, }
@article {pmid40165815, year = {2025}, author = {Battur, M and Aaqil, M and Zheng, J and Lin, HX and Chuluunotgon, B and Zorigtbaatar, T and Zhao, C and Tian, Y}, title = {Exploring the effects of milk-enriched walnut soy sauce: Insights from GC-IMS and metagenomics approach to flavor and microbial shifts.}, journal = {Food chemistry: X}, volume = {27}, number = {}, pages = {102364}, pmid = {40165815}, issn = {2590-1575}, abstract = {This study investigates the impact of milk addition on the fermentation of walnut soy sauce, using Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) and metagenomics to analyze flavor profiles and microbial dynamics. GC-IMS analysis showed significant increases in volatile compounds such as esters (ethyl acetate), aldehydes (hexanal), and alcohols (isoamyl alcohol), enhancing the aroma and taste. Metagenomic analysis revealed that milk increased microbial diversity, with Weissella and Lactobacillus dominating early fermentation. The milk-enriched soy sauce (SYM) exhibited higher amino acid nitrogen (2.67 g/L), and total nitrogen (7.18 g/L) compared to the control, indicating improved nutritional quality. Protease activity peaked at 2438.5 U/g for neutral protease, supporting efficient protein hydrolysis. Relative Odor Activity Value (ROAV) analysis identified 29 key flavor compounds, including 3-methyl butanol and ethyl 2-methyl butyrate, which contributed fruity and buttery notes to SYM. These results suggest that milk enhances microbial growth and improves both flavor and nutritional quality of walnut soy sauce.}, }
@article {pmid40165787, year = {2025}, author = {Huang, Z and Wang, J and He, X and Zhang, M and Ren, X and Yu, W and Yao, S and Ji, K}, title = {Divergent profiles of rhizosphere soil carbon and nitrogen cycling in Pinus massoniana provenances with different types of carbon storage.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1537173}, pmid = {40165787}, issn = {1664-302X}, abstract = {INTRODUCTION: In subtropical China, P. massoniana is a timber tree species which have a great potential for carbon sequestration. However, few studies have investigated how varying levels of carbon storage in P. massoniana provenances affect the soil microbial functional potential related to nutrient cycling within the rhizosphere.<br><br>METHODS: In this investigation, metagenomic sequencing was employed to explore the differences in carbon and nitrogen cycling capabilities among rhizosphere microbial communities within P. massoniana provenances, categorized by high, medium, and low levels of carbon storage.<br><br>RESULTS: Our findings revealed a significant increase in the relative abundance of Acidobacteriota and Ascomycota by 23 and 61%, respectively, whereas Basidiomycota significantly decreased by 8% in the rhizosphere of P. massoniana provenances with high carbon storage compared with those with low carbon storage. The variability in carbon storage among P. massoniana provenances was linked to marked disparities in the presence of key genes essential for carbon and nitrogen cycling within their rhizosphere soils.<br><br>DISCUSSION: Notably, in P. massoniana provenances characterized by high carbon storage, the rhizosphere presented a significantly elevated presence of genes associated with carbon decomposition, carbon assimilation, methane generation, and denitrification, in stark contrast to provenances with medium and low carbon storage. Furthermore, P. massoniana provenances with high carbon storage rates presented increased transformation and availability of soil carbon and nitrogen, along with increased potential for ecological restoration. Moreover, the rhizosphere soil nitrification of P. massoniana provenances with low carbon storage surpassed that of other provenances, leading to increased available nitrogen content and elevated nitrate leaching risk. In the P. massoniana rhizosphere, critical soil factors, including soil organic carbon (SOC), total nitrogen (TN), pH, and nitrate nitrogen (NO3 [-]-N) content, significantly shape the functionality of genes associated with carbon and nitrogen cycling. In conclusion, our study lays a scientific foundation for establishing P. massoniana plantations and identifying P. massoniana provenances with superior ecological value and potential.}, }
@article {pmid40165255, year = {2025}, author = {Xie, B and Dong, C and Zhao, X and Qu, L and Lv, Y and Liu, H and Xu, J and Yu, Z and Shen, H and Shang, Y and Zhao, X and Zhang, J}, title = {Structural and functional alteration of the gut microbiomes in ICU staff: a cross-sectional analysis.}, journal = {Critical care (London, England)}, volume = {29}, number = {1}, pages = {141}, pmid = {40165255}, issn = {1466-609X}, support = {82402568//National Natural Science Foundation of China/ ; 82472223//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/physiology ; *Intensive Care Units/organization &amp; administration/statistics &amp; numerical data ; Male ; Female ; Prospective Studies ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Cohort Studies ; Feces/microbiology ; Health Personnel/statistics &amp; numerical data ; }, abstract = {BACKGROUND: 16S rRNA sequencing has revealed structural alterations in the gut microbiomes of medical workers, particularly those working in intensive care unit (ICU). This study aims to further compare the taxonomic and functional characteristics of gut microbiomes between ICU staff and non-medical individuals using metagenomic sequencing.<br><br>METHODS: A prospective cross-sectional cohort study was conducted, fecal samples from 39 individuals in each group-ICU staff and non-medical subjects were analyzed using metagenomic sequencing. PERMANOVA (using the adonis function) was employed to analyze the genus-level profiles and assess the impact of individual parameters on the gut microbiome. Multiple databases were utilized to annotate and compare the functional differences in gut microbiomes between the two groups.<br><br>RESULTS: We observed that ICU staff exhibited a significant decrease in gut microbiome diversity, characterized by a marked decline in Actinobacteria and a substantial increase in Bacteroides and Bacteroidaceae. CAZy annotation revealed a notable increase in carbohydrate-active enzymes within the ICU staff cohort. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further indicated an elevated risk of endocrine and metabolic disorders, along with enhanced glycan biosynthesis and metabolism. Additionally, KEGG pathway enrichment analysis highlighted significant enrichment in cancer-related pathways. Analysis using the Virulence Factor Database (VFDB) showed a higher abundance of virulence factors associated with immune modulation, invasion, and antimicrobial activity/competitive advantage among ICU staff. Notably, no discernible difference in the presence of antibiotic resistance genes within the gut microbiomes was observed between the two groups. Importantly, all aforementioned differences demonstrated clear gender disparities.<br><br>CONCLUSIONS: Our findings indicated that ICU staff exhibited a reduction in gut microbiome diversity which was associated with an increase in virulence factors and carbohydrate-active enzymes, as well as with a heightened susceptibility to endocrine and metabolic diseases and cancers.}, }
@article {pmid40165201, year = {2025}, author = {Lin, L and Peng, X and Chen, L and Dong, L and Zhong, L}, title = {Case report: novel NFKB2 variant associated with pediatric eosinophilic granulomatosis with polyangiitis (EGPA) in the COVID-19 pandemic.}, journal = {Pediatric rheumatology online journal}, volume = {23}, number = {1}, pages = {35}, pmid = {40165201}, issn = {1546-0096}, mesh = {Humans ; Female ; *COVID-19/complications ; Child ; *NF-kappa B p52 Subunit/genetics ; SARS-CoV-2 ; Churg-Strauss Syndrome/genetics/diagnosis ; Granulomatosis with Polyangiitis/genetics/diagnosis ; }, abstract = {BACKGROUND: Childhood-onset eosinophilic granulomatosis with polyangiitis (cEGPA) is a rare type of systemic autoimmune disorder. Variants in the NFKB2 gene can manifest as common variable immunodeficiency or combined immunodeficiency, often accompanied by autoimmunity and ectodermal dysplasia. Here, we report a case of a Chinese patient who carries NFKB2 variants that coexist with cEGPA, a novel combination which, to our knowledge, has not been previously published.<br><br>CASE PRESENTATION: We reported a 9-year and 10-month-old girl who presented with cough, wheezing, dyspnea, hypereosinophilia, and vasculitis. Notably, she had significant bilateral pulmonary interstitial lesions. We performed metagenomic next-generation sequencing (mNGS), bronchoscopy and immunological analysis. She was considered to have refractory cEGPA after six months of corticosteroid and immunosuppressive treatment. Tapering off corticosteroids posed a challenge, and multiple immunosuppressive agents were ineffective. Our patient suffered from recurrent fever, wheezing, dyspnea and perianal abscess, along with life-threatening infections, including pneumocystis jirovecii pneumonia (PJP) and severe coronavirus disease 2019 (COVID-19) pneumonia during the pandemic. Her cytokines and inflammatory markers showed a profound collapse. She developed significant hypoxemia, which necessitated mechanical ventilation. Primary immunodeficiency gene panel testing revealed a novel de novo variant in NFKB2 (c.2578&#x2009;+&#x2009;2 dup) that was classified as pathogenic. Despite treatment with antibacterial, antiviral, and antifungal agents, biologics, and plasma exchange, she ultimately succumbed to respiratory failure.<br><br>CONCLUSIONS: This case report establishes a novel link between NFKB2 variants and EGPA, particularly in the context of the COVID-19 pandemic. This study expands the spectrum of NFKB2 variants and vividly illustrates the complex interrelationships among autoimmunity, infection, and immunodeficiency.}, }
@article {pmid40165140, year = {2025}, author = {Trivett, H and Darby, AC and Oyebode, O}, title = {Academic and clinical perspectives of metagenome sequencing as a diagnostic tool for infectious disease: an interpretive phenomenological study.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {448}, pmid = {40165140}, issn = {1471-2334}, mesh = {Humans ; *Metagenome ; *Communicable Diseases/diagnosis ; *COVID-19/diagnosis ; Metagenomics/methods ; SARS-CoV-2/genetics ; England ; }, abstract = {BACKGROUND: Effective infectious disease diagnostics (IDD) are vital for informing clinical decision-making regarding the treatment and patient management of disease and infections. In England, conventional clinical methods rely upon culture-dependent techniques, and there has been little shift in the acceptance and integration of culture-independent sequencing methods into routine clinical IDD. This study explored stakeholders' experiences within IDD, including those working in clinical settings and those conducting research at the forefront of microbial genomics. From the participants' experiences, the study aimed to identify barriers and facilitators driving the development and implementation of metagenome sequencing as a routine diagnostic.<br><br>METHODS: Virtual semi-structured interviews were conducted with purposively selected individuals involved in IDD. The interviews explored the experiences of implementing metagenome sequencing as a diagnostic tool and decisions about which diagnostics are used for identifying bacteria-causing infections. Thematic analysis was used to analyse the data, and an Interpretive Phenomenological approach was used throughout.<br><br>RESULTS: Ten individuals were interviewed between July 2021 and October 2021, including clinical scientists, consultants, and professors in academia. Their experience ranged from limited knowledge of metagenome sequencing to an expert understanding of the phenomenon. The thoughts and perspectives of participants of the study could be grouped into five themes: Availability of diagnostics for infectious diseases; Clinical laboratory infrastructure; Ethical Data Sharing: Enhancing metagenomics through Open Access; Case study in action: COVID-19; and The importance of communication to improve developments of new diagnostics. Participants recognised the need for new diagnostics to be implemented to overcome the limitations of current diagnostic approaches but highlighted the barriers to integrating new diagnostics into clinical settings, such as the impact on clinical decision-making, accreditation, and cost. Further, participants felt that lessons could be learnt from using metagenomics in COVID-19 and how other diagnostic platforms have been integrated into clinical settings over the last 20 years.<br><br>CONCLUSIONS: The study provided insights into stakeholders' perspectives and opinions to address the knowledge gap in current literature and identified barriers and facilitators which drive the implementation of metagenome sequencing as a routine IDD in clinical settings. Knowledge of new and upcoming genomic diagnostic testing is not equally distributed throughout the UK, impacting the understanding and drive to integrate metagenome sequencing into routine clinical diagnostics. Improvements in access to new diagnostics could improve patient treatment and management and positively impact population health.}, }
@article {pmid40165002, year = {2025}, author = {Wang, H and Su, Q and Sun, H and Meng, Y and Xing, X and Zheng, H and Li, Y}, title = {Unexpected Microbial and Genetic Diversity in the Gut of Chinese Giant Salamander.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12976}, pmid = {40165002}, issn = {1749-4877}, abstract = {The gut microbiome is crucial for animal health, yet the diversity of the critically endangered Chinese giant salamander's gut microbiota remains largely uncharacterized. In this study, we first conducted a comprehensive landscape survey of the gut microbiome of the Chinese giant salamander using 16S rRNA sequencing across a wide geographic range, identifying a distinct microbial cluster within its habitat. Subsequently, using shotgun metagenomes, we recovered 1518 metagenome-assembled genomes. Notably, 85% of the newly identified genomes could not be assigned to any known bacterial species, indicating a significant presence of novel taxa in Chinese giant salamander intestines. We observed substantial species-level variations in the gut microbiome across different age groups, with some novel species uniquely enriched in specific age populations. From the gut symbionts, we established a gene catalog comprising 3 278 107 non-redundant protein-coding genes, of which 7733 were annotated into recognized KEGG orthology groups. Additionally, we found that the gut microbiota of the Chinese giant salamander exhibits enhanced functional capacities explicitly in lipid metabolism and assimilatory sulfate reduction. Significant variations in the abundance of related enzyme-encoding genes across age groups suggest the unique roles of microbial metabolism in salamander health. By identifying microbial genomes and constructing an integrated gene catalog from metagenomic data, we significantly expand the resources available for research on the gut microbiome of the Chinese giant salamander, paving the way for further investigations into its ecological and health-related implications.}, }
@article {pmid40164980, year = {2025}, author = {Otani, S and Louise Jespersen, M and Brinch, C and Duus Møller, F and Pilgaard, B and Egholm Bruun Jensen, E and Leekitcharoenphon, P and Aaby Svendsen, C and Aarestrup, AH and Sonda, T and Sylvina, TJ and Leach, J and Piel, A and Stewart, F and Sapountzis, P and Kazyoba, PE and Kumburu, H and Aarestrup, FM}, title = {Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2484385}, doi = {10.1080/19490976.2025.2484385}, pmid = {40164980}, issn = {1949-0984}, mesh = {Animals ; *Diet ; *Hominidae/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; *Life Style ; Humans ; Adaptation, Physiological ; Pan troglodytes/microbiology ; Metagenome ; Phylogeny ; Africa ; }, abstract = {In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees. Even amongst shared bacterial communities, several core bacteria have co-diversified to fulfil unique dietary degradation functions within their host populations. These co-evolutionary trends extend to non-bacterial elements, such as mitochondrial DNA, antimicrobial resistance, and parasites. Our findings indicate that microbiome-host co-adaptations have led to both taxonomic and within taxa functional displacements to meet host physiological demands. The microbiome, in turn, transcends its taxonomic interchangeable role, reflecting the lifestyle, ecology and dietary history of its host.}, }
@article {pmid40164860, year = {2025}, author = {Adawiah, A and Meryandini, A and Ridwan, R and Fidriyanto, R and Sarwono, KA and Wiryawan, KG}, title = {The rumen microbiome and metabolome profile of Ongole crossbreed cattle fed probiotics and protected amino acids.}, journal = {Tropical animal health and production}, volume = {57}, number = {3}, pages = {148}, pmid = {40164860}, issn = {1573-7438}, mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Amino Acids/metabolism ; *Animal Feed/analysis ; Male ; *Metabolome ; *Diet/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration &amp; dosage/pharmacology ; Cross-Over Studies ; Dietary Supplements/analysis ; Bacteria/classification/metabolism/genetics ; }, abstract = {This study aimed to investigate the microbial population dynamics and metabolite profiles of Ongole crossbreed cattle (OCC) fed a combination of feed additives using metagenomic and metabolomic analyses. A crossover design was employed, involving four 3-year-old fistulated OCC bulls, each receiving four distinct dietary treatments per experimental period, followed by a washout phase with a basal diet. The treatments consisted of a basal diet (G1) as control, and the addition of feed additives as follows: G2: probiotics (Lactiplantibacillus plantarum); G3: premix; G4: G2 + G3 + amino acids lysine and methionine; and G5: G2 + G3 + amino acids protected with tannin. Rumen fluid was collected for the analysis of microbiome dynamics and metabolite profiles. The bacterial communities in diets G1, G2, G3, and G5 exhibited similar compositions, dominated by Bacteroidota, particularly the genus Prevotella. The G5 diet successfully suppressed the population of archaea, notably Methanosarcinales and Methanobacteriales, which are associated with methane production. A total of 28 significant metabolites (VIP > 1) was identified in rumen fluid, including lipid prenols, phenolic compounds, indoles and derivatives, saturated and unsaturated hydrocarbons, fatty acyls, benzene derivatives, and organooxygen compounds. The volatile compounds profile of rumen fluid showed a marked increase in prenol lipid compounds, especially in the G5 diet. Additionally, Methanosarcinales and Methanobacteriales were negatively correlated with prenol lipid levels. The inclusion of probiotics and protected amino acids alters the microbiome community structure and metabolites, positively affecting ruminant productivity.}, }
@article {pmid40164832, year = {2025}, author = {Litichevskiy, L and Considine, M and Gill, J and Shandar, V and Cox, TO and Descamps, HC and Wright, KM and Amses, KR and Dohnalová, L and Liou, MJ and Tetlak, M and Galindo-Fiallos, MR and Wong, AC and Lundgren, P and Kim, J and Uhr, GT and Rahman, RJ and Mason, S and Merenstein, C and Bushman, FD and Raj, A and Harding, F and Chen, Z and Prateek, GV and Mullis, M and Deighan, AG and Robinson, L and Tanes, C and Bittinger, K and Chakraborty, M and Bhatt, AS and Li, H and Barnett, I and Davenport, ER and Broman, KW and Levy, M and Cohen, RL and Botstein, D and Freund, A and Di Francesco, A and Churchill, GA and Li, M and Thaiss, CA}, title = {Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40164832}, issn = {2058-5276}, abstract = {The gut microbiome changes with age and has been proposed to mediate the benefit of lifespan-extending interventions such as dietary restriction. However, the causes and consequences of microbiome ageing and the potential of such interventions remain unclear. Here we analysed 2,997 metagenomes collected longitudinally from 913 deeply phenotyped, genetically diverse mice to investigate interactions between the microbiome, ageing, dietary restriction (caloric restriction and fasting), host genetics and a range of health parameters. Among the numerous age-associated microbiome changes that we find in this cohort, increased microbiome uniqueness is the most consistent parameter across a second longitudinal mouse experiment that we performed on inbred mice and a compendium of 4,101 human metagenomes. Furthermore, cohousing experiments show that age-associated microbiome changes may be caused by an accumulation of stochastic environmental exposures (neutral theory) rather than by the influence of an ageing host (selection theory). Unexpectedly, the majority of taxonomic and functional microbiome features show small but significant heritability, and the amount of variation explained by host genetics is similar to ageing and dietary restriction. We also find that more intense dietary interventions lead to larger microbiome changes and that dietary restriction does not rejuvenate the microbiome. Lastly, we find that the microbiome is associated with multiple health parameters, including body composition, immune components and frailty, but not lifespan. Overall, this study sheds light on the factors influencing microbiome ageing and aspects of host physiology modulated by the microbiome.}, }
@article {pmid40164697, year = {2025}, author = {Jia, L and Ke, Y and Zhao, S and Liu, J and Luo, X and Cao, J and Liu, Y and Guo, Q and Chen, WH and Chen, F and ,  and Wang, J and Wu, H and Ding, J and Zhao, XM}, title = {Metagenomic analysis characterizes stage-specific gut microbiota in Alzheimer's disease.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {40164697}, issn = {1476-5578}, abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder with a decade-long preclinical pathological period that can be divided into several stages. Emerging evidence has revealed that the microbiota-gut-brain axis plays an important role in AD pathology. However, the role of gut microbiota in different AD stages has not been well characterized. In this study, we performed fecal shotgun metagenomic analysis on a Chinese cohort with 476 participants across five stages of AD pathology to characterize stage-specific alterations in gut microbiota and evaluate their diagnostic potential. We discovered extensive gut dysbiosis that is associated with neuroinflammation and neurotransmitter dysregulation, with over 10% of microbial species and gene families showing significant alterations during AD progression. Furthermore, we demonstrated that microbial gene families exhibited strong diagnostic capabilities, evidenced by an average AUC of 0.80 in cross-validation and 0.75 in independent external validation. In the optimal model, the most discriminant gene families are primarily involved in the metabolism of carbohydrates, amino acids, energy, glycan and vitamins. We found that stage-specific microbial gene families in AD pathology could be validated by an in vitro gut simulator and were associated with specific genera. We also observed that the gut microbiota could affect the progression of cognitive decline in 5xFAD mice through fecal microbiota transplantation, which could be used for early intervention of AD. Our multi-stage large cohort metagenomic analysis demonstrates that alterations in gut microbiota occur from the very early stages of AD pathology, offering important etiological and diagnostic insights.}, }
@article {pmid40164638, year = {2025}, author = {Mills, S and Ijaz, UZ and Lens, PNL}, title = {Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {54}, pmid = {40164638}, issn = {2055-5008}, support = {15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; 15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; EP/P029329/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/V030515/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bioreactors/microbiology ; *Metagenomics/methods ; Bacteria/genetics/classification/isolation &amp; purification ; Microbiota ; High-Throughput Nucleotide Sequencing ; Microbial Consortia/genetics ; Methane/metabolism ; Metagenome ; Phylogeny ; }, abstract = {Different microbial communities are impacted disproportionately by environmental disturbances. The degree to which a community can remain unchanged under a disturbance is referred to as resistance[1]. However, the contributing ecological factors, which infer a community's resistance are unknown. In this study, the impact of historical environmental stability on ecological phenomena and microbial community resistance to shocks was investigated. Three separate methanogenic bioreactor consortia, which were subjected to varying degrees of historical environmental stability, and displayed different levels of resistance to an organic loading rate (OLR) shock were sampled. Their community composition was assessed using high throughput sequencing of 16S rRNA genes and assembly based metagenomics. The effect environmental instability on ecological phenomena such as microbial community assembly, microbial niche breadth and the rare biosphere were assessed in the context of each reactor's demonstrated resistance to an OLR shock. Additionally, metagenome assembled genomes were analysed for functional effects of prolonged stability/instability. The system which was subjected to more environmental instability experienced more temporal variation in community beta diversity and a proliferation of specialists, with more abundant two component regulatory systems. This community was more susceptible to deterministic community assembly and demonstrated a lower degree of resistance, indicating that microbial communities experiencing longer term environmental instability (e.g. variations in pH or temperature) are less able to resist a large disturbance.}, }
@article {pmid39812462, year = {2025}, author = {Kamel, K and Sardo Infirri, S and Riddell, A and Chowdary, P and Batty, P}, title = {Factor VIII Antibodies Demonstrate Type I or Type II Kinetics in Acquired Haemophilia A.}, journal = {Haemophilia : the official journal of the World Federation of Hemophilia}, volume = {31}, number = {2}, pages = {313-318}, pmid = {39812462}, issn = {1365-2516}, mesh = {*Hemophilia A/immunology/blood ; Humans ; *Factor VIII/immunology ; Kinetics ; Male ; Retrospective Studies ; *Autoantibodies/immunology/blood ; Aged ; Middle Aged ; Female ; Adult ; Aged, 80 and over ; }, abstract = {BACKGROUND: Acquired haemophilia A (AHA) is an acquired bleeding disorder resulting from autoantibodies against Factor VIII (FVIII). Previous studies have reported differences in FVIII inhibitor kinetics (type I or type II) in AHA compared to severe haemophilia A.<br><br>AIM: To characterise inhibitor kinetics in AHA and evaluate the proportions displaying type I, II or indeterminate kinetics.<br><br>METHODS: Single-centre retrospective study of inhibitor kinetics in adults with AHA. Type I kinetics were defined as linear FVIII inhibition with &#x2265; 97% FVIII inactivation. Type II kinetics were defined as non-linear kinetics and inability to completely neutralise FVIII. Inhibitor titres were calculated using two methods outlined by the International Council for Standardisation in Haematology.<br><br>RESULTS: Baseline samples from 34 patients were included. Fifteen samples (44.1%) exhibited type I kinetics, 16 samples (47.1%) exhibited type II kinetics and 3 (8.8%) were indeterminate. Plateau mean residual FVIII:C was higher for inhibitors displaying type II compared to type I kinetics (18.6&#xa0;vs. 2.9&#xa0;IU/dL, p < 0.0001). Non-linear regression using a dose-response curve without categorisation for kinetics type yielded a poor fit (R[2] = 38%), which improved with refitting using categories of type I or II kinetics that explained 87% and 85% of the variability. The median difference in inhibitor titre between the two reporting methods was 5% and 15% in the type I and II kinetics groups, respectively.<br><br>CONCLUSION: FVIII autoantibodies demonstrate either type I or type II kinetics. Greater discrepancy in reported inhibitor titres depending on the method used is seen for inhibitors with type II kinetics.}, }
@article {pmid40164558, year = {2025}, author = {Zhou, HY and Zhang, J and Weng, DD}, title = {[One case of recurrent infection with chlamydia psittaci pneumonia].}, journal = {Zhonghua lao dong wei sheng zhi ye bing za zhi = Zhonghua laodong weisheng zhiyebing zazhi = Chinese journal of industrial hygiene and occupational diseases}, volume = {43}, number = {3}, pages = {237-240}, doi = {10.3760/cma.j.cn121094-20240109-00008}, pmid = {40164558}, issn = {1001-9391}, mesh = {Humans ; *Chlamydophila psittaci/isolation &amp; purification ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; Psittacosis/microbiology ; Recurrence ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {This paper analyzed the clinical data of a patient with recurrent infection of chlamydia psittaci pneumonia within 7 months. The patient had a clear history of contact with live poultry, and the clinical manifestations were dry cough, persistent fever, and respiratory failure. Chest CT imaging changes showed lobar consolidation of infected lung lobes, ground-glass shadows, bronchial air-filling signs, and pleural effusion. The two infections were detected in bronchoalveolar lavage fluid by metagenomic next-generation sequencing (mNGS) and pathogen targeted next-generation sequencing (tNGS), respectively, to achieve early diagnosis of chlamydia psittaci pneumonia. New tetracycline drugs were used as the core of treatment for both infections, and rapid improvement was achieved after anti-infection treatment.}, }
@article {pmid40163992, year = {2025}, author = {Lei, H and Zhou, N and Zhang, J and Lin, R and Chen, T and Wu, J and Su, L and Liu, S and Liu, T}, title = {Salinity as a key factor affects viral structure, function, and life strategies in lakes from arid and semi-arid regions.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138075}, doi = {10.1016/j.jhazmat.2025.138075}, pmid = {40163992}, issn = {1873-3336}, abstract = {Salinity impacts lake microorganisms in arid and semiarid zones, affecting climate change. Viruses regulate community structure, facilitate gene transfer, and mediate nutrient cycling. However, studies on the diversity and functional differences of viruses in lakes of varying salinity are limited. Thus, we investigated metagenomic data from 20 lakes in Xinjiang Province, China, to determine viral distribution, virus-host linkage, function, and drivers in lakes of varying salinity. The results showed that salinity shaped the distribution of viral community composition, and Hafunaviridae was the dominant virus in high-salinity lakes. All the metagenome-assembled genomes (MAGs) belonging to Halobacteriota were predicted as hosts, with a lysogenic lifestyle predominating the life strategy, implying their potential protection in salt lakes. Moreover, some auxiliary metabolic genes (AMGs), such as cpeT and PTOX, were related to antioxidant and stress responses, which might help the host survive high salinity stress-induced peroxidation. Notably, the main antibiotic resistance genes (ARGs) carried by viruses, which conferred resistance to polymyxin and trimethoprim, related to the local use of veterinary antibiotics, suggesting that they are potential vehicles for the transmission of ARGs. Overall, these findings suggest that lake systems include unique viral varieties that may influence microbial ecosystems and host metabolism related to environmental adaptability.}, }
@article {pmid40163955, year = {2025}, author = {Du, R and Cui, L and Feng, Y and Lv, X and Gao, Y and Li, A and Wang, Q and Ma, Y}, title = {Enhancing the decomposition and composting of food waste by in situ directional enzymatic hydrolysis: performance, ARGs removal and engineering application.}, journal = {Waste management (New York, N.Y.)}, volume = {200}, number = {}, pages = {114774}, doi = {10.1016/j.wasman.2025.114774}, pmid = {40163955}, issn = {1879-2456}, abstract = {This research utilized food waste (FW) as substrate, innovatively developed a directional multienzyme applied for accelerating FW hydrolysis and composting, and an in situ enzymatic hydrolysis combining in composting has been developed to manage FW. Results showed that the composting was achieved at 4 days and the humification index was increased by 2.60 compared with that of without enzymatic hydrolysis. FTIR analysis revealed that following multienzyme pretreatment, the primary constituents of FW, including protein, starch and lipid, underwent structural breakdown, among which protein exhibited the higher susceptibility to multienzyme action and was the first to disintegrated, and the structure also became looser. Moreover, the total antibiotic resistance gene (ARGs) was reduced more than 90 % in the proposed composting process. Analysis of microbial communities and metagenomes showed that multienzyme pretreatment reshaped microbial communities towards favoring FW hydrolysis and humification. The engineering application analysis further implied that the proposed composting approach is scale flexible, engineering applicable, economic viability and environmentally sustainability. It was anticipated that this study has the potential to trigger a paradigm shift in future in-situ treatment of FW to achieve full resource recovery towards zero solid discharge.}, }
@article {pmid40163458, year = {2025}, author = {Vendrell-Fernández, S and Beamud, B and Abou Haydar, Y and Am de Sousa, J and Burlaud-Gaillard, J and Kornobis, E and Raynal, B and Vinh, J and Bikard, D and Ghigo, JM}, title = {Incomplete lytic cycle of a widespread Bacteroides bacteriophage leads to the formation of defective viral particles.}, journal = {PLoS biology}, volume = {23}, number = {3}, pages = {e3002787}, doi = {10.1371/journal.pbio.3002787}, pmid = {40163458}, issn = {1545-7885}, mesh = {*Bacteriophages/physiology/genetics ; *Virion/ultrastructure ; *Bacteroides/virology/genetics ; *Lysogeny ; Phylogeny ; Retroelements/genetics ; DNA, Viral/genetics ; Genome, Viral ; }, abstract = {Advances in metagenomics have led to the identification of new intestinal temperate bacteriophages. However, their experimental characterization remains challenging due to a limited understanding of their lysogenic-lytic cycle and the common lack of plaque formation in vitro. In this study, we investigated the hankyphage, a widespread transposable phage of prominent Bacteroides symbionts. Hankyphages spontaneously produced virions in laboratory conditions even in the absence of inducer, but virions did not show any evidence of infectivity. To increase virion production and raise the chances of observing infection events, we identified a master repressor of the hankyphage lytic cycle, RepCHP, whose silencing amplified hankyphage gene expression, and enhanced replicative transposition and virion production. However, attempts to infect or lysogenize new host cells with different capsular types remained unsuccessful. Transmission electron microscopy and capsid DNA sequencing revealed an abnormal virion morphology and incomplete DNA packaging of the hankyphage, suggesting that it cannot complete its assembly in laboratory conditions for reasons that are yet to be identified. Still, metavirome and phylogenetic analyses were suggestive of hankyphage horizontal transmission. We could also detect the activity of diversity-generating retroelements (DGRs) that mutagenize the hankyphage tail fiber, and likely contribute to its broad host range. This study sheds light on the life cycle of this abundant intestinal bacteriophage and highlights important gaps in our understanding of the factors required for the completion of its life cycle. Elucidating this puzzle will be critical to gain a better understanding of the hankyphage biology and ecological role.}, }
@article {pmid40163416, year = {2025}, author = {Tordoff, J and Alfonse, LE and Makarova, KS and Ornstein, A and Garrity, AJ and Yan, WX and Scott, DA and Koonin, EV and Cheng, DR}, title = {Initial Characterization of 12 New Subtypes and Variants of Type V CRISPR Systems.}, journal = {The CRISPR journal}, volume = {}, number = {}, pages = {}, doi = {10.1089/crispr.2024.0100}, pmid = {40163416}, issn = {2573-1602}, abstract = {Type V CRISPR systems are highly diverse in sequence, mechanism, and function. Although recent efforts have greatly expanded our understanding of their evolution, the diversity of type V systems remains to be completely explored, and many clades have not been experimentally characterized. In this work, we mined metagenomic databases to identify three new subtypes and nine new variants of Cas12, the effector of Type V systems, and provide experimental and computational characterization of their Protospacer-Adjacent Motif (PAM), interference activity, loci architecture, and tracrRNA dependence. Half of the new Cas12s are found in phages or prophages. New subtypes Cas12o and Cas12p lack the canonical RuvC catalytic residues, suggesting they interfere with the target without cleavage, possibly by blocking transcription or replication. One variant, Cas12f10, displays substantial activity on PAM-less targets. Our work expands the diversity of the functionally characterized Cas12 effectors and provides some promising candidates for genome engineering tools.}, }
@article {pmid40162776, year = {2025}, author = {Haft, DH and Tolstoy, I}, title = {Novel selenoprotein neighborhoods suggest specialized biochemical processes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0141724}, doi = {10.1128/msystems.01417-24}, pmid = {40162776}, issn = {2379-5077}, abstract = {UNLABELLED: Prokaryotic genomes encode selenoproteins sparsely, roughly one protein per 5,000. Finding novel selenoprotein families can expose unknown biological processes that are enabled, or at least enhanced, by having a selenium atom replace a sulfur atom in some cysteine residues. Here, we report the discovery of 18 novel selenoprotein families or second selenocysteine sites in previously unrecognized extensions of protein translations. Most of these families had some confounding factors-too small a family, too few selenoproteins in the family, selenocysteine (U) too close to one end, a skew toward understudied or uncultured lineages, and consequently were missed previously. Discoveries were triggered by observations during the ongoing construction of protein family models for the National Center for Biotechnology Information's RefSeq and Prokaryotic Gene Annotation Pipeline or made by targeted searches for novel selenoproteins in the vicinity of known ones, rather than by any broadly applied genome mining method. Unrelated families TsoA, TsoB, TsoC, and TsoX are adjacent in tso (three selenoprotein operon) loci in the bacterial phylum Thermodesulfobacteriota. TrsS (third radical SAM selenoprotein) occurs strictly in the context of a molybdopterin-dependent aldehyde oxidoreductase. A short carboxy-terminal motif, U-X-X-stop (UXX-star), occurs in selenoproteins with various architectures, usually providing the second U in the protein. The multiple new selenocysteine insertion sites, selenoprotein families, and selenium-dependent operons we curated manually suggest that many more proteins and pathways remain to be discovered; once improved computational methods are applied comprehensively to the latest collections of microbial genomes and metagenomes, they may reveal surprising new biochemical processes.<br><br>IMPORTANCE: Next-generation DNA sequencing and assembly of metagenome-assembled genomes (MAGs) for uncultured species of various microbiomes adds a vast "dark matter" of hard-to-decipher protein sequences. Selenoproteins, optimized by natural selection to encode selenocysteine where cysteine might have been encoded much more easily, carry a strong clue to their function-some specialized aspect of binding or catalysis. Operons with multiple adjacent, but otherwise unrelated, selenoproteins should provide even more vivid information. In this study, efforts in protein family construction and curation, aimed at improving the PGAP genome annotation pipeline, generated multiple novel selenoprotein-containing genomic contexts that may lead to the future characterization of several systems of proteins. Past observations suggest roles in the metabolic handling of trace elements (mercury, tungsten, arsenic, etc.) or of organic compounds refractory to simpler enzymatic pathways. In addition, the work significantly expands the truth set of validated selenoproteins, which should aid future, more automated genome mining efforts.}, }
@article {pmid40162769, year = {2025}, author = {Dickter, JK and Zhao, Y and Parekh, V and Ma, H and Modi, BG and Li, W-Y and Armenian, SH and Wu, X and Abdulla, FR}, title = {Mining metagenomes and metatranscriptomes unveils viruses associated with cutaneous squamous cell carcinoma in hematopoietic stem cell transplant recipients.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0005325}, doi = {10.1128/spectrum.00053-25}, pmid = {40162769}, issn = {2165-0497}, abstract = {UNLABELLED: We investigated the presence of viral DNA and RNA in cutaneous squamous cell carcinoma (cSCC) tumor and normal tissues from nine individuals with a history of hematopoietic stem cell transplantation (HCT). Microbiome quantification through DNA and RNA sequencing (RNA-seq) revealed the presence of 18 viruses in both tumor and normal tissues. DNA sequencing (DNA-seq) identified Torque teno virus, Saimiriine herpesvirus 1, Merkel cell polyomavirus, Human parvovirus B19, Human gammaherpesvirus-4, Human herpesvirus-6, and others. RNA-seq revealed additional viruses such as Tobamovirus, Pinus nigra virus, Orthohepadnavirus, Human papillomavirus-5, Human herpesvirus-7, Human gammaherpesvirus-4, Gammaretrovirus, and others. Notably, DNA-seq indicated that tumor samples exhibited low levels of Escherichia virus in three out of nine subjects and elevated levels of Human gammaherpesvirus-4 in one subject, while normal samples frequently contained Gammaretrovirus and occasionally Escherichia virus. A comparative analysis using both DNA- and RNA-seq captured three common viruses: Abelson murine leukemia virus, Murine type C retrovirus, and Human gammaherpesvirus-4. These findings were corroborated by an independent data set, supporting the reliability of the viral detection methods utilized. The study provides insights into the viral landscape in post-HCT patients, emphasizing the need for comprehensive viral monitoring in this vulnerable population.<br><br>IMPORTANCE: This study is important because it explores the potential role of viruses in the development of cSCC in individuals who have undergone allogeneic HCT. cSCC is common in this population, particularly in those with chronic graft-versus-host disease on long-term immunosuppression. By using advanced metagenomic and metatranscriptomic next-generation sequencing, we aimed to identify viral pathogens present in tumor and adjacent normal tissue. The results could lead to targeted preventive or therapeutic interventions for these high-risk people, potentially improving their outcomes and management of cSCC.}, }
@article {pmid40162572, year = {2025}, author = {Wu, H and Zhang, H and Dong, T and Li, Z and Guo, X and Chen, H and Yao, Y}, title = {Overcoming Extreme Ammonia Inhibition on Methanogenesis by Artificially Constructing a Synergistically Community with Acidogenic Bacteria and Hydrogenotrophic Archaea.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2502743}, doi = {10.1002/advs.202502743}, pmid = {40162572}, issn = {2198-3844}, support = {2024YFD1700500//National Key R&amp;D Program&#xa0;of China/ ; A279021901//Shaanxi Youth Thousand Talents/ ; 2024CY2-GJHX-74//Shaanxi Key R&amp;D Program&#xa0;of China/ ; 2452021112//Chinese Universities Scientific Fund/ ; JCYJ20220530161408019//Shenzhen Natural Science Foundation/ ; 2023KCXTD038//Guangdong Provincial University Innovation Team Project/ ; 2022-K32//Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering/ ; Z111021902//Northwest A&amp;F University Young Talent Project/ ; }, abstract = {High total ammonia nitrogen (TAN) inhibits anaerobic digestion (AD) and cannot be completely eliminated by merely enhancing a stage of AD. This study incorporates TAN-tolerant inoculum into substrates hydrolyzed by Rhizopus mixed agents to simultaneously enhance hydrolysis-acidogenesis-methanogenesis. The results show a 16.46-fold increase in CH4 production under TAN-inhibited (6870.97 mg L-1) conditions, even exceeding the AD without TAN by 21.10%. Model substrates sodium acetate and mixed H2 confirm hydrogenotrophic methanogenesis is the main pathway, with reduced TAN inhibition. Furthermore, a synergistic metabolic microbial community dominated by hydrolytic bacteria JAAYGG01 sp. and DTU014 sp., acidogenic bacteria DTU015 sp., DTU013 sp., and JAAYLO01 sp., and methanogens Methanosarcina mazei and an unclassified species in the Methanoculleus is reconstructed to resist TAN inhibition. Metagenomic combined with metatranscriptomic sequencing identifies that this microbial community carries xynD and bglB to regulate substrate hydrolysis, leading to acetate production through glycolysis, butyrate, and pyruvate metabolism with high acetate kinase activity, thereby CH4 produced primarily via hydrogenotrophic methanogenesis with high coenzyme F420 activity, facilitated by efficient mass transfer processes and quorum sensing regulation. This cleaner strategy obtains higher economic benefit (US$149.02) than conventional AD and can increase 154.64-fold energy production of a 24 000 m3 biogas plant, guided by machine learning.}, }
@article {pmid40162034, year = {2025}, author = {Huang, L and Zheng, D and Li, T and Li, X and Kong, J and Wang, K and Wang, S and Cao, C}, title = {Disseminated Histoplasmosis Due to Anti-IFN-γ Autoantibodies-Associated Immunodeficiency.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1605-1609}, doi = {10.2147/IDR.S513750}, pmid = {40162034}, issn = {1178-6973}, abstract = {BACKGROUND: Disseminated histoplasmosis caused by the temperature-dependent dimorphic fungus Histoplasma capsulatum is an invasive fungal disease rarely reported in southern China. Here, we report a case of disseminated histoplasmosis due to anti-IFN-γ autoantibodies (AIGA)- associated immunodeficiency.<br><br>CASE PRESENTATION: We present the case of a 57-year-old HIV-negative female patient with disseminated histoplasmosis in southern China. The patient showed progressively enlarging multiple clavicular, neck, and upper chest skin nodules and dyspnea, which led to the initial suspicion of pulmonary tuberculosis or lung cancer. Bacterial cultures results were negative. Histopathology of a skin tissue showed infectious granulomas. Disseminated histoplasmosis was diagnosed via next-generation sequencing (mNGS) and fungal culture. Furthermore, enzyme-linked immunosorbent assay results from a peripheral blood confirmed that the patient had a high-titer of AIGA.<br><br>CONCLUSION: This case prompts clinicians to consider histoplasmosis an important differential diagnosis in a region where talaromycosis is highly endemic. This case report emphasizes that clinicians should be vigilant for immunodeficiency and consider testing for AIGA in HIV-negative patients who are suspected of having complex opportunistic infections.}, }
@article {pmid40161798, year = {2025}, author = {Zeamer, AL and Lai, Y and Sanborn, V and Loew, E and Tracy, M and Jo, C and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP}, title = {Microbiome functional gene pathways predict cognitive performance in older adults with Alzheimer's disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.06.641911}, pmid = {40161798}, issn = {2692-8205}, abstract = {Disturbances in the gut microbiome is increasing correlated with neurodegenerative disorders, including Alzheimer's Disease. The microbiome may in fact influence disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby driving disease pathology along the "microbiota-gut-brain-axis". Currently, drivers of cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (age 60+) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiomes. Subjects were classified as healthy controls or as having mild cognitive impairment based on cognitive performance. Those with a diagnosis of Alzheimer's Diseases with confirmed using serum biomarkers. Using metagenomic sequencing, we found that relative species abundances correlated well with cognition status (MCI or AD). Furthermore, gene pathways analyses suggest certain microbial metabolic pathways to either be correlated with cognitive decline or maintaining cognitive function. Specifically, genes involved in the urea cycle or production of methionine and cysteine predicted worse cognitive performance. Our study suggests that gut microbiome composition may predict AD cognitive performance.}, }
@article {pmid40161742, year = {2025}, author = {Wong, MK and Armstrong, E and Heirali, AA and Schneeberger, PHH and Chen, H and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B}, title = {Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.11.642547}, pmid = {40161742}, issn = {2692-8205}, abstract = {UNLABELLED: Composition and function of the gut microbiome is associated with diverse health conditions and treatment responses. Human microbiota-associated (HMA) mouse models are used to establish causal links for these associations but have important limitations. We assessed the fidelity of HMA mouse models to recapitulate ecological responses to a microbial consortium using stools collected from a human clinical trial. HMA mice were generated using different routes of consortium exposure and their ecological features were compared to human donors by metagenomic sequencing. HMA mice were more similar in gut composition to other mice than their respective human donors, with taxa including Akkermansia muciniphila and Bacteroides species enriched in mouse recipients. A limited repertoire of microbes was able to engraft into HMA mice regardless of route of consortium exposure. In publicly available HMA mouse datasets from four distinct health conditions, we confirmed our observation that a taxonomically restricted set of microbes reproducibly engrafts in HMA mice and observed that stool microbiome composition of HMA mice were more like other mice than their human donor. Our data suggest that HMA mice are limited models to assess the ecological impact of microbial consortia, with ecological effects in HMA mice being more strongly associated with host species than donor stool ecology or ecological responses to treatment in humans. Comparisons to published studies suggest this may be due to comparatively large host-species effects that overwhelm ecological effects of treatment in humans that HMA models aim to recapitulate.<br><br>IMPORTANCE: Human microbiota-associated (HMA) mice are models that better represent human gut ecology compared to conventional laboratory mice and are commonly used to test the effect of the gut microbiome on disease or treatment response. We evaluated the fidelity of using HMA mice as avatars of ecological response to a human microbial consortium, MET4. Our results show that HMA mice in our cohort and across other published studies are more similar to each other than the human donors or inoculum they are derived from and harbour a taxonomically restricted gut microbiome. These findings highlight the limitations of HMA mice in evaluating the ecological effects of complex human microbiome-targeting interventions, such as microbial consortia.}, }
@article {pmid40161675, year = {2025}, author = {Secaira-Morocho, H and Jiang, X and Zhu, Q}, title = {Augmenting microbial phylogenomic signal with tailored marker gene sets.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.13.643052}, pmid = {40161675}, issn = {2692-8205}, abstract = {Phylogenetic marker genes are traditionally selected from a fixed collection of whole genomes evenly distributed across major microbial phyla, covering only a small fraction of gene families. And yet, most microbial diversity is found in metagenome-assembled genomes that are unevenly distributed and harbor gene families that do not fit the criteria of universal orthologous genes. To address these limitations, we systematically evaluate the phylogenetic signal of gene families annotated from KEGG and EggNOG functional databases for deep microbial phylogenomics. We show that markers selected from an expanded pool of gene families and tailored to the input genomes improve the accuracy of phylogenetic trees across simulated and real-world datasets of whole genomes and metagenome-assembled genomes. The improved accuracy of trees compared to previous markers persists even when metagenome-assembled genomes lack a fraction of open reading frames. The selected markers have functional annotations related to metabolism, cellular processes, and environmental information processing, in addition to replication, translation, and transcription. We introduce TMarSel, a software tool for automated, systematic, free-from-expert opinion, and tailored marker selection that provides flexibility in the number of markers and annotation databases while remaining robust against uneven taxon sampling and incomplete genomic data.}, }
@article {pmid40161639, year = {2025}, author = {Williams, A and Ravel, J and Kaul, R and Armstrong, E and Huibner, S and Holm, JB}, title = {Temporal Dynamics of the Vaginal Microbiome and Host Immune Markers Before, During, and After Metronidazole Treatment for Bacterial Vaginosis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.13.643085}, pmid = {40161639}, issn = {2692-8205}, abstract = {UNLABELLED: This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment, variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.<br><br>IMPORTANCE: Bacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections among others, is characterized by a dysbiotic vaginal microbiome associated with dominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at initiation of treatment as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during and after metronidazole treatment.}, }
@article {pmid40160274, year = {2025}, author = {Naushad, S and Gao, R and Duceppe, MO and Dupras, AA and Reiling, SJ and Merks, H and Dixon, B and Ogunremi, D}, title = {Metagenomic detection of protozoan parasites on leafy greens aided by a rapid and efficient DNA extraction protocol.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1566579}, doi = {10.3389/fmicb.2025.1566579}, pmid = {40160274}, issn = {1664-302X}, abstract = {INTRODUCTION: Infections with protozoan parasites associated with the consumption of fresh produce is an on-going issue in developed countries but mitigating the risk is hampered by the lack of adequate methods for their detection and identification.<br><br>MATERIALS AND METHODS: We developed a metagenomic next-generation sequencing (mNGS) assay using a MinION sequencer for the identification of parasites in intentionally contaminated lettuce to achieve a more accurate and rapid method than the traditional molecular and microscopy methods commonly used for regulatory purposes. Lettuce (25 g) was spiked with varying numbers of Cryptosporidium parvum oocysts, and microbes washed from the surface of the lettuce were lysed using the OmniLyse device. DNA was then extracted by acetate precipitation, followed by whole genome amplification. The amplified DNA was sequenced by nanopore technology and validated with the Ion Gene Studio S5, and the generated fastq files raw reads were uploaded to the CosmosID webserver for the bioinformatic identification of microbes in the metagenome. To demonstrate the ability of the procedure to distinguish other common food and waterborne protozoan parasites, lettuce was also spiked with C. hominis, C. muris, Giardia duodenalis and Toxoplasma gondii individually or together.<br><br>RESULTS: The efficient lysis of oocysts and cysts was a prerequisite for the sensitive detection of parasite DNA and was rapidly achieved within 3 min. Amplification of extracted DNA led to the generation of 0.16-8.25 &#x3bc;g of DNA (median = 4.10 &#x3bc;g), sufficient to perform mNGS. Nanopore sequencing followed by bioinformatic analysis led to the consistent identification of as few as 100 oocysts of C. parvum in 25 g of fresh lettuce. Similar results were obtained using the Ion S5 sequencing platform. The assay proved useful for the simultaneous detection of C. parvum, C. hominis, C. muris, G. duodenalis and T. gondii.<br><br>DISCUSSION: Our metagenomic procedure led to the identification of C. parvum present on lettuce at low numbers and successfully identified and differentiated other protozoa either of the same genus or of different genera. This novel mNGS assay has the potential for application as a single universal test for the detection of foodborne parasites, and the subtyping of parasites for foodborne outbreak investigations and surveillance studies.}, }
@article {pmid40160273, year = {2025}, author = {Liu, Y and Ying, Y and Li, Y and Zhang, W and Shu, J}, title = {Symbiotic bacteria associated with different species of Curculio (Coleoptera: Curculionidae) and their host plants.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1531847}, doi = {10.3389/fmicb.2025.1531847}, pmid = {40160273}, issn = {1664-302X}, abstract = {Bacteria often play important roles in the host adaptation of phytophagous insects. Beetles of the genus Curculio (Coleoptera: Curculionidae) include pest species that bore into the seeds of trees in the family Fagaceae and damage the cotyledons. At present, there are few studies of the taxonomic diversity and functional effects of symbiotic bacteria involved in changes in host ranges and host adaptation of Curculio. Here, we used 16S rRNA gene Illumina and metagenomic sequencing to compare the composition and functions of the bacterial communities of three species of host plants and several Curculio species combinations: Curculio bimaculatus feeding on Castanopsis sclerophylla, C. bimaculatus feeding on Castanopsis tibetana, and Curculio davidi feeding on Ca. tibetana. The host plants influenced the diversity of symbiotic bacteria, while the Curculio species influenced the community structure of the symbiotic bacteria. Functional predictions showed that symbiotic bacteria contributed to the metabolism of the hosts. However, consistent with the variation in bacteria, the major metabolism-related bacterial genera varied among the treatment groups. Comparisons of metabolic enzymes based on KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation revealed differences in the enzymes involved in insect development and detoxification of plant secondary compounds among the three groups, and the patterns were influenced by the dominance of the Curculio species on the host plants. This study provides valuable insights into the possible role of symbiotic bacteria in Curculio as host insects.}, }
@article {pmid40160271, year = {2025}, author = {Yang, B and Feng, C and Jiang, H and Chen, Y and Ding, M and Dai, H and Zhai, Z and Yang, M and Liang, T and Zhang, Y}, title = {Effects of long-term continuous cropping on microbial community structure and function in tobacco rhizosphere soil.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1496385}, doi = {10.3389/fmicb.2025.1496385}, pmid = {40160271}, issn = {1664-302X}, abstract = {As is well known, continuous cropping can lead to a decrease in crop yield and quality. Despite this, continuous cropping remains prevalent in practical agricultural production, particularly in the case of tobacco cultivation, owing to its high economic value. The samples for this study were collected from a flue-cured tobacco planting base located in Huili County, Liangshan Yi Autonomous Prefecture, Sichuan Province, China. After years of continuous planting, the yield of tobacco in this base has significantly decreased. In order to explain the microecological causes of this phenomenon, we collected non-continuous cropping, continuous cropping for 5 years, and continuous cropping for 10 years of tobacco rhizosphere soil, and analyzed the effects of long-term continuous cropping on nutrients, enzyme activities, microbial community structure, and function of tobacco rhizosphere soil. The results showed that with the continuous cropping, the majority nutrients (except for phosphorus and manganese) in rhizosphere soil decreased significantly, and the rhizosphere microbial community structure changed significantly. Correlation network analysis results showed that changes in the rhizosphere microbial community of tobacco were closely related to soil urease, active organic carbon, and available iron content. The results of functional analysis based on microorganisms and genes showed that the rhizosphere microbiota may change the content of soil nutrients through iron_respiration, sulfur_respiration, and Carbon fixation in prokaryotes pathways. The results of the correlation network analysis and the functional analysis mutually confirmed each other, both emphasizing the important role of soil carbon and iron in shaping the structure of the tobacco rhizosphere microbial community. Based on the results of this study, we propose to improve the microbial community structure of tobacco rhizosphere soil by increasing the levels of readily oxidizable organic carbon, available iron, and soil urease activity in the future, so as to alleviate the negative impact of continuous cropping on crop yield. The results of this study provide theoretical support for modifying the rhizosphere microbial environment through nutrient regulation, thereby enhancing plant growth in the context of continuous tobacco cropping.}, }
@article {pmid40160267, year = {2025}, author = {Kragh, ML and Scheel, NH and Leekitcharoenphon, P and Truelstrup Hansen, L}, title = {Repeated biocide treatments cause changes to the microbiome of a food industry floor drain biofilm model.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1542193}, doi = {10.3389/fmicb.2025.1542193}, pmid = {40160267}, issn = {1664-302X}, abstract = {There is a concern about the development of microbial tolerance and resistance to biocides due to their repeated use within the food industry. This study aimed to develop a floor drain biofilm model and test whether repeated biocide treatment would result in increased tolerance to biocides. Culturomics and shotgun metagenomic analysis of 14 drains and 214 bacterial isolates from three industrial food production environments revealed microbiomes with great diversity and complexity, but with the dominance of a few highly abundant taxa, including Pseudomonas. A representative drain biofilm was created (3 days, 15°C) using 31 whole genome sequenced bacterial isolates from 24 genera. The biofilm model represented 47-58% and 76-81% of the microbial abundance observed in the metagenome and viable microbiota, respectively. The biofilm model was exposed on days 3 and 6 to water or different industrial concentrations of benzalkonium chloride (BC), peracetic acid (PAA), or sodium hypochlorite (SH). Analysis of the viable survivors using MALDI-TOF MS and the regrowing biofilms using 16S rRNA amplicon sequencing showed how the diversity of the biofilm decreased but without any change in biocide tolerance as seen in log reductions (CFU/cm[2]). The use of different biocides did, however, exert significantly different selective pressures on the microbiomes as Citrobacter, Acinetobacter, Aeromonas, and Pseudomonas dominated the biofilm after treatments with SH or PAA, while Serratia and Moraxella dominated after treatments with BC. The dominance of Serratia marcescens could be explained by the carriage of a BC efflux pump (oqxB) and the highest (20 mg/L BC) minimum inhibitory concentration (MIC) result of the drain isolates. In contrast, despite carrying a BC efflux pump (qacH), Listeria monocytogenes ST121 did not show increased survival or presence in the biofilm after BC treatments. Only the highest tested concentration of PAA was able to completely eradicate L. monocytogenes. The developed biofilm model and the repeated biocide treatments enabled a better understanding of how biocides affect the biofilm microbiome. Future research should involve testing biocide rotation strategies to control biofilm regrowth and inactivation of persistent foodborne pathogens in floor drains.}, }
@article {pmid40159059, year = {2025}, author = {Shang, SY and Li, XP and Xu, J and Li, Y and Cao, LQ and Ye, H}, title = {[A case of acute pseudomembranous necrotizing tracheobronchitis in an adult].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {48}, number = {4}, pages = {385-388}, doi = {10.3760/cma.j.cn112147-20240828-00510}, pmid = {40159059}, issn = {1001-0939}, mesh = {Humans ; *Tracheitis/diagnosis/microbiology ; *Bronchitis/microbiology/diagnosis ; *Staphylococcal Infections/diagnosis ; Male ; Staphylococcus aureus/isolation &amp; purification ; Bronchoscopy ; Influenza B virus/isolation &amp; purification ; Adult ; Necrosis ; Influenza, Human/complications ; Middle Aged ; Linezolid/therapeutic use ; }, abstract = {This study presented a rare case of secondary Staphylococcus aureus (S. aureus) infection following influenza B virus infection, resulting in diffuse airway injury and hemorrhagic pneumonia. The patient initially underwent bronchial artery embolization (BAE) due to persistent hemoptysis refractory to conventional hemostatic therapy. Although the hemoptysis was resolved postoperatively, severe hypoxemia persisted. Bronchoscopy revealed diffuse yellow plaques with mucosal erosion and necrosis in the airways. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified S. aureus harboring the Panton-Valentine leukocidin (PVL) genes. Histopathological examination revealed severe acute inflammatory changes consistent with necrotizing airway pathology. A diagnosis of IBV-associated S. aureus infection leading to acute pseudomembranous necrotizing tracheobronchitis and hemorrhagic pneumonia was made. The patient responded favorably to linezolid therapy. Follow-up bronchoscopy revealed multiple granulation tissues in the airways, which were subsequently removed under endoscopic guidance. After ruling out persistent infection, the patient was treated with low-dose oral prednisone, which resulted in significant clinical improvement.}, }
@article {pmid40158829, year = {2025}, author = {Liu, Y and Zhang, Q and Lu, L and Qian, Y and Wu, Y and Hu, D and Xu, Y and Xu, H and Ji, G}, title = {Huang-qin Decoction alleviates Deoxycholic Acid-induced Colorectal Cancer in Mice by Regulating Gut Microbiota.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {119715}, doi = {10.1016/j.jep.2025.119715}, pmid = {40158829}, issn = {1872-7573}, abstract = {Huangqin Decoction (HQD), a traditional Chinese medicine (TCM) formula documented in Shang Han Lun, has demonstrated safety and efficacy in the treatment of ulcerative colitis (UC). Recent studies also suggest that HQD exerts therapeutic effects on colorectal cancer (CRC). However, the underlying mechanisms remain unclear.<br><br>AIMS OF THE STUDY: This study aimed to investigate the therapeutic effects of HQD on CRC and explore its potential mechanisms of action.<br><br>METHODS: The active ingredients and potential targets of HQD were identified through network pharmacology-based analyses. The CRC-related targets were compared with those of HQD. Shared targets were subjected to Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and a protein-protein interaction (PPI) network was constructed. Additionally, APC[min/+] mice were treated with 0.2% deoxycholic acid (DCA) and gavaged with low or high doses of HQD. Tumor morphology was assessed using hematoxylin and eosin (HE) staining. Immunohistochemical staining was performed to evaluate the expression of Ki-67, Caspase-3, and MUC2 in the intestine. Periodic acid-Schiff (PAS) and PAS-alcian blue (PAS-AB) staining were utilized to detect mucin distribution and the number of goblet cells in the intestines of the mice. The mRNA expression levels of interleukin 6 (IL-6), mitogen-activated protein kinase 8 (MAPK8), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), albumin (ALB), and Caspase 3 (CASP3) were quantified using quantitative reverse-transcription PCR (qRT-PCR). Immunofluorescence was employed to assess the degree of apoptosis. Additionally, 16S ribosomal RNA gene sequencing, sequence curation and annotation, and metagenomic sequencing were performed to analyze changes in the composition of the mouse intestinal microbiota and related functions and signaling pathways.<br><br>RESULTS: The active ingredients of HQD were identified. GO and KEGG pathway enrichment analyses indicated that the shared targets were primarily involved in tumor suppression. HQD effectively treated DCA-induced CRC in mice. Furthermore, positive PAS and PAS-AB staining was significantly increased in the intestines of mice treated with HQD. HQD enhanced the abundance of Lachnospiraceae, Firmicutes, Fusobacteria, and Clostridium, while reducing the abundance of Eggerthellales. Additionally, HQD modulated secondary bile acid metabolism, carbohydrate synthesis, and other energy metabolism pathways, which may underlie its therapeutic effects.<br><br>CONCLUSION: HQD effectively treated CRC in mice, and its mechanisms of action may be related to the regulation of the gut microbiota.}, }
@article {pmid40158299, year = {2025}, author = {Borkakoti, N and Ribeiro, AJM and Thornton, JM}, title = {A structural perspective on enzymes and their catalytic mechanisms.}, journal = {Current opinion in structural biology}, volume = {92}, number = {}, pages = {103040}, doi = {10.1016/j.sbi.2025.103040}, pmid = {40158299}, issn = {1879-033X}, abstract = {In this perspective, we analyse the progress made in our knowledge of enzyme sequences, structures and functions in the last 2 years. We review how much new enzyme data have been garnered and annotated, derived from the study of proteins using structural and computational approaches. Recent advances towards capturing 'Catalysis in silico' are described, including knowledge and predictions of enzyme structures, their interactions and mechanisms. We highlight the flood of enzyme data, driven by metagenomic sequencing, the improved enzyme data resources, the high coverage in Protein Data Bank of E.C. classes and the AI-driven structure prediction techniques that facilitate the accurate prediction of protein structures. We note the focus on disordered regions in the context of enzyme regulation and specificity and comment on emerging bioinformatic approaches that capture reaction mechanisms computationally for comparing and predicting enzyme mechanisms. We also consider the drivers of progress in this field in the next five years.}, }
@article {pmid40158160, year = {2025}, author = {Zhu, M and Wang, Q and Yang, Y and Liu, X and Zhang, J and Li, G and Liu, W and Xiang, X and Chen, J}, title = {Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.}, journal = {Nutrition journal}, volume = {24}, number = {1}, pages = {50}, pmid = {40158160}, issn = {1475-2891}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Child ; Male ; Cross-Sectional Studies ; *Metabolome/physiology ; Female ; Child, Preschool ; *Feces/microbiology ; China ; *Diet/methods ; Metabolomics/methods ; Nutritional Status ; Multiomics ; }, abstract = {The gut microbiome can modulate nutrient metabolism to produce many metabolites interacting with the host. However, the intricate interactions among dietary intake, the gut microbiome and metabolites, and host metabolites need to be further explored although some studies have been devoted to it. Here, in a cross-sectional studies, 88 children aged 2-12 years were enrolled from northwestern China. The dietary intake data were collected via a designed food frequency questionnaire to calculate plant-based diet indices (PDIs). Stool and plasma samples were collected for metagenomic and broad-targeted metabolomic analysis. Spearman's rank correlation was used to describe the associations between nutrients/PDIs and the gut microbiota and metabolites. PDI was significantly positively associated with Bilophila wadsworthia, Bacteroides thetaiotaomicron, and Alistipes indistinctus, etc., but was obviously negatively correlated with Roseburia intestinalis, Faecalibacterium prausnitzii, etc. However, these species showed no significant associations with either healthy PDI (hPDI) or unhealthy PDI (uPDI). Interestingly, hPDI was significantly positively related to species, including Ruminococcus bicirculans, and was significantly negatively associated with uPDI, and vice versa. The above correlation trends were also observed between PDIs and predicted gut microbial functional pathways, microbial metabolites and the host metabolome. Notably, the significantly related pathways were focused mainly on substances and energy metabolism. PDI was significantly positively associated with the fecal contents of P-aminobenzoate, chenodeoxycholic acid, 4,6-dihydroxyquinoline, quinoline-4,8-diol, etc., but was significantly negatively associated with those of TMAO, FFA, creatine phosphate, etc. In plasma, PDI was significantly positively associated with sarcosine, ornithine, L-histidine, etc., but was distinctly negatively correlated with FFAs, carnitine C2:0, etc. Strikingly, the healthy plant-based diet index (hPDI) is correlated with increased levels of metabolites related to tryptophan metabolism, whereas the unhealthy PDI (uPDI) is linked to increased levels of metabolites associated with tyrosine and sphingolipid metabolism, which are pathways commonly associated with Western diets. Our studies provide reliable data support and a comprehensive understanding of the effects of dietary intake on the gut microbiome and microbial and host metabolites and lay a foundation for further studies of the diet-gut microbiota-microbial metabolites and host metabolism.}, }
@article {pmid40158141, year = {2025}, author = {Jiang, Y and Aton, M and Zhu, Q and Lu, YY}, title = {Modeling microbiome-trait associations with taxonomy-adaptive neural networks.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {87}, pmid = {40158141}, issn = {2049-2618}, support = {RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; }, mesh = {Humans ; *Neural Networks, Computer ; *Microbiota ; Metagenomics/methods ; Bacteria/classification/genetics ; Computer Simulation ; }, abstract = {The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun metagenomic sequencing technologies have produced vast amounts of microbiome data, analyzing such data is highly challenging due to its sparsity, noisiness, and high feature dimensionality. Here, we develop MIOSTONE, an accurate and interpretable neural network model for microbiome-disease association that simulates a real taxonomy by encoding the relationships among microbial features. The taxonomy-encoding architecture provides a natural bridge from variations in microbial taxa abundance to variations in traits, encompassing increasingly coarse scales from species to domains. MIOSTONE has the ability to determine whether taxa within the corresponding taxonomic group provide a better explanation in a data-driven manner. MIOSTONE serves as an effective predictive model, as it not only accurately predicts microbiome-trait associations across extensive simulated and real datasets but also offers interpretability for scientific discovery. Both attributes are crucial for facilitating in silico investigations into the biological mechanisms underlying such associations among microbial taxa. Video Abstract.}, }
@article {pmid40157594, year = {2025}, author = {Wang, C and Fan, S and Li, M and Ye, Y and Li, Z and Long, W and Li, Y and Huang, Z and Jiang, Q and Yang, W and Yang, R and Tang, D}, title = {A 7-year feed study on the long-term effects of genetically modified maize containing cry1Ab/cry2Aj and EPSPS genes on gut microbiota and metabolite profiles across two generations of cynomolgus macaques.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {}, number = {}, pages = {115419}, doi = {10.1016/j.fct.2025.115419}, pmid = {40157594}, issn = {1873-6351}, abstract = {The health implications of genetically modified (GM) crops remain controversial relative to their non-GM counterparts, particularly regarding long-term dietary exposure. Although the gut microbiome is a key health indicator, studies investigating the impact of GM crop consumption on intestinal microbiota remain limited. This study presents a comprehensive 7-year evaluation of GM maize expressing cry1Ab/cry2Aj and G10evo-EPSPS proteins through metagenomic and metabolomic analyses. We assessed the effects of GM maize consumption on gut microbiota diversity and metabolite profiles in cynomolgus macaques (Macaca fascicularis) compared with non-GM maize. Three diet regimens were implemented: a conventional compound feed (CK group), diet formulation containing 70% non-GM maize (Corn group), and diet formulation containing 70% GM maize (Tg group). The results demonstrated that feeding GM maize to the first (F0) and second (F1) generations of monkeys did not substantially affect the composition, community structure, or function of the intestinal microbiome, as indicated by species composition and diversity analyses. Minor differences in intestinal metabolites were observed but were not directly linked to transgenic maize consumption. Collectively, long-term intake of maize with cry1Ab/cry2Aj and g10evo-epsps genes had no adverse effects on macaques or their offspring.}, }
@article {pmid40157532, year = {2025}, author = {Pienaar, RD and Herrero, S and Cerqueira de Araujo, A and Krupa, F and Abd-Alla, AMM and Herniou, EA}, title = {High-throughput screening reveals high diversity and widespread distribution of viruses in black soldier flies (Hermetia illucens).}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108322}, doi = {10.1016/j.jip.2025.108322}, pmid = {40157532}, issn = {1096-0805}, abstract = {Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (Hermetia illucens, BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. A high-throughput pipeline allowed the simultaneous investigation of 203 next generation sequencing datasets. This revealed the presence of seven viruses belonging to the families Dicistroviridae, Iflaviridae, Rhabdoviridae, Solinviviridae, Inseviridae, Lebotiviridae, and an unclassified Bunyavirales. Here we describe five viruses, which were detected in BSF from multiple origins, outlining the diversity of naturally occurring viruses associated with BSF colonies. As this viral community may also include BSF pathogens, we developed molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.}, }
@article {pmid40157487, year = {2025}, author = {Li, J and Zhu, L and Li, X and Han, X and Yi, J and Wu, Y and Wang, M}, title = {Characterization and Risk-quantification of Antibiotic Resistome in Grain-based and Non-grain Cropping Soils.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126147}, doi = {10.1016/j.envpol.2025.126147}, pmid = {40157487}, issn = {1873-6424}, abstract = {Microbial contamination in soils, encompassing human bacterial pathogens (HBPs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs), poses a significant threat to human health via the food chain. Currently, there is a lack of comprehensive assessments of microbial contamination and associated health risks of ARGs in agricultural soils. In this study, metagenomic sequencing was used to evaluate microbial contamination in grain-based cropping soils (rice cultivation) and non-grain cropping soils (vegetable cultivation and aquaculture). The results showed that the diversity and abundance of HBPs and VFGs were significantly higher in non-grain soils. Further resistome analysis revealed higher abundances of high-risk (from 0.014 to 0.018 - 0.023) and "last-resort" ARGs (from 0.007 to 0.034 - 0.046) in non-grain soils. Besides ARGs abundance, health risk quantification revealed that non-grain soils exhibited 1.49 to 2.14-fold greater ARG-related risks than grain-based soils. Additionally, stronger network associations were found between HBPs, ARGs, and mobile genetic elements (MGEs) in non-grain soils. This study indicated that the non-grain cropping pattern of soils elevated the risk of microbial contamination and ARGs health risk, which provided an important basis for accurately quantifying the risk of microbial contamination in different agricultural soils.}, }
@article {pmid40157184, year = {2025}, author = {Qiao, X and Kong, X and Zhou, H and Fan, X and Yuan, J and Zhang, Y}, title = {Deciphering the inhibitory mechanisms of polystyrene microplastics on thermophilic methanogens from the insights of microbial metabolite profiling and metagenomic analyses.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138054}, doi = {10.1016/j.jhazmat.2025.138054}, pmid = {40157184}, issn = {1873-3336}, abstract = {Due to the utilization of food packaging bags, a substantial amount of polystyrene microplastics (PS MPs) are introduced into the food waste (FW) treatment system during the pre-treatment process, potentially impacting the subsequent biochemical treatment system. In order to investigate the mechanism by which PS MPs affect anaerobic methanogenesis metabolism in thermophilic condition, this study analyzed the characteristics of methanogenesis in thermophilic anaerobic digestion (AD) of FW under different concentrations of PS MPs (100 μm, 10-200 mg/L). The results revealed a negative correlation between PS MPs concentration and methane (CH4) yield from FW. When the concentration of PS MPs reached 200 mg/L, CH4 yield decreased by 47.8 %. Further mechanistic investigations revealed that while the presence of PS MPs at lower concentrations could alleviate its adverse impact on methanogenesis by enhancing EPS content, the accumulation of reactive oxygen species (ROS) persisted with increasing PS MPs concentration, thereby inhibiting the activities of key enzymes involved in solubilization and acidification metabolisms (e.g., acetate kinase and F420). Metagenomics analysis indicated that the presence of PS MPs down-regulate abundance of genes for quorum sensing and CH4 metabolism pathways. These findings not only unveil potential detrimental effects of PS MPs on AD systems but also provide novel insights into comprehending and controlling the impact of MPs pollution on environmental preservation and energy recovery processes.}, }
@article {pmid40157173, year = {2025}, author = {Weiting, S and Chen, W and Xiao, L and Yanqiu, H}, title = {Enhanced acid reduction in lactic acid bacteria: Breeding through irradiation-induced mutation and functional assessment.}, journal = {International journal of food microbiology}, volume = {435}, number = {}, pages = {111161}, doi = {10.1016/j.ijfoodmicro.2025.111161}, pmid = {40157173}, issn = {1879-3460}, abstract = {High concentrations of citric acid (CA), malic acid (MA), and tartaric acids (TA) are the primary contributors to the sour taste of fruit and fruit products. However, lactic acid bacteria that are capable of efficiently degrading these organic acids are scarce. Here, three brands of sauerkraut (Xinxi, X; Yuyuan, Y; and Zou Youcai, Z) with various doses of [60]Co γ-irradiation could be treated to induce mutations in their associated lactic acid bacteria and then the abilities of the resulting microbial communities to degrade CA, MA, and TA were evaluated. Sauerkraut X treated with 0.4 kGy irradiation demonstrated the greatest ability of acid reduction. Metagenomic analyses of irradiated (0.4 kGy) and non-irradiated bacterial communities from sauerkraut X revealed a slight decrease in microbial diversity due to irradiation, with a substantial decline in the relative abundance of Lactiplantibacillus xiangfangensis. Concurrently, the relative abundance of dominant acid-reducing lactic acid bacteria such as Levilactobacillus brevis, Pediococcus ethanolidurans, and Lentilactobacillus parafarraginis increased. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed an increase in metabolism-related genes after irradiation, indicating that fatty acid synthesis and aspartate metabolism might be key pathways involved in the enhanced degradation of CA, MA, and TA. Analysis using the Carbohydrate-Active enzymes Database (CAZy) database revealed that glycoside hydrolase (GH) and glycosyltransferase (GT) genes were the most abundant carbohydrate-associated enzyme genes in the bacterial community of sauerkraut X. This finding proved that the oligosaccharides and monosaccharides produced by GH and GT might indirectly affect rates of organic acid degradation. Three highly effective acid-reducing lactic acid bacteria from the microbial community of irradiated sauerkraut X a were isolated and identified via 16S rRNA sequencing as Pediococcus ethanolidurans, Levilactobacillus brevis, and Loigolactobacillus coryniformis. The individual strains showed degradation rates as high as 92.02 % for citric acid (Pediococcus ethanolidurans), 83.04 % for malic acid (Levilactobacillus brevis), and 90.33 % for TA (Loigolactobacillus coryniformis). This study provides a theoretical basis and technical support for the development of enhanced microbial strains that can reduce the acid content of fruit materials.}, }
@article {pmid40156973, year = {2025}, author = {Zhong, S and Li, B and Chen, Q and Zhang, J and Cai, H and An, R and Liu, G and Zhou, S}, title = {Identifying groundwater anthropogenic disturbances and their predominant impact on microbial nitrogen cycling at a former contamination site adjacent to Baiyangdian Lake.}, journal = {Water research}, volume = {280}, number = {}, pages = {123544}, doi = {10.1016/j.watres.2025.123544}, pmid = {40156973}, issn = {1879-2448}, abstract = {Groundwater ecosystems face increasing threat from declining water quality due to intensified urbanization, agricultural, and industrial activities. Accurately identifying anthropogenic disturbances remains challenging, and their effects on microbial nitrogen cycling are still largely unknown. Here, by collecting 64 groundwater samples from an aquifer beneath the Tanghe sewage reservoir in the North China Plain, we conducted a full-spectrum screening of 228 physiochemical indices, 47 nitrogen cycling genes (NCGs) and 2182 metagenome-assembled genomes (MAGs) harboring NCGs. Unmix model identified antibiotic usage, industrial manufacturing, and agricultural practices as the predominant pollution sources, explaining 49.6-92.2 % (averaged 81.0 %) of the variations in aquifer attributes. These activities were primary drivers governing distributions of groundwater NCGs and NCG-hosts, with fragmented denitrification processes being prevalent. Antibiotic usage and industrial activities were probably associated with suppressed nitrogen cycling, while agriculture had a positive effect. Notably, we observed enhanced mutualistic interactions within NCG-hosts and increased enrichment of NCG-antibiotic resistance gene (ARG), NCG-mental resistance gene (MRG), and NCG-ARG-MRG co-hosts under high anthropogenic stresses, suggesting microbial adaptation to optimize nutrient and energy metabolism. This study provided new insight into how groundwater nitrogen cycling responds to anthropogenic disturbances, offering valuable information for developing groundwater management and pollution control strategies.}, }
@article {pmid40156579, year = {2025}, author = {Sanghani, A and Antaliya, K and Patel, R and Dave, S and Tipre, D}, title = {Revealing Microbial Functionalities and Ecological Roles in Rajpardi Lignite Mine: Insights from Metagenomics Analysis.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovaf048}, pmid = {40156579}, issn = {1472-765X}, abstract = {The present study employs a metagenomics approach to evaluate microbial communities' ecological functions and potential within the Rajpardi lignite mine of Gujarat, India. Through whole genome shotgun sequencing on the Illumina Miseq platform, we obtained 10,071,318 sequences, which unveiled a diverse and abundant microbial community primarily composed of Proteobacteria, Acidobacteria, and Nitrospirae. Comprehensive taxonomic profiling and gene prediction was carried out using the SqueezeMeta pipline, which highlighted significant contributions to carbohydrate, amino acid, and energy metabolism. The detection of antimicrobial resistance (AMR) and stress resistance genes, such as blaTEM and merA, suggests that these microbes possess the ability to adapt to harsh environmental conditions. Genome binning revealed species such as Acidiphilum sp. 20-67-58, emphasising the nature of these communities as they adapted to an acidic environment. This finding highlights the crucial role of microbes in biogeochemical cycles, emphasizing their potential in bioremediation, pollutant degradation, and ecosystem restoration.}, }
@article {pmid40156577, year = {2025}, author = {Kop, LFM and Koch, H and Martins, PD and Suarez, C and Karačić, S and Persson, F and Wilén, BM and Hagelia, P and Jetten, MSM and Lücker, S}, title = {High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf032}, pmid = {40156577}, issn = {1574-6941}, abstract = {Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7±15% but a wide range between 1.2-61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome (MAG) analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.}, }
@article {pmid40156536, year = {2025}, author = {Sarker, S and Klukowski, N and Talukder, S and Athukorala, A and Uddin, MJ}, title = {Opportunistic sampling from the near-threatened Alexandrine parakeet uncovers genomes of a novel parvovirus and beak and feather disease virus.}, journal = {Australian veterinary journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/avj.13442}, pmid = {40156536}, issn = {1751-0813}, support = {DE200100367//Australian Research Council/ ; }, abstract = {Birds are known to harbour a wide range of pathogenic viruses, including the beak and feather disease virus (BFDV; species, Circovirus parrot), which poses a significant threat to the conservation of endangered avian species. This study reports the genomic identification and characterisation of a novel psittaciform chaphamaparvovirus (PsChPV-6) and BFDV, sequenced from the faecal samples of healthy Alexandrine parakeets (Psittacula eupatria). PsChPV-6 is a linear, single-stranded DNA virus consisting of 4232 nucleotides (nt) with a high A + T content and five predicted open reading frames (ORFs). Key proteins encoded by PsChPV-6, such as the nonstructural protein 1 (NS1) and major capsid protein VP1, demonstrate strong sequence similarities to other avian parvoviruses, with conserved motifs in NS1 crucial for viral replication. The presence of a previously uncharacterised ORF1 region suggests strain-specific viral features that warrant further exploration. BFDV is a circular single-stranded DNA virus in the Circoviridae family and was also identified in the samples. Phylogenetic analysis positioned PsChPV-6 within the Chaphamaparvovirus genus, closely related to parvoviruses from diverse avian species, whereas BFDV was grouped with strains from Australian cockatoos and other nonpsittacine birds, suggesting potential cross-species transmission. These findings contribute to a deeper understanding of the genetic diversity and evolutionary dynamics of these viral pathogens in bird populations, underscoring the importance of ongoing surveillance to evaluate their ecological and veterinary impacts.}, }
@article {pmid40156205, year = {2025}, author = {Huyghe, CET and Fages, A and Ronco, F and Indermaur, A and Schedel, FDB and Kimirei, I and Makasa, L and Tschopp, P and Salzburger, W}, title = {Metagenomic Insights Into the Dietary Diversity of the Adaptive Radiation of Cichlid Fishes in Lake Tanganyika.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17743}, doi = {10.1111/mec.17743}, pmid = {40156205}, issn = {1365-294X}, support = {189970//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, abstract = {Diet specialisation is a main driver of diversification in many adaptive radiations. Therefore, identifying diet items is essential to characterise trophic specialisations and to understand the dynamics of dietary adaptations. In this study, we explored the trophic niches of 56 species from the adaptive radiation of cichlid fishes in Lake Tanganyika, encompassing all major phylogenetic lineages and feeding specialisations. We employed a metagenomic sequencing approach to identify the food sources of the investigated species at high taxonomic resolution, sequencing over 400 digestive content samples from wild-caught individuals at around 50 million paired-end read depth per sample. Our analyses revealed Arthropoda, Chordata (fishes), Bacillariophyta and Streptophyta as the primary diet phyla of the Tanganyikan cichlids. Moreover, we confirmed the presence of other food sources and identified taxa not previously documented to be part of the cichlids' diet. Based on their dietary compositions, the Tanganyikan cichlids can be grouped into herbivores, invertivores, piscivores and mixed feeders. Further, we showed that trophic disparity in the radiation is shaped by rapid divergence and documented cases of dietary niche convergence. Diet composition correlated with carbon and nitrogen stable isotope values, gut length, and body morphology. Differences in diet-such as the consumption of diatoms, streptophytes and chlorophytes versus fish and arthropods-were associated with changes in body, upper oral jaw and lower pharyngeal jaw shape. Collectively, this study presents a comprehensive and detailed diet classification of the Tanganyikan cichlids, highlighting the power of metagenomic approaches in delineating dietary adaptations.}, }
@article {pmid40155949, year = {2025}, author = {Song, J and Lin, LA and Tang, C and Chen, C and Yang, Q and Zhang, D and Zhao, Y and Wei, HC and Linghu, K and Xu, Z and Chen, T and He, Z and Liu, D and Zhong, Y and Zhu, W and Zeng, W and Chen, L and Song, G and Chen, M and Jiang, J and Zhou, J and Wang, J and Chen, B and Ying, B and Wang, Y and Geng, J and Lin, JW and Chen, L}, title = {DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {76}, pmid = {40155949}, issn = {1474-760X}, mesh = {*Metagenomics/methods ; Humans ; *Nanopore Sequencing/methods ; *Sequence Analysis, RNA/methods ; COVID-19/virology/genetics ; Gene Expression Profiling/methods ; Transcriptome ; Glioma/genetics ; High-Throughput Nucleotide Sequencing/methods ; SARS-CoV-2/genetics ; Software ; Malaria ; }, abstract = {Nanopore direct RNA sequencing (DRS) is a powerful tool for RNA biology but suffers from low basecalling accuracy, low throughput, and high input requirements. We present DEMINERS, a novel DRS toolkit combining an RNA multiplexing workflow, a Random Forest-based barcode classifier, and an optimized convolutional neural network basecaller with species-specific training. DEMINERS enables accurate demultiplexing of up to 24 samples, reducing RNA input and runtime. Applications include clinical metagenomics, cancer transcriptomics, and parallel transcriptomic comparisons, uncovering microbial diversity in COVID-19 and m[6]A's role in malaria and glioma. DEMINERS offers a robust, high-throughput solution for precise transcript and RNA modification analysis.}, }
@article {pmid40155846, year = {2025}, author = {Zhang, Z and Tian, L}, title = {Validation of mNGS results using extensive lab and clinical data.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {173}, pmid = {40155846}, issn = {1471-2180}, mesh = {Humans ; Retrospective Studies ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Mycoplasma pneumoniae/genetics/isolation &amp; purification ; Male ; Adult ; Middle Aged ; Female ; Tuberculosis/microbiology/diagnosis ; Aged ; Adolescent ; Young Adult ; Child ; }, abstract = {PURPOSE: Interpreting the results of metagenomic next-generation sequencing (mNGS) presents a significant challenge in both clinical and laboratory contexts.<br><br>METHODS: A retrospective analysis was conducted to validate mNGS findings, with a particular emphasis on Mycobacterium tuberculosis, Mycoplasma pneumoniae, and Pneumocystis jirovecii as representative pathogens, examined from both clinical and laboratory perspectives.<br><br>RESULTS: Based on a comprehensive clinical analysis, the mNGS demonstrated detection accuracies for M. tuberculosis, M. pneumoniae, and P. jirovecii of 87.0% (60 out of 69; 95% confidence interval [CI], 77.04%-92.99%), 97.6% (81 out of 83; 95% CI, 91.63%-99.34%), and 78.9% (45 out of 57; 95% CI, 66.72%-87.53%), respectively. Conversely, when incorporating laboratory confirmation from a variety of detection methodologies, the accuracy rates for mNGS in identifying M. tuberculosis, M. pneumoniae, and P. jirovecii were 92.7% (51 out of 55; 95% CI, 82.74%-97.14%), 82.3% (51 out of 62; 95% CI, 70.96%-89.80%), and 83.9% (26 out of 31; 95% CI, 67.36%-92.91%), respectively. Additionally, our analysis revealed no statistically significant difference in read counts and relative abundances between mNGS results deemed clinically as false positives and those considered true positives (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: In contemporary clinical practice, the detection of positive results from mNGS is notably high from both laboratory and clinical standpoints. Nonetheless, the interpretation of results with low read counts presents significant challenges for both clinical and laboratory environments under current conditions.}, }
@article {pmid40155693, year = {2025}, author = {Refahi, M and Sokhansanj, BA and Mell, JC and Brown, JR and Yoo, H and Hearne, G and Rosen, GL}, title = {Enhancing nucleotide sequence representations in genomic analysis with contrastive optimization.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {517}, pmid = {40155693}, issn = {2399-3642}, support = {1936791//National Science Foundation (NSF)/ ; 1919691//National Science Foundation (NSF)/ ; 2107108//National Science Foundation (NSF)/ ; }, mesh = {*Genomics/methods ; Sequence Analysis, DNA/methods ; Base Sequence ; Algorithms ; Metagenomics/methods ; }, abstract = {Analysis of genomic and metagenomic sequences is inherently more challenging than that of amino acid sequences due to the higher divergence among evolutionarily related nucleotide sequences, variable k-mer and codon usage within and among genomes of diverse species, and poorly understood selective constraints. We introduce Scorpio (Sequence Contrastive Optimization for Representation and Predictive Inference on DNA), a versatile framework designed for nucleotide sequences that employ contrastive learning to improve embeddings. By leveraging pre-trained genomic language models and k-mer frequency embeddings, Scorpio demonstrates competitive performance in diverse applications, including taxonomic and gene classification, antimicrobial resistance (AMR) gene identification, and promoter detection. A key strength of Scorpio is its ability to generalize to novel DNA sequences and taxa, addressing a significant limitation of alignment-based methods. Scorpio has been tested on multiple datasets with DNA sequences of varying lengths (long and short) and shows robust inference capabilities. Additionally, we provide an analysis of the biological information underlying this representation, including correlations between codon adaptation index as a gene expression factor, sequence similarity, and taxonomy, as well as the functional and structural information of genes.}, }
@article {pmid40155620, year = {2025}, author = {Kazarina, A and Wiechman, H and Sarkar, S and Richie, T and Lee, STM}, title = {Recovery of 679 metagenome-assembled genomes from different soil depths along a precipitation gradient.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {521}, pmid = {40155620}, issn = {2052-4463}, support = {2020-67019-31803//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; 2238633//National Science Foundation (NSF)/ ; OIA-1656006//National Science Foundation (NSF)/ ; }, mesh = {*Soil Microbiology ; *Metagenome ; Metagenomics ; Bacteria/genetics/classification ; Kansas ; Soil/chemistry ; Archaea/genetics ; }, abstract = {Soil contains a diverse community of organisms; these can include archaea, fungi, viruses, and bacteria. In situ identification of soil microorganisms is challenging. The use of genome-centric metagenomics enables the assembly and identification of microbial populations, allowing the categorization and exploration of potential functions living in the complex soil environment. However, the heterogeneity of the soil-inhabiting microbes poses a tremendous challenge, with their functions left unknown, and difficult to culture in lab settings. In this study, using genome assembling strategies from both field core samples and enriched monolith samples, we assembled 679 highly complete metagenome-assembled genomes (MAGs). The ability to identify these MAGs from samples across a precipitation gradient in the state of Kansas (USA) provided insights into the impact of precipitation levels on soil microbial populations. Metabolite modeling of the MAGs revealed that more than 80% of the microbial populations possessed carbohydrate-active enzymes, capable of breaking down chitin and starch.}, }
@article {pmid40155586, year = {2025}, author = {Bebawy, AS and Saad, BT and Saad, MT and Mosaad, GS and Gomaa, FAM and Alshahrani, MY and Aboshanab, KM}, title = {Evaluation of the taxonomic classification tools and visualizers for metagenomic analysis using the Oxford nanopore sequence database.}, journal = {Journal of applied genetics}, volume = {}, number = {}, pages = {}, pmid = {40155586}, issn = {2190-3883}, abstract = {Microbial metagenomic identification is generally attributed to the specificity and type of the bioinformatic tools, including classifiers and visualizers. In this study, the performance of two major classifiers, Centrifuge and Kraken2, and two visualizers (Recentrifuge and Krona) has been thoroughly investigated for their efficiency in the identification of the microorganisms using the Whole-Genome Sequence (WGS) database and four targeted databases including NCBI, Silva, Greengenes, and Ribosomal Database Project (RDP). Two standard DNA metagenomic library replicates, Zymo and Zymo-1, were used as quality control. Results showed that Centrifuge gave a higher percentage of Pseudomonas aeruginosa, Escherichia coli, and Salmonella enterica identification than Kraken2. Compared to Recentrifuge, Kraken2 was more accurate in identifying Staphylococcus aureus, Listeria monocytogenes, Bacillus subtilis, and Cryptococcus neoformans. The results of the rest of the detected microorganisms were generally consistent with the two classifiers. Regarding visualizers, both Recentrifuge and Krona provided similar results regarding the abundance of each microbial species regardless of the classifier used. The differences in results between the two mentioned classifiers may be attributed to the specific algorithms each method uses and the sequencing depth. Centrifuge uses a read mapping approach, while Kraken2 uses a k-mer-based system to classify the sequencing reads into taxonomic groups. In conclusion, both Centrifuge and Kraken2 are effective tools for microbial classification. However, the choice of classifier can influence the accuracy of microbial classification and, therefore, should be made carefully, depending on the desired application, even when the same reference database is used.}, }
@article {pmid40154870, year = {2025}, author = {Yang, JT and Zhang, Y and Xiong, SY and Wei, HJ and Zhang, WT and Lian, XL and Xu, XL and Jiang, HX and Sun, J}, title = {Microplastics Reduced the Natural Attenuation of Antibiotic Resistance Genes in Fertilized Soils.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126144}, doi = {10.1016/j.envpol.2025.126144}, pmid = {40154870}, issn = {1873-6424}, abstract = {The prolonged application of mulch and manure in agriculture has led to significant microplastic (MP) pollution in fertilized soils, raising global concerns about its potential impacts on soil health and ecosystem function. However, the effects of MP exposure on antibiotic resistance genes (ARGs) and microbial communities in fertilized soils are unknown. Therefore, we comprehensively explored the trends and drivers of ARGs during their natural abatement under the stress of conventional and biodegradable MP addition in fertilized soils using a soil microcosm experiment and metagenomic. The findings indicated that the presence of polybutylene succinate MPs (PBS-MPs) reduced the natural attenuation rate of ARGs in fertilized soils while increasing the fraction of high-risk ARGs in soils. Microbial communities and mobile genetic elements (MGEs) mainly drove the inhibitory effect of MPs on ARG abatement. Interestingly, most potential hosts for the coexistence of ARGs, metal resistance genes (MRGs), and MGEs were annotated as pathogens, such as Escherichia spp., Salmonella spp., and Klebsiella spp. In addition, MP stress in fertilized soil may lead to long-term contamination by highly virulent and antibiotic-resistant Escherichia coli. MPs influence the distribution of carbon sources, which in turn reduces the diversity and stability of soil microbial communities, while simultaneously promoting the colonization of crucial ARG hosts, like Dyella spp. This ultimately prolonged the high-risk state for ARG proliferation in the soil. This study highlights the significant risk posed by MPs to the persistence and spread of ARGs in fertilized soils. These results provide valuable insights for managing MP contamination in agricultural systems, emphasizing the need for sustainable practices to mitigate the long-term environmental risks associated with MP pollution.}, }
@article {pmid40154751, year = {2025}, author = {Jiang, X and Zhao, Y and Zhang, W and Zheng, Q and Li, D and Zhang, G and Zhou, T}, title = {Chlorotetracycline-driven modulation of substrate utilization and metabolic traits in sludge anaerobic fermentation for optimized methane production.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132449}, doi = {10.1016/j.biortech.2025.132449}, pmid = {40154751}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) is a highly efficient and promising method for treating waste activated sludge (WAS). Nevertheless, the presence of chlortetracycline (CTC) in WAS introduced uncertainty into the AD process. This study revealed thatthe cumulative methane yield was increased by 27.5 % with the CTC concentration at 50 mg/kg dry sludge by enhancing hydrolysis, acidification and methanogenesis during which specific microbial communities were enriched and related functional genes were enhanced. Subsequent investigations foundthe accumulation of extracellular polymeric substances (EPS) was improved and methane-producing microorganisms (e.g., Bacteroidetes and Euryarchaeota) were also enriched under CTC exposure. Metagenomic analysis further elucidated thatCTC significantly increased functional genes related to bacterial secretion system and metabolism of organic matter for methane production (e.g., pyruvate metabolism and methane metabolism). This study shed light on the substantial impact of CTC on the AD of WAS and provided a promising strategy for improvements in anaerobic fermentation.}, }
@article {pmid40154110, year = {2025}, author = {Alameer, RM and Tayeb, H and Magrashi, A and Alqasabi, A and Nazmi, A and Yamani, A and Almaghrabi, RS}, title = {Diagnosis of donor-derived Malassezia restricta &amp;Aspergillus species invasive fungal infection in renal transplant recipient using next generation sequencing - A report of 2 cases and literature review.}, journal = {Journal of infection and public health}, volume = {18}, number = {5}, pages = {102742}, doi = {10.1016/j.jiph.2025.102742}, pmid = {40154110}, issn = {1876-035X}, abstract = {Diagnosing donor-derived fungal infection in solid organ transplant recipients can be particularly challenging and is associated with high mortality. Here, we report two cases of Malassezia restricta and Aspergillus spp donor-derived fungal infection in renal transplant recipients leading to graft loss. Fortunately, both patients achieved full recovery with the administration of antifungal therapy.}, }
@article {pmid40154057, year = {2025}, author = {Chen, H and Zhong, S and Liu, Z and Hu, Z and Wang, C and Zhou, Y and Xu, N and Zhao, F and Li, D and Hu, Y}, title = {Microbiome-metabolomic insights into the systemic regulation in Fangxian Huangjiu fermentation.}, journal = {Food chemistry}, volume = {481}, number = {}, pages = {143980}, doi = {10.1016/j.foodchem.2025.143980}, pmid = {40154057}, issn = {1873-7072}, abstract = {Metabolic forces drive microecological succession in Huangjiu fermentation. This study investigates the dynamic metabolic-microbial interplay during Fangxian Huangjiu fermentation. Temporal changes of metabolome and microbiome revealed a syntropic relationship that purified the microbial community with convergent metabolic patterns. With species turnover driving microbial community structure, early-stage microbiomes exhibited great functional diversity. Functions related to energy and molecular building blocks were enriched at the end of early stage, and contributed greatly to microbial adaptation, highlighting the importance of metabolic forces in shaping community structure. Proteobacteria were identified as key facilitators of diverse metabolic activities, and Enterobacter emerged as a fundamental microbial community particularly for materials transformation. Correlation analysis enriched amino acid metabolism pathways. Further, Pantoea ananatis and Wickerhamomyces anomalus were isolated to enhance sphingosine-1-phosphate, γ-aminobutyric acid, and creatine levels without altering physicochemical properties. The study offers insights into the regulation of Huangjiu fermentation, and suggested potential micobiome manipulation to optimize characteristics.}, }
@article {pmid40154039, year = {2025}, author = {Li, J and Huang, Z and Zhang, R}, title = {Unmasking Prototheca wickerhamii: A rare case of cutaneous infection and its implications for clinical practice.}, journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases}, volume = {29}, number = {3}, pages = {104525}, doi = {10.1016/j.bjid.2025.104525}, pmid = {40154039}, issn = {1678-4391}, abstract = {Prototheca, an opportunistic pathogenic algae widely found in nature, has emerged as a potential public health concern. Most cases occur in immunocompromised individuals, with infections in immunocompetent patients being relatively rare. Due to their non-specific clinical presentation and limited awareness among clinicians, Prototheca infections are often misdiagnosed, resulting in delayed treatment. Recent advances in species identification and antifungal susceptibility testing have provided important tools for diagnosis and therapy. Here, we report a case of recurrent facial infection in a 76-year-old immunocompetent man. Skin biopsy revealed an infectious granuloma, and fungal culture identified yeast-like colonies. Fluorescence staining and scanning electron microscopy revealed abundant spores, while metagenomic sequencing confirmed the infection as Prototheca wickerhamii. The patient was successfully treated with long-term itraconazole and dipotassium glycyrrhizinate capsules. This case highlights the importance of early and accurate diagnosis in the management of Prototheca skin infections and reviews the therapeutic strategies used.}, }
@article {pmid40153957, year = {2025}, author = {Huang, M and Mu, G and Mai, F and Zhou, Y and Li, X and Yang, Q and Shao, B and Wang, J and Tong, Y}, title = {Methane cycling in typical emerging proglacial lakes on the Tibetan Plateau: Insights into the metabolic mechanisms mediated by microorganisms.}, journal = {Water research}, volume = {280}, number = {}, pages = {123533}, doi = {10.1016/j.watres.2025.123533}, pmid = {40153957}, issn = {1879-2448}, abstract = {A large number of high-latitude emerging proglacial lakes have formed on the Tibetan Plateau (TP) due to the global warming and deglaciation. These lakes have the potential to emit methane (CH4) because of the exposure of cryopreserved organic carbon, leading to their significance in regional carbon turnover and cycling. However, previous studies have focused more on human-impacted lakes (e.g., eutrophic lakes), resulting in limited research on the mechanisms of CH4 cycling in the proglacial lakes. In this study, we demonstrated that three typical emerging high-latitude proglacial lakes (∼5500 m a.s.l.) on the TP exhibited a diffusive emission flux of 32.39 ± 11.66 μmol/m[2]/d during the summer. The δ[13]C-CH4 values (-50.10 ± 0.56‰) suggested a biogenic origin of CH4 through the acetoclastic pathway in the lakes. Metagenome sequencing further showed that microbes involved in methanogenesis were dominated by Methanosarcina (36.74 ± 0.07 % of total methanogens). Significant CH4 consumption was observed in the proglacial lakes. The microbes involved in the CH4 consumption were dominated by Methylobacter (48.50 ± 0.17 % of total methanotrophs). A Mantel test demonstrated that dissolved iron (Fe) was a key factor controlling the structure of the CH4 cycling microbial communities. Functional gene and co-occurrence network analyses indicated that members of Pseudomonadota, Bacteroidota, and Actinomycetota may be involved in CH4 cycling by providing methanogenic substrates (i.e., acetyl coenzyme A) and consuming CH4 oxidative intermediates (i.e., methanol, formaldehyde, and formic acid). This study emphasized the ecological significance of emerging proglacial lakes in CH4 releases. It broadened the current understanding of cryophilic CH4 cycling microbes and their mechanisms, that enhances our knowledge of the carbon cycle on the TP.}, }
@article {pmid40153355, year = {2025}, author = {Klištincová, N and Koreňová, J and Rešková, Z and Čaplová, Z and Burdová, A and Farkas, Z and Polovka, M and Drahovská, H and Pangallo, D and Kuchta, T}, title = {Bacterial consortia of ewes´ whey in the production of bryndza cheese in Slovakia.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovaf047}, pmid = {40153355}, issn = {1472-765X}, abstract = {Whey from previous production is often used as a natural starter in the technology of traditional cheeses, including bryndza-cheese in Slovakia. Therefore, studying its bacterial community and isolating new potential natural starters is important for improving the characterisitics of final product. Composition of bacterial consortia of fresh and fermented whey in the production of raw ewes´ milk-based bryndza-cheese from 8 small or medium-sized producers was analysed. Culture-based microbiological analysis and culture-independent analysis based on 16S rRNA gene sequencing by MiSeq and MinION were used. Results showed the dominance of lactococci or streptococci, with 3 - 8 log CFU ml-[1] of Lactobacillus sensu lato in all whey samples. Potential natural starters comprising Lacticaseibacillus paracasei/casei, Lactiplantibacillus plantarum, Lentilactobacillus parabuchneri, Lactobacillus helveticus, Lactobacillus diolivorans, Levilactobacillus brevis, Limosilactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus gasseri and Lentilactobacillus otakiensis were isolated. Coliforms were also present in all samples, with no consistently lower values in fermented whey samples. Some samples contained pseudomonads and/or acinetobacters. Coagulase positive staphylococci were present at relevant levels in samples from 4 producers. The results revealed that whey is a source of natural starters due to the presence of lactobacilli.}, }
@article {pmid40153196, year = {2025}, author = {Erickson, I and Davidson, S and Choi, H and Rho, S and Guignet, M and Peagler, K and Thummel, K and Ericsson, A and Barker-Haliski, M}, title = {Intestinal dysbiosis alters acute seizure burden and antiseizure medicine activity in Theiler's virus model of encephalitis.}, journal = {Epilepsia}, volume = {}, number = {}, pages = {}, doi = {10.1111/epi.18395}, pmid = {40153196}, issn = {1528-1167}, support = {//University of Washington/ ; }, abstract = {OBJECTIVE: Brain infection with Theiler's murine encephalomyelitis virus (TMEV) in C57BL/6J mice produces an etiologically relevant model of acquired seizures. Dietary changes can modify seizure presentation following TMEV brain infection and influence intestinal microbiome diversity and composition. Intestinal dysbiosis may thus similarly affect seizure burden and antiseizure medicine (ASM) activity in this model, independent of pharmacokinetic effects. We thus sought to define the influence of antibiotic (ABX)-induced gut dysbiosis on acute seizure presentation, anticonvulsant activity of carbamazepine (CBZ), and CBZ pharmacokinetics with TMEV infection.<br><br>METHODS: Male C57BL/6J mice (4-5&#x2009;weeks old) received oral ABX or saline (SAL) once daily beginning on arrival through day 7 after TMEV infection (postinfection [p.i.]). Mice were infected with TMEV or phosphate-buffered saline on day 0. Mice received intraperitoneal (20&#x2009;mg/kg) CBZ or vehicle (VEH) twice daily on days 3-7 p.i. and were assessed for handling-induced seizures 30&#x2009;min after treatment. Plasma was collected on day 7 p.i. at 15 and 60&#x2009;min after CBZ administration for bioanalysis.<br><br>RESULTS: TMEV infection induced acute seizures, but ABX-induced gut dysbiosis altered seizure presentation. There were 75% SAL-VEH, 35% SAL-CBZ, 35% ABX-VEH, and 72% ABX-CBZ mice with seizures during the 7-day monitoring period. There was a significant pretreatment&#x2009;&#xd7;&#x2009;ASM interaction (p&#x2009;=&#x2009;.0001), with differences in seizure burden in SAL- versus ABX-pretreated mice (p&#x2009;=&#x2009;.004). CBZ significantly increased latency to seizure presentation, an effect absent in ABX-CBZ mice. Plasma CBZ concentrations did not differ between SAL and ABX pretreatment groups, suggesting that ABX did not influence CBZ pharmacokinetics.<br><br>SIGNIFICANCE: ABX-induced gut dysbiosis markedly altered acute disease trajectory with TMEV-induced encephalitis, reflecting a novel contribution of the gut microbiome to seizure presentation. ABX-induced gut dysbiosis also significantly changed acute seizure control by CBZ, but did not influence plasma CBZ concentrations. The gut-brain axis is thus an underrecognized contributor to TMEV infection-induced seizures, ASM activity, and disease burden.}, }
@article {pmid40152616, year = {2025}, author = {Yao, J and Zeng, Y and Hong, X and Wang, M and Zhang, Q and Chen, Y and Gou, M and Xia, Z-Y and Tang, Y-Q}, title = {Phages-bacteria interactions underlying the dynamics of polyhydroxyalkanoate-producing mixed microbial cultures via meta-omics study.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0020025}, doi = {10.1128/msystems.00200-25}, pmid = {40152616}, issn = {2379-5077}, abstract = {The dynamics of the structure of polyhydroxyalkanoate-producing mixed microbial cultures (PHA-MMCs) during enrichment and maintenance is an unsolved problem. The effect of phages has been proposed as a cause of dynamic changes in community structure, but evidence is lacking. To address this question, five PHA-MMCs were enriched, and biological samples were sampled temporally to study the interactions between phage and bacterial members by combining metagenomics and metatranscriptomics. A total of 963 metagenome-assembled genomes (MAGs) and 4,294 phage operational taxonomic units (pOTUs) were assembled from bulk metagenomic data. The dynamic changes in the structure of phage and bacterial communities were remarkably consistent. Structural equation modeling analysis showed that phages could infect and lyse dominant species to vacate ecological niches for other species, resulting in a community succession state in which dominant species alternated. Seven key auxiliary metabolic genes (AMGs), phaC, fadJ, acs, ackA, phbB, acdAB, and fadD, potentially contributing to PHA synthesis were identified from phage sequences. Importantly, these AMGs were transcribed, indicating that they were in an active expression state. The meta-analysis provides the first catalog of phages in PHA-MMCs and the AMGs they carry, as well as how they affect the dynamic changes in bacterial communities. This study provides a reference for subsequent studies on understanding and regulating the microbial community structure of open microbial systems.IMPORTANCEThe synthesis of biodegradable plastic PHA from organic waste through mixed microbial cultures (PHA-MMCs), at extremely low cost, has the potential for expanded production. However, the dynamics of dominant species in PHA-MMCs are poorly understood. Our results demonstrate for the first time the impact of phages on the structure of bacterial communities in the PHA-MMCs. There are complex interactions between the PHA producers (e.g., Azomonas, Paracoccus, and Thauera) and phages (e.g., Casadabanvirus and unclassified Hendrixvirinae). Phage communities can regulate the activity and structure of bacterial communities. In addition, the AMGs related to PHA synthesis may hitchhike during phage-host infection cycles, enabling their dissemination across bacterial communities, and phages may act as a critical genetic reservoir for bacterial members, facilitating access to PHA synthesis-related functional traits. This study highlights the impact of phages on bacterial community structure, suggesting that phages have the potential to be used as a tool for better controlling the microbial community structure of PHA-MMCs.}, }
@article {pmid40152185, year = {2025}, author = {Allos, H and Hasbun, R}, title = {Aseptic meningitis: a foundation review.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1097/QCO.0000000000001105}, pmid = {40152185}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: This review addresses the multifaceted nature of aseptic meningitis, a condition with diverse infectious and noninfectious etiologies. Despite its common presentation in clinical settings, over half of the cases remain without an identified cause, necessitating a comprehensive examination of diagnostic and management strategies. The increasing availability of advanced molecular diagnostics and the challenge of distinguishing bacterial from nonbacterial cases make this an opportune time to explore its implications for clinical practice.<br><br>RECENT FINDINGS: The literature highlights the pivotal role of advanced molecular diagnostics, such as multiplex PCR and metagenomic sequencing, in improving the identification of pathogens in aseptic meningitis. Enteroviruses remain the leading cause, but pathogens like Herpesviridae, arboviruses, and nonviral agents such as fungi and spirochetes also contribute significantly. New diagnostic algorithms and clinical models are emerging to distinguish bacterial from viral meningitis, reducing unnecessary treatments.<br><br>SUMMARY: Aseptic meningitis management is evolving with advancements in diagnostic technologies that allow for earlier pathogen identification, improving patient outcomes and minimizing healthcare costs. These findings underscore the importance of timely and accurate diagnostics and tailored therapeutic strategies in both clinical and research settings. Enhanced awareness of noninfectious causes is also crucial for comprehensive care.}, }
@article {pmid40152095, year = {2025}, author = {Wu, S and Luo, Y and Wei, F and Li, Y and Fan, J and Chen, Y and Zhang, W and Li, X and Xu, Y and Chen, Z and Xia, C and Hu, M and Li, P and Gu, Q}, title = {Lactic acid bacteria target NF-κB signaling to alleviate gastric inflammation.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo06308b}, pmid = {40152095}, issn = {2042-650X}, abstract = {Helicobacter pylori (H. pylori) infection and the resulting gastric inflammation are major contributors to gastric cancer development. Probiotics, particularly Lactobacillus, are promising for their anti-inflammatory potential, yet their exact mechanisms in inhibiting H. pylori-induced inflammation are unclear. In our previous study, Lactiplantibacillus plantarum ZJ316 (L. plantarum ZJ316) demonstrated strong anti-inflammatory effects against H. pylori infection in vivo, but its precise mechanisms were not fully understood. Here, we aimed to investigate how L. plantarum ZJ316 inhibits the inflammatory response to H. pylori infection. Our results demonstrated that L. plantarum ZJ316 effectively reduced the expression of pro-inflammatory cytokines in H. pylori-infected AGS cells. Mechanistically, L. plantarum ZJ316 inhibited the NF-κB signaling pathway by preventing the degradation of IκBα, suppressing p65 phosphorylation, and blocking the nuclear translocation of phosphorylated p65. Treatment with the NF-κB inhibitor BAY 11-7082 further decreased tumor necrosis factor-α (TNF-α), interleukin-8 (IL-8), and interleukin-1β (IL-1β) levels, confirming the inhibitory effect of L. plantarum ZJ316 on the NF-κB pathway. In H. pylori-infected mice, oral administration of L. plantarum ZJ316 significantly alleviated inflammatory cell infiltration, reduced TNF-α and pepsinogen II (PGII) levels, and increased interleukin-10 (IL-10) levels in serum. A comparative metagenomic analysis of the gastric microbiota revealed a decrease in Prevotella and Desulfovibrio, alongside an increase in Ligilactobacillus and Akkermansia, supporting the protective effects of L. plantarum ZJ316 and correlating with their decreased inflammatory response. In summary, administration of L. plantarum ZJ316 demonstrated robust anti-inflammatory effects against H. pylori infection by suppressing NF-κB signaling and promoting favorable changes in the gastric microbiota composition. Therefore, L. plantarum ZJ316 holds promise as a novel functional food for protecting the body against H. pylori infection.}, }
@article {pmid40151642, year = {2025}, author = {Cai, X and Cho, JY and Chen, L and Liu, Y and Ji, F and Salgado, K and Ge, S and Yang, D and Yu, H and Shao, J and Futreal, PA and Sepesi, B and Gibbons, D and Chen, Y and Wang, G and Cheng, C and Wu, M and Zhang, J and Hsiao, A and Xia, T}, title = {Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112162}, pmid = {40151642}, issn = {2589-0042}, abstract = {Understanding the effect of gut microbiota function on immune checkpoint inhibitor (ICI) responses is urgently needed. Here, we integrated 821 fecal metagenomes from 12 datasets to identify differentially abundant genes and construct random forest models to predict ICI response. Gene markers demonstrated excellent predictive performance, with an average area under the curve (AUC) of 0.810. Pathway analyses revealed that quorum sensing (QS), ABC transporters, flagellar assembly, and amino acid biosynthesis pathways were enriched between responders (R) and non-responders (NRs) across 12 datasets. Furthermore, luxS, manA, fliC, and trpB exhibited consistent changes between R and NR across 12 datasets. Follow-up microbiota transplant experiments showed that inter-species signaling by different QS autoinducer-2 (AI-2) molecules (synthesized by luxS) can act on overall community function to promote the colonization of Akkermansia muciniphila, which is associated with superior ICI responses. Together, our data highlight the role of gut microbiota function in modulating the microbiome and antitumor immunity.}, }
@article {pmid40151403, year = {2025}, author = {Otsuki, A and Inoue, R and Imai, T and Miura, H and Nishida, A and Inatomi, O and Andoh, A}, title = {Characterization of the gut phageome of Japanese patients with ulcerative colitis under endoscopic remission.}, journal = {Journal of clinical biochemistry and nutrition}, volume = {76}, number = {2}, pages = {202-209}, pmid = {40151403}, issn = {0912-0009}, abstract = {This study aimed to analyze the gut phageome in Japanese patients with ulcerative colitis (UC) in endoscopic remission. Fecal samples were collected from 35 UC patients and 22 healthy controls. The gut microbiome was analyzed using 16S rRNA amplicon sequencing, and the phageome was profiled through shotgun metagenomic sequencing. Compared to healthy controls, UC patients showed a significant reduction in phageome richness (observed species and Chao1 index). Principal coordinate analysis revealed a significant difference in beta-diversity between UC and healthy controls (p = 0.001). The abundance of temperate phages was higher in UC (15.2%) compared to healthy controls (5.9%), although this was not statistically significant (p = 0.088). Temperate phages associated with Coprococcus sp., Bacteroides sp. KFT8, and Faecalibacterium prausnitzii, as well as virulent phages associated with Ruminococcus gnavus and Lactobacillus farciminis, were increased in UC patients. Conversely, phages associated with Thermosipho affectus, Bacteroides sp. OF03-11BH, and Odoribacter splanchnicus were decreased in UC patients. Phages associated with the genera Odoribacter (p = 0.0004), Ruminococcus (p = 0.009), and Veillonella (p = 0.013) were significantly reduced in UC patients. The gut phageome of inactive UC patients exhibited notable alterations in viral composition compared to healthy controls. These results suggest that changes in the gut phageome might be involved in the pathogenesis of UC.}, }
@article {pmid40151093, year = {2025}, author = {Liu, D and Zhang, W and Zhu, L and Gong, J and Huang, Y and Li, Z and He, J}, title = {Autoinducer-2 Quorum Sensing Is an Active Universal Signaling System in Sociomicrobiology.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {e024}, doi = {10.1002/jobm.70024}, pmid = {40151093}, issn = {1521-4028}, support = {//This study was supported by National Natural Science Foundation of China (grants 32371495 and 32171424), Hubei Province Technology Innovation Plan Project (2024BCB028), and Wuhan Science and Technology Major Project (grant 2023020302020708)./ ; }, abstract = {Autoinducer-2 (AI-2) is a bacterial quorum sensing (QS) signaling molecule that regulates inter-specific and intraspecific bacterial communication in complex ecological environments. Here, we systematically analyzed the distribution of AI-2 QS-related proteins (synthases and receptors) in the domain bacteria, explored the evolution and development of AI-2 receptors, and analyzed the AI-2 regulatory networks using human intestinal metagenomic data. The results show that AI-2 QS-related proteins are distributed in 17 bacterial phyla, accounting for approximately 36.80% of the total genomes. Based on the ability of bacteria to synthesize and receive AI-2 signals, we divided bacteria into four major categories, namely Prosumer, Producer, Monitor, and Immunizer. The Gram-positive bacteria are mainly responsible for producing the AI-2 signals, while Gram-negative bacteria are more likely to respond to AI-2. Evolutionary analysis shows that the AI-2 receptor CahR is mainly derived from the methyl-accepting chemotaxis protein (MCP). Based on the length difference of the ligand-binding domains, we further speculate that AI-2 binding activates CahR through either allostery or aggregation mode. Using human intestinal metagenomic data, we found a strong correlation between AI-2 signaling and c-di-GMP signaling. These findings will have an important impact on the AI-2 QS research and accelerate its development.}, }
@article {pmid40150979, year = {2025}, author = {Yildirim, EA and Laptev, GY and Ilina, LA and Ponomareva, ES and Brazhnik, EA and Smetannikova, TS and Novikova, NI and Turina, DG and Filippova, VA and Dubrovin, AV and Dubrovina, AS and Kalitkina, KA and Klyuchnikova, IA and Zaikin, VA and Griffin, DK and Romanov, MN}, title = {Metagenomic Composition and Predicted Metabolic Pathway Analyses of the Endometrial and Rectal Microbiota in Dairy Cows Following the Introduction of a Complex Feed Additive.}, journal = {Frontiers in bioscience (Elite edition)}, volume = {17}, number = {1}, pages = {25725}, doi = {10.31083/FBE25725}, pmid = {40150979}, issn = {1945-0508}, support = {24-16-00131//Russian Science Foundation/ ; }, mesh = {Animals ; Cattle/microbiology ; Female ; *Animal Feed ; *Rectum/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; Metabolic Networks and Pathways ; Metagenomics ; Dairying ; }, abstract = {BACKGROUND: The microbiome composition in dairy cows (Bos taurus) directly impacts on health and reproductive performance. This study aimed to determine the metagenomic composition and predicted microbial community functions in the endometrium and rectal chyme of cows fed a complex feed additive (CFA). The latter included the Bacillus mucilaginosus 159 strain, a short-chain fatty acid, plus essential oils.<br><br>METHODS: Clinically healthy cows were divided into two groups (n = 15 in each): (I) a control group fed the standard diet, and (II) an experimental group. CFA was introduced into the diet of Group II during the entire transit period at a dose of 50 g per animal per day; moreover, all animals received Pen-Strep 400 antibiotics to prevent endometritis and other pathologies. The microbial community composition from the endometrium and rectal chyme biotopes was assessed using targeted next-generation sequencing.<br><br>RESULTS: Significant changes were observed in the composition and predicted metabolic pathways due to the CFA administration, with the endometrial microbiota being more responsive to CFA than the intestinal chyme microbiome. Remarkably, the Actinobacteriota representatives disappeared in the endometrium of Group II animals compared to controls, whose content ranged from 0.34 to 3.3%. The use of CFA also resulted in a less pronounced effect in four predicted metabolic pathways for microbial degradation of catechol in the endometrium compared to controls (p < 0.05).<br><br>CONCLUSIONS: Our findings support the concept of a relationship between the gut microbiome and the reproductive system microflora of cows, as we observed changes in the composition and predicted metabolic pathways of the endometrial microbiota after orally administering CFA. This emphasizes the need for an integrated approach combining the correction of microecological disorders in the intestines and the reproductive system simultaneously.}, }
@article {pmid40150359, year = {2025}, author = {Liu, Y and Dong, X and Sun, L and Cui, H and Kang, J and Bu, N and Zhang, Y and Qi, Z and Li, Z and Zhang, Z and Zhao, L}, title = {Analysis of the Microbial Community Structure of Ixodes persulcatus at Each Developmental Stage.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/ani15060830}, pmid = {40150359}, issn = {2076-2615}, support = {32260887//National Natural Science Foundation of China/ ; }, abstract = {Ticks are the second most significant vector of pathogens worldwide. Ixodes persulcatus is one of the dominant tick species in Inner Mongolia that can carry and transmit various pathogenic microorganisms. However, only one specific pathogen has been detected in a particular developmental stage of I. persulcatus, moreover metagenomic analysis has been conducted only in the adult tick stage. In this study, we used I. persulcatus at different developmental stages (first-generation female adult ticks, eggs, larval ticks, engorged larval ticks, nymphal ticks, engorged nymphal ticks, and second-generation adult ticks) from Inner Mongolia as materials for nucleic acid extraction. Subsequently, we constructed Illumina PE250 and Illumina PE150 libraries and sequenced them on the Illumina NovaSeq 6000 platform. Finally, we used molecular biology software and sequence analysis platform to analyze microbial community structures. Illumina PE250 sequencing revealed that the seven developmental stages of I. persulcatus were annotated to 21 phyla, 43 classes, 104 orders, 188 families, 391 genera, and 556 species of bacteria. Among them, 4 phyla and 14 genera were present at all developmental stages, with Proteobacteria being the dominant phylum and Rickettsia spp. being the dominant genus. In addition, Rickettsia had the highest relative abundance in the seven developmental stages. All developmental stages were annotated to a certain abundance of Brucella spp. Illumina PE150 sequencing revealed that the three samples (X-I-YDCP: first-generation adult ticks; X-I-MIX: mixed samples of eggs, larval ticks, and nymphal ticks; X-I-EDCP: second-generation adult ticks) of I. persulcatus were annotated to six orders, 28 families, 72 genera, and 158 species of viruses, of which 46 genera and 80 species were found in all three sample species. To the best of our knowledge, this is the first study that comprehensively analyzed the microbial community composition of I. persulcatus at different developmental stages. Based on the study outcomes, certain abundance of Rickettsia japonica, bovine viral diarrhea virus, and African swine fever virus were annotated to I. persulcatus.}, }
@article {pmid40149936, year = {2025}, author = {Zhan, J and Cheng, J and Chang, W and Su, Y and Yue, X and Wu, C}, title = {Absolute Quantitative Metagenomic Analysis Provides More Accurate Insights for the Anti-Colitis Effect of Berberine via Modulation of Gut Microbiota.}, journal = {Biomolecules}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/biom15030400}, pmid = {40149936}, issn = {2218-273X}, mesh = {*Berberine/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Metagenomics/methods ; Colitis, Ulcerative/microbiology/drug therapy ; Mice ; Bacteria/drug effects/genetics/classification ; Male ; Butyric Acid/pharmacology ; Disease Models, Animal ; }, abstract = {Current gut microbiota studies often rely on relative quantitative sequencing. However, under certain circumstances, while the relative quantitative abundance of these bacteria may remain stable, the absolute quantities of specific bacteria can vary considerably. Since the function of bacteria is directly linked to their total numbers, absolute quantification is crucial. This study aims to identify the optimal method for microbiome analysis by comparing relative and absolute quantitative sequencing. Using ulcerative colitis, which is closely associated with gut microbiota, as a disease model and berberine (which affects microbiota) versus sodium butyrate (which does not) as drugs, relative and absolute quantitative methods were used to evaluate the varying effects of the different drugs on the regulation of gut microbiota in UC-affected animals. The regulatory effects of BBR on gut microbiota were further synthesized as identified in earlier studies using an individual-based meta-analysis, and we compared these findings with our absolute sequencing results. The results from absolute sequencing were more consistent with the actual microbial community, suggesting that relative abundance measurements might not accurately reflect the true abundance of microbial species. Moreover, meta-analysis results were only partially consistent with absolute quantitative sequencing and sometimes directly opposed, suggesting that relative quantitative sequencing analyses are prone to misinterpretation and incorrect correlation of results. This study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.}, }
@article {pmid40149684, year = {2025}, author = {Zhao, X and Xu, J and Wu, D and Chen, N and Liu, Y}, title = {Gut Microbiota in Different Treatment Response Types of Crohn's Disease Patients Treated with Biologics over a Long Disease Course.}, journal = {Biomedicines}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/biomedicines13030708}, pmid = {40149684}, issn = {2227-9059}, support = {(No. RDJP2022-15 to X.Z., No. RDJP2023-22 to J.X.)//Scientific Research Development Funds of Peking University 401 People's Hospital/ ; No. CFH2024-4-4089 to J.X.//the Capital Health Research and Development of Special/ ; (82370555 to J.X., 400 No. 82370537, 82341228 to Y.L.)//the National Natural Science Foundation of China/ ; (No. XZ2024ZR-ZY012(Z) to X.Z.//the Xizang Autono- 402 mous Region Natural Science Foundation Group Medical Aid Project/ ; }, abstract = {Background and Aims: Crohn's disease (CD) is a chronic inflammatory bowel disease (IBD) with a globally increasing prevalence, partially driven by alterations in gut microbiota. Although biological therapy is the first-line treatment for CD, a significant proportion of patients experience a primary non-response or secondary loss of response over time. This study aimed to explore the differences in gut microbiota among CD patients with divergent long-term responses to biological therapy, focusing on a long disease course. Methods: Sixteen CD patients who applied the biological agents for a while were enrolled in this study and were followed for one year, during which fecal specimens were collected monthly. Metagenomic analysis was used to determine the microbiota profiles in fecal samples. The response to biological therapy was evaluated both endoscopically and clinically. Patients were categorized into three groups based on their response: R (long-term remission), mA (mild active), and R2A group (remission to active). The differences in the gut microbiota among the groups were analyzed. Results: Significant differences in fecal bacterial composition were observed between the groups. The R2A group exhibited a notable decline in gut microbial diversity compared to the other two groups (p < 0.05). Patients in the R group had higher abundances of Akkermansia muciniphila, Bifidobacterium adolescentis, and Megasphaera elsdenii. In contrast, Veillonella parvula, Veillonella atypica, and Klebsiella pneumoniae were higher in the R2A group. Conclusions: Gut microbial diversity and specific bacterial significantly differed among groups, reflecting distinct characteristics between responders and non-responders.}, }
@article {pmid40149628, year = {2025}, author = {Kaczka, A and Błońska, A and Chojnacki, C and Gąsiorowska, A and Błasiak, J and Popławski, T and Chojnacki, J}, title = {Periodic Changes in the Gut Microbiome in Women with the Mixed Type of Irritable Bowel Syndrome.}, journal = {Biomedicines}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/biomedicines13030652}, pmid = {40149628}, issn = {2227-9059}, abstract = {Background: The mixed type of irritable bowel syndrome (IBS-M) is characterized by recurrent constipation and diarrhea. The cause of the variability of these symptoms is not sufficiently understood. The aim of this study was to perform metagenomic and metabolic assessment of the gut microbiome in constipation and diarrheal period of IBS-M. Methods: This study included 30 women, aged 28-47 years old, with the symptoms which aligned with those of IBS-M, according to the Rome IV Criteria. Results: In both periods of the disease, the dysbiosis index (DI), the Shannon diversity index (SDI), the hydrogen-methane and ammonia breath tests, as well as the selected bacterial metabolites (-p-hydroxyphenyl acetic acid (HPA), 3-indoxyl sulfate (Indican, 3-IS)), and hippuric acid (A) in urine, were determined. The dysbiosis index (DI) in the period of constipation was 3.73 ± 0.90 points, and in the diarrheal period it did not change significantly 3.93 ± 0.75 points (p > 0.05). During the diarrheal period, the diversity of bacteria increases from 2.16 ± 0.59 to 2.74 ± 0.50 points on the Shannon dietary index (p < 0.001). The gut microbiome profile also changed, especially during the diarrheal period where an abundance of Bifidobacterium spp. and Lactobacillus spp. decreased significantly. In addition, during this period, the levels of hydrogen and ammonia in breath air increased, while the methane level decreased. The differences also concern the results of urinary metabolites, especially related to hippuric acid and indican. During the diarrheal period, the levels of hydrogen and ammonia ions increased, while the methane level decreased. The differences also concern the results of urinary metabolites, especially related to hippuric acid and indican. Conclusions: In patients with IBS-M, periodic changes in the profile and metabolism of the gut microbiome occur, which coexist with recurrent symptoms such as constipation and diarrhea.}, }
@article {pmid40149502, year = {2025}, author = {Hailu, G and Legesse, M and Mulu, A and Medhin, G and Tsegaye, MM and Alemayehu, DH and Ayele, A and Gebreegziabxier, A and Tayachew, A and Aguine, A and Dejene, H and Tessema, SK and Onywera, H and Stanislas, AE and Abate, E and Marcello, A and Bitew, M}, title = {SARS-CoV-2 Genetic Variants Identified in Selected Regions of Ethiopia Through Whole Genome Sequencing: Insights from the Fifth Wave of COVID-19.}, journal = {Genes}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/genes16030351}, pmid = {40149502}, issn = {2073-4425}, mesh = {Humans ; Ethiopia/epidemiology ; *COVID-19/virology/epidemiology/transmission ; *SARS-CoV-2/genetics/pathogenicity ; Male ; Female ; Adult ; *Whole Genome Sequencing/methods ; *Genome, Viral ; Middle Aged ; Phylogeny ; Genetic Variation ; Young Adult ; Adolescent ; }, abstract = {BACKGROUND: The COVID-19 pandemic highlighted SARS-CoV-2 variants with increased transmissibility and immune evasion. In Ethiopia, where cases surged, the understanding of the virus's dynamics was limited. This study analyzed SARS-CoV-2 variants during the fifth wave, crucial for guiding vaccines, therapeutics, diagnostics, and understanding disease severity.<br><br>METHOD: From June to August 2022, 150 SARS-CoV-2-positive samples were randomly selected from the Ethiopian Public Health Institute repository. Sixty-three high-quality genome sequences were analyzed.<br><br>RESULTS: Of the 63 sequences, 70% were from males and 30% from females, with a median age of 34. Omicron dominated (97%, 61/63), primarily clade 22A (64%, 40/63), followed by 22B (18%, 11/63) and 21K (14%, 9/63). Delta accounted for 3.2% (2/63). Omicron was identified in all (25) vaccinated study participants. Ethiopian sequences showed limited evolutionary divergence and lower genetic diversity compared to global sequences.<br><br>CONCLUSION: Omicron was the predominant variant during Ethiopia's fifth wave, indicating recent community transmission. Despite minor genetic diversity differences, ongoing surveillance remains critical for tracking variants and informing public health interventions.}, }
@article {pmid40149437, year = {2025}, author = {Alharbi, SM and Al-Sulami, N and Al-Amrah, H and Anwar, Y and Gadah, OA and Bahamdain, LA and Al-Matary, M and Alamri, AM and Bahieldin, A}, title = {Metagenomic Characterization of the Maerua crassifolia Soil Rhizosphere: Uncovering Microbial Networks for Nutrient Acquisition and Plant Resilience in Arid Ecosystems.}, journal = {Genes}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/genes16030285}, pmid = {40149437}, issn = {2073-4425}, mesh = {*Rhizosphere ; *Soil Microbiology ; Mycorrhizae/genetics/classification ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics/methods ; Metagenome ; Ecosystem ; Microbiota/genetics ; Plant Roots/microbiology ; Fungi/genetics/classification ; }, abstract = {Background/Objectives:Maerua crassifolia, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in M. crassifolia's rhizosphere remain underexplored. Methods: Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of M. crassifolia. Results: The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus clarus, Rhizophagus irregularis and Funneliformis geosporum, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as Sphingomonas spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. Conclusions: Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant-root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial-fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of M. crassifolia, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability.}, }
@article {pmid40149106, year = {2025}, author = {Olsen, NS and Riber, L}, title = {Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/antibiotics14030296}, pmid = {40149106}, issn = {2079-6382}, support = {NNF23OC0086264//Novo Nordisk Foundation/ ; }, abstract = {Extensive use of antibiotics in human healthcare as well as in agricultural and environmental settings has led to the emergence and spread of antibiotic-resistant bacteria, rendering many infections increasingly difficult to treat. Coupled with the limited development of new antibiotics, the rise of antimicrobial resistance (AMR) has caused a major health crisis worldwide, which calls for immediate action. Strengthening AMR surveillance systems is, therefore, crucial to global and national efforts in combating this escalating threat. This review explores the potential of metagenomics, a sequenced-based approach to analyze entire microbial communities without the need for cultivation, as a transformative and rapid tool for improving AMR surveillance strategies as compared to traditional cultivation-based methods. We emphasize the importance of monitoring mobile genetic elements (MGEs), such as integrons, transposons, plasmids, and bacteriophages (phages), in relation to their critical role in facilitating the dissemination of genetic resistance determinants via horizontal gene transfer (HGT) across diverse environments and clinical settings. In this context, the strengths and limitations of current bioinformatic tools designed to detect AMR-associated MGEs in metagenomic datasets, including the emerging potential of predictive machine learning models, are evaluated. Moreover, the controversial role of phages in AMR transmission is discussed alongside the potential of phage therapy as a promising alternative to conventional antibiotic treatment.}, }
@article {pmid40148934, year = {2025}, author = {de Campos, GM and Clemente, LG and Lima, ARJ and Cella, E and Fonseca, V and Ximenez, JPB and Nishiyama, MY and de Carvalho, E and Sampaio, SC and Giovanetti, M and Elias, MC and Slavov, SN}, title = {Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {88}, pmid = {40148934}, issn = {1743-422X}, support = {2022/00910-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/11944-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/11944-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/11944-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/23205-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 403075/2023-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Anelloviridae/genetics/classification/isolation &amp; purification ; *Torque teno virus/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; DNA Virus Infections/virology/blood ; Plasma/virology ; Algorithms ; Metagenome ; Genome, Viral/genetics ; }, abstract = {BACKGROUND: Viral metagenomics has expanded significantly in recent years due to advancements in next-generation sequencing, establishing it as the leading method for identifying emerging viruses. A crucial step in metagenomics is taxonomic classification, where sequence data is assigned to specific taxa, thereby enabling the characterization of species composition within a sample. Various taxonomic classifiers have been developed in recent years, each employing distinct classification approaches that produce varying results and abundance profiles, even when analyzing the same sample.<br><br>METHODS: In this study, we propose using the identification of Torque Teno Viruses (TTVs), from the Anelloviridae family, as indicators to evaluate the performance of four short-read-based metagenomic classifiers: Kraken2, Kaiju, CLARK and DIAMOND, when evaluating human plasma samples.<br><br>RESULTS: Our results show that each classifier assigns TTV species at different abundance levels, potentially influencing the interpretation of diversity within samples. Specifically, nucleotide-based classifiers tend to detect a broader range of TTV species, indicating higher sensitivity, while amino acid-based classifiers like DIAMOND and CLARK display lower abundance indices. Interestingly, despite employing different algorithms and data types (protein-based vs. nucleotide-based), Kaiju and Kraken2 performed similarly.<br><br>CONCLUSION: Our study underscores the critical impact of classifier selection on diversity indices in metagenomic analyses. Kaiju effectively assigned a wide variety of TTV species, demonstrating it did not require a high volume of reads to capture diversity. Nucleotide-based classifiers like CLARK and Kraken2 showed superior sensitivity, which is valuable for detecting emerging or rare viruses. At the same time, protein-based approaches such as DIAMOND and Kaiju proved robust for identifying known species with low variability.}, }
@article {pmid40148927, year = {2025}, author = {Feng, Z and Lorenc, N and O'Brien, B and Sun, G and Li, Z and Jung, D and Ronholm, J}, title = {Deep culturing the fecal microbiota of healthy laying hens.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {32}, pmid = {40148927}, issn = {2524-4671}, abstract = {BACKGROUND: The microbiota is implicated in several aspects of livestock health and disease. Understanding the structure and function of the poultry microbiota would be a valuable tool for improving their health and productivity since the microbiota can likely be optimized for metrics that are important to the industry such as improved feed conversion ratio, lower greenhouse gas emissions, and higher levels of competitive exclusion against pathogens. Most research into understanding the poultry microbiota has relied on culture-independent methods; however, the pure culture of bacteria is essential to elucidating the roles of individual bacteria in the microbiota and developing novel probiotic products for poultry production.<br><br>RESULTS: In this study, we have used a deep culturing approach consisting of 76 culture conditions to generate a culture collection of 1,240 bacterial isolates from healthy chickens. We then compared the taxonomy of cultured isolates to the taxonomic results of metagenomic sequencing to estimate what proportion of the microbiota was cultured. Metagenomic sequencing detected DNA from 545 bacterial species while deep culturing was able to produce isolates for 128 bacterial species. Some bacterial families, such as Comamonadaceae and Neisseriaceae were only detected via culturing - indicating that metagenomic analysis may not provide a complete taxonomic census of the microbiota. To further examine sub-species diversity in the poultry bacteriome, we whole genome sequenced 114 Escherichia coli isolates from 6 fecal samples and observed a great deal of diversity.<br><br>CONCLUSIONS: Deep culturing and metagenomic sequencing approaches to examine the diversity of the microbiota within an individual will yield different results. In this project we generated a culture collection of enteric bacteria from healthy laying hens that can be used to further understand the role of specific commensals within the broader microbiota context and have made this collection available to the community. Isolates from this collection can be requested by contacting the corresponding author and will be provided at cost.}, }
@article {pmid40148567, year = {2025}, author = {Austin, GI and Brown Kav, A and ElNaggar, S and Park, H and Biermann, J and Uhlemann, AC and Pe'er, I and Korem, T}, title = {Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40148567}, issn = {2058-5276}, support = {R01HD106017//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD114715//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; T15LM007079//U.S. Department of Health &amp; Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; U54DK104309//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; }, abstract = {Every step in common microbiome profiling protocols has variable efficiency for each microbe, for example, different DNA extraction efficiency for Gram-positive bacteria. These processing biases impede the identification of signals that are biologically interpretable and generalizable across studies. 'Batch-correction' methods have been used to address these issues computationally with some success, but they are largely non-interpretable and often require the use of an outcome variable in a manner that risks overfitting. We present DEBIAS-M (domain adaptation with phenotype estimation and batch integration across studies of the microbiome), an interpretable framework for inference and correction of processing bias, which facilitates domain adaptation in microbiome studies. DEBIAS-M learns bias-correction factors for each microbe in each batch that simultaneously minimize batch effects and maximize cross-study associations with phenotypes. Using diverse benchmarks including 16S rRNA and metagenomic sequencing, classification and regression, and a variety of clinical and molecular targets, we demonstrate that using DEBIAS-M improves cross-study prediction accuracy compared with commonly used batch-correction methods. Notably, we show that the inferred bias-correction factors are stable, interpretable and strongly associated with specific experimental protocols. Overall, we show that DEBIAS-M facilitates improved modelling of microbiome data and identification of interpretable signals that generalize across studies.}, }
@article {pmid40147547, year = {2025}, author = {Liu, H and Sun, R and Wu, Y and Feng, J and Fan, G and Chen, S and Li, L}, title = {Molecular detection and identification of goose astrovirus in GuangDong Province, China.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105745}, doi = {10.1016/j.meegid.2025.105745}, pmid = {40147547}, issn = {1567-7257}, abstract = {In recent years, Goose Astrovirus (GAstV) has become a major pathogen in China, afflicting geese with significant clinical manifestations like gout and urate deposits in organs. Notably, similar symptoms have emerged in ducks. From 2023 to 2024, 126 liver samples were collected from ducks in Guangdong Province, where farms reported emaciation, paralysis, and deaths. Metagenomic analysis pinpointed GAstV as the primary pathogen, with a 43.65 % confirmed positive rate via qPCR. A new strain, GD2406, was identified, showing 97.5 %-98.8 % similarity to 30 GAstV-2 strains in GenBank. GD2406 displayed 98.3 % and 97.7 % identity with the duck strains HNNY0620 and SDTA, and 98.3 % and 98.4 % identity with highly virulent GAstV strains HNKF-1 and HNSQ-6. Phylogenetic analysis indicated a genetic closeness between GD2406 and the goose strain HB01. There were 13 amino acid mutations, mainly within ORF2, and a single mutation differing from HNKF-1 and HNSQ-6, hinting at significant pathogenic potential for both ducks and geese. This study is the first to report GAstV causing severe symptoms and mortality in Muscovy ducks in Guangdong Province, suggesting ducks could be key hosts and underscoring the risk of cross-species transmission.}, }
@article {pmid40147421, year = {2025}, author = {Goswami, P and Ji, R and Shen, J and Roberts, AP and Lin, W}, title = {Genomic and metabolic characterisation of a novel species Magnetominusculus dajiuhuensis DJH-1[Ts] sp. nov. from an acidic peatland.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {3}, pages = {126605}, doi = {10.1016/j.syapm.2025.126605}, pmid = {40147421}, issn = {1618-0984}, abstract = {Magnetotactic bacteria (MTB) are recognised widely for their ability to synthesise intracellular magnetite (Fe3O4) and/or greigite (Fe3S4) nanocrystals and align with Earth's magnetic field. They are crucial for understanding prokaryotic organelle biogenesis. MTB members of the Nitrospirota phylum (previously known as the Nitrospirae phylum) are of interest due to their important ecological roles in the biogeochemical cycling of iron and sulphur. Here, we introduce Magnetominusculus dajiuhuensis DJH-1[Ts], a newly discovered Nitrospirota MTB species that thrives in the acidic Dajiuhu Peatland of central China. By combining electron microscopy, 16S rRNA gene-based analysis and genome-resolved metagenomics, we elucidate its distinctive morphology, genomic features, and metabolic functions. The metagenome-assembled genome, assigned to the genus Magnetominusculus, family Magnetobacteriaceae, order Thermodesulfovibrionales, class Thermodesulfovibrionia according to the GTDB taxonomy, reveals an obligate anaerobe that lives in central China's largest wetland. We propose the formal name Magnetominusculus dajiuhuensis DJH-1[Ts] sp. nov., following the SeqCode system. Genomic and metabolic characterisation of this novel species suggests its potential role in nitrogen, sulphur, and carbon metabolism in aquatic biogeochemistry, particularly in peatlands. The genome of this novel strain indicates that it harnesses the Wood-Ljungdahl pathway for carbon fixation and acetate metabolism in anaerobic conditions, while its potential role in nitrogen cycling is characterised by denitrification and nitrogen fixation. It also participates in reduction of sulphate to sulphide, indicating a role in sulphur cycling in its ecological niche. Taken together, the discovery and characterisation of Magnetominusculus dajiuhuensis DJH-1[Ts] provide new insights into MTB diversity and ecological functions, particularly in peatland biogeochemistry.}, }
@article {pmid40147302, year = {2025}, author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD}, title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.}, journal = {Water research}, volume = {280}, number = {}, pages = {123511}, doi = {10.1016/j.watres.2025.123511}, pmid = {40147302}, issn = {1879-2448}, abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.}, }
@article {pmid40147232, year = {2025}, author = {Wang, J and Ge, Y}, title = {Unveiling the latitudinal dependency of global patterns in soil prokaryotic gene content.}, journal = {The Science of the total environment}, volume = {974}, number = {}, pages = {179224}, doi = {10.1016/j.scitotenv.2025.179224}, pmid = {40147232}, issn = {1879-1026}, abstract = {Prokaryotic genomic traits offer insights into their functional roles, evolutionary processes, and ecological interactions, but global patterns in soil microbial genomes remain poorly understood. In this study, we examined 6436 metagenome-assembled genomes (MAGs) from global soil environments to explore the driving factors of prokaryotic gene content. Through random forest analysis, we found that, among numerous potential influencing factors such as climate, soil physicochemical properties, and human activities, geographic latitude was the primary factor affecting prokaryotic gene content. Our results showed a marked decrease in gene content from the tropics to the poles, with polar MAGs containing 10.4 % and 13.3 % fewer genes than those in tropical and temperate zones, respectively. This decline correlates with shifts in key metabolic processes, such as nitrogen fixation and energy conversion. Furthermore, we assessed interspecies metabolic interactions using Metabolic Resource Overlap (MRO) and Metabolic Interaction Potential (MIP) metrics. Our analysis revealed significantly lower MRO in high-latitude microbial communities, yet comparable MIP values to those in lower latitudes, indicating that reduced competition may contribute to genomic streamlining. These findings highlight the significant influence of latitude and interspecies interactions on microbial genomic characteristics, advancing our comprehension of microbial ecological adaptations.}, }
@article {pmid38630846, year = {2024}, author = {Phan, HV and Tsitsiklis, A and Maguire, CP and Haddad, EK and Becker, PM and Kim-Schulze, S and Lee, B and Chen, J and Hoch, A and Pickering, H and van Zalm, P and Altman, MC and Augustine, AD and Calfee, CS and Bosinger, S and Cairns, CB and Eckalbar, W and Guan, L and Jayavelu, ND and Kleinstein, SH and Krammer, F and Maecker, HT and Ozonoff, A and Peters, B and Rouphael, N and ,  and Montgomery, RR and Reed, E and Schaenman, J and Steen, H and Levy, O and Diray-Arce, J and Langelier, CR}, title = {Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology.}, journal = {Science translational medicine}, volume = {16}, number = {743}, pages = {eadj5154}, pmid = {38630846}, issn = {1946-6242}, support = {U19 AI090023/AI/NIAID NIH HHS/United States ; U19 AI118608/AI/NIAID NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; S10 OD026880/OD/NIH HHS/United States ; U19 AI077439/AI/NIAID NIH HHS/United States ; U19 AI118610/AI/NIAID NIH HHS/United States ; U19 AI167891/AI/NIAID NIH HHS/United States ; U19 AI167903/AI/NIAID NIH HHS/United States ; U19 AI128913/AI/NIAID NIH HHS/United States ; R01 AI132774/AI/NIAID NIH HHS/United States ; S10 OD030463/OD/NIH HHS/United States ; R01 AI135803/AI/NIAID NIH HHS/United States ; U19 AI089992/AI/NIAID NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; U19 AI128910/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Aged ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged, 80 and over ; *COVID-19 ; SARS-CoV-2 ; Prospective Studies ; Multiomics ; Chemokines ; }, abstract = {Age is a major risk factor for severe coronavirus disease 2019 (COVID-19), yet the mechanisms behind this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host immune response in the blood and the upper airway, as well as the nasal microbiome in a prospective, multicenter cohort of 1031 vaccine-naïve patients hospitalized for COVID-19 between 18 and 96 years old. We performed mass cytometry, serum protein profiling, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody assays, and blood and nasal transcriptomics. We found that older age correlated with increased SARS-CoV-2 viral abundance upon hospital admission, delayed viral clearance, and increased type I interferon gene expression in both the blood and upper airway. We also observed age-dependent up-regulation of innate immune signaling pathways and down-regulation of adaptive immune signaling pathways. Older adults had lower naïve T and B cell populations and higher monocyte populations. Over time, older adults demonstrated a sustained induction of pro-inflammatory genes and serum chemokines compared with younger individuals, suggesting an age-dependent impairment in inflammation resolution. Transcriptional and protein biomarkers of disease severity differed with age, with the oldest adults exhibiting greater expression of pro-inflammatory genes and proteins in severe disease. Together, our study finds that aging is associated with impaired viral clearance, dysregulated immune signaling, and persistent and potentially pathologic activation of pro-inflammatory genes and proteins.}, }
@article {pmid40146796, year = {2025}, author = {Li, J and Zhu, Y and Chang, Q and Gong, Y and Wan, J and Xu, S}, title = {Comparative Analysis of Microbiological Profiles and Antibiotic Resistance Genes in Subjects with Colorectal Cancer and Healthy Individuals.}, journal = {Polish journal of microbiology}, volume = {74}, number = {1}, pages = {71-81}, doi = {10.33073/pjm-2025-006}, pmid = {40146796}, issn = {2544-4646}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Male ; Middle Aged ; Female ; *Bacteria/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Aged ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Adult ; }, abstract = {Alteration of the gut microbiota (GM) is associated with various diseases, including colorectal cancer (CRC). With the development of next-generation sequencing techniques, metagenomic sequencing, along with metabolic function and antibiotic-resistant gene analyses, has been used to investigate differences in GM between CRC patients and healthy controls. Fecal samples were obtained from seven CRC patients and six healthy subjects, and the sequencing data were analyzed for similarity, a-diversity, principal component analysis (PCA), and linear discriminant analyses (LDA). Regarding Actinobacteria, 3 orders, 5 families, 9 genera, and 19 species were identified with no differences between the CRC and control groups, while the levels of Bifidobacterium bifidum and Bifidobacterium dentium were higher, and the level of Bifidobacterium breve was lower in the CRC group compared to the healthy controls (p = 0.053). Otherwise, 2 genera (Leuco-nostoc and Salmonella) and 7 species of bacteria (Parabacteroides merdae, Alistipes shahii, Alistipes finegoldii, Clostridium nexile, Salmonella enterica, unclassified Salmonella, Enterobacter cloacae) were found to be significantly differently distributed between CRC patients and healthy controls. PCA-LDA successfully classified these 2 groups with satisfactory accuracy (84.52% for metabolic function and 77.38% for resistant genes). These findings underscore the potential of GM as a diagnostic tool for CRC, offering a promising avenue for non-invasive screening and risk assessment. The identification of specific microbial signatures, particularly those linked to metabolic functions and resistance traits, could open new doors for understanding the role of the microbiome in CRC progression and treatment resistance.}, }
@article {pmid40146759, year = {2025}, author = {Guan, Y and Guo, H and Xia, D and Liu, Y and Wang, X}, title = {Migration of heavy metals and microbial metabolic regulation mechanisms in the co-fermentation of coal slime and sawdust.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/09593330.2025.2482966}, pmid = {40146759}, issn = {1479-487X}, abstract = {Heavy metals (HMs) significantly affect the anaerobic fermentation of coal slime (CS), while sawdust serves as a promising substrate for methane bioconversion and an effective adsorbent for HMs. To explore the migration of HMs and improve the conversion efficiency of CS and sawdust to biomethane, experiments were conducted on the co-fermentation of CS and sawdust with different mass ratios. FT-IR, ICP-MS, SEM-EDS, and metagenomic sequencing were employed to elucidate the regulation mechanism of microorganisms after adding sawdust in altering the toxicological environment. The results revealed that the optimum mass ratio of CS to sawdust was 2:1. Oxygen-containing functional groups in CS were removed, and the fatty structure was degraded. Addition of sawdust promoted the further degradation of CS and migration of various HMs. Metal elements such as Fe, Mg, Co, and Cd had also been detected on its surface. Bacillota (39.05%) was significantly enriched, which effectively improved the microbial community structure. The abundance of species with metal detoxification functions increased. The types and abundance of transporters related to toxic metal ions increased in families such as ATP-binding Cassette Superfamily (ABC) and Resistance-Nodulation-Cell Division Superfamily (RND), which would further aid in cellular homeostasis. Moreover, the addition of sawdust promoted the expression of metal resistance genes (MRGs). Multi-MRGs were primarily linked to Cu, As, and Zn, with an increased abundance of bacterial species contributing to key MRGs such as copA, ziaA, and actP. These findings offer valuable insights that support the clean and efficient utilization of CS and sawdust.}, }
@article {pmid40145240, year = {2025}, author = {Zhou, Y and Oba, K and Xu, T and Kuroiwa, M and Hori, T and Terada, A}, title = {Actively N2O-Reducing Oxygen-Tolerant Microbial Consortium Attained by Using a High-Dilution-Rate Chemostat Fed with Methanol.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12732}, pmid = {40145240}, issn = {1520-5851}, abstract = {Nitrous oxide-reducing bacteria (N2ORB) are generally considered the only biological sink for the potent greenhouse gas N2O. Although N2O consumption activities by diverse heterotrophic N2ORB have been detected, knowledge gaps remain about the phylogenies, physiologies, and activities of N2ORB. Here, we successfully enriched a methylotrophic N2ORB consortium under intermittent oxygen and N2O supplies. [15]N tracer analysis showed that the N2O consumption activity of the enriched consortium was higher than its N2O production activity in the presence of either a single or multiple electron acceptors (i.e., nitrogen oxides). The observed maximum N2O consumption was 80.7 μmol·g-biomass[-1]·h[-1]. Quantitative PCR results showed that clade I nosZ bacteria overwhelmed clade II nosZ bacteria at high (0.41 mmol·min[-1]) and low (0.08 mmol·min[-1]) N2O loading rates. The dilution rate and N2O loading rate affected the microbial community composition and activity. A higher N2O loading rate stimulated active and oxygen-tolerant N2ORB that boosted N2O consumption by approximately 50% in the presence of oxygen. Metagenomic analysis unraveled the predominance of a novel methylotrophic N2ORB, possessing entire denitrifying genes and high-affinity terminal oxidase genes, from the reactor with a high N2O loading rate. The unique physiological traits of the consortium enriched by methanol shed light on a novel function─aerobic N2O consumption by N2ORB─and pave the way for innovative N2O mitigation strategies applying powerful N2O sinks in engineered systems.}, }
@article {pmid40144527, year = {2025}, author = {Wang, J and Ren, W and Sun, Z and Liu, S and Han, Z and Wang, Y and Zeng, Y and Meng, J and Yao, X}, title = {Impact of intragastric administration of donkey milk on mouse immunity utilizing gut microbiomics and plasma metabolomics.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1486406}, pmid = {40144527}, issn = {2297-1769}, abstract = {INTRODUCTION: Donkey milk demonstrates closer compositional resemblance to human milk compared to bovine milk, positioning it as an optimal nutritional substitute for infants with cow's milk allergy. Furthermore, its rich profile of bioactive compounds suggests potential immunomodulatory properties. This study systematically investigated the effects of donkey milk supplementation on murine immune function and gut microbiome dynamics, thereby providing mechanistic insights to support its clinical development in functional food applications.<br><br>METHODS: Following daily intragastric administration of 10 mL/kg of body weight of donkey milk (DM) or distilled water (DW) to the mice for 28 consecutive days, liver tissues were harvested for immunological profiling, with concurrent collection of blood samples for plasma metabolomic analysis and fecal specimens for gut microbiome characterization. Subsequently, the modulatory effects of donkey milk supplementation on immune parameters, intestinal microbiota composition, and plasma metabolic profiles were systematically evaluated.<br><br>RESULTS: Immunity analysis revealed that intragastric administration of DM raised the levels of IL-6 and TNF-&#x3b1; cytokines in mouse liver. In addition, DM modulated the composition of both the murine gut microbiome and plasma metabolites. One-hundred and forty-five differentially-produced metabolites were identified, most prominently nicotinamide, L-valine, and &#x3b2;-estradiol, that are primarily associated with valine, leucine, and isoleucine biosynthesis and degradation, nicotinate and nicotinamide metabolism, and unsaturated fatty acid biosynthesis. Alterations at phylum, genus, and species levels were evident in the fecal microbiota of mice after intragastric administration of DM. In particular, an increased abundance of the Lactobacillus bacterium was observed. Correlation analysis of differential metabolites and microbiomes indicated a correspondence between Falsiroseomonas and Salipiger species and the antioxidant coenzyme Q that has the potential to activate the immune system.<br><br>CONCLUSION: The data collectively suggest that DM may adjust the murine gut microbiome and plasma metabolites thereby potentially improving immunity in mice.}, }
@article {pmid40144403, year = {2025}, author = {Li, Z and Zou, D and Liu, R and Pan, J and Huang, J and Ma, J and Huang, L and He, J and Fu, L and Zheng, X and Wang, M and Fang, J and Dong, H and Li, M and Huang, L and Dai, X}, title = {A hunting ground for predatory bacteria at the Zhenbei seamount in the South China Sea.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf042}, pmid = {40144403}, issn = {2730-6151}, abstract = {Seamounts are critical marine biodiversity hot spots, while the metabolic activity of their microbial community remains largely unknown. In this study, we investigated the diversity and activity of free-living and particle-attached microorganisms in the surface, middle, and bottom layers of seawater at the Zhenbei seamount in the South China Sea using omics approaches, including 16S ribosomal RNA (rRNA)/16S rDNA ratio analysis. Over 20 phyla were detected, with Proteobacteria, Actinobacteriota, Cyanobacteria, Bacteroidota, Thaumarchaeota, and Planctomycetota being predominant. Surprisingly, Bdellovibrionota and Myxococcota, the two well-known predatory bacteria, exhibited exceptionally higher rRNA/rDNA ratios than the other phyla, with rRNA abundances being 10- or even 200-fold higher than their rDNA abundances. These metabolically active predatory bacteria are mainly uncultured species. A total of 23 Myxococcota metagenome-assembled genomes (MAGs) and 12 Bdellovibrionota MAGs were assembled. The most highly overexpressed genes frequently detected in these MAGs were those that encode flagellum and pilus proteins as well as T4-like virus tail tube protein, indicating that these predator bacteria were likely active in hunting. Our results suggest that seamounts may serve as hunting grounds for predatory bacteria, which may be involved in controlling the flows of elements and energy in the seamount microbial communities and, thus, in shaping the seamount ecosystems.}, }
@article {pmid40143870, year = {2025}, author = {Hu, Y and Zhou, J and Lin, X}, title = {Akkermansia muciniphila helps in the recovery of lipopolysaccharide-fed mice with mild intestinal dysfunction.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1523742}, pmid = {40143870}, issn = {1664-302X}, abstract = {BACKGROUND: Mild intestinal dysfunction, linked to subtle yet significant health issues, can be induced by lipopolysaccharide (LPS), a Gram-negative bacterial component that disrupts gut function and triggers inflammation. Akkermansia muciniphila has shown promise as a probiotic for gut health due to its roles in mucin degradation and short-chain fatty acid production. This study explores the therapeutic effects of Akkermansia muciniphila on LPS-induced mild intestinal dysfunction in mice.<br><br>METHODS: Thirty-eight 6-week-old C57BL/6 mice were split into control (n&#x202f;=&#x202f;19) and LPS-treated (n&#x202f;=&#x202f;19) groups. LPS-treated mice received 300&#x202f;&#x3bc;g/kg/day of LPS for 4&#x202f;weeks, followed by Akkermansia muciniphila supplementation at 41&#x202f;mg/kg/day (Akk1) or 82&#x202f;mg/kg/day (Akk2) for another 4&#x202f;weeks. Gut microbiota was analyzed via metagenomic sequencing, and gene expression was evaluated through transcriptomics.<br><br>RESULTS: LPS significantly altered gut microbiota, reducing diversity and increasing pathogenic genera like Lachnoclostridium. Akkermansia muciniphila supplementation, particularly at higher doses, partially restored gut microbiota by increasing beneficial genera such as Muribaculum. Transcriptomics showed that LPS induced immune and inflammatory responses, while Akkermansia muciniphila reduced these effects by modulating pathways like TNF and NF-kappa B signaling.<br><br>CONCLUSION: Akkermansia muciniphila mitigates LPS-induced gut dysfunction by restoring microbiota balance and modulating immune responses, highlighting its potential as a therapeutic agent for gut health.}, }
@article {pmid40143862, year = {2025}, author = {Sujatha, S and Sindhura, KAV and Koti, PS and Hiremath, S and Muttappagol, M and Vinay Kumar, HD and Shankarappa, KS and Venkataravanappa, V and Reddy, KMS and Reddy, CNL}, title = {Influence of weather and seasonal factors on whitefly dynamics, associated endosymbiotic microbiomes, and Begomovirus transmission causing tomato leaf curl disease: insights from a metagenomic perspective.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1555058}, pmid = {40143862}, issn = {1664-302X}, abstract = {INTRODUCTION: Bemisia tabaci (Gennadius) is a globally significant agricultural pest, responsible for transmitting over 120 plant viruses, including those from the Begomovirus genus, which contribute to considerable crop losses. The species complex comprises cryptic species, associated with a diverse array of bacterial endosymbionts that play essential roles in host nutrition, virus transmission, and overall host adaptability. These endosymbionts are classified into primary and secondary categories, with primary endosymbionts forming obligatory, long-term associations, and secondary endosymbionts influencing factors such as biotype differentiation and vector competency. Notably, these microbial communities enhance B. tabaci's capacity to transmit viruses, including the tomato leaf curl virus (ToLCuV), which poses a significant threat to tomato production.<br><br>METHODS: In this study, we examined the population dynamics of B. tabaci across three major tomato-growing regions in Karnataka, South India, focusing on their seasonal associations with endosymbionts and the incidence of tomato leaf curl disease (ToLCuD). Multiple regression analysis was employed to assess the influence of weather parameters on whitefly populations and disease prevalence. Additionally, we constructed a metagenomic profile to evaluate the effects of geographical location, seasonality, environmental factors, and agricultural practices on the bacterial communities associated with B. tabaci. Species-specific primers were used to validate the presence and diversity of these bacterial communities.<br><br>RESULTS: Meteorological data revealed a positive correlation between temperature and B. tabaci populations, which corresponded with an increased incidence of ToLCuD. Genetic characterization of the whitefly identified Asia II-5 and Asia II-7 cryptic species as the dominant forms in the surveyed regions, with Portiera emerging as the most prevalent endosymbiont. A more in-depth analysis of the microbial communities associated with B. tabaci, utilizing 16S rRNA metagenomic sequencing, revealed a dominance of the Proteobacteria phylum. The endosymbiotic bacterial consortium was primarily composed of Candidatus Portiera, Candidatus Hamiltonella, Candidatus Rickettsia, and Candidatus Arsenophonus.<br><br>DISCUSSION: The metagenomic analysis revealed a highly diverse array of bacterial communities, with 92% of sequences classified under Proteobacteria, representing a spectrum of microbial types associated with B. tabaci ranging from parasitic and pathogenic to mutualistic. Within this phylum, Alphaproteobacteria were predominant, known for their role as facultative symbionts, while Gammaproteobacteria provided essential nutrients to arthropods, enhancing their survival and fitness. The interplay of continuous and intensive tomato cultivation, elevated temperatures, favorable host plants, and abundant viral inoculum creates an ideal environment for the proliferation of B. tabaci and the widespread transmission of ToLCuD. The presence of diverse cryptic species of B. tabaci, which are efficient viral vectors, further complicates the situation. These findings underscore the urgent need for integrated management strategies globally to control both whitefly populations and ToLCuD, ensuring the protection of tomato crops and the sustainability of farmer livelihoods.}, }
@article {pmid40143285, year = {2025}, author = {Popov, N and Sonets, I and Evdokimova, A and Molchanova, M and Panova, V and Korneenko, E and Manolov, A and Ilina, E}, title = {AliMarko: A Pipeline for Virus Identification Using an Expert-Guided Approach.}, journal = {Viruses}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/v17030355}, pmid = {40143285}, issn = {1999-4915}, support = {122030900069-4//Russian State/ ; }, mesh = {*Phylogeny ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation &amp; purification ; *Feces/virology ; Animals ; *Genome, Viral ; Humans ; Metagenome ; Chiroptera/virology ; Computational Biology/methods ; Software ; Sequence Analysis, RNA/methods ; }, abstract = {Viruses are ubiquitous across all kingdoms of cellular life, posing a significant threat to human health, and analyzing viral communities is challenging due to their genetic diversity and lack of a single, universally conserved marker gene. To address this challenge, we developed the AliMarko pipeline, a tool designed to streamline virus identification in metagenomic data. Our pipeline uses a dual approach, combining mapping reads with reference genomes and a de novo assembly-based approach involving an HMM-based homology search and phylogenetic analysis, to enable comprehensive detection of viral sequences, including low-coverage and divergent sequences. We applied our pipeline to total RNA sequencing of bat feces and identified a range of viruses, quickly validating viral sequences and assessing their phylogenetic relationships. We hope that the AliMarko pipeline will be a useful resource for the scientific community, facilitating the interpretation of viral communities and advancing our understanding of viral diversity and its impact on human health.}, }
@article {pmid40143275, year = {2025}, author = {Sarana da Silva, A and de Campos, GM and Altizani, GM and de Carvalho, E and Barros, AC and Cella, E and Kashima, S and Sampaio, SC and Elias, MC and Giovanetti, M and Scrideli, CA and Slavov, SN}, title = {Utilizing Viral Metagenomics to Characterize Pathogenic and Commensal Viruses in Pediatric Patients with Febrile Neutropenia.}, journal = {Viruses}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/v17030345}, pmid = {40143275}, issn = {1999-4915}, support = {17/23205-8; 21/11944-6; 2022/10278-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 403075/2023-8; 305111/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Humans ; *Metagenomics/methods ; Child ; Male ; Female ; Child, Preschool ; *Febrile Neutropenia/virology ; Adolescent ; Viruses/classification/genetics/isolation &amp; purification ; Infant ; Herpesviridae/genetics/classification/isolation &amp; purification ; Oropharynx/virology ; Neoplasms/virology/complications ; Metagenome ; }, abstract = {Febrile neutropenia (FN) is one of the most common complications in pediatric oncology patients. It has a complex etiologic nature, which in the majority of cases remains unclear. Intervention often follows empirical treatment protocols, mainly using broad-spectrum antibiotics. To evaluate potential viral etiologic agents, this study applied viral metagenomics to paired plasma and oropharyngeal samples obtained from pediatric patients with oncological diseases diagnosed with FN. Metagenomic sequencing was performed on 15 pediatric patients with oncological diseases and FN at the outpatient clinic of Pediatric Oncology at the University Hospital of the Faculty of Medicine of Ribeirão Preto, University of São Paulo. As a control group, we included 15 pediatric patients with oncological diseases in remission or undergoing treatment. Clinically relevant viruses identified by metagenomics in FN patients predominantly included herpesviruses and viruses found in the respiratory tract, like adenoviruses. Direct molecular confirmation was performed on all of them. Anelloviruses, represented by various genera and species in all groups, were also highly prevalent. The data obtained in this study show that viruses might also have possible implications for the etiology of FN. However, due to the complex nature of this disease, more studies are necessary to evaluate their causal relationship. The results obtained in our study may serve to improve patient treatment and ensure adequate management.}, }
@article {pmid40142589, year = {2025}, author = {Chen, X and Gao, L and Kou, Y and Wang, X and Li, X and He, H and Wang, M}, title = {Composition, Distribution and Mobility Potential of the Antibiotic Resistome in Sediments from the East China Sea Revealed by Metagenomic Analysis.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030697}, pmid = {40142589}, issn = {2076-2607}, support = {41806131//National Natural Science Foundation of China/ ; 42120104006//National Natural Science Foundation of China/ ; ZR2024QD036//Natural Science Foundation of Shandong Province/ ; }, abstract = {Marine sediments are recognized as crucial reservoirs of antibiotic resistance genes (ARGs). However, the antibiotic resistome in sediments of the East China Sea, an area heavily impacted by human activities, has not been thoroughly studied. Here, we conducted a systematic investigation into the antibiotic resistome in these sediments using metagenomic analysis. Overall, we detected eighty ARG subtypes and nineteen ARG types. Beta-lactams were the dominant ARG type, and Gammaproteobacteria was the main ARG host in this study. Mobile genetic elements (MGEs) were not major drivers of ARG profiles. Although the ARG host communities significantly differed between the spring and autumn (p < 0.05), the antibiotic resistome remained stable across the two seasons. The assembly of ARGs and their hosts was governed by stochastic processes, and a high ratio of stochastic processes implied its crucial role in the assembly and stabilization of the antibiotic resistome. Co-occurrence network analysis revealed an important role of Deltaproteobacteria in the stabilization of ARG profiles across seasons. Environmental parameters (e.g., temperature and density) played certain roles in the stabilization of the antibiotic resistome between spring and autumn. Moreover, nine human pathogen bacteria (HPB) were detected in this study. We also found that the health risks caused by ARGs were relatively higher in the spring. Our results will provide a strong foundation for the development of targeted management strategies to mitigate the further dissemination and spread of ARGs in marine sediments.}, }
@article {pmid40142582, year = {2025}, author = {Peng, Y and Jiang, L and Wu, J and Yang, J and Guo, Z and Miao, M and Peng, Z and Chang, M and Miao, B and Liu, H and Liang, Y and Yin, H and He, Q and Liu, X}, title = {Red Mud Potentially Alleviates Ammonia Nitrogen Inhibition in Swine Manure Anaerobic Digestion by Enhancing Phage-Mediated Ammonia Assimilation.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030690}, pmid = {40142582}, issn = {2076-2607}, support = {Grant No. 2018YFC1800400//the National Key Research and Development Program of China/ ; Grant No. 51909282//the National Natural Science Foundation of China/ ; Grant No. 2022JJ40583//the Natural Science Foundation of Hunan Province of China/ ; Grant No. 2022WK2017//the Hunan Provincial Key Research and Development Plan/ ; Grant No. 2023NK2030//the Hunan Provincial Key Research and Development Plan/ ; }, abstract = {Red mud has been demonstrated to improve the methane production performance of anaerobic digestion (AD). However, the influence of red mud on ammonia nitrogen inhibition during AD through the mediating role of bacteria-phages interactions in this process remains poorly understood. Thus, this study investigated the impact of red mud on nitrogen metabolism in AD and characterized the phage and prokaryotic communities through a metagenomic analysis. The results showed that red mud significantly increased methane production by 23.1% and promoted the conversion of ammonia nitrogen into organic nitrogen, resulting in a 4.8% increase in total nitrogen. Simultaneously, it enriched the key microbial genera Methanothrix, Proteinophilum, and Petrimonas by 0.5%, 0.8%, and 2.7%, respectively, suggesting an enhancement in syntrophic acetate oxidation with greater ammonia tolerance. A viral metagenomic analysis identified seven nitrogen-metabolism-related auxiliary metabolic genes (AMGs), with glnA (encoding glutamine synthetase) being the most abundant. Compared to the control treatments, the red mud treatments led to a higher abundance of temperate phages and an increased number of AMGs. Furthermore, two new hosts carrying glnA (Mycolicibacteria smegmatis and Kitasatopola aureofaciens) were predicted, indicating that red mud expanded the host range of phages and promoted the spread of AMGs. Overall, our findings highlight the importance of phages in alleviating ammonia nitrogen inhibition and provide a novel understanding of the role of red mud in the AD of swine manure.}, }
@article {pmid40142572, year = {2025}, author = {Yi, Q and Zhang, G and Wang, T and Li, J and Kang, W and Zhang, J and Liu, Y and Xu, Y}, title = {Comparative Analysis of Metagenomic Next-Generation Sequencing, Sanger Sequencing, and Conventional Culture for Detecting Common Pathogens Causing Lower Respiratory Tract Infections in Clinical Samples.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030682}, pmid = {40142572}, issn = {2076-2607}, support = {2022-PUMCH-B-074//National High Level Hospital Clinical Research Funding/ ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary tool for infectious disease diagnostics. The necessity of mNGS in real-world clinical practice for common Lower Respiratory Tract Infections (LRTI) needs further evaluation. A total of 184 bronchoalveolar lavage fluid (BALF) samples and 322 sputa associated with LRTI were fully examined. The detection performance was compared between mNGS and standard microbiology culture, using Sanger sequencing as the reference method. 52.05% (165/317) of sputa showed identical results for all three methods. Compared to Sanger sequencing, the same results obtained by mNGS were 88.20% (284/322). In 2.80% (9/322) of cases, Sanger sequencing detected more microorganisms, while mNGS detected more in 9% (29/322) of cases. For BALF, 49.41% (85/172) of cases showed identical results for all three methods. In 91.30% (168/184) of cases, identical results were produced by both mNGS and Sanger sequencing. mNGS detected more species in 7.61% (14/184) of cases, whereas in 2.80% (2/184) instances, the Sanger sequencing detected more microorganisms than mNGS. In the 184 BALF samples, 66 samples were identified as having co-infections by mNGS, Sanger sequencing identified 64 samples, and cultures identified 22 samples. Our study demonstrates that mNGS offers a significant advantage over conventional culture methods in detecting co-infections. For common bacterial pathogens, conventional culture methods are sufficient for detection. However, mNGS provides comprehensive pathogen detection and is particularly useful for identifying rare and difficult-to-culture pathogens.}, }
@article {pmid40142491, year = {2025}, author = {Kioukis, A and Camargo, AP and Pavlidis, P and Iliopoulos, I and Kyrpides, NC and Lagkouvardos, I}, title = {Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030598}, pmid = {40142491}, issn = {2076-2607}, support = {710//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//Joint Genome Institute/ ; }, abstract = {The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as Archaea from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the 'Global Archaea Diversity' (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the Archaea, offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life.}, }
@article {pmid40142462, year = {2025}, author = {Hadian, S and Smith, DL and Supronienė, S}, title = {Modulating the Plant Microbiome: Effects of Seed Inoculation with Endophytic Bacteria on Microbial Diversity and Growth Enhancement in Pea Plants.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030570}, pmid = {40142462}, issn = {2076-2607}, abstract = {Understanding plant microbe interactions is crucial for achieving sustainable agriculture. This study investigated the effects of inoculating pea plants (Pisum sativum) with two endophytic Bacillus strains, AR11 and AR32, isolated from Artemisia species and characterized by phosphate solubilization, nitrogen fixation, and pathogen antagonism. Utilizing cutting-edge methods such as rarefaction curves, rank abundance modeling, and metagenomic analysis, this research provides a detailed understanding of how these bacterial strains influence plant associated microbiomes. AR11 significantly enhanced microbial diversity, while AR32 showed a moderate effect. Beta diversity analyses revealed distinct shifts in microbial community composition, with AR11-treated samples enriched with beneficial taxa such as Paenibacillus, Flavobacterium, and Methylotenera, known for their roles in nutrient cycling, pathogen suppression, and plant health promotion. This innovative methodological framework surpasses traditional approaches by offering a comprehensive view of ecological and functional microbiome shifts. The study highlights the potential of nonhost bacteria as biostimulants and their role in developing microbiome engineering strategies to enhance plant resilience. These findings contribute to sustainable agriculture by demonstrating how microbial inoculants can be employed to enhance crop productivity and environmental resilience in diverse agricultural systems.}, }
@article {pmid40142456, year = {2025}, author = {Zhu, S and Guo, Z and Liu, L and Gao, Y and Bai, L and Chen, Y and Zha, M}, title = {Complex Probiotics Relieve Constipation Through Regulation of the Intestinal Microbiota in Kittens.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030563}, pmid = {40142456}, issn = {2076-2607}, support = {2024LHMS03043//The Natural Science Foundation of Inner Mongolia, China/ ; 2022 - Science and Technology Xing Meng - Quality improvement - 02//Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; SPYQ202001//The Cultivation Project for Excellent Youth of Inner Mongolia Agricultural University/ ; }, abstract = {The early developmental phase is a critical window for feline growth, during which immature digestive systems are susceptible to microbiome imbalances caused by environmental stressors. Our research employed macrogenomic analysis to evaluate how complex probiotic formulations influence growth metrics and gastrointestinal flora in juvenile felines. Two dozen healthy kittens were equally divided into the control group and the probiotics group following a 5-day environmental adaptation phase. Fecal scores were recorded daily for all kittens. Fresh fecal samples were collected on days 1 and 14 for macrogenomic analysis. The results showed a significantly lower rate of constipation in the probiotics group compared to the control group (p < 0.05). However, no significant differences were observed in intestinal microbial diversity or structure between the two groups. Metagenomic analysis revealed a higher relative abundance of Bifidobacterium animalis in the probiotics group compared to the control group (p < 0.05). Additionally, the probiotics group exhibited lower relative abundances of Lachnospiraceae bacterium 2 1 58FAA, Lachnospiraceae bacterium 1 1 57FAA, and Acidaminococcus intestini compared to the control group (p < 0.05). These results suggest that complex probiotics can regulate the intestinal microbiota, improve constipation, and promote intestinal health in kittens.}, }
@article {pmid40142431, year = {2025}, author = {Aires, C and Maioto, R and Inês, A and Dias, AA and Rodrigues, P and Egas, C and Sampaio, A}, title = {Microbiome and Microbiota Within Wineries: A Review.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030538}, pmid = {40142431}, issn = {2076-2607}, abstract = {The main goal of this work is to review the winery's microbiota, from the grape to the winery's microbial niches (fermentation tanks, surfaces, air), and their risks to wine and human health. The impact of climate change on the winery microbiome and related challenges are also discussed. Microbial diversity in wineries depends on several factors, such as the grape variety and its ripeness, temperature, relative humidity and the diverse activities of the winemaking process. Winery surfaces and equipment allow the establishment of a microbial community that can impact wine quality, the health of winery workers and visitors and even wine consumers. In the context of climate change, changes in the sugar content, phenolic compounds and the profile of hexoses and amino acids are already evident. These changes interfere with the fermentation microbiota and the quality of the wines, which are more alcoholic and less acidic. Furthermore, periods of drought or heavy rain favor species associated with berry diseases, including some capable of producing mycotoxins or harmful biogenic amines. In order to understand the impact of these changes on microbial communities, the use of various techniques will be discussed, such as flow cytometry, fluorescence in situ hybridization (FISH), quantitative polymerase chain reaction (qPCR) and metagenomic methods.}, }
@article {pmid40142426, year = {2025}, author = {Needle, DB and Reboul, G and Mitchell, PK and Rothenheber, D and Marra, NJ and Cronk, BD and Patel, NG and Goodman, LB}, title = {Application of Amplicon Metagenomics to Identify Fungal Pathogens in Formalin-Fixed Paraffin-Embedded Samples: Proof of Concept in Animals with Fungal Pathologies.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030533}, pmid = {40142426}, issn = {2076-2607}, support = {1U18FD006716//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network (FDA Vet-LIRN)/ ; 1R03DE033304-01A1/NH/NIH HHS/United States ; }, abstract = {The identification of fungal pathogens in formalin-fixed paraffin-embedded (FFPE) tissues is an unmet need in human and animal medicine, and sequence-agnostic approaches are needed to identify emerging pathogens. Eleven FFPE biopsy specimens with etiologic diagnoses of fungal disease based on standard testing of paired fresh tissue samples were utilized here to evaluate metabarcoding approaches. The cases included tissues from three dogs, three cats, one box turtle, one goat, one common loon, and one gray tree frog. The diagnoses from the fresh tissues in these cases were Microsporum canis, Penicillium sp., Exophiala sp. (likely E. jeanselmei), Verticillium sp., Rhizopus sp., atypical Cryptococcus neoformans, Conidiobolus spp., Aspergillus fumigatus, Cryptococcus neoformans var grubii, Batrachochytrium dendrobatidis, Fusarium solani, Blastomyces dermatitidis, Coccidiodes immitis, and Histoplasma capsulatum. We compared the ITS1 and 28S D1 rRNA gene genetic markers in combination with several bioinformatic strategies to identify fungal pathogens in the FFPE tissue samples, with a success rate of 9/11. These methods could allow diagnosticians who receive only FFPE tissues and see fungal pathogens to speciate the pathogens and could be of value in retrospective studies wherein FFPE tissue is the only archived tissue. Furthermore, these techniques could be of use to researchers investigating polymicrobial communities where DNA preservation is suboptimal.}, }
@article {pmid40142417, year = {2025}, author = {Chao, S and Chen, Y and Wu, J and Zhang, Y and Song, L and Li, P and Sun, Y and Hu, Y and Wang, H and Jiang, Y and Lv, B}, title = {Exserohilum turcicum Alters Phyllosphere Microbiome Diversity and Functions-Implications for Plant Health Management.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030524}, pmid = {40142417}, issn = {2076-2607}, support = {2024-02-08-00-12-F00021//Shanghai Agriculture Applied Technology Development Program, China/ ; 32302635//National Natural Science Foundation of China/ ; 22ZR1442500//Natural Science Foundation of Shanghai/ ; SAAS Application Basic Study 2025(08)//2025 SAAS Project on Agricultural Science and Technology Innovation Supporting Area/ ; 016//Shanghai Academy of Agricultural Sciences 2022/ ; 20DZ2255300//Shanghai Engineering Research Center of Specialty Maize/ ; 2023ZD04062//the Science and Technology Innovation 2030 Biological Breeding-Major Projects/ ; 23DZ2290700//Shanghai "Science and Technology Innovation Action Plan" Professional Technical Service Platform Project/ ; }, abstract = {The phyllosphere represents the largest biological surface on Earth and serves as an untapped reservoir of functional microbiota. The phyllosphere microbiome has the potential to mitigate plant diseases; however, limited information exists regarding its role in maintaining plant health. In this study, metagenomic sequencing was employed to analyze the microbiomes of the adaxial and abaxial leaf surfaces of healthy (CKWT) and diseased (EWT) maize, with the aim of dissecting the influence of Exserohilum turcicum on phyllosphere microbiome function. E. turcicum altered the alpha and beta diversity of the phyllosphere microbiome, with the Shannon diversity and Chao1 index values significantly reduced in EWT. More beneficial microbes accumulated in the CKWT phyllosphere, whereas pathogenic microbes decreased. E. turcicum may have altered the balance between commensal and pathogenic microorganisms. The species and abundances of microorganisms on the two sets of leaf surfaces were also altered after inoculation with E. turcicum. Further analysis of disease-resistance-related metabolic pathways and abundances of antibiotic-resistance genes revealed that E. turcicum altered the abundance of the functional microbiome and modified the microbiome differences between adaxial and abaxial leaf surfaces. In conclusion, the results reveal that microbial diversity in the maize phyllosphere can influence the microbiome and regulate microbial functions to support plant health. These findings enhance our understanding of how E. turcicum affects the phyllosphere microbiome and provide a theoretical basis for biological control of E. turcicum.}, }
@article {pmid40142410, year = {2025}, author = {Hassen, AI and Muema, EK and Diale, MO and Mpai, T and Bopape, FL}, title = {Non-Rhizobial Endophytes (NREs) of the Nodule Microbiome Have Synergistic Roles in Beneficial Tripartite Plant-Microbe Interactions.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030518}, pmid = {40142410}, issn = {2076-2607}, support = {A-089//Department of Agriculture Land Reform and Rural Development/ ; }, abstract = {Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant-microbe interactions that occur in the soil rhizosphere and one of the oldest plant-microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs).}, }
@article {pmid40141768, year = {2025}, author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM}, title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/life15030423}, pmid = {40141768}, issn = {2075-1729}, support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; }, abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.}, }
@article {pmid40140988, year = {2025}, author = {Yan, Q and Huang, L and Li, S and Zhang, Y and Guo, R and Zhang, P and Lei, Z and Lv, Q and Chen, F and Li, Z and Meng, J and Li, J and Wang, G and Chen, C and Ullah, H and Cheng, L and Fan, S and You, W and Zhang, Y and Ma, J and Sha, S and Sun, W}, title = {The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {30}, pmid = {40140988}, issn = {1756-994X}, mesh = {Humans ; *Virome/genetics ; *Viruses/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; China ; Female ; Feces/virology ; Male ; Metagenomics/methods ; Genome, Viral ; Asian People/genetics ; East Asian People ; }, abstract = {BACKGROUND: The gut viral community has been increasingly recognized for its role in human physiology and health; however, our understanding of its genetic makeup, functional potential, and disease associations remains incomplete.<br><br>METHODS: In this study, we collected 11,286 bulk or viral metagenomes from fecal samples across large-scale Chinese populations to establish a Chinese Gut Virus Catalogue (cnGVC) using a de novo virus identification approach. We then examined the diversity and compositional patterns of the gut virome in relation to common diseases by analyzing 6311 bulk metagenomes representing 28 disease or unhealthy states.<br><br>RESULTS: The cnGVC contains 93,462 nonredundant viral genomes, with over 70% of these being novel viruses not included in existing gut viral databases. This resource enabled us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we profiled the gut virome in large-scale populations, assessed sex- and age-related variations, and identified 4238 universal viral signatures of diseases. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC&#x2009;=&#x2009;0.698) and high-risk patients from controls (AUC&#x2009;=&#x2009;0.761), and its predictive ability was also validated in external cohorts.<br><br>CONCLUSIONS: Our resources and findings significantly expand the current understanding of the human gut virome and provide a comprehensive view of the associations between gut viruses and common diseases. This will pave the way for novel strategies in the treatment and prevention of these diseases.}, }
@article {pmid40140753, year = {2025}, author = {Yan, Z and Wang, Y and Zeng, W and Hui, J and Yang, B and Xu, J and Miao, Y and Xia, R}, title = {Antibiotic-driven pathogen replacement events in a kidney transplant recipient with ADPKD: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {423}, pmid = {40140753}, issn = {1471-2334}, support = {82270784//National Natural Science Foundation of China/ ; 2023A1515012276//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2024CL-GX03//Clinical High-tech and Major Technology Projects in Guangzhou Area/ ; }, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Polycystic Kidney, Autosomal Dominant/complications/surgery ; *Anti-Bacterial Agents/therapeutic use ; Male ; Transplant Recipients ; Middle Aged ; Nephrectomy ; Enterococcus faecium/isolation &amp; purification/drug effects ; }, abstract = {BACKGROUND: Retaining the native bilateral kidneys after transplantation is a common treatment for patients with end-stage autosomal dominant polycystic kidney disease. However, this strategy poses the risks of potential complications from polycystic kidney infection. The efficiency of antibiotic therapy and the optimal time for native nephrectomy in managing these infections remain uncertain.<br><br>CASE PRESENTATION: We report a case of a kidney transplant recipient with retained bilateral polycystic kidneys who experienced recurrent cyst and bloodstream infections, accompanied by antibiotic-driven pathogen replacement. After multiple failed attempts at antibiotic therapy, the patient subsequently underwent unilateral polycystic kidney resection. Subsequently, a new infection episode occurred, leading to the other native nephrectomy. Cystic tissue and fluid samples were collected from both shallow and deep layers of the polycystic kidneys, along with peripheral blood and urine samples. These samples were analyzed using microbial culture, metagenome sequencing, and digital polymerase chain reaction to identify infectious pathogens. Pathogen replacement occurred across different infection episodes, with the dominant bacterial species being Escherichia coli, Klebsiella aerogenes, and Enterococcus faecium, in succession.<br><br>CONCLUSIONS: This case highlights the replacement of dominant pathogens under antibiotic selection pressure in polycystic kidney infections, primarily involving gram-negative bacilli. When initial and subsequent antibiotic therapy fail, re-evaluation of the cyst infection definition is necessary, and preemptive native nephrectomy should be considered.}, }
@article {pmid40140741, year = {2025}, author = {Zhao, X and Liu, X and Wang, Z and Wei, S and Wu, Z}, title = {Metagenomic next-generation sequencing for the diagnosis of Corynebacterium striatum meningitis: case report and literature review.}, journal = {BMC neurology}, volume = {25}, number = {1}, pages = {127}, pmid = {40140741}, issn = {1471-2377}, support = {20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; 20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; 20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; [2023]14-73//Shanxi Provincial Department of Education/ ; }, mesh = {Humans ; Male ; Aged ; *Corynebacterium/isolation &amp; purification/genetics ; *Corynebacterium Infections/diagnosis/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Meningitis, Bacterial/diagnosis/drug therapy/microbiology ; }, abstract = {OBJECTIVE: To report a case of Corynebacterium striatum meningitis and conduct a comprehensive literature review to determine the clinical presentation, microbiology, and treatment approaches for these patients.<br><br>MATERIALS AND METHODS: A 75-year-old male patient presented with headache and fever; however, bacterial cultures of cerebrospinal fluid (CSF) yielded negative results. Metagenomic next-generation sequencing (mNGS) of CSF subsequently identified Corynebacterium striatum meningitis as the causative agent for meningitis. A systematic search was performed across various databases encompassing systematic reviews, cohort studies, case series, and case reports involving patients diagnosed with Corynebacterium striatum meningitis regardless of age. Clinical presentation characteristics and the most frequently employed diagnostic technologies were obtained. A narrative summary of the findings is presented.<br><br>RESULTS: Corynebacterium striatum meningitis patients do not exhibit any specific age or sex predisposition or distinctive symptoms or signs. In patients with Corynebacterium striatum meningitis, CSF tests typically reveal an increased number of white blood cells (predominantly polymorphonuclear cells), elevated protein levels, and decreased glucose levels. Notably, the prevalence of antibiotic-resistant strains of Corynebacterium striatum has increased in recent years, leading to a gradual rise in antibiotic treatment failure rates. It is predicted that by 2030, vancomycin may be the sole effective drug available.<br><br>CONCLUSION: The possibility of Corynebacterium striatum infection should be considered during clinical diagnosis and laboratory testing procedures for bacterial meningitis. mNGS can serve as a supplementary gold standard in the diagnosis of bacterial meningitis, effectively enhancing the detection rate of rare pathogens.}, }
@article {pmid40140706, year = {2025}, author = {Best, L and Dost, T and Esser, D and Flor, S and Gamarra, AM and Haase, M and Kadibalban, AS and Marinos, G and Walker, A and Zimmermann, J and Simon, R and Schmidt, S and Taubenheim, J and Künzel, S and Häsler, R and Franzenburg, S and Groth, M and Waschina, S and Rosenstiel, P and Sommer, F and Witte, OW and Schmitt-Kopplin, P and Baines, JF and Frahm, C and Kaleta, C}, title = {Metabolic modelling reveals the aging-associated decline of host-microbiome metabolic interactions in mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40140706}, issn = {2058-5276}, support = {859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; FOR5042//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 416 418087534//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Aging is accompanied by considerable changes in the gut microbiome, yet the molecular mechanisms driving aging and the role of the microbiome remain unclear. Here we combined metagenomics, transcriptomics and metabolomics from aging mice with metabolic modelling to characterize host-microbiome interactions during aging. Reconstructing integrated metabolic models of host and 181 mouse gut microorganisms, we show a complex dependency of host metabolism on known and previously undescribed microbial interactions. We observed a pronounced reduction in metabolic activity within the aging microbiome accompanied by reduced beneficial interactions between bacterial species. These changes coincided with increased systemic inflammation and the downregulation of essential host pathways, particularly in nucleotide metabolism, predicted to rely on the microbiota and critical for preserving intestinal barrier function, cellular replication and homeostasis. Our results elucidate microbiome-host interactions that potentially influence host aging processes. These pathways could serve as future targets for the development of microbiome-based anti-aging therapies.}, }
@article {pmid40140705, year = {2025}, author = {Garrido-Sanz, D and Keel, C}, title = {Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40140705}, issn = {2058-5276}, abstract = {Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.}, }
@article {pmid40140473, year = {2025}, author = {Brown, AA and Widdowson, M and Brandt, S and Mohammadzadeh, P and Rosenberg, JB and Jepsen, JRM and Ebdrup, BH and Hernández-Lorca, M and Bønnelykke, K and Chawes, B and Stokholm, J and Thorsen, J and Ibrahimi, P and Li, X and Sørensen, SJ and Rasmussen, MA}, title = {Associations of the gut microbiome and inflammatory markers with mental health symptoms: a cross-sectional study on Danish adolescents.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10378}, pmid = {40140473}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Adolescent ; Cross-Sectional Studies ; Female ; Denmark/epidemiology ; *Inflammation/metabolism ; *Attention Deficit Disorder with Hyperactivity/metabolism/microbiology ; *Biomarkers ; *Depression/metabolism ; Anxiety/microbiology ; Mental Health ; Stress, Psychological/metabolism ; Feces/microbiology ; }, abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder that often persists into adulthood and is accompanied by comorbid mental health problems. This cross-sectional cohort study analyzed 411 18-year-olds from the Danish COPSAC2000 birth cohort to investigate the relationship between the gut microbiome, fasting and postprandial systemic inflammation, ADHD symptoms, and symptoms of anxiety, stress, and depression. ADHD was assessed using the Adult ADHD Self-Report Scale (ASRS), while depression, stress, and anxiety were evaluated with the Depression, Anxiety, and Stress Scale 21 (DASS-21). Fecal metagenomic data and inflammation levels, measured as glycosylated protein A (GlycA), were analyzed following a standardized meal challenge. In males, higher ADHD symptom scores correlated significantly with increased abundance of a tryptophan biosynthesis pathway (MetaCyc Metabolic Pathways Database) and elevated fasting and postprandial GlycA levels (p < 0.05). While the severity of depression, anxiety, and stress symptoms showed weak associations with GlycA and the gut microbiome, our findings indicate a significant link between ADHD symptoms and postprandial inflammation, warranting further investigation into underlying mechanisms.}, }
@article {pmid40140149, year = {2025}, author = {Ananda, A and Brigiyanti, LN and Widhiastuty, MP and Haryati, T and Suharti,  and Ma'ruf, IF and Akhmaloka, }, title = {Characterization and molecular dynamics simulation of Lk2 lipase expressed in Pichia pastoris.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {342}, pmid = {40140149}, issn = {1573-4978}, support = {12/II.7/HK/2023//RIIM Research Project Program, National Research and Innovation/ ; }, mesh = {*Lipase/genetics/metabolism/chemistry/isolation &amp; purification ; *Molecular Dynamics Simulation ; Substrate Specificity ; Pichia/genetics/metabolism ; Hydrogen-Ion Concentration ; Fungal Proteins/genetics/metabolism/chemistry ; Recombinant Proteins/metabolism/genetics/isolation &amp; purification/chemistry ; Molecular Docking Simulation ; Hydrolysis ; Saccharomycetales ; }, abstract = {BACKGROUND: Lipase is a versatile enzyme that serves as a biocatalyst in various industries. lk2 was successfully isolated from household waste compost through a metagenomic approach.<br><br>MATERIALS AND METHODS: lk2 from plasmid pPICZ&#x3b1;A- lk2 was integrated into chromosomes of Pichia. pastoris GS115 using the electroporation method. Lk2 was expressed on Pichia. pastoris by methanol induction. The enzyme was purified through Ion Metal Affinity Chromatography Ni-NTA. The purified enzyme was characterized based on hydrolytic activity and in silico analysis.<br><br>RESULTS: Lk2 was successfully expressed as an extracellular protein in Pichia pastoris. The cell-free supernatant exhibited hydrolysis activity to para-nitro phenyl laurate. The purified protein showed 15 times activity compared to cell-free supernatant and the size at around 35&#xa0;kDa following gel electrophoresis. The enzyme showed optimum activity at 60[o]C and pH 8. Lk2 preferred para nitro phenyl laurate as substrate. The enzyme's preference for medium-long carbon chains was corroborated by in silico analysis, which revealed favorable interactions between the enzyme and substrate, including affinity binding energy and optimal orientation of catalytic pocket to the substrate. Furthermore, the radius of gyration analysis of the Lk2 showed that the best structural compactness of Lk2 was at 60[o]C. This is in line with the optimal temperature of Lk2 activity. In addition, docking analysis found important substrate binding residues, including Tyr30, Ser85, Leu121, Leu163, Leu166, Leu 233, and Leu254 beside Ser85, Asp231, and His253 as triad catalytic.<br><br>CONCLUSION: Lk2 belongs to a thermotolerant and alkaline lipase, prefers a medium-length carbon chain as substrate and is confirmed by in silico analysis. Several amino acid residues were probed to be important for substrate binding residues. The data give valuable information to develop the possibility of Lk2 as an industry's enzyme.}, }
@article {pmid40139349, year = {2025}, author = {Bilton, TP and Hickey, SM and Jonker, A and McRae, K and Hess, MK and Perry, BJ and Bryson, B and Henry, H and Bain, W and Booker, F and Veenvliet, B and Peers-Adams, J and Pile, G and Waller, E and Janssen, PH and Tiplady, KM and Reid, P and Muetzel, S and Agnew, M and Dodds, KG and McEwan, JC and Rowe, SJ}, title = {Milk fatty acids and rumen composition as proxy measures of enteric methane.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-25876}, pmid = {40139349}, issn = {1525-3198}, abstract = {Genomic selection is a powerful tool to reduce methane emissions in ruminants. However, it requires large-scale on-farm phenotypic measures of methane. Current technologies to measure methane emissions have several limitations and may not be suitable for lactating animals. Because enteric methane is closely linked to the fermentation process in the rumen, which in turn affects milk composition, breeding for low-methane ruminants may change the rumen microbial and milk composition. Consequently, these compositions may provide proxy measures of methane for use in selective breeding of low-methane ruminants. We investigated the effect on rumen and milk composition in sheep bred for divergent methane yield and the potential for generating proxy measures of methane emissions from rumen or milk samples in lactating ewes. Four hundred genotyped lactating ewes from a sheep research flock bred specifically for high and low-methane emissions had methane measured and rumen and milk samples collected approximately 6 wk post-lambing across 4 lactation years. Rumen samples were processed to generate VFA and metagenomic profiles of the rumen microbial community, and fatty acid profiles and mid-infrared spectra were generated for the milk samples. Although no differences in total fat, protein, and lactose percentages in the milk were found, the milk fatty acid profiles differed between methane selection lines, with higher PUFA and branched-chain fatty acids levels, and lower total SFA contents in ewes from the low-methane line. Higher proportions of acetate relative to propionate were found in the rumen samples from the low-methane ewes. Predictions of methane were obtained from the rumen VFA and metagenomic profiles and the fatty acid profiles and mid-infrared spectra from milk. These predictions formed the proxy methane measures and were heritable (between 0.12 to 0.36) and correlated (between 0.29 and 0.42) with the measured methane values. The genetic correlation between proxies and measured methane was between 0.52 and 0.71. The estimated efficiency of indirect selection for methane was higher for the milk sample proxies (49%-75%) than the rumen metagenomic profiles (45%-47%) and rumen VFA profiles (12%-38%). These results suggest that milk fatty acid, MIR spectroscopic, and rumen microbial composition phenotypes have the potential to be used as proxy measures of methane in lactating ruminants, with the milk-based proxies showing greater promise. Results show that the number of animals with methane proxy measures could be increased substantially and will enable access to breeding technology in countries with limited methane measurement infrastructure.}, }
@article {pmid40139294, year = {2025}, author = {Hou, Y and Jia, R and Zhou, L and Zhang, L and Sun, W and Li, B and Zhu, J}, title = {Integrated rice-fish farming dynamically altered the metal resistances and microbial-mediated iron, arsenic, and mercury biotransformation in paddy soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126107}, doi = {10.1016/j.envpol.2025.126107}, pmid = {40139294}, issn = {1873-6424}, abstract = {Given the global concern over heavy metal contamination in agricultural soil, comprehensive and in-depth investigations into the microbial ecological impacts of different agricultural practices on soil heavy metals and their biotransformation processes are both urgent and necessary. We employed metagenomic sequencing to investigate the impacts of integrated rice-fish farming on metal concentrations, metal resistance genes (MRGs), and microbial-mediated Fe, As, and Hg biotransformation processes within rice field. Our findings revealed that integrated rice-fish farming significantly reduced both the diversity and total abundance of MRGs. It also reduced the soil Al, Cd, Cu, Fe, Hg, Ni, Se, V, and Zn levels, with a marked correlation observed between metal concentration and MRGs profiles. Furthermore, integrated rice-fish farming markedly altered the microbial-mediated biotransformation processes for Fe, As, and Hg. It notably upregulated the abundance of Fe biotransformation genes, particularly those involved in the Fe gene regulation, oxidation, reduction, and storage. Biotransformation genes responsible for the As (III) oxidation and As methylation also exhibited increased abundances, along with mercury methylation and demethylation genes. Through metagenome assembled genomes (MAGs), we identified the Mycobacterium aubagnese from paddy soil which contained As oxidation genes and other multiple MRGs, exhibiting strong As remediation potential. Our findings demonstrated the potential of integrated rice-fish farming to reduce soil metal concentrations and mitigate soil metal pollution.}, }
@article {pmid40139249, year = {2025}, author = {Taylor, JT and Lee, V and Dearlove, T and Jolly, M and Wierenga, JR and Dubrulle, J and Hodgkinson-Bean, J and Hunter, S and Gartrell, B and Morgan, K and McInnes, K and French, N and Holmes, EC and Geoghegan, JL}, title = {A Metagenomic Investigation into Apteryx rowi Dermatosis Identifies Multiple Novel Viruses and a Highly Abundant Nematode.}, journal = {Journal of wildlife diseases}, volume = {}, number = {}, pages = {}, doi = {10.7589/JWD-D-24-00115}, pmid = {40139249}, issn = {1943-3700}, abstract = {Sporadic cases of dermatosis have been reported in wild Ōkārito Rowi (Apteryx rowi), a species of brown kiwi, for over a decade. The disease exhibits distinctive features, including lesions, lichenification, and feather loss. Swab samples and full-thickness skin biopsies were collected during a survey of affected kiwi in 2023 for a metatranscriptome-based, total infectome investigation to identify any possible microbial agents associated with the disease. Our approach identified novel viruses as well as a species of nematode in high relative abundance. We found a highly abundant hepacivirus within the Flaviviridae, but only in some mild cases of dermatitis across all sample types, and in both active and chronic infections. In addition, we found a significant shift in the taxonomic composition of the nonviral microbiome within severe chronic dermatitis cases, particularly an increased abundance of transcripts from a Eucoleus sp. parasitic. Although determining the primary cause of disease in critically endangered wildlife such as Rowi remains challenging, our detection of novel and highly abundant microorganisms opens new lines of inquiry to investigate their potential association with dermatosis in this nationally iconic species.}, }
@article {pmid40139192, year = {2025}, author = {Munneke, MJ and Yuan, Y and Preisner, EC and Shelton, CD and Carroll, DT and Kirchoff, NS and Dickson, KP and Cantu, JO and Douglass, MV and Calcutt, MW and Gibson-Corley, KN and Nicholson, MR and Byndloss, MX and Britton, RA and de Crécy-Lagard, V and Skaar, EP}, title = {A thiouracil desulfurase protects Clostridioides difficile RNA from 4-thiouracil incorporation, providing a competitive advantage in the gut.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2025.03.001}, pmid = {40139192}, issn = {1934-6069}, abstract = {Nucleotides are essential building blocks for major cellular macromolecules and are critical for life. Consequently, bacterial pathogens must acquire or synthesize nucleotides during infection. Clostridioides difficile is the most common hospital-acquired gastrointestinal infection, and nutrient acquisition is critical for pathogenesis. However, the impact of nucleotide metabolism on C. difficile infection remains unclear. Here, we discover that 4-thiouracil (4-TU), a pyrimidine analog present in the human gut, is toxic to commensal bacteria. 4-TU hijacks the uracil salvage pathway for incorporation into RNA through the uracil phosphoribosyltransferase activity encoded by PyrR and Upp. C. difficile can salvage 4-TU as a pyrimidine source through the enzymatic action of a thiouracil desulfurase (TudS), thereby contributing to C. difficile fitness in mice fed 4-TU or MiniBioreactor models of infection containing exogenous 4-TU. Collectively, these results reveal a molecular mechanism for C. difficile to utilize a poisonous pyrimidine analog in the vertebrate gut to outcompete commensal microbes.}, }
@article {pmid40138989, year = {2025}, author = {Uprety, T and Swan, M and Kennedy, L and Bryant, U and Cassone, L and Loynachan, A and Janes, J and Evely, MM and Calvaruso, FC and Quick, M and Morgan, J and Abdelrazek, S and Lahmers, K and Carter, C and Erol, E}, title = {Retrospective investigation of 43 necropsy cases of Tyzzer disease in foals and partial genome sequence of Clostridium piliforme by shotgun metagenomics.}, journal = {Veterinary microbiology}, volume = {304}, number = {}, pages = {110489}, doi = {10.1016/j.vetmic.2025.110489}, pmid = {40138989}, issn = {1873-2542}, abstract = {Clostridium piliforme is an obligate intracellular filamentous bacterium that causes Tyzzer disease (TD) in many animals. The disease manifests as severe, multifocal necrotizing hepatitis, with a high fatality rate in foals. Through retrospective investigation, we detected C. piliforme in 43 equine necropsy cases from 2012 to 2024. Positive cases were diagnosed from February to July, peaking in May. The age of affected foals ranged from 4 days to 2 months. Histologically, all cases had necrotizing hepatitis with multifocal, coalescing pinpoint, tan or reddish foci. Since only a partial 16S rRNA gene sequence was available for the horse strain of C. piliforme, we used shotgun metagenomics to obtain its genome sequence from the liver of a necropsied foal with TD. The sequences obtained were compared against the NCBI NT/NR database with the highest number of reads and contigs aligning to Clostridium species. A complete 16S rRNA gene was obtained, showing the highest identity to a 16S rRNA gene of the horse strain of C. piliforme (99.05 %), followed by 98.02-96.71 % identities to rabbit and rodent strains of C. piliforme, indicating cross-species variation. Additional identified genes included alveolysin, exo-α-sialidase, flagellar and spore formation/vegetation, providing the first genetic evidence of virulence factors for C. piliforme. Furthermore, presence of genes encoding multidrug export and multidrug resistance proteins suggested C. piliforme could develop resistance to beta-lactams and fluoroquinolones. This study provides the first partial genome sequence of C. piliforme using a shotgun metagenomics hepatic sampling approach on a foal with TD.}, }
@article {pmid40138908, year = {2025}, author = {Díaz-García, C and Sánchez-Osuna, M and Serra-Compte, A and Karakatsanidou, I and Gómez-Sánchez, I and Fidalgo, B and Barbuzana-Armas, C and Fittipaldi, M and Rosselli, R and Vinyoles, J and González, S and Pich, OQ and Espasa, M and Yáñez, MA}, title = {Mapping antimicrobial resistance landscape at a city scale sewage network.}, journal = {The Science of the total environment}, volume = {974}, number = {}, pages = {179127}, doi = {10.1016/j.scitotenv.2025.179127}, pmid = {40138908}, issn = {1879-1026}, abstract = {Wastewater is a valuable source for monitoring contaminants of biotic or abiotic origin. Antimicrobial resistance (AMR) has emerged as a public health threat that consists of the ability of microorganisms to resist the effects of antimicrobial compounds, rendering them very difficult or impossible to eradicate in case of infection. Considering the dissemination of antimicrobial resistance genes (ARGs) to a wide number of ecosystems, there is a need for the identification of hotspots that concentrate antimicrobial resistance determinants. A comprehensive investigation conducted at a city-scale in Sabadell (Barcelona, Spain) has integrated both phenotypic and genotypic methodologies, including metagenomics and culture-based techniques coupled with whole-genome sequencing (WGS), to monitor ARG presence in seven different spots of the sewage system. Metagenomics approach identified 262 ARG variants across analyzed sampling sites, grouped into 15 resistance categories. The most prevalent ARGs were macrolides-lincosamides-class B streptogramins (MLSB) (35.1 %) and beta-lactams (28.7 %), including carbapenems (5.9 %) and cephalosporins (5.3 %). MLSB resistance featured dominant msr(E) and mph(E) genes, the most abundant ARGs in our study. ARGs conferring resistance to beta-lactam were dominated by blaOXA-464, blaOXA-491, and blaNPS. Key genes for carbapenem (blaOXA-372, blaKPC-2) and cephalosporin (blaOXA-10, blaOXA-1) resistance were identified. The hospital sector exhibited the highest relative abundance of ARGs, dominated by beta-lactams, MLSB, and aminoglycosides. Wastewater treatment plant (WWTP) entrance points and residential areas displayed similar ARG profiles, while WWTP effluent and industrial zones had the lowest ARG levels. WWTP significantly reduced ARG presence (93.3 %). The characterization of antibiotic-resistant bacterial isolates found that most abundant ARGs were predominantly plasmid-borne, favoring ARG spread across bacterial genera. This finding confirmed the significant role of plasmids in ARG dissemination, increasing both diversity and prevalence within waterborne bacterial communities. City-scale surveillance programs can play a pivotal role in guiding effective measures to reduce the dissemination of AMR and mitigate their environmental impact.}, }
@article {pmid40138872, year = {2025}, author = {Liang, T and Jiang, T and Liang, Z and Li, L and Chen, Y and Chen, T and Yang, L and Zhang, N and Dong, B and Xie, X and Gu, B and Wu, Q}, title = {Gut microbiota-driven BCAA biosynthesis via Staphylococcus aureus -expressed acetolactate synthase impairs glycemic control in type 2 diabetes in South China.}, journal = {Microbiological research}, volume = {296}, number = {}, pages = {128145}, doi = {10.1016/j.micres.2025.128145}, pmid = {40138872}, issn = {1618-0623}, abstract = {An increase in branched-chain amino acid (BCAA) levels can result in insulin resistance at different stages of type 2 diabetes (T2D), however, the causes of this increase are unclear. We performed metagenomics and metabolomics profiling in patients with prediabetes (PDM), newly diagnosed diabetes (NDDM), and post-medication type 2 diabetes (P2DM) to investigate whether altered gut microbes and metabolites could explain the specific clinical characteristics of different disease stages of T2D. Here we identify acetolactate synthase (ALS) a BCAA biosynthesis enzyme in Staphylococcus aureus as a cause of T2D insulin resistance. Compared with healthy peoples, patients with PDM, NDDM, and P2DM groups, especially in P2DM group, have increased faecal numbers of S. aureus. We also demonstrated that insulin administration may be a risk factor for S. aureus infection in T2D. The presence of ALS-positive S. aureus correlated with the levels of BCAAs and was associated with an increased fasting blood glucose (FBG) and insulin resistance. Humanized microbiota transplantation experiment indicated that ALS contributes to disordered insulin resistance mediated by S. aureus. We also found that S. aureus phage can reduced the FBG levels and insulin resistance in db/db mice. The ALS-positive S. aureus are associated with insulin resistance in T2D, opening a new therapeutic avenue for the prevention or treatment of diabetes.}, }
@article {pmid40138860, year = {2025}, author = {Li, G and Srinivasan, V and Tooker, NB and Wang, D and Onnis-Hayden, A and Bott, C and Dombrowski, P and Pinto, A and Gu, AZ}, title = {Metagenomic analysis revealed community-level metabolic differences between full-scale EBPR and S2EBPR systems.}, journal = {Water research}, volume = {280}, number = {}, pages = {123509}, doi = {10.1016/j.watres.2025.123509}, pmid = {40138860}, issn = {1879-2448}, abstract = {Side-Stream Enhanced Biological Phosphorus Removal (S2EBPR) has emerged as a promising technology addressing certain challenges of conventional Enhanced Biological Phosphorus Removal (EBPR), notably stability in phosphorus removal, yet the underlying mechanisms are not fully understood. Metagenomic analysis presents a powerful approach to elucidate community-level metabolic differences between EBPR and S2EBPR configurations. In this study, we compared three EBPR and three S2EBPR activated sludge communities using metagenomic analysis at taxonomy, key functional pathways/genes, and polyphosphate-metabolism marker genes. Our analysis revealed larger genus-level diversity variance in S2EBPR communities, indicating distinct microbial community compositions influenced by different operational configurations. A higher diversity index in the S2EBPR than the EBPR was observed, and a higher Ca. Accumulibacter abundance was detected in EBPRs, whereas the fermentative candidate PAOs genera, including Ca. Phosphoribacter and Ca. Promineifilum, were more abundant in S2EBPR systems. EBPR and S2EBPR groups displayed similar gene and pathway abundance patterns related to core metabolisms essential for carbon and nitrogen metabolism. PolyP-metabolism marker gene phylogeny analysis suggested that exopolyphosphatase gene (ppx) showed better distinctions between EBPR and S2EBPR communities than polyphosphate kinase gene (ppk). This also highlighted the needs in fine-cale microdiversity analysis and finding novel Ca. Accumulibacter clades and species as resolved using the ppk gene. These findings provide valuable insights into AS community dynamics and metabolic functionalities, paving the way for further research into optimizing phosphorus removal processes in wastewater treatment systems.}, }
@article {pmid40138725, year = {2025}, author = {Stachler, E and Gnirke, A and McMahon, K and Gomez, M and Stenson, L and Guevara-Reyes, C and Knoll, H and Hill, T and Hill, S and Messer, KS and Arizti-Sanz, J and Albeez, F and Curtis, E and Samani, P and Wewior, N and O'Connor, DH and Vuyk, W and Khoury, SE and Schnizlein, MK and Rockey, NC and Broemmel, Z and Mina, M and Madoff, LC and Wohl, S and O'Connor, L and Brown, CM and Ozonoff, A and Park, DJ and MacInnis, BL and Sabeti, PC}, title = {Establishing Methods to Monitor Influenza (A)H5N1 Virus in Dairy Cattle Milk, Massachusetts, USA.}, journal = {Emerging infectious diseases}, volume = {31}, number = {13}, pages = {}, doi = {10.3201/eid3113.250087}, pmid = {40138725}, issn = {1080-6059}, abstract = {Highly pathogenic avian influenza A(H5N1) virus has caused a multistate outbreak among US dairy cattle, spreading across 16 states and infecting hundreds of herds since its onset. We rapidly developed and optimized PCR-based detection assays and sequencing protocols to support H5N1 molecular surveillance. Using 214 retail milk samples from 20 states for methods development, we found that H5N1 virus concentrations by digital PCR strongly correlated with quantitative PCR cycle threshold values; digital PCR exhibited greater sensitivity. Metagenomic sequencing after hybrid selection was best for higher concentration samples, whereas amplicon sequencing performed best for lower concentrations. By establishing these methods, we were able to support the creation of a statewide surveillance program to perform monthly testing of bulk milk samples from all dairy cattle farms in Massachusetts, USA, which remain negative to date. The methods, workflow, and recommendations described provide a framework for others aiming to conduct H5N1 surveillance efforts.}, }
@article {pmid40138143, year = {2025}, author = {Ali, KA and He, LX and Gao, F and Xia, ZA and Huang, H and Zeng, H and Hu, WH}, title = {Pathogen Detection in Spinal Infections: Next-Generation Sequencing Versus Conventional Microbiological Methods.}, journal = {Current medical science}, volume = {}, number = {}, pages = {}, pmid = {40138143}, issn = {2523-899X}, support = {(2023AFB646)//Hubei Provincial Natural Science Foundation of China/ ; (No. 2023020201010155)//Innovation Program of Wuhan Basic Research/ ; (2022135)//Educational Research Program of Huazhong University of Science and Technology/ ; }, abstract = {OBJECTIVE AND BACKGROUND: Early and accurate diagnosis of spinal infections, including spinal tuberculosis, is pivotal for effective treatment but remains challenging. This study aims to assess the diagnostic yield of metagenomic next-generation sequencing (mNGS) compared with that of conventional microbiological tests (CMTs) in identifying pathogens associated with spinal pathologies, with a special focus on infections leading to surgical interventions.<br><br>METHODS: We enrolled 85 patients who underwent spinal surgery, comprising 63 patients with clinically diagnosed spinal infections, including patients with spinal tuberculosis, and 22 patients with noninfectious spinal conditions. The procedures involved irrigation and debridement for persistent wound drainage, with subsequent DNA extraction from plasma and joint fluid for mNGS and CMT analysis.<br><br>RESULTS: Significantly increased C-reactive protein (CRP) levels were observed in patients with infections. The mNGS approach showed greater diagnostic sensitivity (92.06%) for detecting pathogens, including Mycobacterium tuberculosis, than did CMTs (36.51%). Despite its low specificity, mNGS had considerable negative predictive value (70.59%), underscoring its utility in ruling out infections.<br><br>CONCLUSIONS: The mNGS offers superior sensitivity over CMTs in the diagnosis of a variety of spinal infections, notably spinal tuberculosis. This study highlights the potential of mNGS in enhancing the diagnosis of complex spinal infections, thereby informing targeted treatment strategies.}, }
@article {pmid40138008, year = {2025}, author = {Davasaz Tabrizi, E and Sevil, M and Arican, E}, title = {Bioinformatic strategies in metagenomics of chronic prostatitis.}, journal = {World journal of urology}, volume = {43}, number = {1}, pages = {188}, pmid = {40138008}, issn = {1433-8726}, mesh = {Male ; *Prostatitis/microbiology ; Humans ; Adult ; *Metagenomics ; *Computational Biology ; Chronic Disease ; Young Adult ; Middle Aged ; Microbiota/genetics ; }, abstract = {PURPOSE: Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a prevalent urological condition in young men, significantly affecting quality of life due to persistent discomfort and neuropsychological symptoms. Despite its high prevalence, the etiology of CP/CPPS remains poorly understood. This study investigated urinary microbiota differences between CP/CPPS patients and healthy controls to identify microbial contributors, antibiotic resistance genes (ARGs), and virulence factors of dominant bacteria, as well as to explore potential therapeutic targets.<br><br>METHODS: Urine samples were collected from 58 CP/CPPS patients and 25 controls. Symptom severity was assessed by a specialist urologist using the NIH Chronic Prostatitis Symptom Index and UPOINT classification. Bacterial-specific 16&#xa0;S rRNA sequencing was performed using nanopore technology, with bioinformatics analyses conducted via ONT guppy 5.0.11, NCBI and SLV 16&#xa0;S bacterial taxonomic databases, UPGMA hierarchical clustering, and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC). Pairwise comparisons were analyzed using the Mann-Whitney U test.<br><br>RESULTS: Distinct microbial diversity patterns were observed between patients and controls. Bacillus species were significantly enriched in CP/CPPS patients, while Enterococcus species predominated in controls. Younger patients exhibited unique microbiome profiles compared to older groups. Bioinformatics analyses identified ARGs and virulence factors associated with Bacillus species, implicating them in localized inflammation. Antibiotics like pleuromutilin or vancomycin were identified as potential therapeutic options, though experimental validation was beyond the study's scope.<br><br>CONCLUSION: These findings highlight microbial imbalances and provide a foundation for microbiome-targeted therapeutic strategies for CP/CPPS management in the future. Additionally, the identification of bacterial virulence factors and ARG provides insights into the potential mechanisms driving persistent symptoms. Future research with larger cohorts and experimental validation of the suggested therapeutic options may contribute to more effective treatment for CP/CPPS.}, }
@article {pmid40137749, year = {2025}, author = {Mao, W and Wang, J and Li, T and Wu, J and Wang, J and Wen, S and Huang, J and Shi, Y and Zheng, K and Zhai, Y and Li, X and Long, Y and Lu, J and Guo, C}, title = {Hybrid Capture-Based Sequencing Enables Highly Sensitive Zoonotic Virus Detection Within the One Health Framework.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/pathogens14030264}, pmid = {40137749}, issn = {2076-0817}, support = {2023YFVA1005//National Natural Science Foundation of China International (Regional) Cooperation and Ex-change Project/ ; 51000-12240016//Startup Fund for Young Researchers of Sun Yat-sen University/ ; z1-2023005//Discipline Cluster of Oncology, Wenzhou Medical University/ ; }, mesh = {Animals ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *One Health ; *SARS-CoV-2/genetics/isolation &amp; purification ; Cattle ; Metagenomics/methods ; Genome, Viral/genetics ; Zoonoses/virology/diagnosis ; COVID-19/diagnosis/virology ; Viruses/genetics/isolation &amp; purification ; Sensitivity and Specificity ; Limit of Detection ; }, abstract = {Hybrid capture-based target enrichment prior to sequencing has been shown to significantly improve the sensitivity of detection for genetic regions of interest. In the context of One Health relevant pathogen detection, we present a hybrid capture-based sequencing method that employs an optimized probe set consisting of 149,990 probes, targeting 663 viruses associated with humans and animals. The detection performance was initially assessed using viral reference materials in a background of human nucleic acids. Compared to standard metagenomic next-generation sequencing (mNGS), our method achieved substantial read enrichment, with increases ranging from 143- to 1126-fold, and enhanced detection sensitivity by lowering the limit of detection (LoD) from 10[3]-10[4] copies to as few as 10 copies based on whole genomes. This method was further validated using infectious samples from both animals and humans, including bovine rectal swabs and throat swabs from SARS-CoV-2 patients across various concentration gradients. In both sample types, our hybrid capture-based sequencing method exhibited heightened sensitivity, increased viral genome coverage, and more comprehensive viral identification and characterization. Our method bridges a critical divide between diagnostic detection and genomic surveillance. These findings illustrate that our hybrid capture-based sequencing method can effectively enhance sensitivity to as few as 10 viral copies and genome coverage to >99% in medium-to-high viral loads. This dual capability is particularly impactful for emerging pathogens like SARS-CoV-2, where early detection and genomic characterization are equally vital, thereby addressing the limitations of metagenomics in the surveillance of emerging infectious diseases in complex samples.}, }
@article {pmid40137713, year = {2025}, author = {Shaw, CA and Soltero-Rivera, M and Profeta, R and Weimer, BC}, title = {Case Report: Shift from Aggressive Periodontitis to Feline Chronic Gingivostomatitis Is Linked to Increased Microbial Diversity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/pathogens14030228}, pmid = {40137713}, issn = {2076-0817}, support = {UL1 TR001860/NH/NIH HHS/United States ; }, mesh = {Animals ; Cats ; *Microbiota/genetics ; *Cat Diseases/microbiology/diagnosis ; *Aggressive Periodontitis/microbiology ; Stomatitis/microbiology/veterinary ; Bacteria/genetics/classification/isolation &amp; purification ; Disease Progression ; Mouth/microbiology ; Metagenomics ; Male ; }, abstract = {Aggressive Periodontitis (AP) and Feline Chronic Gingivostomatitis (FCGS) are two oral inflammatory diseases in cats with unknown etiology. Both conditions present with severe inflammation of the oral cavity and in FCGS it is found with additional deterioration of the non-keratinized mucosa. The oral microbiome is increasingly implicated in disease progression, but little is known about shifts in the microbial community during the AP and FCGS progression. To that end, we used deep metagenomic sequencing with total RNA on three longitudinal samples of the oral microbiome in a cat first diagnosed with AP that progressed to FCGS. This deep sequencing approach revealed that increased diversity at both the genus and species levels marked the shift from AP to FCGS, including increases in Porphyromonas and Treponema species, and decreased Streptobacillus species. The metatranscriptomes were then probed for expression of antimicrobial resistance genes and virulence factors. Disease-related genes that include cheY, and ompP5 were expressed in early AP and FCGS, while others like galU were only expressed in one or the other disease state. Both genus and species-level shifts were observed along the longitudinal microbiome samples with a noted increase in species diversity in the FCGS-associated microbiome. Corroborating that functional shifts accompany taxonomic changes, the AMR and virulence factor expression similarly changed between the sampling points. Together, these taxonomic and functional shifts indicate that AP and FCGS are potentially linked and may be marked by changes in the oral microbiome, which supports the development of microbial-based clinical diagnostics and therapeutics.}, }
@article {pmid40137232, year = {2025}, author = {Krivonos, DV and Fedorov, DE and Klimina, KM and Veselovsky, VA and Kovalchuk, SN and Pavlenko, AV and Yanushevich, OO and Andreev, DN and Sokolov, FS and Fomenko, AK and Devkota, MK and Andreev, NG and Zaborovsky, AV and Tsaregorodtsev, SV and Evdokimov, VV and Krikheli, NI and Bely, PA and Levchenko, OV and Maev, IV and Govorun, VM and Ilina, EN}, title = {Gut Mycobiome Changes During COVID-19 Disease.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {3}, pages = {}, pmid = {40137232}, issn = {2309-608X}, support = {&#x2116; 122030900064-9//The government task/ ; &#x2116;056-00108-22-01//The government task/ ; }, abstract = {The majority of metagenomic studies are based on the study of bacterial biota. At the same time, the COVID-19 pandemic has prompted interest in the study of both individual fungal pathogens and fungal communities (i.e., the mycobiome) as a whole. Here, in this work, we investigated the human gut mycobiome during COVID-19. Stool samples were collected from patients at two time points: at the time of admission to the hospital (the first time point) and at the time of discharge from the hospital (the second time point). The results of this study revealed that Geotrichum sp. is more represented in a group of patients with COVID-19. Therefore, Geotrichum sp. is elevated in patients at the time of admission to the hospital and underestimated at the time of discharge. Additionally, the influence of factors associated with the diversity of fungal gut microbiota was separately studied, including disease severity and age factors.}, }
@article {pmid40136572, year = {2025}, author = {Malik, Y and Ali, I and Sajjad, A and Jing, L and Iqbal, I and Rehman, AU and Azam, T and Chen, X}, title = {Bacterial Diversity at Himalayan Pink Salt Extraction Site.}, journal = {Biology}, volume = {14}, number = {3}, pages = {}, pmid = {40136572}, issn = {2079-7737}, abstract = {Table salt, or sodium chloride, is extensively utilized in the culinary business as a flavoring agent, texture garnishing [...].}, }
@article {pmid40136549, year = {2025}, author = {Pizzi, S and Conti, A and Di Canito, A and Casagrande Pierantoni, D and Foschino, R and Setati, ME and Vigentini, I}, title = {Endophytic Diversity in Vitis vinifera with Different Vineyard Managements and Vitis sylvestris Populations from Northern Italy: A Comparative Study of Culture-Dependent and Amplicon Sequencing Methods.}, journal = {Biology}, volume = {14}, number = {3}, pages = {}, pmid = {40136549}, issn = {2079-7737}, support = {150549//Italy/South Africa Joint Research Programme (ISARP) 2023-2025/ ; }, abstract = {This study aimed to investigate the endophytic microbial populations associated with wild and domesticated grapevines using both culture-based and culture-independent methods. Through culture-based methods, 148 endophytes were identified. The dominant fungal species included Aureobasidium pullulans, Alternaria alternata, and Cladosporium allicinum, while predominant bacterial species were Ralstonia pikettii, Nocardia niigatensis, and Sphingomonas echinoides. Culture-independent methods employed metagenomic techniques to explore microbial biodiversity, focusing on targeted amplification of bacterial 16S rRNA as well as fungal ITS and 26S rRNA gene regions. The main bacterial species identified included Halomonas sp., Sphingomonas sp. and Massilia sp., whereas the fungal population was dominated by Cladosporium sp., Malassezia sp. and Mucor sp. The findings revealed that vineyard management practices did not lead to statistically significant variations in microbial communities. The consistent presence of these genera across all samples suggests that they are stable components of the grapevine endophytic microbiota, remaining relatively unaffected by external environmental factors.}, }
@article {pmid40136543, year = {2025}, author = {Claros, MG and Bullones, A and Castro, AJ and Lima-Cabello, E and Viruel, M&#xc1; and Suárez, MF and Romero-Aranda, R and Fernández-Pozo, N and Veredas, FJ and Belver, A and Alché, JD}, title = {Multi-Omic Advances in Olive Tree (Olea europaea subsp. europaea L.) Under Salinity: Stepping Towards 'Smart Oliviculture'.}, journal = {Biology}, volume = {14}, number = {3}, pages = {}, pmid = {40136543}, issn = {2079-7737}, support = {TED2021-130015B-C21//Agencia Estatal de Investigaci&#xf3;n/ ; TED2021-130015B-C22//Agencia Estatal de Investigaci&#xf3;n/ ; PID2020-113324GB-I00//Agencia Estatal de Investigaci&#xf3;n/ ; PID2020-115853RR-C33//Agencia Estatal de Investigaci&#xf3;n/ ; PID2021-125805OA-I00//Agencia Estatal de Investigaci&#xf3;n/ ; RED2022-134072-T//Agencia Estatal de Investigaci&#xf3;n/ ; RYC2020-030219-I//Agencia Estatal de Investigaci&#xf3;n/ ; EMERGIA20_00286//Consejer&#xed;a de Econom&#xed;a, Conocimiento, Empresas y Universidad, Junta de Andaluc&#xed;a/ERDF-UE/ ; UMA20-FEDERJA-029//Consejer&#xed;a de Econom&#xed;a, Conocimiento, Empresas y Universidad, Junta de Andaluc&#xed;a/ERDF-UE/ ; PYC20 RE 009 CSIC EEZ//Consejer&#xed;a de Econom&#xed;a, Conocimiento, Empresas y Universidad, Junta de Andaluc&#xed;a/ERDF-UE/ ; }, abstract = {Soil salinisation is threatening crop sustainability worldwide, mainly due to anthropogenic climate change. Molecular mechanisms developed to counteract salinity have been intensely studied in model plants. Nevertheless, the economically relevant olive tree (Olea europaea subsp. europaea L.), being highly exposed to soil salinisation, deserves a specific review to extract the recent genomic advances that support the known morphological and biochemical mechanisms that make it a relative salt-tolerant crop. A comprehensive list of 98 olive cultivars classified by salt tolerance is provided, together with the list of available olive tree genomes and genes known to be involved in salt response. Na[+] and Cl[-] exclusion in leaves and retention in roots seem to be the most prominent adaptations, but cell wall thickening and antioxidant changes are also required for a tolerant response. Several post-translational modifications of proteins are emerging as key factors, together with microbiota amendments, making treatments with biostimulants and chemical compounds a promising approach to enable cultivation in already salinised soils. Low and high-throughput transcriptomics and metagenomics results obtained from salt-sensitive and -tolerant cultivars, and the future advantages of engineering specific metacaspases involved in programmed cell death and autophagy pathways to rapidly raise salt-tolerant cultivars or rootstocks are also discussed. The overview of bioinformatic tools focused on olive tree, combined with machine learning approaches for studying plant stress from a multi-omics perspective, indicates that the development of salt-tolerant cultivars or rootstocks adapted to soil salinisation is progressing. This could pave the way for 'smart oliviculture', promoting more productive and sustainable practices under salt stress.}, }
@article {pmid40134914, year = {2025}, author = {Xu, J and Zeng, H and Li, H and Lin, X and Lin, T}, title = {Severe pneumonia caused by Chlamydia abortus complicated by hemophagocytic syndrome: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1547766}, pmid = {40134914}, issn = {2296-858X}, abstract = {BACKGROUND: Pneumonia caused by Chlamydia abortus (C. abortus) is uncommon, particularly when complicated by severe acute respiratory distress syndrome (ARDS) and multiple organ dysfunction syndrome (MODS). Hemophagocytic lymphohistiocytosis (HLH) is a rare and potentially fatal disease characterized by the uncontrolled activation and non-malignant expansion of macrophages and T lymphocytes. This report describes a case of severe pneumonia complicated by hemophagocytic lymphohistiocytosis, caused by Chlamydia abortus.<br><br>CASE INTRODUCTION: A 42-year-old female with no history of underlying medical conditions, no known exposure to poultry or avian animals, and no consumption of undercooked sheep or ewes contaminated with infected placenta, presented to the respiratory medicine department with a 3-day history of fever, cough, and sputum production. Initially diagnosed with community-acquired pneumonia, she was treated with piperacillin-tazobactam for 5 days. However, despite 12 h of high-flow oxygen therapy, her oxygenation did not improve, and she was transferred to the ICU, where she received additional treatments, including moxifloxacin and methylprednisolone. Her condition worsened further, prompting the initiation of veno-venous extracorporeal membrane oxygenation (VV-ECMO) and bronchoalveolar lavage for metagenomic next-generation sequencing (mNGS) analysis. The mNGS results identified Chlamydia abortus with a count of 180,791, leading to the cessation of moxifloxacin and the addition of omadacycline to her regimen. After 13 days of ECMO therapy, her condition improved, and the ECMO was discontinued. The endotracheal tube was successfully removed 15 days after intubation. However, 3 days later, the patient developed recurrent fever, pancytopenia, elevated ferritin, blood lipids, soluble CD25, and decreased natural killer cell activity, leading to a diagnosis of hemophagocytic lymphohistiocytosis (HLH). She was treated with ruxolitinib, etoposide, and other supportive medications. Despite treatment, her condition continued to deteriorate. Three days later, the family opted to discontinue therapy due to financial constraints. She passed away 12 h later.<br><br>CONCLUSION: Chlamydia abortus infection can result in severe acute respiratory distress syndrome (ARDS), necessitating prompt diagnosis and active clinical intervention. This case is unique due to the rare occurrence of HLH following Chlamydia abortus infection, a pathogen not commonly associated with this condition. Metagenomic next-generation sequencing (mNGS) offers a distinct advantage in rapidly and accurately identifying rare pathogen infections, while extracorporeal membrane oxygenation (ECMO) can be an effective treatment for severe pneumonia caused by Chlamydia abortus. It highlights the importance of early recognition and management of HLH in patients with severe, unexplained infections, particularly in those with unusual pathogens. Additionally, Chlamydia abortus infection may be complicated by HLH. Clinicians should remain vigilant for patients presenting with unexplained high fever, hepatosplenomegaly, and pancytopenia, and HLH screening should be initiated promptly. Early intervention can significantly improve patient survival rates.}, }
@article {pmid40134637, year = {2025}, author = {Armstrong, E and Kulikova, M and Yee, N and Rishu, A and Muscedere, J and Sibley, S and Maslove, D and Boyd, JG and Evans, G and Detsky, M and Marshall, J and Taggart, LR and Friedrich, JO and Tsang, JLY and Duan, E and Ali Firdous, K and McCullagh, D and Findlater, A and Fowler, R and Daneman, N and Coburn, B}, title = {Impact of Antibiotic Duration on Gut Microbiome Composition and Antimicrobial Resistance: A Substudy of the BALANCE Randomized Controlled Trial.}, journal = {Open forum infectious diseases}, volume = {12}, number = {3}, pages = {ofaf137}, pmid = {40134637}, issn = {2328-8957}, abstract = {BACKGROUND: Maintaining a diverse gut microbiome and minimizing antimicrobial resistance gene (ARG) carriage through reduced antibiotic utilization may decrease antimicrobial resistance. We compared gut microbiome disruption and ARG carriage following 7 or 14 days of antibiotics for treatment of bacteremia in a substudy of the BALANCE randomized controlled trial.<br><br>METHODS: The BALANCE randomized controlled trial enrolled 3631 participants with bacteremia, who were randomized 1:1 to receive 7 or 14 days of antibiotics. Rectal swabs were collected from 131 participants and analyzed with metagenomic sequencing to characterize the gut microbiome and ARGs. The primary outcome was change in gut microbiome diversity at day 7 vs 14.<br><br>RESULTS: Forty-one participants (n = 28 in the 14-day group, n = 13 in the 7-day group) had samples available for the primary analysis, with an imbalance in piperacillin-tazobactam exposure between groups. Change in gut microbiome diversity at day 7 vs 14 was comparable between the 14-day group (median, 0.07; IQR, -0.46 to +0.51) and 7-day group (median, 0.19; IQR, -0.77 to +0.22; P = .49). Change in ARG abundance at day 7 vs 14 did not differ by treatment duration, nor did the abundance of individual ARGs. We did not observe any change in gut microbiome diversity or ARG carriage at enrollment vs day 7.<br><br>CONCLUSIONS: In this subset of patients from the BALANCE randomized controlled trial, we did not detect greater gut microbiome disruption or ARG carriage among participants who received 14 vs 7 days of antibiotics, but we were limited by small sample size and imbalances between groups.}, }
@article {pmid40134271, year = {2025}, author = {Orme, W and Grimm, SL and Vella, DSN and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Coarfa, C and Madan, A}, title = {Relationships of Personality Traits With the Taxonomic Composition of the Gut Microbiome Among Psychiatric Inpatients.}, journal = {The Journal of neuropsychiatry and clinical neurosciences}, volume = {}, number = {}, pages = {appineuropsych20240126}, doi = {10.1176/appi.neuropsych.20240126}, pmid = {40134271}, issn = {1545-7222}, abstract = {OBJECTIVE: Through the brain-gut-microbiome axis, myriad psychological functions that affect behavior share a dynamic, bidirectional relationship with the intestinal microbiome. Little is known about the relationship between personality-a stable construct that influences social- and health-related behaviors-and the bacterial ecosystem. The authors of this exploratory study examined the relationship between general and maladaptive personality traits and the composition of the gut microbiome.<br><br>METHODS: In total, 105 psychiatric inpatients provided clinical data and fecal samples. Personality traits were measured with the five-factor model of personality, the Structured Clinical Interview for DSM-IV Axis II Personality Disorders, and the Personality Inventory for DSM-5; 16S ribosomal DNA sequencing and whole-genome shotgun sequencing methods were used on fecal samples. Machine learning (ML) was used to identify personality traits associated with bacterial variability and specific taxa.<br><br>RESULTS: Supervised ML techniques were used to classify traits of social detachment (maximum area under the receiver operating characteristic curve [AUROC]=0.944, R[2]>0.20), perceptual disturbance (maximum AUROC=0.763, R[2]=0.301), and hoarding behaviors (maximum AUROC=0.722) by using limited sets of discriminant bacterial species or genera. Established bacterial genera associated with psychosis (e.g., Peptococcus and Coprococcus) were associated with traits of perceptual disturbance. Hoarding behaviors were associated with a defined gut microbial composition that included Streptococcus, a known contributor to the development of pediatric autoimmune neuropsychiatric disorders.<br><br>CONCLUSIONS: Observations from this study are consistent with recent findings demonstrating person-to-person interactions as a mode of gut microbiome transmission. This study adds to the emerging literature on the intricate connections between brain and gut function, expanding the interdisciplinary field of psychiatric microbiology.}, }
@article {pmid40133835, year = {2025}, author = {Gao, N and Feng, S and Yu, X and Zhao, J and Wan, Y and Yao, Z and Li, D}, title = {Diagnostic value of metagenomic next-generation sequencing combined by medical thoracoscopy surgery among infectious pleural effusion patients.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {407}, pmid = {40133835}, issn = {1471-2334}, support = {ZR2014HQ050//Natural Science Foundation of Shandong province/ ; }, mesh = {Humans ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Female ; Middle Aged ; *Metagenomics/methods ; *Pleural Effusion/microbiology/diagnosis ; Aged ; *Thoracoscopy/methods ; Adult ; Bacteria/isolation &amp; purification/genetics/classification ; Aged, 80 and over ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a novel method for identifying pathogens in infectious diseases. This study aimed to explored the application value of mNGS in diagnosing pulmonary infections with pleural effusion, confirmed by medical thoracoscopy.<br><br>METHODS: We retrospectively reviewed 25 patients with pulmonary infections and pleural effusion between July 2020 and December 2021. All patients had their diagnosis confirmed by medical thoracoscopy to obtain tissue samples for both traditional testing and mNGS. Samples included pleural effusion, successive sputum, and tissue obtained through medical thoracoscopy. We wanted to assess how effective mNGS was in accurately diagnosing these infections.<br><br>RESULTS: This study found that the positive predictive value of mNGS (76% (19/25)) was significantly higher than that of traditional testing (32% (8/25)). The most commonly identified pathogens were Mycobacterium tuberculosis (n&#x2009;=&#x2009;5), followed by Fusobacterium nucleatum (n&#x2009;=&#x2009;4), Torque teno virus (n&#x2009;=&#x2009;4), Streptococcus intermedius (n&#x2009;=&#x2009;3), Peptostreptococcus stomatis (n&#x2009;=&#x2009;2), Porphyromonas endodontalis (n&#x2009;=&#x2009;2), and Campylobacter rectus (n&#x2009;=&#x2009;2). The percentage of mNGS-positive cases was significantly higher than that from traditional testing for bacteria, but the superiority of mNGS for tuberculosis detection was insignificant. Ten cases were identified with mixed infections by mNGS, while no mixed infections were found by traditional testing.<br><br>CONCLUSIONS: Our study showed that using mNGS in combination with biopsy samples obtained through medical thoracoscopy resulted in higher positive rates compared to traditional tests and provided more evidence of pathogens for patients with infectious pleural effusion.}, }
@article {pmid40133828, year = {2025}, author = {Lei, H and Liao, J and Lin, Y and Liu, T and Lei, W and Gao, W}, title = {Application of metagenomic next-generation sequencing in treatment guidance for deep neck space abscess.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {166}, pmid = {40133828}, issn = {1471-2180}, support = {82000950, 81972528, 82273053, 82203783//National Natural Science Foundation of China/ ; 82000950, 81972528, 82273053, 82203783//National Natural Science Foundation of China/ ; 2020YFC1316903//National Key Research and Development Program of China/ ; 2017004//Sun Yat-sen University/ ; 202201011050//Guangzhou Science, Technology and Innovation Commission/ ; 24QNPY345//Young Teacher Foundation of Sun Yat-sen University/ ; }, mesh = {Humans ; Male ; Female ; *High-Throughput Nucleotide Sequencing/methods ; *Neck/microbiology ; Middle Aged ; *Metagenomics/methods ; Retrospective Studies ; *Abscess/microbiology/drug therapy ; Adult ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Aged ; Bacteria/genetics/isolation &amp; purification/classification/drug effects ; Treatment Outcome ; }, abstract = {BACKGROUND: Infectious etiologies of deep neck space abscess (DNSA) by conventional culture tests can be challenging, which also leads to frequent irrational antibiotic usage. Metagenomic next-generation sequencing (mNGS), as a novel method for analyzing the complex microbial ecosystem from clinical samples, has been utilized in clinical research and practice of various infectious diseases but deep neck space abscess. We here aimed to explore the clinical value of mNGS for pathogen detection and treatment guidance in DNSA patients compared with conventional culture tests.<br><br>METHODS: One hundred six patients diagnosed with DNSA were retrospectively enrolled and allocated into mNGS group and culture group according to whether mNGS was conducted. The pathogen detection effectiveness was of mNGS was compared with conventional culture. Effectiveness of mNGS-modified antimicrobial therapy was evaluated by comparing the treatment outcomes between two groups.<br><br>RESULTS: mNGS showed a significantly higher detection rate than conventional culture (p&#x2009;<&#x2009;0.05) with faster result acquisition. Treatment success rate of patients in the mNGS group was significantly higher than in the culture group (RR: 1.22, 95%CI: 1.07-1.82, p&#x2009;=&#x2009;0.033). Besides, patients in the mNGS group had shorter duration of irrational antimicrobial therapy, shorter hospital stay and less medical costs (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: mNGS is an effective technology for facilitating pathogen detection and improving treatment outcomes of DNSA patients.}, }
@article {pmid40133298, year = {2025}, author = {Bhanu, P and Buchke, S and Hemandhar-Kumar, N and Varsha, P and Kiran, SKR and Vikneswaran, G and Alva, A and Basavaraj, GS and Kumar, J}, title = {Comparative metagenomic analysis of the oral microbiome in COVID-19 patients and healthy individuals.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10303}, pmid = {40133298}, issn = {2045-2322}, support = {20210001//Bangalore Bioinnovation Centre/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology ; *Mouth/microbiology/virology ; *Microbiota/genetics ; *Metagenomics/methods ; *SARS-CoV-2/genetics/isolation &amp; purification ; Male ; Female ; Adult ; Middle Aged ; Metagenome ; Aged ; }, abstract = {COVID-19, caused by SARS-CoV-2, affects multiple body systems, including the oral cavity, where it may disrupt the oral microbiome in ways that contribute to disease pathology. Understanding the long-term interaction between SARS-CoV-2 and the oral microbiome is crucial, as it may reveal microbial markers valuable for diagnosing or monitoring persistent health issues in COVID-19 survivors. Metagenomic sequencing revealed significant microbial shifts in the oral microbiome of COVID-19 patients, showing reduced microbial diversity and increased prevalence of opportunistic pathogens compared to healthy individuals. Alpha diversity measures indicated lower microbial diversity and evenness, while beta diversity analyses demonstrated distinct microbial community compositions. Core microbiome analysis identified unique taxa in COVID-19 patients that may contribute to disease pathology, while differential abundance analysis highlighted specific taxa shifts, including an increase in potential pathogens. Our findings advance the understanding of microbial changes in the oral microbiome associated with COVID-19 and suggest potential targets for microbiome-based interventions. While these results indicate associations with possible health impacts, further research is needed to determine causative links and long-term implications for COVID-19 survivors. This foundational research highlights the potential for microbiome science to inform diagnostic tools, such as microbial markers for disease progression, and therapeutic approaches, including targeted probiotics, which could ultimately support better patient outcomes and public health strategies.}, }
@article {pmid40132505, year = {2025}, author = {Wang, L and Zhang, W and Yao, J and Qi, Z and Liu, Y and Li, Z and Qu, J and Ma, Y and Zhang, Y}, title = {Effect of freeze-thaw cycle aging on biochar application in DEHP contaminated Mollisols: Insights from soil properties and microbial community.}, journal = {Ecotoxicology and environmental safety}, volume = {294}, number = {}, pages = {118082}, doi = {10.1016/j.ecoenv.2025.118082}, pmid = {40132505}, issn = {1090-2414}, abstract = {Biochar holds significant promise for remediation of organic pollutants. However, the impact of biochar on di-(2-ethylhexyl) phthalate (DEHP)-contaminated Mollisols after freeze-thaw cycles is largely unknown, according to the seasonal traits observed at high latitudes. In this study, fresh biochar (BC) was produced from corn straw, and freeze-thaw aging biochar (FBC) was prepared by simulating winter temperatures in the Mollisol region of Northeast China using BC as a precursor. Pot experiments were conducted to evaluate the effects of freeze-thaw aging on the detoxification efficiency of biochar, the improvement of soil physical and chemical properties, and the regulation of soil microbial community structure and functional genes. The results indicated that biochar after freeze-thaw cycling significantly improved the physical and chemical properties of Mollisols compared with the control, reducing DEHP content by 99.08 % after 28 days. Metagenomic sequencing further revealed the presence of microorganisms and genetic elements potentially involved in DEHP degradation in the soil. The treatment group with freeze-thaw aging biochar exhibited higher microbial diversity and abundance, particularly in Proteobacteria, Bacteroides, and Firmicutes. Analysis of the DEHP degradation pathway via benzoic acid route revealed an increase in the abundance of degraded functional genes/enzymes (benC-xylZ, pacL, catB, pcaG, mhpE, and mhpF). The up-regulation of nitrogen fixation genes and nitrification genes (amoB, hao, narG, nifD, and vnfH) along with a 49.19 % increase in soil microbial biomass nitrogen suggested that freeze-thaw aging biochar benefited nitrogen cycling. Furthermore, the feasibility of applying biochar to high-latitude agricultural settings was validated using pakchoi (Brassica rapa L. ssp. chinensis) as a test crop. These findings suggest that the freeze-thaw aging process enhances the effectiveness of biochar in remediating DEHP-contaminated Mollisols. This study offers a novel perspective on the restoration and improvement of Mollisol productivity in high-latitude regions through biochar application.}, }
@article {pmid40132340, year = {2025}, author = {Roselli, WR and de Oliveira Miraglia, FF and de Mello Malta, F and Fernandes, GBP and Ribas, GC and de Oliveira Godeiro Júnior, C and Amgarten, DE and Nunes, FCG and Trindade, M and de Almeida Junior, JN and Martino, MDV and Santana, RAF and Pinho, JRR and Doi, AM}, title = {Diagnosis of Cladophialophora bantiana cerebral infection by clinical metagenomics.}, journal = {Diagnostic microbiology and infectious disease}, volume = {112}, number = {3}, pages = {116822}, doi = {10.1016/j.diagmicrobio.2025.116822}, pmid = {40132340}, issn = {1879-0070}, abstract = {PURPOSE: Cladophialophora bantiana is a rare cause of severe central nervous system phaeohyphomycosis.<br><br>RESULTS: A 44-year-old woman from Northeastern Brazil with a history of scotomas, mental confusion, and impaired coordination presented Magnetic Resonance Imaging with vasogenic edema and nodular enhancement in the left occipital lobe. Brain biopsy showed neutrophilic exudate with eosinophils, macrophages, giant multinucleated cells, and septate hyphae with a brown-colored birefringent wall and acute angle branching. Metagenomic analysis of the biopsy's total RNA revealed the presence of RNA sequences highly similari to C. bantiana. Culture confirmed the presence of olivaceous-gray suede-like to floccose colonies, with septate dematiaceous hyphae and long conidia chains from undifferentiated conidiophores, consistent with C. bantiana.<br><br>CONCLUSIONS: This case highlights the potential of metagenomic testing as a tool for early diagnosis of infections caused by uncommon fungal pathogens. To our knowledge, this is the first report of C. bantiana central nervous system infection in Brazil.}, }
@article {pmid40135889, year = {2025}, author = {Nielsen, ME and Søgaard, KK and Karst, SM and Krarup, AL and Albertsen, M and Nielsen, HL}, title = {Application of rapid Nanopore metagenomic cell-free DNA sequencing to diagnose bloodstream infections: a prospective observational study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0329524}, doi = {10.1128/spectrum.03295-24}, pmid = {40135889}, issn = {2165-0497}, abstract = {Bloodstream infections are a major cause of mortality, often leading to sepsis or septic shock. Rapid initiation of effective antimicrobial therapy is essential for survival; however, the current gold standard for identifying pathogens in bloodstream infections, blood culturing, has limitations with long turnaround time and poor sensitivity. This delay in refining empirical broad-spectrum antimicrobial treatments contributes to increased mortality and the development of antimicrobial resistance. In this study, we developed a metagenomic next-generation sequencing assay utilizing the Oxford Nanopore Technologies platform to sequence microbial cell-free DNA from blood plasma. We demonstrated proof of concept in a prospective observational clinical study including patients (n = 40) admitted to the emergency ward on suspicion of bloodstream infection. Study samples were drawn from the same venipuncture as a blood culture sample from the included patients. Nanopore metagenomic sequencing confirmed all microbiological findings in patients with positive blood cultures (n = 11) and identified pathogens relevant to the acute infection in an additional 11 patients with negative blood cultures. This proof-of-concept study demonstrates that culture-independent Nanopore metagenomic sequencing directly on blood plasma could be a feasible supplementary test for infection diagnostics in patients admitted with severe infections or sepsis. These findings support further studies on Nanopore metagenomic sequencing for sepsis diagnostics in larger cohorts to validate and expand the results from this study.IMPORTANCEThis study demonstrates the potential of Nanopore metagenomic sequencing as a rapid, culture-independent diagnostic tool for bloodstream infections, identifying pathogens missed by conventional blood cultures. The study highlights the method's promise in improving pathogen detection and warrants further validation in larger clinical studies.}, }
@article {pmid40135776, year = {2025}, author = {Wang, J and Liu, Q and Jin, S and Yang, B and Wang, C and Tan, Y and Feng, W and Tao, J and Wang, H and Wang, Y and Yang, S and Cui, L}, title = {Characterization of bile microbiota in patients with obstructive jaundice associated with biliary tract diseases.}, journal = {Clinical and translational gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ctg.0000000000000841}, pmid = {40135776}, issn = {2155-384X}, abstract = {BACKGROUND: Cholangiocarcinoma (CHOL), a malignant tumor of the biliary system, is particularly concerning due to its high malignancy and poor prognosis, often leading to obstructive jaundice. The advent of metagenomic sequencing(mNGS) technology has expanded diagnostic capabilities, including the identification of microbes within tumors and their potential role in cancer progression.<br><br>OBJECTIVE: This study aims to explore the bacterial composition in bile from patients with obstructive jaundice of different etiologies and to investigate the association between bile microbiota and biochemical analytes, as well as their potential as biomarkers for diagnosis of obstructive jaundice diseases.<br><br>METHODS: Bile samples from patients with obstructive jaundice admitted to Beijing Friendship Hospital were collected and subjected to 16S rRNA and metagenomic sequencing. The study included patients diagnosed with benign biliary stricture, gallstone, and cholangiocarcinoma. Clinical data and bile chemical components were analyzed. The potential functional roles of the identified microbiota were predicted using bioinformatics tools.<br><br>RESULTS: The study enrolled 13 patients with benign biliary stricture, 19 with gallstones, and 10 with cholangiocarcinoma. Significant differences in bile chemical components and microbial diversity were observed among the groups. The bile microbiota was dominated by distinct phyla and genera across the groups, with Proteobacteria and Fusobacteriota enriched in benign biliary stricture, Firmicutes and Desulfobacterota in cholangiocarcinoma, and Synergistota in gallstone patients. Functional analysis revealed differences in gene functions related to metabolism and other biological processes. A correlation between bile microbiota and biochemical markers was established, and the combination of differential microbiota showed potential as a diagnostic marker for obstructive jaundice of different etiologies.<br><br>CONCLUSION: Bile microbiota varies significantly among patients with obstructive jaundice of different etiologies. The identified microbial signatures and their functional roles could serve as novel diagnostic markers and provide insights into the pathogenesis of biliary diseases.}, }
@article {pmid40135668, year = {2025}, author = {Nassar, R and Nassar, M and Mohamed, L and Senok, A and Williams, D}, title = {Characterization and ex vivo modelling of endodontic infections from the Arabian Gulf region.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.14227}, pmid = {40135668}, issn = {1365-2591}, support = {MBRU-CMRG2020-11//Mohammed Bin Rashid University of Medicine and Health Sciences/ ; 2201100262//University of Sharjah/ ; }, abstract = {AIM: The microbiota of endodontic infections in patients from the Arabian Gulf region (AGR) is largely unexplored. While research in different global regions has investigated the microbial composition of such infections, studies using shotgun metagenomic sequencing (SMS) alongside culture-dependent techniques (CDT) are limited. There are also few in vitro biofilm models that reflect the microbial profiles of endodontic infections. Therefore, by employing SMS and CDT, this research aimed to explore compositional and functional microbial profiles of endodontic infections from the AGR. The research also sought to develop ex vivo biofilms directly from endodontic infection samples.<br><br>METHODOLOGY: SMS and CDT were used to analyze 32 root canal samples from necrotic pulp. Patients' samples were categorized into two cohorts: symptomatic (n&#x2009;=&#x2009;19) and asymptomatic (n&#x2009;=&#x2009;13). Samples underwent sequencing followed by bioinformatic analysis to investigate microbial composition, resistome, virulome, and functional differences. Two representative samples (8R, 15R) were selected to develop ex vivo biofilms on hydroxyapatite coupons. Similarity between inoculum and developed biofilms was assessed using SMS and CDT. The reproducibility of developed biofilms was assessed based on microbial composition and relative abundance at the species level using correlation coefficient analysis.<br><br>RESULTS: Endodontic samples had high bacterial diversity, with a total of 366 bacterial species detected across the two cohorts. Several antibiotic resistance (n&#x2009;=&#x2009;59) and virulence (n&#x2009;=&#x2009;82) genes were identified, with no significant differences between the cohorts. CDT identified 28 bacterial species, with 71.4% of the isolated bacteria having phenotypic resistance to clinically relevant antibiotics. SMS showed that the ex vivo biofilms were polymicrobial. Biofilm derived from sample 15R had 9 species and was dominated by Enterococcus faecalis, while sample 8R had 12 species and was dominated by Streptococcus mutans. Pearson correlation analysis demonstrated a significant positive correlation between biological biofilm replicates, confirming the reproducibility of biofilm formation.<br><br>CONCLUSIONS: There was high bacterial diversity in root canal samples from necrotic pulp. Samples were shown to contain antibiotic resistance and virulence genes, with no differences evident between symptomatic and asymptomatic infections. A high number of isolated bacteria were resistant to clinically used antibiotics. Ex vivo biofilm models from clinical samples were successfully developed and reproducibly reflected a polymicrobial composition.}, }
@article {pmid40135504, year = {2025}, author = {Pelto, J and Auranen, K and Kujala, JV and Lahti, L}, title = {Elementary methods provide more replicable results in microbial differential abundance analysis.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf130}, pmid = {40135504}, issn = {1477-4054}, support = {952914//European Union's Horizon 2020 research and innovation programme/ ; }, mesh = {*Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Humans ; Reproducibility of Results ; Computational Biology/methods ; Bacteria/genetics/classification ; }, abstract = {Differential abundance analysis (DAA) is a key component of microbiome studies. Although dozens of methods exist, there is currently no consensus on the preferred methods. While the correctness of results in DAA is an ambiguous concept and cannot be fully evaluated without setting the ground truth and employing simulated data, we argue that a well-performing method should be effective in producing highly reproducible results. We compared the performance of 14 DAA methods by employing datasets from 53 taxonomic profiling studies based on 16S rRNA gene or shotgun metagenomic sequencing. For each method, we examined how the results replicated between random partitions of each dataset and between datasets from separate studies. While certain methods showed good consistency, some widely used methods were observed to produce a substantial number of conflicting findings. Overall, when considering consistency together with sensitivity, the best performance was attained by analyzing relative abundances with a nonparametric method (Wilcoxon test or ordinal regression model) or linear regression/t-test. Moreover, a comparable performance was obtained by analyzing presence/absence of taxa with logistic regression.}, }
@article {pmid40132013, year = {2025}, author = {Halo, BA and Aljabri, YAS and Yaish, MW}, title = {Drought-induced microbial dynamics in cowpea rhizosphere: Exploring bacterial diversity and bioinoculant prospects.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0320197}, doi = {10.1371/journal.pone.0320197}, pmid = {40132013}, issn = {1932-6203}, mesh = {*Rhizosphere ; *Vigna/microbiology/genetics ; *Droughts ; *Soil Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Biodiversity ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Microbiota ; Plant Roots/microbiology ; }, abstract = {Rhizospheric bacterial communities in plants contribute to drought resilience by promoting plant-soil interactions, yet their biodiversity and ecological impacts are not fully characterized. In cowpeas, these interactions may be crucial in enhancing tolerance to drought conditions. In this study, cowpea plants were subjected to drought treatment, the soil attached to the roots was collected, environmental DNA (e-DNA) was extracted, and the bacterial communities were identified as amplicon sequence variants (ASVs) by metagenomics analysis of the 16S rRNA gene. Microbial communities under drought and control conditions were analyzed using taxonomy and diversity metrics. The sequencing results revealed 5,571 ASVs, and taxonomic analysis identified 1,752 bacterial species. Alpha and beta diversity analyses showed less conserved microbial community structures and compositions among the samples isolated from the rhizosphere under drought conditions compared to untreated samples, implying the enhancement effect of drought on species' biodiversity and richness. The differential accumulation analysis of the bacterial community identified 75 species that accumulated significantly (P ≤ 0.05) in response to drought, including 13 species exclusively present, seven absent, and 46 forming a high-abundance cluster within the hierarchical heatmap. These species were also grouped into specific clades in the phylogenetic tree, suggesting common genetic ancestry and potentially shared traits associated with drought tolerance. The differentially accumulated bacterial list included previously characterized species from drought and saline habitats. These findings suggest that drought stress significantly alters the composition and abundance of epiphytic bacterial communities, potentially impacting the rhizosphere's ecological balance and interactions with cowpeas. The results highlight microbial adaptations that enhance plant resilience through improved stress mitigation, providing meaningful understandings for advancing sustainable agriculture and developing microbial-based strategies to boost crop productivity in drought-prone regions.}, }
@article {pmid40131885, year = {2025}, author = {Elsakhawy, OK and Roozitalab, A and Abouelkhair, MA}, title = {Genome sequence of a Tetraparvovirus ungulate 1 strain from a cow in Tennessee, USA.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0129124}, doi = {10.1128/mra.01291-24}, pmid = {40131885}, issn = {2576-098X}, abstract = {We report the genome sequence of a strain belonging to the species Tetraparvovirus ungulate 1 (hereafter referred to as UTPV1-1882), identified in a 4-month-old cow with respiratory disease in Tennessee, USA. The sequence data will improve the existing genomic database, which currently lacks information on these viruses in the United States.}, }
@article {pmid40131631, year = {2025}, author = {Pavan, E and Pavón, JAR and Nunes, MRT and Carrasco, MM and Dos Santos, MAM and Slhessarenko, RD}, title = {Anellovirus species in the serum of acute febrile patients from Mato Grosso, central Western Brazil, 2019.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {40131631}, issn = {1678-4405}, support = {FAPEMAT.0290384/2018//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Mato Grosso/ ; 88887.838336/2023-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 309750/2020-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304781/2019-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 144451/2023-9 (PIBIC)//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {The Anelloviridae family is one of the most diverse group of viruses within human virome, comprising 155 species distributed across 30 genera, four of which infect humans. Using a metagenomic approach to examine the frequency and diversity of viruses in the serum of patients with acute febrile illness in Mato Grosso during 2019, we identified and characterized two complete, three nearly complete and nine partial anellovirus genomes, including eleven putatively new species. Alphatorquevirus was the most prevalent genus (50%; n = 7), followed by Gammatorquevirus (35.7%; n = 5) and Betatorquevirus (14.3%; n = 2), consistent with global reports showing its dominance within Anelloviridae. Additionally, 65% of genomes were recovered from children, supporting higher anellovirus diversity and load in younger individuals.}, }
@article {pmid40131463, year = {2025}, author = {Liu, H and Gan, Y and He, B and Liu, H and Zhuo, H and Tang, J and Xie, B and Shen, G and Ren, H and Jiang, X}, title = {mNGS technique was used to analyze the microbiome structure of intervertebral disc tissue in 99 patients with degenerative disc disease.}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {}, number = {}, pages = {}, pmid = {40131463}, issn = {1432-0932}, abstract = {OBJECTIVE: Whether bacterial hypotoxic infection in the intervertebral disc is the cause of disc degenerative disease (DDD) is controversial. The mNGS technique can provide valuable insights by obtaining more comprehensive evidence of the presence of bacteria in the intervertebral disc. This study was designed to analyze the characteristics of intervertebral microbiome structure in patients with lumbar disc degenerative disease and its correlation with clinical indicators.<br><br>METHODS: A total of 104 patients with lumbar&#xa0;disc degenerative diseases were included in this study. The surgically removed lumbar intervertebral disc tissues were collected for clinical culture and metagenomic second-generation sequencing (mNGS), and the consistency of the two microbial detection methods was compared.According to the collected clinical information, patients were grouped according to the modified Pfirrmann grading, Modic typing and age, and the differences of microbial communities detected by mNGS among different groups were compared, including &#x3b1; diversity analysis, &#x3b2; diversity analysis, species abundance difference analysis, etc. Spearman correlation between clinical features and generic relative abundance was calculated.<br><br>RESULTS: The effective culture results of 104 intervertebral disc tissue samples were only 19 cases positive, with a positive rate of 18.3% (19/104), and the mNGS detection results were positive in 99 cases, with a positive rate of 95.2% (99/104). According to the 19 samples with positive culture, nearly half 47.4% (9/19) of staphylococcus species were positive, and all the positive species were basically epidermal common colonization species or environmental common bacteria. At the same time, we conducted two times of mNGS sequencing for these 19 samples, and the consistency rate between the two sequencing results and the culture results was 84.2% (16/19). According to the results of mNGS detection, 250 species from 110 genera were detected in 99 positive samples. The results of group analysis showed that patients with lower degree of disc degeneration (modified Pfirrmann&#x2009;&#x2264;&#x2009;4) and young patients (age&#x2009;<&#x2009;45&#xa0;years) had more abundant microbial communities in disc tissue (P&#x2009;<&#x2009;0.05).&#xa0;Correlation analysis showed that there was a positive correlation between Arcobacter skirrowii and improved Pfirrmann classification at the species level (P&#x2009;<&#x2009;0.01). There was a negative correlation between pseudomonas&#xa0;thermotolerans and modified Pfirrmann classification (P&#x2009;<&#x2009;0.05). There was a positive correlation between Staphylococcus hominis and Modic typing scores (P&#x2009;<&#x2009;0.05). Staphylococcus&#xa0;arlettae was negatively correlated with age (P&#x2009;<&#x2009;0.05). At the genus level, Arcobacter had a significant positive correlation with the modified Pfirrmann grade and Modic classification (P&#x2009;<&#x2009;0.05), Corynebacterium had a significant negative correlation with the modified Pfirrmann grade (P&#x2009;<&#x2009;0.05), and Pseudomonas had a significant negative correlation with age (P&#x2009;<&#x2009;0.05). After our follow-up of six months to one year, two of the patients included in this study eventually developed severe lumbar disc infection, and the rest did not develop infection.<br><br>CONCLUSIONS: This study proves that hypotoxic infection may be involved in the degeneration of intervertebral disc, and the bacterial species that cause this occult infection may be more abundant than previously thought. In addition, there was a significant correlation between the biome structure of these bacteria and clinical indicators. The hypothesis of the cause of this insidious infection has the potential to change the way the disease is treated.}, }
@article {pmid40131352, year = {2025}, author = {Lu, W and Ji, R and Li, W}, title = {Invasive pulmonary and central nervous system aspergillosis: A case report and literature review.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2025.02528}, pmid = {40131352}, issn = {1588-2640}, abstract = {Invasive aspergillosis primarily affects individuals with compromised immune systems. This study endeavors to suggest the importance of early diagnosis and treatment related to central nervous system (CNS) aspergillosis. Recognizing the typical and atypical imaging characteristics of CNS aspergillosis enables the early and aggressive treatment of an otherwise rapidly fatal infection. We reported a case of an elderly patient with a history of non-Hodgkin lymphoma and prostate cancer who underwent repeated chemotherapy and subsequently experienced a sudden disturbance of consciousness. The diagnosis was affirmed through metagenomic next-generation sequencing (mNGS) of sputum and cerebrospinal fluid. The treatment encompassed systemic antifungal agents and intrathecal injection of amphotericin B. Metagenomic sequencing of sputum and cerebrospinal fluid detected Aspergillus fumigatus and Aspergillus flavus, leading to a diagnosis of invasive pulmonary and CNS aspergillosis. Although the patient actively received combined systemic antifungal drugs (voriconazole and amphoteric B liposome) and intrathecal injection of amphotericin B, he ultimately succumbed to the infection. A review of similar cases from PubMed and Medline from 2014 to 2024, encompassing 64 patients, showed that while early diagnosis and combination therapy have improved survival rates, outcomes remain suboptimal. Invasive aspergillosis has a high mortality rate and requires early diagnosis and treatment. Metagenomic sequencing of pathogenic microorganisms constitutes a convenient approach to facilitate the early diagnosis of aspergillosis. Voriconazole is the preferred treatment for invasive aspergillosis. When CNS aspergillosis emerges, it might be necessary to combine other systemic antifungal agents with intrathecal injection of amphotericin B.}, }
@article {pmid40131312, year = {2025}, author = {Herazo-Álvarez, J and Mora, M and Cuadros-Orellana, S and Vilches-Ponce, K and Hernández-García, R}, title = {A review of neural networks for metagenomic binning.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf065}, pmid = {40131312}, issn = {1477-4054}, support = {2022-21221825//National Agency for Research and Development/ ; EQM210185//Fondequip/ ; }, mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; Humans ; Machine Learning ; Metagenome ; Deep Learning ; }, abstract = {One of the main goals of metagenomic studies is to describe the taxonomic diversity of microbial communities. A crucial step in metagenomic analysis is metagenomic binning, which involves the (supervised) classification or (unsupervised) clustering of metagenomic sequences. Various machine learning models have been applied to address this task. In this review, the contributions of artificial neural networks (ANN) in the context of metagenomic binning are detailed, addressing both supervised, unsupervised, and semi-supervised approaches. 34 ANN-based binning tools are systematically compared, detailing their architectures, input features, datasets, advantages, disadvantages, and other relevant aspects. The findings reveal that deep learning approaches, such as convolutional neural networks and autoencoders, achieve higher accuracy and scalability than traditional methods. Gaps in benchmarking practices are highlighted, and future directions are proposed, including standardized datasets and optimization of architectures, for third-generation sequencing. This review provides support to researchers in identifying trends and selecting suitable tools for the metagenomic binning problem.}, }
@article {pmid40130931, year = {2025}, author = {Xia, T and Yang, J and Chen, S and Li, H and Xu, S and Guo, K and Hou, S}, title = {Recovery of 26 metagenome-assembled genomes from the phycosphere of the marine diatom Skeletonema tropicum.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0101324}, doi = {10.1128/mra.01013-24}, pmid = {40130931}, issn = {2576-098X}, abstract = {Metagenome-assembled genomes (MAGs) were recovered from the phycosphere of marine diatom Skeletonema tropicum, which has been long-term maintained in artificial seawater. Most MAGs were found to be highly complete (>90%) with minimum contaminations (<5%), which could serve as reference genomes to investigate the interactions between Skeletonema and their phycosphere microbiota.}, }
@article {pmid40130924, year = {2025}, author = {Fuchsman, CA and Cram, JA and Huntemann, M and Riley, R and Foster, B and Foster, B and Roux, S and Palaniappan, K and Mukherjee, S and Reddy, T and Daum, C and Copeland, A and Chen, I-MA and Ivanova, NN and Kyrpides, NC and Graham, D and Eloe-Fadrosh, EA and Malkin, SY}, title = {Size-fractionated metagenomic depth profiles from two sulfidic stations in the Chesapeake Bay.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0008425}, doi = {10.1128/mra.00084-25}, pmid = {40130924}, issn = {2576-098X}, abstract = {We present 45 size-fractionated metagenomes collected from two stratified Chesapeake Bay mainstem stations during bottom water sulfidic conditions. This data set enables investigations into shifts in community structure and genomic potential across redox gradients and particle associations (free-living [0.2-3 µm], small [3-30 µm], medium [30-180 µm], and large [>180 µm] fractions).}, }
@article {pmid40130858, year = {2025}, author = {Vaccaro, M and Pilat, AM and Gusmano, L and Pham, MTN and Barich, D and Gibson, A and Epalle, M and Frost, DJ and Volin, E and Slimak, ZC and Menke, CC and Fennessy, MS and Slonczewski, JL}, title = {Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0303424}, doi = {10.1128/spectrum.03034-24}, pmid = {40130858}, issn = {2165-0497}, abstract = {UNLABELLED: Microbial communities of small freshwater bodies interact dynamically with environmental factors in unknown ways. Longitudinal sampling of four ponds in Knox County, Ohio, revealed relationships among antibiotic resistance genes (ARGs) and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration, and metagenomes were analyzed by short-read sequencing. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database. The top 30 ARGs showed increased abundance at the end of the growing season. The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and acid stress response (mtrA). The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannic acids). Acidity amplifies the transmembrane pH difference component of the proton-motive force, thus increasing the cell's energy available for pump function and ARG expression. Association with microbial taxa was tested by the Kraken2/Bracken predictor of taxa profiles. The ARG profiles showed the strongest acid dependence in ponds with a high proportion of Proteobacteria, whereas a pond with high Cyanobacteria showed the lowest ARG counts. Efflux pumps such as SmeABC and transcriptional activation by MtrA incur large energy expenditures whose function may be favored at low external pH, where the cell's proton-motive force is maximal.<br><br>IMPORTANCE: Compared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes (ARGs). Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity of freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes how aquatic ARG prevalence may depend on environmental factors such as pH and tannic acid levels.}, }
@article {pmid40130853, year = {2025}, author = {Lisha, W and Jiao, Q and Mengyuan, C and Jiajia, Q and Tianbin, T and Yilan, W and Linjie, H and Sufei, Y}, title = {Clinical evaluation of negative mNGS reports in sterile body fluids and tissues.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0201324}, doi = {10.1128/spectrum.02013-24}, pmid = {40130853}, issn = {2165-0497}, abstract = {Regarding metagenomics next-generation sequencing (mNGS) negative literature, there have been much discussions about methodology; thus, we collected clinical and laboratory information for retrospective evidence-based research. We retrospectively analyzed 150 negative mNGS results of patients suspected of having aseptic body fluid infections and divided them into a plasma group, cerebrospinal fluid (CSF) group, and others group according to the sample types. Based on the final laboratory and clinical diagnoses, the diagnostic accuracy of excluding infections in the plasma, CSF, and others groups of negative mNGS results were 72.0%, 40.4%, and 30.2%, respectively. The false-negative rates of the CSF and others group were relatively high. The positive impact rates of clinical application in the plasma, CSF, and others groups were 68.0%, 40.4%, and 25.6%, respectively. Three factors, including patient department distribution, admission symptoms, and doctors' judgment of patient infection were used to analyze the reasons for uncertain negative or false-negative results in mNGS. The clinical information analysis of false-negative patients' aims were to reduce the false-negative rate and improve the diagnostic accuracy of mNGS. On the selection of sampling timing in mNGS, within half a month after a patient develops suspected symptoms of infection, the earlier the mNGS test, the higher the true-negative rate.IMPORTANCEThere has been little research carried out on the diagnostic value of negative metagenomics next-generation sequencing (mNGS) results in clinical practice, especially for sterile body fluids. In the present study, plasma negative mNGS results showed the highest diagnostic accuracy for excluding infection. However, the cerebrospinal fluid and other mNGS false-negative rates were 59.6% and 69.8%, respectively. Our findings emphasized the role of negative mNGS results in practical clinical applications and clarified that patients, mNGS sampling time, and doctor's decision making were the key factors for the diagnosis of clinical infections. More attention should be paid to the diagnostic role of mNGS true negatives, the analysis of clinical patterns of false negatives, and improving the diagnostic accuracy of mNGS.}, }
@article {pmid40130725, year = {2025}, author = {Filis, G and Bezantakou, D and Rigkos, K and Noti, D and Saridis, P and Zarafeta, D and Skretas, G}, title = {ProteoSeeker: A Feature-Rich Metagenomic Analysis Tool for Accessible and Comprehensive Metagenomic Exploration.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2414877}, doi = {10.1002/advs.202414877}, pmid = {40130725}, issn = {2198-3844}, support = {T2EDK-02899//Operational Program Competitiveness, Entrepreneurship, and Innovation of the NSRF 2014-2020/ ; ATTP4-0340328//Operational Program "Attica 2014-2020" of the NSRF 2014-2020/ ; 101&#xa0;079&#xa0;363//Horizon Europe Programme/ ; 101&#xa0;087&#xa0;471//Horizon Europe Programme/ ; 101087471//HORIZON EUROPE Widening participation and spreading excellence/ ; }, abstract = {The vast majority of microbial diversity remains unculturable, limiting access to novel biotechnological resources. Advances in metagenomics have expanded the understanding of microbial communities, yet targeted protein discovery remains challenging. This study introduces ProteoSeeker, a command-line tool for streamlined metagenomic protein identification and annotation. ProteoSeeker operates in two primary modes: i) Seek mode, which screens the proteins according to user-defined protein families, and ii) Taxonomy mode, which uncovers the taxonomy of the host organisms. By automating key steps, ProteoSeeker reduces computational complexity, enabling time-efficient and comprehensive metagenomic analysis for both specialized and nonspecialized users. The efficiency of ProteoSeeker to achieve targeted enzyme discovery is demonstrated by identifying extremophilic enzymes with desired biochemical features, such as amylases for starch hydrolysis and carbonic anhydrases for CO2 capture applications. By democratizing functional metagenomics, ProteoSeeker is anticipated to accelerate biotechnology, synthetic biology, and biomedical research and innovation.}, }
@article {pmid40130207, year = {2025}, author = {Lewin, S and Wehrhan, M and Wende, S and Sommer, M and Kolb, S}, title = {Variation of N cycle guilds of the rye rhizosphere microbiome is driven by crop productivity along a tillage erosion catena.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf020}, doi = {10.1093/ismeco/ycaf020}, pmid = {40130207}, issn = {2730-6151}, abstract = {Tillage erosion poses threats to crop yields. A transition towards more sustainable agricultural practices may be advanced by harnessing ecosystem services provided by plant microbiomes. However, targeting microbiomes at the agroecosystem scale necessitates bridging the gap to microscale structures of microbiomes. We hypothesized that differences of microbial nitrogen (N) cycle guilds in the rhizosphere of rye align with a soil catena that has been formed by tillage erosion. The rhizosphere was sampled at four sites, which captured a complete tillage erosion gradient from extremely eroded to depositional soils. The gene abundances characteristic of microbial N cycle guilds were assessed via metagenomics. The eroded sites showed the lowest plant productivity and soil mineral N availability, which was associated with an enrichment of glnA in the rhizosphere. Genes associated with dissimilatory nitrate-to-ammonium reducers and diazotrophy prevailed in the eroded soil profiles. The strongest correlations of the biomasses of rye plants along the catena with N cycle functions were observed for norBC. Thus, tillage erosion as a legacy of agricultural management aligns with substantial differences in rhizosphere microbiome functionality in N cycling. These microbiome differences were linked to plant shoot properties. Thus, the dynamics of the microbiome can be indirectly assessed by remote sensing.}, }
@article {pmid40130011, year = {2025}, author = {Keenum, I and Jackson, SA and Eloe-Fadrosh, E and Schriml, LM}, title = {A standards perspective on genomic data reusability and reproducibility.}, journal = {Frontiers in bioinformatics}, volume = {5}, number = {}, pages = {1572937}, doi = {10.3389/fbinf.2025.1572937}, pmid = {40130011}, issn = {2673-7647}, abstract = {Genomic and metagenomic sequence data provides an unprecedented ability to re-examine findings, offering a transformative potential for advancing research, developing computational tools, enhancing clinical applications, and fostering scientific collaboration. However, effective and ethical reuse of genomics data is hampered by numerous technical and social challenges. The International Microbiome and Multi'Omics Standards Alliance (IMMSA, https://www.microbialstandards.org/) and the Genomic Standards Consortium (GSC, https://gensc.org) hosted a 5-part seminar series "A Year of Data Reuse" in 2024 to explore challenges and opportunities of data reuse and reproducibility across disparate domains of the genomic sciences. Addressing these challenges will require a multifaceted approach, including common metadata reporting, clear communication, standardized protocols, improved data management infrastructure, ethical guidelines, and collaborative policies that prioritize transparency and accessibility. We offer strategies to enable responsible and technically feasible data reuse, recognition of data reproducibility challenges, and emphasizing the importance of cross-disciplinary efforts in the pursuit of open science and data-driven innovation.}, }
@article {pmid40129931, year = {2025}, author = {Lee, G and Rosa, BA and Fernandez-Baca, MV and Martin, J and Ore, RA and Ortiz, P and Cabada, MM and Mitreva, M}, title = {Distinct gut microbiome features characterize Fasciola hepatica infection and predict triclabendazole treatment outcomes in Peruvian patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1555171}, doi = {10.3389/fcimb.2025.1555171}, pmid = {40129931}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; Peru ; Animals ; *Fasciola hepatica/drug effects/genetics ; *Fascioliasis/drug therapy/microbiology ; *Triclabendazole/therapeutic use ; Treatment Outcome ; *Anthelmintics/pharmacology/therapeutic use ; Female ; Male ; Adult ; Middle Aged ; Bacteria/classification/genetics/drug effects/isolation &amp; purification ; Metagenomics ; Young Adult ; Feces/microbiology/parasitology ; }, abstract = {BACKGROUND: Fasciola hepatica, a globally distributed helminth, causes fasciolosis, a disease with significant health and economic impacts. Variability in triclabendazole (TCBZ) efficacy and emerging resistance are remaining challenges. Evidence suggests that the gut microbiome influences host-helminth interactions and is associated with anthelmintic effects, but its association with human F. hepatica infection and TCBZ efficacy is not well understood.<br><br>METHODS: In this study, we investigated the relationship between Fasciola hepatica infection and the gut microbiome through metagenomic shotgun sequencing of 30 infected and 60 age- and sex-matched uninfected individuals from Peru. Additionally, we performed a longitudinal analysis to evaluate microbiome dynamics in relation to TCBZ treatment response.<br><br>RESULTS AND DISCUSSION: Infection was associated with specific microbial taxonomic and functional features, including higher abundance of Negativibacillus sp900547015, Blautia A sp000285855, and Prevotella sp002299635 species, and enrichment of microbial pathways linked to survival under stress and depletion of pathways for microbial growth. Unexpectedly, we identified that responders to TCBZ treatment (who cleared infection) harbored many microbiome features significantly different relative to non-responders, both before and after treatment. Specifically, the microbiomes of responders had a higher abundance Firmicutes A and Bacteroides species as well as phospholipid synthesis and glucuronidation pathways, while non-responders had higher abundance of Actinobacteria species including several from the Parolsenella and Bifidobacterium genera, and Bifidobacterium shunt and amino acid biosynthesis pathways.<br><br>CONCLUSIONS: Our findings underscore the impact of helminth infection on gut microbiome and suggest a potential role of gut microbiota in modulating TCBZ efficacy, offering novel insights into F. hepatica-microbiome interactions and paving the way for microbiome-informed treatment approaches.}, }
@article {pmid40129370, year = {2025}, author = {Lázaro, &#xc1; and Gómez-Ramírez, P and Vila-Donat, P and Cimbalo, A and Manyes, L}, title = {Effects of pumpkin and fermented whey on fecal microbiota profile against AFB1 and OTA exposure in Wistar rats.}, journal = {Toxicology mechanisms and methods}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/15376516.2025.2484636}, pmid = {40129370}, issn = {1537-6524}, abstract = {Mycotoxins perturb the gut microbiota performance. Bioactive compounds have been recently used as a new food strategy to diminish mycotoxins bioaccessibility and prevent their toxic effects on human and animal health. Male and female Wistar rats were exposed orally to twelve different diets containing aflatoxin B1 (AFB1) and/or ochratoxin A (OTA) with or without fermented whey (FW) and pumpkin (P) for 28 days. Fecal microbiota using 16S rRNA gene sequencing and subsequent metagenomics analysis were analyzed to study the effect of 28 day-exposure through diet of contaminated and enriched feed. QIIME 2 microbiome analysis package (version 2024.5) was used to analyze the demultiplexed data. Mycotoxins-functional ingredients combination contributed more to microbial phylogenetic faith α-diversity rather than the functional ingredients alone, while the same combination reported a microbial α-diversity enhancement in comparison to the mycotoxins alone. Proteobacteria phylum was reduced in rat samples fed with contaminated diets (AFB1, OTA and AFB1 + OTA), while there was an increase - although not in all groups - when adding the functional ingredients. The main difference between the sexes was found in FW + AFB1 + OTA group, with males (25%) showing higher % of Proteobacteria than females (1.86%). Phylogenetic diversity faith only focuses on microbial genetic (dis)similarity, not considering the biological function. Morganella morganii, a Proteobacteria found in some groups presents anticancer activity, but it is also related to inflammatory bowel disease and colorectal cancer. To sum up, both mycotoxins and functional ingredients trigger changes in the microbiota profile of Wistar rats in a sex-specific manner.}, }
@article {pmid40129261, year = {2025}, author = {Boden, JS and Som, SM and Brazelton, WJ and Anderson, RE and Stüeken, EE}, title = {Evaluating Serpentinization as a Source of Phosphite to Microbial Communities in Hydrothermal Vents.}, journal = {Geobiology}, volume = {23}, number = {2}, pages = {e70016}, doi = {10.1111/gbi.70016}, pmid = {40129261}, issn = {1472-4669}, support = {NE/V010824/1//Natural Environment Research Council/ ; 80NSSC19K1427//NASA Planetary Science Division ISFM Program/ ; OCE-1536405//National Science Foundation/ ; 80NSSC18K0829//NASA Astrobiology Program/ ; 80NSSC19K1427//NASA Astrobiology Program/ ; }, mesh = {*Hydrothermal Vents/microbiology ; *Phosphites/chemistry/metabolism ; Microbiota ; Bacteria/genetics/metabolism/classification ; Phosphorus/metabolism/analysis ; }, abstract = {Previous studies have documented the presence of phosphite, a reduced and highly soluble form of phosphorus, in serpentinites, which has led to the hypothesis that serpentinizing hydrothermal vents could have been an important source of bioavailable phosphorus for early microbial communities in the Archean. Here, we test this hypothesis by evaluating the genomic hallmarks of phosphorus usage in microbial communities living in modern hydrothermal vents with and without influence from serpentinization. These genomic analyses are combined with results from a geochemical model that calculates phosphorus speciation during serpentinization as a function of temperature, water:rock ratio, and lithology at thermodynamic equilibrium. We find little to no genomic evidence of phosphite use in serpentinizing environments at the Voltri Massif or the Von Damm hydrothermal field at the Mid Cayman Rise, but relatively more in the Lost City hydrothermal field, Coast Range Ophiolite Microbial Observatory, The Cedars, and chimney samples from Old City hydrothermal field and Prony Bay hydrothermal field, as well as in the non-serpentinizing hydrothermal vents at Axial Seamount. Geochemical modeling shows that phosphite production is favored at ca 275°C-325°C and low water:rock ratios, which may explain previous observations of phosphite in serpentinite rocks; however, most of the initial phosphate is trapped in apatite during serpentinization, suppressing the absolute phosphite yield. As a result, phosphite from serpentinizing vents could have supported microbial growth around olivine minerals in chimney walls and suspended aggregates, but it is unlikely to have fueled substantial primary productivity in diffusely venting fluids during life's origin and evolution in the Archean unless substrates equivalent to dunites (composed of > 90 wt% olivine) were more common.}, }
@article {pmid40128855, year = {2025}, author = {DeVeaux, AL and Hall-Moore, C and Shaikh, N and Wallace, M and Burnham, CD and Schnadower, D and Kuppermann, N and Mahajan, P and Ramilo, O and Tarr, PI and Dantas, G and Schwartz, DJ}, title = {Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {82}, pmid = {40128855}, issn = {2049-2618}, support = {R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; T32GM139774/GM/NIGMS NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; Male ; *Metagenomics/methods ; Infant, Newborn ; *Fever/microbiology ; *Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Urinary Tract Infections/microbiology ; Case-Control Studies ; Bacterial Infections/microbiology ; Metagenome ; }, abstract = {BACKGROUND: Extraintestinal bacterial infections (EBIs), e.g., urinary tract infection, bacteremia, and meningitis, occur in approximately 10% of febrile infants younger than 60 days. Although many EBI-causing species commonly reside in the infant gut, proof that the digestive system is a pre-infection habitat remains unestablished.<br><br>RESULTS: We studied a cohort of febrile term infants&#x2009;<&#x2009;60&#xa0;days old who presented to one of thirteen US emergency departments in the Pediatric Emergency Care Applied Research Network from 2016 to 2019. Forty EBI cases and 74 febrile controls matched for age, sex, and race without documented EBIs were selected for analysis. Shotgun sequencing was performed of the gut microbiome and of strains cultured from the gut and extraintestinal site(s) of EBI cases, including blood, urine, and/or cerebrospinal fluid. Using a combination of EBI isolate genomics and fecal metagenomics, we detected an intestinal strain presumptively isogenic to the EBI pathogen (>&#x2009;99.999% average nucleotide identity) in 63% of infants with EBIs. Although there was no difference in gut microbiome diversity between cases and controls, we observed significantly increased Escherichia coli relative abundance in the gut microbiome of infants with EBIs caused by E. coli. Infants with E. coli infections who were colonized by the putatively isogenic pathogen strain had significantly higher E. coli phylogroup B2 abundance in their gut, and their microbiome was more likely to contain virulence factor loci associated with adherence, exotoxin production, and nutritional/metabolic function.<br><br>CONCLUSIONS: The intestine plausibly serves as a reservoir for EBI pathogens in a subset of febrile term infants, prompting consideration of new opportunities for surveillance and EBI prevention among colonized, pre-symptomatic infants. Video Abstract.}, }
@article {pmid40128848, year = {2025}, author = {Byrne, SR and DeMott, MS and Yuan, Y and Ghanegolmohammadi, F and Kaiser, S and Fox, JG and Alm, EJ and Dedon, PC}, title = {Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {81}, pmid = {40128848}, issn = {2049-2618}, support = {T32-ES007020//NIEHS Training Grant in Environmental Toxicology/ ; R01-OD028099-01//NIH Transformative Award/ ; R01-OD028099-01//NIH Transformative Award/ ; P30-ES002109//NIEHS Core Center Grant/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Feces/microbiology ; *Bacteria/genetics/classification/metabolism ; Mice ; Animals ; Epigenesis, Genetic ; Epigenome ; Female ; Male ; Phosphates/metabolism ; }, abstract = {BACKGROUND: Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome. Here we optimized and applied fecal DNA extraction, mass spectrometric, and metagenomics technologies to characterize the landscape and temporal dynamics of gut microbes possessing PT modifications.<br><br>RESULTS: Exploiting the nuclease-resistance of PTs, mass spectrometric analysis of limit digests of PT-containing DNA reveals PT dinucleotides as part of genomic consensus sequences, with 16 possible dinucleotide combinations. Analysis of mouse fecal DNA revealed a highly uniform spectrum of 11 PT dinucleotides in all littermates, with PTs estimated to occur in 5-10% of gut microbes. Though at similar levels, PT dinucleotides in fecal DNA from 11 healthy humans possessed signature combinations and levels of individual PTs. Comparison with a widely distributed microbial epigenetic mark, m[6]dA, suggested temporal dynamics consistent with expectations for gut microbial communities based on Taylor's Power Law. Application of PT-seq for site-specific metagenomic analysis of PT-containing bacteria in one fecal donor revealed the larger consensus sequences for the PT dinucleotides in Bacteroidota, Bacillota (formerly Firmicutes), Actinomycetota (formerly Actinobacteria), and Pseudomonadota (formerly Proteobacteria), which differed from unbiased metagenomics and suggested that the abundance of PT-containing bacteria did not simply mirror the spectrum of gut bacteria. PT-seq further revealed low abundance PT sites not detected as dinucleotides by mass spectrometry, attesting to the complementarity of the technologies. Video Abstract CONCLUSIONS: The results of our studies provide a benchmark for understanding the behavior of an abundant and chemically reactive epigenetic mark in the human gut microbiome, with implications for inflammatory conditions of the gut.}, }
@article {pmid40128686, year = {2025}, author = {Sun, N and Zhang, J and Guo, W and Cao, J and Chen, Y and Gao, D and Xia, X}, title = {Comparative analysis of metagenomic next-generation sequencing for pathogenic identification in clinical body fluid samples.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {165}, pmid = {40128686}, issn = {1471-2180}, support = {SY202214//Suqian Sci&amp;Tech Program/ ; SY202214//Suqian Sci&amp;Tech Program/ ; 81601857//National Natural Science Foundation of China/ ; YKK18216//Health Technology Development Special Foundation of Nanjing City/ ; YKK18216//Health Technology Development Special Foundation of Nanjing City/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Body Fluids/microbiology/virology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; Male ; Middle Aged ; Female ; Adult ; Aged ; Sensitivity and Specificity ; Young Adult ; Adolescent ; Cell-Free Nucleic Acids/genetics ; DNA, Bacterial/genetics ; Child ; Aged, 80 and over ; Child, Preschool ; }, abstract = {OBJECTIVES: This study aims to evaluate and compare the effectiveness of metagenomic next-generation sequencing (mNGS) in identifying pathogens from clinical body fluid samples, with a specific focus on the application of microbial cell-free DNA (cfDNA) mNGS.<br><br>METHODS: A total of 125 clinical body fluid samples were collected. All samples underwent mNGS targeting whole-cell DNA (wcDNA), with 30 samples also analyzed for cfDNA mNGS and 41 subjected to 16S rRNA NGS for comparative analysis. Patient clinical data, including culture results, were obtained from electronic medical records.<br><br>RESULTS: In comparison to cfDNA mNGS, the mean proportion of host DNA in wcDNA mNGS was 84%, significantly lower than the 95% observed in cfDNA mNGS (p&#x2009;<&#x2009;0.05). Using culture results as a reference, concordance rates were 63.33% (19/30) for wcDNA mNGS and 46.67% (14/30) for cfDNA mNGS. Additionally, wcDNA mNGS showed greater consistency in bacterial detection with culture results, achieving a rate of 70.7% (29/41) compared to 58.54% (24/41) for 16S rRNA NGS. The sensitivity and specificity of wcDNA mNGS for pathogen detection in body fluid samples were 74.07% and 56.34%, respectively, when compared to culture results.<br><br>CONCLUSION: Whole-cell DNA mNGS demonstrates significantly higher sensitivity for pathogen detection and identification compared to both cfDNA mNGS and 16S rRNA NGS in clinical body fluid samples, particularly those associated with abdominal infections. However, the compromised specificity of wcDNA mNGS highlights the necessity for careful interpretation in clinical practice.}, }
@article {pmid40128614, year = {2025}, author = {Diener, C and Holscher, HD and Filek, K and Corbin, KD and Moissl-Eichinger, C and Gibbons, SM}, title = {Author Correction: Metagenomic estimation of dietary intake from human stool.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42255-025-01284-z}, pmid = {40128614}, issn = {2522-5812}, }
@article {pmid40128575, year = {2025}, author = {Yun, H and Seo, JH and Kim, YG and Yang, J}, title = {Impact of scented candle use on indoor air quality and airborne microbiome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10181}, pmid = {40128575}, issn = {2045-2322}, support = {RS-2023-00244833//National Research Foundation of Korea/ ; }, mesh = {*Air Pollution, Indoor/analysis ; *Microbiota ; *Particulate Matter/analysis ; *Air Microbiology ; Humans ; Bacteria/classification/isolation &amp; purification ; Environmental Monitoring/methods ; Extracellular Vesicles ; }, abstract = {Indoor air quality has become a growing concern worldwide due to its significant impact on human health, particularly in residential environments where people spend most of their time. Many studies have examined particulate matter (PM) in indoor air and indoor bioaerosols. However, there is a significant lack of research on airborne micro-sized bacteria (m-AB) and nano-sized bacterial extracellular vesicles (n-ABE), particularly those produced by common household activities, such as burning scented candles. This study investigates changes in PM concentrations and indoor microbiome composition resulting from candle use. Air samples were collected from three locations in residential homes: at the candle-lit spot (CL), 3 m away (3m_CL), and 6 m away (6m_CL). PM10 concentrations peaked at 1.52 times the baseline at the source after 5 min of burning, while PM2.5 and PM1 remained elevated at 3m_CL and 6m_CL over time. Before burning, dominant m-AB genera included Phyllobacterium and Pseudomonas, while post-burning, Phyllobacterium myrsinacearum in n-ABE significantly increased, marking its first detection in indoor air. This suggests that existing airborne bacteria may undergo growth or apoptosis due to combustion byproducts. These findings highlight the importance of improving ventilation in indoor spaces to minimize health risks from prolonged exposure to airborne particles and bacterial vesicles.}, }
@article {pmid40128554, year = {2025}, author = {Toma, R and Hu, L and Banavar, G and Vuyisich, M}, title = {Preparation of robust synthetic control samples and their use in a metatranscriptomic clinical test.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10101}, pmid = {40128554}, issn = {2045-2322}, mesh = {Humans ; Reproducibility of Results ; *Transcriptome ; Metagenomics/methods ; Gene Expression Profiling/methods ; }, abstract = {Metatranscriptomics (MT) has the potential to revolutionize the field of molecular diagnostics. Due to the complexity of MT diagnostic models, positive and negative control materials for specific disease indications can be difficult to obtain. Controls must often be sourced directly from patients. This introduces logistical burdens, assay variability, and limits high throughput clinical laboratory operations. To overcome this limitation, we developed a method for generating Synthetic Control (SC) samples, which duplicate the nucleic acid signature of complex clinical specimens and produce the desired test outcome. SCs can be easily and cost-effectively produced in large quantities (> 100,000 SCs per amplification cycle), enabling high throughput diagnostic testing. Here, we report the generation of Synthetic Positive Control (SPC) samples. SPCs were validated and implemented in a clinical laboratory. The SPCs produced robust positive signals (average OC risk score of 0.996) and high levels of reproducibility (%CV of 0.29%) in a high throughput automated CLIA laboratory. SCs are a novel and useful method for the generation of high quality controls for MT-based diagnostic tests, and their adoption could herald the widespread use of MT tests in molecular diagnostics.}, }
@article {pmid40128535, year = {2025}, author = {Han, H and Wang, Z and Zhu, S}, title = {Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2865}, pmid = {40128535}, issn = {2041-1723}, support = {62272105//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Metagenomics/methods ; *Benchmarking ; *Metagenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Metagenomic binning is a culture-free approach that facilitates the recovery of metagenome-assembled genomes by grouping genomic fragments. However, there remains a lack of a comprehensive benchmark to evaluate the performance of metagenomic binning tools across various combinations of data types and binning modes. In this study, we benchmark 13 metagenomic binning tools using short-read, long-read, and hybrid data under co-assembly, single-sample, and multi-sample binning, respectively. The benchmark results demonstrate that multi-sample binning exhibits optimal performance across short-read, long-read, and hybrid data. Moreover, multi-sample binning outperforms other binning modes in identifying potential antibiotic resistance gene hosts and near-complete strains containing potential biosynthetic gene clusters across diverse data types. This study also recommends three efficient binners across all data-binning combinations, as well as high-performance binners for each combination.}, }
@article {pmid40128181, year = {2025}, author = {Yan, W and Shi, X and Zhao, Y and Liu, X and Jia, X and Gao, L and Yuan, J and Liao, A and Yasui, H and Wang, X and Wang, X and Zhang, R and Wang, H}, title = {Microbiota-reprogrammed phosphatidylcholine inactivates cytotoxic CD8 T cells through UFMylation via exosomal SerpinB9 in multiple myeloma.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2863}, pmid = {40128181}, issn = {2041-1723}, support = {2022-YGJC-61;2022-MS-219//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; }, mesh = {Female ; Animals ; Mice ; Humans ; Cell Line ; *T-Lymphocytes, Cytotoxic/immunology ; *Gastrointestinal Microbiome ; *Phosphatidylcholines/immunology/metabolism ; *Multiple Myeloma/genetics/immunology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Exosomes/immunology/metabolism ; *Serpins/genetics/immunology/metabolism ; *Membrane Proteins/genetics/immunology/metabolism ; }, abstract = {Gut microbiome influences tumorigenesis and tumor progression through regulating the tumor microenvironment (TME) and modifying blood metabolites. However, the mechanisms by which gut microbiome and blood metabolites regulate the TME in multiple myeloma (MM) remain unclear. By employing16S rRNA gene sequencing coupled with metagenomics and ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, we find that Lachnospiraceae are high and phosphatidylcholine (PC) are low in MM patients. We further show that Lachnospiraceae inhibits PC production from MM cells and enhances cytotoxic CD8 T cell function. Mechanistically, PC promotes Sb9 mRNA maturation in MM cells by LIN28A/B via lysophosphatidic acid, thus enhances exosamal Sb9 production. Exosamal Sb9 then reduces GZMB expression by suppressing tumor protein p53 (TP53) UFMylation via the competitive binding of TP53 with the ubiquitin-fold modifier conjugating enzyme 1 in CD8 T cells. We thus show that Lachnospiraceae and PC may be potential therapeutic targets for MM treatment.}, }
@article {pmid40128138, year = {2025}, author = {Bai, M and Zhou, Z and Yin, M and Wang, M and Gao, X and Zhao, J}, title = {Corrigendum to "The use of metagenomic and untargeted metabolomics in the analysis of the effects of the Lycium barbarum glycopeptide on allergic airway inflammation induced by Artemesia annua pollen" [J. Ethnopharmacol. (2025) 337(Pt 1) 118816].}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {119657}, doi = {10.1016/j.jep.2025.119657}, pmid = {40128138}, issn = {1872-7573}, }
@article {pmid40127879, year = {2025}, author = {Mirsalami, SM and Mirsalami, M}, title = {Assessing microbial ecology and antibiotic resistance genes in river sediments.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105738}, doi = {10.1016/j.meegid.2025.105738}, pmid = {40127879}, issn = {1567-7257}, abstract = {Anthropogenic activities greatly affect the Karon River leading to deterioration of water quality. This investigation utilizes environmental genomic techniques to delineate microbial populations, examine functional genomics, and evaluate the occurrence of virulence determinants and antibiotic resistance genes (ARGs) in fluvial sediment. Taxonomic assessment identified that Firmicutes were the predominant phyla, with Bacillus being the most abundant genus across samples. Functional analysis revealed the metabolic capabilities of sediment-associated bacteria, linking them to biogeochemical processes and potential health impacts. The S2 samples exhibited the highest virulence factor genes, while the S3 samples had the most ARGs (30), highlighting concerns about pathogenicity. Analyzing ARGs provides critical insights into environmental data collected, such as water quality parameters (e.g., nutrient concentrations, pH) or pollution levels, prevalence, and distribution of these resistance factors within the sediment samples, helping to identify potential hotspots of antibiotic resistance in the Karon River ecosystem. The study identified similar operational taxonomic units (OTUs) across sampling sites at the phylogenetic level, indicating a consistent presence of certain microbial taxa. However, the lack of variation in functional classification suggests that while these taxa may be present, they are not exhibiting significant differences in metabolic capabilities or functional roles. These findings emphasize the significance of metagenomic methods in understanding microbial ecology and antibiotic resistance in aquatic environments, suggesting a need for further research into the restoration of microbial functions related to ARGs and virulence factors.}, }
@article {pmid40127846, year = {2025}, author = {Brito, J and Frade-González, C and Almenglo, F and González-Cortés, JJ and Valle, A and Durán-Ruiz, MC and Ramírez, M}, title = {Anoxic desulfurization of biogas rich in hydrogen sulfide through feedback control using biotrickling filters: Operational limits and multi-omics analysis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132439}, doi = {10.1016/j.biortech.2025.132439}, pmid = {40127846}, issn = {1873-2976}, abstract = {Biodesulfurization is crucial for sustainable biogas purification from hydrogen sulfide (H2S). This study investigates the operational limits of anoxic biotrickling filters (BTFs) for treating biogas with high H2S concentrations (up to 20,000 ppmv) using nitrite, along with simulated interruptions in H2S supply. The BTF achieved a maximum elimination capacity of 312 g S-H2S m[-3] h[-1] with an H2S removal efficiency of 98 % at an empty bed residence time of 284 s. A proportional-integral-derivative (PID) feedback control system was successfully employed to maintain an H2S outlet concentration close to the requisite setpoint (100 and 500 ppmv) by adjusting the nitrite flow rate, thereby minimizing its accumulation. Continuous nitrite feeding after interruptions in H2S supply was essential to avoid H2S release due to sulfate-reducing bacteria. Multi-omics analyses, combining metagenomics and proteomics, revealed Sulfurimonas as the dominant sulfur-oxidizing bacteria, which downregulates most enzyme genes involved in nitrogen and sulfur metabolism in response to substrate starvation. These findings underscore the resilience of BTFs under extreme conditions and the value of multi-omics approaches in understanding microbial population dynamics, positioning BTFs as a robust solution for large-scale biogas purification.}, }
@article {pmid40127751, year = {2025}, author = {Lim, TW and Huang, S and Burrow, MF and McGrath, C}, title = {A randomised crossover clinical trial of the efficacy of an ultrasonic cleaner combined with a denture cleanser on the microbiome on removable dentures among community-dwelling older adults.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {105709}, doi = {10.1016/j.jdent.2025.105709}, pmid = {40127751}, issn = {1879-176X}, abstract = {OBJECTIVE: To evaluate and characterise the microbial compositional changes of removable dentures after interventions by comparing the efficacy of the test arm (a portable self-operated ultrasonic cleaner combined with an enzymatic peroxide-based denture cleanser solution) to the control arm (immersion of the denture in the same cleanser solution followed by conventional brushing).<br><br>MATERIALS AND METHODS: A prospective, single-blind, block-randomised, two-period crossover, controlled clinical trial was conducted, involving 56 community-dwelling older adults wearing removable acrylic dentures. They were block-randomized into the test/control or control/test denture cleaning sequence. Type IIB Restriction-site Associated DNA for Microbiome metagenomic sequencing was adopted to characterize the species-resolved microbial composition for denture biofilm.<br><br>RESULTS: For the intervention effect, the overall microbial richness in both arms was not significantly different based on the Chao 1 index (P=0.343). However, Beta diversity analysis (Jaccard qualitative distance matrix) demonstrated significant differences in the microbial community structures between the Test and Control arms after interventions, confirmed by the Permanova test (R[2]=0.01118, P=0.034). Among the opportunistic pathogenic bacteria, Pseudomonas aeruginosa was detected as one of the top 30 species by relative abundance at the end of the clinical trial, and Enterobacter kobei was significantly enriched in the control arm, as determined by LEfSe analysis.<br><br>CONCLUSIONS: The microbial community of denture biofilm samples after both interventions were significantly 'shifted' and had limited numbers of opportunistic pathogens, suggesting the interventions equally effective in mitigating the overall number of pathogenic bacteria.<br><br>CLINICAL SIGNIFICANCE: Denture cleaning intervention using ultrasonic cleaner combined with immersion in denture cleanser solution appears to be effective in shifting the denture microbiome with reduced pathogenic bacteria among community-dwelling denture wearers.}, }
@article {pmid40127491, year = {2025}, author = {Penner, M and Klein, OJ and Gantz, M and Nintzel, FEH and Prowald, AC and Boss, S and Barker, P and Dupree, P and Hollfelder, F}, title = {Fluorogenic, Subsingle-Turnover Monitoring of Enzymatic Reactions Involving NAD(P)H Provides a Generalized Platform for Directed Ultrahigh-Throughput Evolution of Biocatalysts in Microdroplets.}, journal = {Journal of the American Chemical Society}, volume = {}, number = {}, pages = {}, doi = {10.1021/jacs.4c11804}, pmid = {40127491}, issn = {1520-5126}, abstract = {Enzyme engineering and discovery are crucial for a sustainable future bioeconomy. Harvesting new biocatalysts from large libraries through directed evolution or functional metagenomics requires accessible, rapid assays. Ultrahigh-throughput screening formats often require optical readouts, leading to the use of model substrates that may misreport target activity and necessitate bespoke synthesis. This is a particular challenge when screening glycosyl hydrolases, which leverage molecular recognition beyond the target glycosidic bond, so that complex chemical synthesis would have to be deployed to build a fluoro- or chromogenic substrate. In contrast, coupled assays represent a modular "plug-and-play" system: any enzyme-substrate pairing can be investigated, provided the reaction can produce a common intermediate which links the catalytic reaction to a detection cascade readout. Here, we establish a detection cascade producing a fluorescent readout in response to NAD(P)H via glutathione reductase and a subsequent thiol-mediated uncaging reaction, with a low nanomolar detection limit in plates. Further scaling down to microfluidic droplet screening is possible: the fluorophore is leakage-free and we report 3 orders of magnitude-improved sensitivity compared to absorbance-based systems, with a resolution of 361,000 product molecules per droplet. Our approach enables the use of nonfluorogenic substrates in droplet-based enrichments, with applicability in screening for glycosyl hydrolases and imine reductases (IREDs). To demonstrate the assay's readiness for combinatorial experiments, one round of directed evolution was performed to select a glycosidase processing a natural substrate, beechwood xylan, with improved kinetic parameters from a pool of >10[6] mutagenized sequences.}, }
@article {pmid40127066, year = {2025}, author = {Pankovics, P and Takáts, K and Urbán, P and Mátics, R and Reuter, G and Boros, &#xc1;}, title = {Identification of a potential interspecies reassortant rotavirus G and avastrovirus 2 co-infection from black-headed gull (Chroicocephalus ridibundus) in Hungary.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0317400}, doi = {10.1371/journal.pone.0317400}, pmid = {40127066}, issn = {1932-6203}, mesh = {*Rotavirus/genetics/isolation &amp; purification ; Animals ; Hungary ; *Reassortant Viruses/genetics/isolation &amp; purification ; *Charadriiformes/virology ; *Phylogeny ; *Genome, Viral ; Avastrovirus/genetics/isolation &amp; purification/classification ; Coinfection/virology ; Rotavirus Infections/virology/veterinary ; Bird Diseases/virology/epidemiology ; Feces/virology ; Astroviridae Infections/virology/veterinary ; }, abstract = {The black-headed gull is the most common nesting gull species in Hungary. Based on the lifestyle and feeding habits of the black-headed gull, which is highly adapted to the human environment, they can be carriers and spreaders of potential human and other animal pathogens. Between 2014 and 2018 within the framework of the "Life Bird Ringing program" a total of 7 faecal samples were collected from gulls and one sample (MR04) was randomly selected for viral metagenomics and mass sequencing. 95.4% and 4% of the reads were classified into family Seadornaviridae and Astroviridae, respectively, and then were verified by RT-PCR method. In this study, the complete genome of a potential interspecies reassortant rotavirus (RV) strain gull/MR04_RV/HUN/2014 (PP239049-PP239059) and the partial ORF1ab, complete ORF2 of a novel avian nephritis virus strain gull/MR04_AAstV/HUN/2014 (PP239060) was discussed. The strain gull/MR04_RV/HUN/2014 was closely related to rotavirus G (RVG) viruses based on the proteins VP1-VP3, VP6, NSP2, NSP3, and NSP5, but it was more related to the human rotavirus B (RVB) strain Bang373 based on the NSP1, NSP4 and VP7, VP4 proteins, which is assumed to be the result of reassortment between different RVG-RVB rotavirus species. The strain gull/MR04_AAstV/HUN/2014 belonged to the genus Avastrovirus species avastrovirus 2 (AAstV-2) and is related to members of group 6 of avian nephritis viruses (ANVs), but based on the genetic distances it may be the first representative of a separate group. Additional gull samples were found to be negative by RT-PCR. Gulls, which are well adapted to the human environment, could potentially spread enterically transmitted viral pathogens like interspecies reassortant rotaviruses (RVG/RVB), but further molecular surveillance is needed to explore more deeply the viral communities of gulls or other related species adapted to human environments.}, }
@article {pmid40127030, year = {2025}, author = {Abraham, A and Green, A and Ferrolino, J and Flerlage, T and Gowen, A and Allison, KJ and Suliman, AY and Bhakta, N and McArthur, J and Srinivasan, S and Hayden, RT and Hijano, DR}, title = {Utility and Safety of Bronchoalveolar Lavage for Diagnosis and Management of Respiratory Illnesses in Immunocompromised Children.}, journal = {Journal of the Pediatric Infectious Diseases Society}, volume = {14}, number = {3}, pages = {}, doi = {10.1093/jpids/piaf015}, pmid = {40127030}, issn = {2048-7207}, support = {//American Lebanese Syrian Associated Charities/ ; }, mesh = {Humans ; *Immunocompromised Host ; Retrospective Studies ; *Bronchoalveolar Lavage ; Child ; Child, Preschool ; Female ; Male ; *Respiratory Tract Infections/diagnosis/drug therapy ; Infant ; Adolescent ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: Acute respiratory illnesses (ARIs) in immunocompromised children have diverse causes, which can obscure accurate diagnosis and lead to unnecessary antimicrobial use. The risk-benefit ratio of bronchoalveolar lavage (BAL) in these patients is debated. This study aimed to evaluate the safety, yield, and utility of BAL in managing ARIs in immunocompromised children.<br><br>METHODS: This retrospective review examined BALs performed on immunocompromised children with ARI at St. Jude Children's Research Hospital between 2016 and 2021. Microbiological and molecular test results were reviewed from BAL, respiratory tract, and blood within 7 days of the BAL. The final ARI diagnosis was determined by the primary team, changes in antimicrobial management and adverse events were assessed.<br><br>RESULTS: BAL identified a potential pathogen in 84/137 (61.3%) of ARI episodes. BAL results contributed to changes in antimicrobial management in 120 (87.6%) cases and contributed to the ARI diagnosis in 106 (77.3%) cases. In 81 (59.1%) cases, ARI diagnosis was established solely from BAL results (infectious [33.3%], noninfectious [63%], multifactorial [3.7%]). BAL results usually agreed with the ARI diagnosis, but 31/137 (22.6%) were not concordant. Post-BAL, only 5 (3.6%) had increased supplemental oxygen&#x2005;>&#x2005;24 hours, and 3 (3.4%) required new, persistent intubation. Consolidative or nodular pulmonary lesions and post-hematopoietic cell transplant had the highest BAL yields, with no significant differences based on the diffuseness of lesions.<br><br>CONCLUSIONS: BAL is a safe, high-yield diagnostic procedure in immunocompromised children, with results leading to changes in clinical management of ARI. Prospective studies are needed to generate BAL guidelines for ARI in this population.}, }
@article {pmid40126889, year = {2025}, author = {Cheng, GB and Bongcam-Rudloff, E and Schnürer, A}, title = {Metagenomic Exploration Uncovers Several Novel 'Candidatus' Species Involved in Acetate Metabolism in High-Ammonia Thermophilic Biogas Processes.}, journal = {Microbial biotechnology}, volume = {18}, number = {3}, pages = {e70133}, doi = {10.1111/1751-7915.70133}, pmid = {40126889}, issn = {1751-7915}, support = {2018-01341//Svenska Forskningsr&#xe5;det Formas/ ; }, mesh = {*Ammonia/metabolism ; *Biofuels ; *Acetates/metabolism ; *Bioreactors/microbiology ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenomics ; Archaea/metabolism/genetics/classification ; Anaerobiosis ; Hot Temperature ; Metabolic Networks and Pathways/genetics ; Metagenome ; Methane/metabolism ; }, abstract = {Biogas reactors operating at elevated ammonia levels are commonly susceptible to process disturbances, further augmented at thermophilic temperatures. The major cause is assumed to be linked to inhibition followed by an imbalance between different functional microbial groups, centred around the last two steps of the anaerobic digestion, involving acetogens, syntrophic acetate oxidisers (SAOB) and methanogens. Acetogens are key contributors to reactor efficiency, acting as the crucial link between the hydrolysis and fermentation steps and the final methanogenesis step. Their major product is acetate, at high ammonia levels further converted by SAOB and hydrogenotrophic methanogens to biogas. Even though these functionally different processes are well recognised, less is known about the responsible organism at elevated temperature and ammonia conditions. The main aim of this study was to garner insights into the penultimate stages in three thermophilic reactors (52°C) operated under high ammonia levels (FAN 0.7-1.0 g/L; TAN 3.6-4.4 g/L). The primary objective was to identify potential acetogens and SAOBs. Metagenomic data from the three reactors were analysed for the reductive acetyl-CoA pathway (Wood-Ljungdahl Pathway) and glycine synthase reductase pathway. The results revealed a lack of true acetogens but uncovered three potential SAOB candidates that harbour the WLP, 'Candidatus Thermodarwinisyntropha acetovorans', 'Candidatus Thermosyntrophaceticus schinkii', 'Candidatus Thermotepidanaerobacter aceticum', and a potential lipid-degrader 'Candidatus Thermosyntrophomonas ammoiaca'.}, }
@article {pmid40126871, year = {2025}, author = {Yang, S}, title = {The Economics of Cell-Free DNA Metagenomic Next-Generation Sequencing for Pathogen Detection.}, journal = {Clinical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/clinchem/hvaf027}, pmid = {40126871}, issn = {1530-8561}, }
@article {pmid40126624, year = {2025}, author = {Orellana, E and Zampieri, G and De Bernardini, N and Guerrero, LD and Erijman, L and Campanaro, S and Treu, L}, title = {Sustainable Food Waste Management in Anaerobic Digesters: Prediction of the Organic Load Impact by Metagenome-Scale Metabolic Modeling.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c11180}, pmid = {40126624}, issn = {1520-5851}, abstract = {The increasing urbanization has led to rising waste and energy demands, necessitating innovative solutions. A sustainable food waste management approach involves anaerobic codigestion with sewage sludge, enhancing biogas production while managing waste. Although this technology has been successfully tested, the biological mechanisms determining its efficiency are still poorly understood. This study leverages genome-scale metabolic modeling of 138 metagenome-assembled genomes to explore species interactions in lab-scale anaerobic reactors fed with sewage sludge to increasing proportions of food waste. The models showed positive correlations with experimental biogas production (CH4: r = 0.54, CO2: r = 0.66), validating their reliability. The dominant methanogen, Methanothrix sp., adapted its metabolism based on feedstock, affecting methane yields, which ranged from 2.5 to 3 mmol/g of volatile solids·h with sewage sludge to 10-14 mmol/g of VS·h with high food waste. The integration of extracellular enzymes into the models highlighted the role in methane production of pectin degradation, protein hydrolysis, and lipid metabolism, mediated by Proteiniphilum sp., Kiritimatiellae sp., and Olb16 sp. The study identified 475 mutualistic interactions involving amino acid, hydrogen, acetate, and phosphate exchange and 44 competitive interactions in hydrolytic and fermentative processes. These insights can help optimize anaerobic digestion and sustainable waste management in urban settings.}, }
@article {pmid40126388, year = {2025}, author = {Zhang, Q and Su, T and Pan, Y and Wang, X and Zhang, C and Qin, H and Li, M and Li, Q and Li, X and Guo, J and Wu, L and Qin, L and Liu, T}, title = {Malus hupehensis leaves: a functional beverage for alleviating hepatic inflammation and modulating gut microbiota in diabetic mice.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo05325g}, pmid = {40126388}, issn = {2042-650X}, abstract = {Malus hupehensis leaves (MHL), consumed as a daily beverage in Chinese folk tradition and recently recognized as a new food material, are abundant in polyphenols and bioactive compounds that demonstrate hypoglycemic, lipid-lowering, and anti-inflammatory effects. However, the antidiabetic mechanisms have not been fully elucidated. This study aimed to investigate the protective mechanisms of Malus hupehensis leaves' extract (MHLE) against type 2 diabetes mellitus (T2DM). The results showed that MHLE effectively ameliorated glucose and lipid metabolic abnormalities in db/db mice, and attenuated hepatic macrophage activation. Transcriptomic analysis of the liver revealed that MHLE primarily affects genes involved in inflammatory responses and inhibited the TLR4/MAPK pathway to reduce hepatic inflammation. Metagenomic sequencing identified changes in gut microbiota composition and showed that MHLE restored the abundance of Lachnospiraceae bacterium, Oscillospiraceae bacterium, and Clostridia bacterium while reducing the abundance of Escherichia coli, thereby ameliorating gut dysbiosis. The integrated regulation of metabolism, immune response, and the microbial environment by MHLE significantly alleviated symptoms of T2DM. This study offers strong scientific evidence for the potential use of MHL as a functional food.}, }
@article {pmid40125310, year = {2025}, author = {Xiao, Y and Jing, D and Xiao, H and Mao, M and Kuang, Y and Shen, M and Lv, C and Jian, X and Peng, C and Chen, X}, title = {Metagenomics Analysis of Altered Gut Microbiome in Psoriasis and the Mediation Analysis: A Case-Control Study.}, journal = {Psoriasis (Auckland, N.Z.)}, volume = {15}, number = {}, pages = {45-54}, doi = {10.2147/PTT.S505283}, pmid = {40125310}, issn = {2230-326X}, abstract = {PURPOSE: Psoriasis is an inflammatory disease linked to gut microbiome dysbiosis. However, the mechanisms underlying gut microbiome changes caused by dietary habits in psoriasis remain unclear.<br><br>PATIENTS AND METHODS: We performed a case-control study including 64 psoriasis patients and 64 age-, sex-, and body mass index (BMI)-matched controls. Stool samples were collected for metagenomics sequencing. The differential abundance analysis was performed to identify differentially abundant taxa between psoriasis and control groups. The dietary intake frequency information of each included subject was obtained through face-to-face interviews. Mediation analysis was used to identify potential mediators of the gut microbiome alterations in psoriasis.<br><br>RESULTS: The gut microbiome of psoriasis patients was significantly alterated when compared to controls. Anaerostipes Hadrus, Blautia Wexlerae, and the other six species may be beneficial to psoriasis. However, Prevotella Copri and Eggerthellaceae could be pathogenic bacteria. The study also identified correlations between specific dietary habits and psoriasis, with the largest correlation observed between poultry consumption and psoriasis (OR=0.735, P=0.001), followed by red meat (OR=0.784, P=0.007) and fresh vegetables (OR=0.794, P=0.028). Mediation analysis revealed that Anaerostipes hadrus, Dorea longicatena, and Eggerthella lenta mediated the association between poultry and psoriasis.<br><br>CONCLUSION: The characteristics of intestinal flora in psoriasis patients were significantly different from controls. Intestinal flora mediated the association between diet and psoriasis to some extent. This study provides new insights for adjuvant treatments of psoriasis through dietary and intestinal microbiota interventions.}, }
@article {pmid40125276, year = {2025}, author = {Zhu, X and Angelidaki, I and Zhang, T and Ju, F}, title = {Metagenomics Disentangles Differential Resistome Traits and Risks in Full-Scale Anaerobic Digestion Plants under Ambient, Mesophilic, and Thermophilic Conditions.}, journal = {ACS environmental Au}, volume = {5}, number = {2}, pages = {183-196}, doi = {10.1021/acsenvironau.4c00071}, pmid = {40125276}, issn = {2694-2518}, abstract = {Anaerobic digestion (AD) systems are vital for converting organic waste to green bioenergy but also serve as a non-negligible environmental reservoir for antibiotic-resistance genes (ARGs) and resistant bacteria of environmental and human health concerns. This study profiles the antibiotic resistome of 90 full-scale biogas reactors and reveals that AD microbiomes harbor at least 30 types and 1257 subtypes of ARGs, of which 16% are located on plasmids showing potential mobility. The total abundance of AD-ARGs ranges widely from 0.13 to 7.81 copies per cell and is distributed into 42-739 subtypes, significantly influenced (P < 0.05) by operational conditions like digestion temperature and substrate types. Compared with the ambient and mesophilic digesters, the thermophilic digesters harbor a significantly lower abundance and diversity as well as greatly reduced mobility and host pathogenicity levels (all P < 0.05) of ARGs, revealing that a higher digestion temperature mitigates the overall resistome risks. The comprehensive analysis of basic traits and key traits of the AD resistome is demonstrated to provide crucial quantitative and qualitative insights into the diversity, distribution pattern, and health risks of ARGs in full-scale AD systems. The revealed knowledge offers new guidance for improving environmental resistome management and developing oriented mitigation strategies to minimize the unwanted spread of clinically important antimicrobial resistance from AD systems.}, }
@article {pmid40124740, year = {2025}, author = {Brucato, N and Lisant, V and Kinipi, C and Kik, A and Besnard, G and Leavesley, M and Ricaut, FX}, title = {Influence of betel nut chewing on oral microbiome in Papua New Guinea.}, journal = {Evolution, medicine, and public health}, volume = {13}, number = {1}, pages = {36-44}, doi = {10.1093/emph/eoae030}, pmid = {40124740}, issn = {2050-6201}, abstract = {BACKGROUND AND OBJECTIVES: For thousands of years, betel nut has been used as a psychoactive agent in Asian and Oceanian populations. Betel nut chewing was associated with the alteration of human oral microbiome and with diseases such as oral cancer and periodontitis, but only in populations of Asian cultural background. We studied the influence of betel nut chewing on the oral microbiome in Papua New Guinea, where half of the population uses betel nut and the prevalence of these diseases is one of the highest in the world.<br><br>METHODOLOGY: We characterized the oral microbiomes of 100 Papua New Guineans. We defined two cohorts of betel chewers (n&#x2005;=&#x2005;50) and non-chewers (n&#x2005;=&#x2005;50) based on a genetic approach to identify the presence of betel nut in saliva. We statistically compared the alpha and beta microbial diversities between the two cohorts. We performed linear discriminant analyses to identify bacterial species more prevalent in each cohort.<br><br>RESULTS: We found that oral microbial diversity is significantly different between betel chewers and non-chewers. The dysbiosis observed in betel chewers, led to an increase of pathogenic bacterial species including Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, known to be in the aetiology of periodontal diseases.<br><br>CONCLUSIONS AND IMPLICATIONS: Our study strongly supports the alteration of human oral microbiome by betel nut use, potentially leading to periodontal diseases. It also shows the need to consider local specificities (e.g. different habits, betel nut types, and oral microbial diversities) to better characterize the impact of betel nut chewing on health.}, }
@article {pmid40124696, year = {2025}, author = {Li, S and Zhang, S and Zhou, T and Ge, Z and Li, Y and Zhang, J and Zhu, Y and Li, S}, title = {The second generation metagenomic sequencing of cerebrospinal fluid for diagnosis of non-eschar scrub typhus.}, journal = {Oxford medical case reports}, volume = {2025}, number = {3}, pages = {omae198}, doi = {10.1093/omcr/omae198}, pmid = {40124696}, issn = {2053-8855}, abstract = {Tsutsugamushi disease, is an infectious disease transmitted by ticks and caused by the rickettsiella. It is characterized by eschar, fever, rash, and flu-like symptoms. However, diagnosing atypical cases without an eschar and with negative Weil-Felix test results poses a significant diagnostic challenge. This study presents a noteworthy case of non-eschar typhus which was effectively diagnosed using advanced next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) samples.}, }
@article {pmid40124394, year = {2025}, author = {Ma, CM and Zhang, FS and Zhao, XH and Yang, Y and Wang, B and Wang, Y and Liu, XF and Bian, X and Xu, ZX and Zhang, G and Qu, LZ and Zhang, N}, title = {Genistein improves depression-like behavior in rats by regulating intestinal flora and altering glutamate gene expression.}, journal = {Current research in food science}, volume = {10}, number = {}, pages = {101020}, doi = {10.1016/j.crfs.2025.101020}, pmid = {40124394}, issn = {2665-9271}, abstract = {Depression is a mental disorder, and genistein is known to have antidepressant effects, but its mechanism of action is still unclear. Here, the mechanism of genistein improving depression based on gut microbiota was explored using classic behavioral indicators of depression combined with genomic technology. The behavioral evaluation showed that rats gavaged with 20-40 mg/kg genistein showed an increase in body weight, glucose preference, absenteeism score, body temperature, and 5-hydroxytryptamine (5-HT) content, while a decrease in adrenocorticotropic hormone (ACTH) and corticosterone (CORT) content compared to the depression rat model group, but there was no significant difference compared to the positive control (fluoxetine). The results of high-throughput sequencing showed that genistein increased the relative abundance of Firmicutes and Actinobacteriota and decreased the relative abundance of Bacteroidota at the phylum level. At the genus level, the abundance of Bifidobacterium, a short-chain fatty acid producing bacterium, was increased. Furthermore, metagenome results revealed that the antidepressant effect of genistein can be achieved by promoting glutamate metabolism, increasing glutamic acid decarboxylase (GAD) expression levels, promoting γ-aminobutyric acid (GABA) synthesis, and indirectly increasing 5-HT levels.}, }
@article {pmid40124227, year = {2025}, author = {Sun, C and Dong, Q and An, H and Liu, Y and Lv, W and Liu, W and Ji, H and Yang, X}, title = {Responses of Soil Microbial Communities and Functions in an Alpine Grassland of the Qinghai Lake Basin With Grazing Disturbance.}, journal = {Ecology and evolution}, volume = {15}, number = {3}, pages = {e71082}, doi = {10.1002/ece3.71082}, pmid = {40124227}, issn = {2045-7758}, abstract = {Soil ecosystems host diverse microbial communities, which are influenced by various environmental factors, soil properties, vegetation characteristics, and anthropogenic activities, such as livestock grazing. Grazing serves as a critical management practice in the alpine grasslands of the Qinghai-Tibet Plateau, affecting soil microbial communities and their functions through processes such as forage consumption, trampling, and the deposition of feces and urine. In this study, we utilized the scientific and technological platform "Alpine Grassland-Livestock Adaptive Management Technology Platform" in Qinghai Province to examine the effects of grazing intensity on soil microbial communities and functions. Experimental treatments included different grazing intensities (light grazing, moderate grazing, and heavy grazing), along with a no-grazing control. Metagenomic sequencing technology was employed to investigate the impact of these grazing intensities on the microbial community composition and functional attributes in alpine grasslands. The results indicated that: (1) Actinobacteria, Proteobacteria, and Chloroflexi were the dominant bacterial communities in the soil, while Ascomycota, Mucoromycota, and Basidiomycota represented the primary fungal communities. (2) Grazing had a greater impact on soil fungal communities than on bacterial communities, altering the Shannon diversity index and Simpson index of soil fungal communities. (3) Soil pH and soil moisture were important factors influencing changes in soil microbial communities. (4) Functional analysis focusing on the "nitrogen metabolism" pathway indicated that under light grazing conditions, the relative abundance of multiple functional genes, particularly those involved in denitrification, decreased.}, }
@article {pmid40123920, year = {2025}, author = {Jimenez, K and Kong, Y and Zhang, Y and Ferketic, D and Nagori, SK and Yang, J and Yulo, AA and Kramer, B and Prado, OG and Cason, T and Chowdhry, R and Kemsley, A and Espinosa, LM and Steele, JA and Griffith, J and Jay, JA}, title = {Evaluation of a modified IDEXX method for antimicrobial resistance monitoring of extended Beta-lactamases-producing Escherichia coli in impacted waters near the U.S.-Mexico border.}, journal = {One health (Amsterdam, Netherlands)}, volume = {20}, number = {}, pages = {100997}, pmid = {40123920}, issn = {2352-7714}, abstract = {As part of a One Health approach, the World Health Organization (WHO) has deemed extended beta-lactamases-producing Escherichia coli (ESBL-Ec) as an appropriate proxy for antimicrobial resistance (AMR) in human, animal, and environmental samples. Traditional methods for ESBL-Ec quantification involve a labor-intensive process of membrane filtration, culturing in the presence and absence of antibiotics, and colony confirmation. The emerging modified IDEXX method utilizes IDEXX Colilert-18 test kits, recognized by the USEPA for the enumeration of total coliforms and E. coli in water samples, modified with cefotaxime for measurement of ESBL-Ec in environmental samples. However, this method has yet to be validated for ocean or sewage-contaminated water and has not been compared against the plate-based method with mTEC for surface water. In this study, ESBL-Ec in ocean and river waters of the Tijuana River Estuary were analyzed by three methods: membrane filtration using mTEC plates (as outlined in USEPA Method 1603), membrane filtration using TBX plates (as outlined in the WHO Tricycle Protocol), and Colilert-18 spiked with cefotaxime (Hornsby et al., 2023). Levels of ESBL-Ec were elevated in the Tijuana River Estuary and nearby ocean samples, as high as 2.2 × 10[6] CFU/100 mL. The modified IDEXX method correlated with membrane filtration methods using selective mTEC (r = 0.967, p < 0.001, n = 14) and TBX (r = 0.95, p < 0.001, n = 14) agars. These results indicate that the modified IDEXX method can be used as a more accessible alternative to the traditional culturing methods as a screening tool for antibiotic resistance in urban aquatic environments. Advantages of the IDEXX-based method including portability, lower Biosafety Level requirements, fewer dilutions to stay within the dynamic range, greater ease of maintaining sterility during analysis, and less required staff training are discussed. Future studies into the validity of the modified IDEXX method compared to qPCR and metagenomic sequencing are needed.}, }
@article {pmid40123796, year = {2025}, author = {Kim, SH and Kwak, MJ and Hwang, JK and Keum, J and Jin, HY and Lee, CY and Tanpure, RS and Kim, YJ and Hoh, JK and Park, JY and Chung, W and Jeon, BH and Park, HK}, title = {Altered heme metabolism and hemoglobin concentration due to empirical antibiotics-induced gut dysbiosis in preterm infants.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {937-945}, pmid = {40123796}, issn = {2001-0370}, abstract = {BACKGROUND: High-risk infants are usually treated with empirical antibiotics after birth, regardless of the evidence of infection; however, their gut microbiome and metabolome have seldom been studied. This study investigated the influence of antibiotic exposure on the gut microbiome and associated metabolic pathways in term and preterm infants.<br><br>METHODS: Thirty-six infants within 10 days of birth who were admitted to a neonatal intensive care unit/newborn nursery unit were divided into four groups based on maturity (gestational age) and use of empirical antibiotics. Genomic DNA was extracted from the fecal samples and underwent high-throughput 16S rRNA amplicon sequencing using the Illumina platforms. Taxonomic classification, diversity analysis, and metagenomic function prediction were performed.<br><br>RESULTS: Preterm infants with empirical antibiotics showed a significantly decreased population of Firmicutes (p&#x202f;=&#x202f;0.003) and an increased population of Proteobacteria (p&#x202f;<&#x202f;0.001) compared to other groups. At the genus level, the populations of Raoultella (p&#x202f;=&#x202f;0.065) and Escherichia (p&#x202f;=&#x202f;0.052) showed an increased trend. The change in microbial composition was correlated with increased heme biosynthesis and decreased hemoglobin levels.<br><br>CONCLUSION: Collectively, our finding suggested that empirical antibiotic exposure in preterm infants alters the gut microbiome, potentially leading to adverse health outcomes. This dysbiosis may affect heme metabolism, increasing the risk of anemia in these vulnerable infants. Therefore, antibiotic use should be carefully tailored to minimize potential harm.}, }
@article {pmid40123706, year = {2025}, author = {Min, S and Lu, Q and Zhang, Y}, title = {A Case of Severe Community-Acquired Pneumonia Caused by Coinfection of Five Pathogens.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1515-1519}, pmid = {40123706}, issn = {1178-6973}, abstract = {INTRODUCTION: Severe pneumonia is a serious pulmonary infection, and its high morbidity and mortality are associated with underlying diseases, treatment-induced immunodeficiency, co-infection of multiple pathogens, and increase of multi-resistant pathogens; For severe community-acquired pneumonia (SCAP) in immunocompromised patients, most of which are infected with rare atypical pathogens, mNGS as an unbiased and hypothesis-free approach to rapidly detect potential infectious agents in pulmonary mixed infections. The cases of simultaneous co-infection of five non-respiratory core pathogens represented by Nocardia farcinica have not been reported.<br><br>CASE PRESENTATION: This article will elaborate on a case of immunocompromised patient with nephrotic syndrome after corticosteroid treatment, who was diagnosed as SCAP after hospital admission and relevant laboratory examination. Bronchoalveolar lavage fluid (BALF) metagenome next-generation sequencing (mNGS) method identified as Nocardia farcinica, Aspergillus fumigatus, Pneumocystis jirovecii, cytomegalovirus and human coronavirus OC43 five pathogens co-infection, the patient improved and he was discharged after receiving the combination treatment of imipenem, ganciclovir, compound sulfamethoxazole, and fluconazole.<br><br>CONCLUSION: For SCAP patients with immunocompromised, there may be possible co-infection of multiple rare pathogens, low positive rate of conventional laboratory tests, mNGS can quickly and accurately identify pathogens, which can be used for targeted drug treatment, promote the early recovery of patients and reduce the abuse of broad-spectrum antibiotics.}, }
@article {pmid40122890, year = {2025}, author = {Nori, SRC and Walsh, CJ and McAuliffe, FM and Moore, RL and Van Sinderen, D and Feehily, C and Cotter, PD}, title = {Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {49}, pmid = {40122890}, issn = {2055-5008}, support = {H2020-MSCA-COFUND-2019-945385//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; 18/CRT/6214//Science Foundation Ireland (SFI)/ ; }, mesh = {Female ; *Vagina/microbiology ; Humans ; *Lactobacillus/genetics/classification/isolation &amp; purification ; *Metagenomics/methods ; *Lactobacillus crispatus/genetics/isolation &amp; purification ; Pregnancy ; Microbiota ; Ireland ; Host Microbial Interactions ; Metagenome ; Genome, Bacterial ; Gardnerella vaginalis/genetics/isolation &amp; purification/classification ; }, abstract = {The vaginal microbiome, a relatively simple, low diversity ecosystem crucial for female health, is often dominated by Lactobacillus spp. Detailed strain-level data, facilitated by shotgun sequencing, can provide a greater understanding of the mechanisms of colonization and host-microbe interactions. We analysed 354 vaginal metagenomes from pregnant women in Ireland to investigate metagenomic community state types and strain-level variation, focusing on cell surface interfaces. Our analysis revealed multiple subspecies, with Lactobacillus crispatus and Lactobacillus iners being the most dominant. We found genes, including putative mucin-binding genes, distinct to L. crispatus subspecies. Using 337 metagenome-assembled genomes, we observed a higher number of strain-specific genes in L. crispatus related to cell wall biogenesis, carbohydrate and amino acid metabolism, many under positive selection. A cell surface glycan gene cluster was predominantly found in L. crispatus but absent in L. iners and Gardnerella vaginalis. These findings highlight strain-specific factors associated with colonisation and host-microbe interactions.}, }
@article {pmid40122843, year = {2025}, author = {Ashraf, S and Jerome, H and Bugembe, DL and Ssemwanga, D and Byaruhanga, T and Kayiwa, JT and Downing, R and Salazar-Gonzalez, JF and Salazar, MG and Shepherd, JG and Wilkie, C and Davis, C and Logan, N and Vattipally, SB and Wilkie, GS and da Silva Filipe, A and Ssekagiri, A and Namuwulya, P and Bukenya, H and Kigozi, BK and McConnell, WW and Willett, BJ and Balinandi, S and Lutwama, J and Kaleebu, P and Bwogi, J and Thomson, EC}, title = {Uncovering the viral aetiology of undiagnosed acute febrile illness in Uganda using metagenomic sequencing.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2844}, pmid = {40122843}, issn = {2041-1723}, support = {MC_UU_00034/6//RCUK | Medical Research Council (MRC)/ ; MC_PC_ MR/Y002814/1//RCUK | Medical Research Council (MRC)/ ; 102789/Z/13/A//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; Uganda/epidemiology ; *Metagenomics/methods ; Female ; Male ; Adult ; Adolescent ; Middle Aged ; Child ; Young Adult ; Child, Preschool ; Fever/virology/diagnosis ; Prospective Studies ; Viruses/genetics/isolation &amp; purification/classification ; Virus Diseases/epidemiology/virology/diagnosis ; Disease Outbreaks ; Aged ; Acute Disease ; Yellow Fever/epidemiology/virology/diagnosis ; Dengue/epidemiology/virology/diagnosis ; Infant ; Rift Valley Fever/epidemiology/diagnosis/virology ; Hemorrhagic Fever, Crimean/epidemiology/diagnosis/virology ; }, abstract = {Viruses associated with acute febrile illness in Africa cause a spectrum of clinical disease from mild to life-threatening. Routine diagnostic methods are insufficient to identify all viral pathogens in this region. In this study, 1281 febrile Ugandan patients were prospectively recruited as part of the CDC-UVRI Acute Febrile Illness Study and pre-screened for common pathogens. 210/1281 undiagnosed samples, and 20 additional samples from viral outbreaks were subjected to metagenomic sequencing. Viral pathogens were identified in 44/230 (19%), including respiratory, hepatitis, blood-borne, gastrointestinal and vector-borne viruses. Importantly, one case of Crimean-Congo haemorrhagic fever and two cases each of Rift Valley fever, dengue and yellow fever were detected in 7/230 (3%) of cases. Le Dantec virus, last reported in 1969, was also identified in one patient. The presence of high-consequence and (re-)emerging viruses of public health concern highlights the need for enhanced population-based diagnostic surveillance in the African region.}, }
@article {pmid40122128, year = {2025}, author = {Zhang, D and Wang, Q and Li, D and Chen, S and Chen, J and Zhu, X and Bai, F}, title = {Gut microbiome composition and metabolic activity in metabolic associated fatty liver disease.}, journal = {Virulence}, volume = {}, number = {}, pages = {2482158}, doi = {10.1080/21505594.2025.2482158}, pmid = {40122128}, issn = {2150-5608}, abstract = {OBJECTIVE: Metabolic Associated Fatty Liver Disease (MAFLD) impacts approximately 25% of the global population. The objective of our study was to elucidate the characteristics of the gut microbiome and alterations in plasma metabolites among MAFLD patients.<br><br>METHODS: Between April 2023 and July 2023, 60 patients with MAFLD, along with 60 age, ethnicity, and sex-matched healthy controls (HCs), were enrolled from Inner Mongolia Autonomous Region, China. Analysis of gut microbiota composition and plasma metabolic profiles was conducted using metagenome sequencing and LC-MS.<br><br>RESULTS: LEfSe analysis identified five pivotal species: Eubacterium rectale, Dialister invisus, Pseudoruminococcus massiliensis, GGB3278 SGB4328, and Ruminococcaceae bacteria. In subgroup analysis, Eubacterium rectale tended to be increased by more than 2 times and more than double in the non-obese MAFLD group, and MAFLD with moderate hepatic steatosis&#xff08;HS&#xff09;respectively. Combinations of phenomics and metabolomics yielded the highest accuracy (AUC&#x2009;=&#x2009;0.97) in the MAFLD diagnosis. Combinations of phenomics and metagenomics yielded the highest accuracy (AUC&#x2009;=&#x2009;0.94) in the prediction of the MAFLD HS progress. Plasma samples identified 172 metabolites mainly composed of fatty acid metabolites such as propionic acid and butyric acid analogues. Ruminococcaceae bacteria have a strong positive correlation with &#x3b2;-Alanine, Uric acid and L-Valine. Pseudoruminococcus massiliensis have a strong positive correlation with &#x3b2;-Alanine.<br><br>CONCLUSION: Increases in Eubacterium rectale and decreases in Dialister invisus seem to be indicative of MAFLD patients. Eubacterium rectale may predicts HS degree of MAFLD and play an important role in the development of non-obese MAFLD. Eubacterium rectale can generate more propionic acid and butyric acid analogues to absorb energy and increase lipid synthesis, and ultimately cause MAFLD. The observed association between Ruminococcaceae bacteria and &#x3b2;-Alanine or Uric acid in these patients could offer fresh insights into the disease mechanism.}, }
@article {pmid40122011, year = {2025}, author = {Yin, M and Li, P and Chen, C and Jia, R and Xia, B and Liu, Y and Liu, A and Liu, L and Li, ZH}, title = {Bioremediation potential of sulfadiazine-degrading bacteria: Impacts on ryegrass growth and soil functionality.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {138012}, doi = {10.1016/j.jhazmat.2025.138012}, pmid = {40122011}, issn = {1873-3336}, abstract = {The extensive use of antibiotics, particularly sulfadiazine (SDZ), has led to significant environmental contamination and the proliferation of antibiotic resistance genes (ARGs). This study investigates the bioremediation potential of two SDZ-degrading bacterial strains, Acinetobacter sp. M9 and Enterobacter sp. H1, and their impact on ryegrass (Lolium perenne) growth and the inter-root microenvironment in SDZ-contaminated soils. A pot experiment combined with amplicon and metagenomic sequencing revealed that inoculation with M9 and H1 significantly enhanced ryegrass growth by alleviating oxidative stress, increasing chlorophyll content, and improving soil nutrient availability. The strains also promoted SDZ degradation efficiency and improved carbon and nitrogen cycling through the upregulation of key functional genes. Furthermore, microbial community analysis demonstrated increased alpha diversity, shifts in dominant taxa, and functional enrichment in pollutant degradation pathways. The dynamics of ARGs revealed a decrease in aminoglycoside, rifamycin, and streptomycin resistance genes, while sulfonamide resistance genes increased due to the residual SDZ stress. These findings highlight the potential of M9 and H1 as sustainable bioremediation agents to mitigate antibiotic contamination, improve soil health, and support plant growth in polluted environments.}, }
@article {pmid40121909, year = {2025}, author = {Thomson, R and Le, C and Wang, L and Batstone, DJ and Zhou, Y and Oehmen, A}, title = {Higher order volatile fatty acid metabolism and atypical polyhydroxyalkanoate production in fermentation-enhanced biological phosphorus removal.}, journal = {Water research}, volume = {280}, number = {}, pages = {123503}, doi = {10.1016/j.watres.2025.123503}, pmid = {40121909}, issn = {1879-2448}, abstract = {Enhanced biological phosphorus removal (EBPR) is an established wastewater treatment process, but its wider implementation has been limited by factors like high temperature and low carbon availability. Fermentation-enhanced EBPR (F-EBPR) processes have shown promise in addressing these limitations, but the underlying mechanisms are not fully understood. This study investigates the metabolism of higher order (C4-5) volatile fatty acids (VFAs) in F-EBPR systems using a combination of carbon isotope labelling and shotgun metagenomic sequencing analyses. Results show that butyrate (HBu) uptake leads to the formation of both typical (C4-5) and atypical (C6+) polyhydroxyalkanoates (PHAs) through a combination ofβ-oxidation and standard condensation pathways, while the putative role of HBu oxidisers were identified relative to substrate composition in F-EBPR processes. Metagenomic analysis reveals the presence of genes required for higher order VFA metabolism in both polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs). This study also highlights the limitations of current models in describing F-EBPR processes and emphasises the need for improved models that account for higher order VFA metabolism and microbial community dynamics.}, }
@article {pmid40121477, year = {2025}, author = {Zhang, Q and Feng, Y and Xia, Y and Shao, Q and Zhao, M and Xu, P and Tang, T and Liu, J and Jin, B and Liu, S and Jiang, C}, title = {Clinical efficacy of metagenomic next-generation sequencing for the detection of pathogens in peritoneal dialysis-related peritonitis: a prospective cohort study.}, journal = {European journal of medical research}, volume = {30}, number = {1}, pages = {198}, pmid = {40121477}, issn = {2047-783X}, support = {2021- LCYJ- PY- 12//Fundings for Clinical Trials from the Affiliated Drum Tower Hospital, Medical School of Nanjing University/ ; YKK21090//Nanjing Healthcare Science and Technology Development Special Fund Project/ ; }, mesh = {Humans ; *Peritonitis/microbiology/diagnosis ; *Peritoneal Dialysis/adverse effects ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Middle Aged ; Prospective Studies ; *Metagenomics/methods ; Aged ; Adult ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been reported to improve pathogen identification in infectious diseases. This prospective cohort study aimed to explore the etiological diagnostic value of mNGS in peritoneal dialysis (PD)-related peritonitis.<br><br>METHODS: Patients with PD-related peritonitis were consecutively recruited at the Nephrology Department of Nanjing Drum Tower Hospital. PD effluent samples for mNGS and culture were collected simultaneously. The positive rate, detection time, and consistency of mNGS and culture were compared.<br><br>RESULTS: From August 1, 2021 to August 31, 2022, 38 patients with 41 episodes of PD-related peritonitis were enrolled. The positive rate of mNGS was higher than that of culture, although not statistically significant (92.7% vs 78.0%, P&#x2009;=&#x2009;0.109). The average reporting time of mNGS was significantly shorter than that of culture (30.4&#x2009;&#xb1;&#x2009;10.5 vs 86.9&#x2009;&#xb1;&#x2009;22.2&#xa0;h, P&#x2009;<&#x2009;0.001). mNGS identified more co-pathogens and unusual pathogens than culture, with multiple pathogens being detected in nearly half of the samples. Among the 30 samples that tested positive by both methods, 27 (90%) showed completely (13 cases) or partly (14 cases) matched results between mNGS and culture. Fourteen patients (with 14 episodes of peritonitis) had used antibiotics within 2&#xa0;weeks before specimen collection. Antibiotic usage led to a significant decrease in the culture-positive rate (57.1% vs 88.9%, P&#x2009;=&#x2009;0.042), while the mNGS-positive rate remained unaffected (92.9% vs 92.6%, P&#x2009;=&#x2009;1.000).<br><br>CONCLUSIONS: This study revealed that mNGS exhibited higher sensitivity and shorter reporting time compared to culture in detecting pathogens in PD-related peritonitis. For samples that yielded positive results by both methods, the consistency between mNGS and culture was substantial. mNGS may offer a novel approach for the etiological diagnosis of PD-associated peritonitis, particularly in cases involving prior antibiotic use and unusual pathogens.}, }
@article {pmid40121075, year = {2025}, author = {Omura, SN and Nureki, O}, title = {General and robust sample preparation strategies for cryo-EM studies of CRISPR-Cas9 and Cas12 enzymes.}, journal = {Methods in enzymology}, volume = {712}, number = {}, pages = {23-39}, doi = {10.1016/bs.mie.2025.01.052}, pmid = {40121075}, issn = {1557-7988}, mesh = {*Cryoelectron Microscopy/methods ; *CRISPR-Cas Systems ; *CRISPR-Associated Proteins/genetics/chemistry/metabolism ; Gene Editing/methods ; CRISPR-Associated Protein 9/genetics/chemistry/metabolism ; Bacterial Proteins/genetics/chemistry/metabolism ; Endodeoxyribonucleases ; }, abstract = {Cas9 and Cas12 are RNA-guided DNA endonucleases derived from prokaryotic CRISPR-Cas adaptive immune systems that have been repurposed as versatile genome-engineering tools. Computational mining of genomes and metagenomes has expanded the diversity of Cas9 and Cas12 enzymes that can be used to develop versatile, orthogonal molecular toolboxes. Structural information is pivotal to uncovering the precise molecular mechanisms of newly discovered Cas enzymes and providing a foundation for their application in genome editing. In this chapter, we describe detailed protocols for the preparation of Cas9 and Cas12 enzymes for cryo-electron microscopy. These methods will enable fast and robust structural determination of newly discovered Cas9 and Cas12 enzymes, which will enhance the understanding of diverse CRISPR-Cas effectors and provide a molecular framework for expanding CRISPR-based genome-editing technologies.}, }
@article {pmid40121033, year = {2025}, author = {Wong, MK and Boukhaled, GM and Armstrong, E and Liu, R and Heirali, AA and Yee, NR and Tsang, J and Spiliopoulou, P and Schneeberger, PHH and Wang, BX and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B}, title = {Microbial Ecosystem Therapeutics 4 (MET4) elicits treatment-specific IgG responses associated with changes in gut microbiota in immune checkpoint inhibitor recipients with advanced solid tumors.}, journal = {Journal for immunotherapy of cancer}, volume = {13}, number = {3}, pages = {}, doi = {10.1136/jitc-2024-010681}, pmid = {40121033}, issn = {2051-1426}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Neoplasms/immunology/drug therapy/therapy ; *Immunoglobulin G/blood/immunology ; Male ; Female ; Middle Aged ; Aged ; }, abstract = {BACKGROUND: Gut microbiome modulation has shown promise in its potential to treat cancer in combination with immunotherapy. Mechanistically, the pathways and routes by which gut microbiota may influence systemic and antitumor immunity remain uncertain. Here, we used blood and stool samples from Microbial Ecosystem Therapeutic 4 (MET4)-IO, an early-phase trial testing the safety and engraftment of the MET4 bacterial consortium in immune checkpoint inhibitor recipients, to assess how MET4 may affect systemic immunity.<br><br>METHODS: Circulating antibody responses induced by MET4 were assessed using an antimicrobial antibody flow cytometry assay on pretreatment and post-treatment plasma. Antibody responses were associated with taxonomic changes in stool identified by metagenomic sequencing. Mass cytometry was performed on peripheral blood mononuclear cells to identify shifts in circulating immune subsets associated with antibody responses.<br><br>RESULTS: Increases in circulating anti-MET4 immunoglobulin G (IgG) responses were measured by flow cytometry post-consortium treatment in MET4 recipients, but not untreated control participants, with five individuals displaying notably higher antibody responses. Stronger IgG responses were associated with greater increases in multiple taxa, including MET4 microbe Collinsella aerofaciens, which was previously linked with immune checkpoint response. However, these taxa were not enriched in the IgG-bound fraction post-MET4 treatment. Greater increases in circulating B cells and FoxP3[+] CD4[+] T cells post-MET4 treatment were observed in the blood of high IgG responders, while CD14[+] and CD16[+] monocyte populations were decreased in these individuals.<br><br>CONCLUSION: These results demonstrate the induction of treatment-specific circulating humoral immunity by a bacterial consortium and suggest potential mechanisms by which gut microbes may contribute to antitumor immunity.}, }
@article {pmid40120232, year = {2025}, author = {Ebmeyer, S and Kristiansson, E and Larsson, DGJ}, title = {Unraveling the origins of mobile antibiotic resistance genes using random forest classification of large-scale genomic data.}, journal = {Environment international}, volume = {198}, number = {}, pages = {109374}, doi = {10.1016/j.envint.2025.109374}, pmid = {40120232}, issn = {1873-6750}, abstract = {Understanding in which environments and under what conditions chromosomal antibiotic resistance genes (ARGs) acquire increased mobility is crucial to effectively mitigate their emergence in and dissemination among pathogens. In order to identify the conditions and environments facilitating these processes, it is valuable to know from which bacterial species mobile ARGs were mobilized initially, before their dissemination to other species. In this study, we used data generated from > 1.5 million publicly available bacterial genome assemblies to train a random forest classifier to identify the origins of mobile genes. Analysis of the models' predictions revealed the previously unknown origins of 12 mobile ARG groups, which confer resistance to 4 different classes of antibiotics. This included ARGs conferring resistance to tetracyclines, an antibiotic class for which, to the best of our knowledge, no recent origins of ARGs have previously been convincingly demonstrated. All identified origin species in this study are known opportunistic pathogens, and some are the origin of multiple mobile ARGs. An analysis of public metagenomes from different sources indicates that most of the origin species are particularly abundant in municipal wastewaters, a few were highly abundant in animal feces and three were most common in environments polluted with waste from antibiotic manufacturing. This study highlights environments where these origin species thrive and where there is a need for limiting antibiotic selection pressures.}, }
@article {pmid40120189, year = {2025}, author = {Sun, Q and Li, D and He, Y and Ping, Q and Wang, L and Li, Y}, title = {Improved anaerobic digestion of waste activated sludge under ammonia stress by nanoscale zero-valent iron/peracetic acid pretreatment and hydrochar regulation: Insights from multi-omics analyses.}, journal = {Water research}, volume = {279}, number = {}, pages = {123497}, doi = {10.1016/j.watres.2025.123497}, pmid = {40120189}, issn = {1879-2448}, abstract = {This study developed a novel strategy combining a nanoscale zero-valent iron (nZVI)/peracetic acid (PAA) pretreatment and hydrochar regulation to enhance anaerobic digestion of waste activated sludge (WAS) under ammonia-stressed conditions. The strategy significantly enhanced methane production at ammonia concentrations below 3000 mg/L, with the regulation groups (AN3000/REG) achieving a 50.1 % increase in cumulative methane yield. Metagenomic analysis demonstrated a 14.2 % enrichment of key functional microorganisms, including syntrophic fatty acid-oxidizing bacteria and hydrogenotrophic methanogens, in the AN3000/REG groups. Some of them promote the conversion of butyrate and valerate to acetate through the upregulation of key genes in the fatty acid β-oxidation pathway, thereby supplying sufficient substrates for acetoclastic methanogenesis. Beyond enhancing acetoclastic methanogenesis, the AN3000/REG groups exhibited significant upregulation of other metabolic pathways, with a 34.2 % increase in syntrophic acetate oxidation-hydrogenotrophic methanogenesis genes and a 17.1 % increase in methanol/methylotrophic methanogenesis-related genes. These findings were further validated by the metatranscriptomic and metaproteomic combination analyses. Furthermore, the AN3000/REG groups exhibited a significant enhancement in direct interspecies electron transfer, with functional microbes (e.g., Geobacter, Methanosarcina, and Methanobacterium), pili, and cytochrome c showing significant increases of 1.38-fold, 12.7-fold, and 5.6-fold, respectively. This might be due to the synergistic effects of nZVI and hydrochar in the regulation groups. Additionally, metabolomic analyses revealed that the regulation strategy improved the microbial adaptability to ammonia stress by modulating metabolic products, such as alkaloids. Our study not only provides a promising strategy for alleviating ammonia inhibition during the anaerobic digestion of WAS but also provides a strong basis for understanding the underlying mechanism under ammonia-stressed conditions.}, }
@article {pmid40119849, year = {2025}, author = {Riva, A and Sahin, E and Volpedo, G and Catania, NT and Venara, I and Biagioli, V and Balagura, G and Amadori, E and De Caro, C and Cerulli Irelli, E and Di Bonaventura, C and Zara, F and Sezerman, OU and Russo, E and Striano, P}, title = {Medication-resistant epilepsy is associated with a unique gut microbiota signature.}, journal = {Epilepsia}, volume = {}, number = {}, pages = {}, doi = {10.1111/epi.18367}, pmid = {40119849}, issn = {1528-1167}, support = {MDBR-23-004-STXBP1//Fingerprinting a multiomics biomarker profile in patients with STXBP1-RD/ ; PNRR-MUR-M4C2 PE0000006//MNESYS/ ; }, abstract = {OBJECTIVE: Dysfunction of the microbiota-gut-brain axis is emerging as a new pathogenic mechanism in epilepsy, potentially impacting on medication response and disease outcome. We investigated the composition of the gut microbiota in a cohort of medication-resistant (MR) and medication-sensitive (MS) pediatric patients with epilepsy.<br><br>METHODS: Children with epilepsy of genetic and presumed genetic etiologies were evaluated clinically and subgrouped into MR and MS. Age-matched healthy controls (HCs) were also recruited. A food diary was used to evaluate nutritional habits, and the Rome IV questionnaire was used to record gastrointestinal symptoms. The microbiota composition was assessed in stool samples through 16S rRNA. &#x3b1;-Diversity (AD) and &#x3b2;-diversity (BD) were calculated, and differential abundance analysis was performed using linear multivariable models (significance: p.adj&#x2009;<&#x2009;.05).<br><br>RESULTS: Forty-one patients (MR:MS&#x2009;=&#x2009;20:21) with a mean age of 7.2&#x2009;years (&#xb1;4.6 SD) and 27 age-matched HCs were recruited. No significant differences in AD were found when comparing patients and HCs. Significant positive correlation was found between AD and age (Chao1 p.adj&#x2009;=&#x2009;.0004, Shannon p.adj&#x2009;=&#x2009;.0004, Simpson p.adj&#x2009;=&#x2009;.0028). BD depicted a different bacterial profile in the epilepsy groups compared to HCs (MS vs. HC: Bray-Curtis F&#x2009;=&#x2009;1.783, p&#x2009;=&#x2009;.001; Jaccard F&#x2009;=&#x2009;1.24, p&#x2009;=&#x2009;.001; MR vs. HC: Bray-Curtis F&#x2009;=&#x2009;2.24, p&#x2009;=&#x2009;.001; Jaccard F&#x2009;=&#x2009;1.364, p&#x2009;=&#x2009;.001). At the genus level, the epilepsy groups were characterized by a significant increase in Hungatella (MS vs. HC: +4.95 log2 change; MR vs. HC: +6.72 log2 change); the [Eubacterium] siraeum group changed between the MR and MS subgroups.<br><br>SIGNIFICANCE: Epileptic patients display unique gut metagenomic signatures compared to HCs. Moreover, a different ratio of the butyrate-producing [Eubacterium] siraeum group suggests dissimilarities between patients based on the response to antiseizure medications.}, }
@article {pmid40119394, year = {2025}, author = {Guo, R and Chang, Y and Wang, D and Sun, H and Gu, T and Zong, Y and Zhou, S and Huang, Z and Chen, L and Tian, Y and Xu, W and Lu, L and Zeng, T}, title = {Interaction between cecal microbiota and liver genes of laying ducks with different residual feed intake.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {30}, pmid = {40119394}, issn = {2524-4671}, support = {CARS-42//China Agriculture Research System of MOF and MARA/ ; 2021C02068//Zhejiang Province Agricultural New Breeding Major Science and Technology Special Project/ ; LZ23C170001//Zhejiang Provincial Natural Science Foundation of China/ ; 32472892//National Natural Science Foundation of China/ ; 2022YFD1300100//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: The gut microbiota exerts a critical influence on energy metabolism homeostasis and productive performance in avian species. Given the diminishing availability of arable land and intensifying competition for finite resources between livestock production and human populations, the agricultural sector faces dual imperatives to enhance productive efficiency while mitigating ecological footprints. Within this paradigm, optimizing nutrient assimilation efficiency in commercial waterfowl operations emerges as a strategic priority. This investigation employs an integrated multi-omics approach framework (metagenomic, metabolomic, and transcriptomic analyses) to elucidate the mechanistic relationships between cecal microbial consortia and feed conversion ratios in Shan Partridge ducks.<br><br>RESULTS: Based on the analysis of metagenome data, a total of 34 phyla, 1033 genera and 3262 species of bacteria were identified by metagenomic sequencing analysis. At the phylum level, 31 phylums had higher mean abundance in the low residual feed intake (LRFI) group than in the high residual feed intake (HRFI) group. Among them, the expression of microbiome Elusimicrobiota was significantly higher in the LRFI group than in the HRFI group (P&#x2009;<&#x2009;0.05). And we also found a significant differences in secondary metabolites biosynthesis, transport, and catabolism pathways between the two groups in microbial function (P&#x2009;<&#x2009;0.05). Based on metabolomic analysis, 17 different metabolites were found. Among them, Lipids and lipid molecules accounted for the highest proportion. Whereas the liver is very closely related to lipid metabolism, we are close to understanding whether an individual's energy utilization efficiency is related to gene expression in the liver. We selected six ducks from each group of six ducks each for liver transcriptome analysis. A total of 322 differential genes were identified in the transcriptome analysis results, and 319 genes were significantly down-regulated. Among them, we found that prostaglandin endoperoxide synthase 2 (PTGS2) might be a key hub gene regulating RFI by co-occurrence network analysis. Interestingly, the differential gene PTGS2 was enriched in the arachidonic acid pathway at the same time as the differential metabolite 15-deoxy-delta12,14-prostaglandin J2 (15d-PGJ2). In addition, the results of the association analysis of differential metabolites with microorganisms also revealed a significant negative correlation between 15d-PGJ2 and Elusimicrobiota.<br><br>CONCLUSION: Based on comprehensive analysis of the research results, we speculate that the Elusimicrobiota may affect the feed utilization efficiency in ducks by regulating the expression of the PTGS2 gene.}, }
@article {pmid40119266, year = {2025}, author = {Zhou, Y and Ren, D and Li, Y and Gui, S}, title = {A case of septic shock caused by drug-resistant Edwardsiella tarda and literature review.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {393}, pmid = {40119266}, issn = {1471-2334}, support = {SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; }, mesh = {Humans ; *Shock, Septic/microbiology/drug therapy ; *Edwardsiella tarda/drug effects/isolation &amp; purification/genetics ; Female ; Adult ; *Enterobacteriaceae Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Piperacillin, Tazobactam Drug Combination/therapeutic use ; Microbial Sensitivity Tests ; }, abstract = {BACKGROUND: Edwardsiella tarda (E. tarda) causes highly mortality, which is rare in septic patients. We herein reported a case of septic shock caused by drug-resistant E. tarda.<br><br>CASE PRESENTATION: We herein describe a 32-year-old female with septic shock who had the medical history of abortion 1 month ago and "systemic lupus erythematosus and rheumatoid arthritis" presented abdominal pain, diarrhea, and dyspnea as the primary symptoms and rapidly deteriorated to MODS following breakfast (undercooked fish porridge) in the ICU. Sepsis surviving bundle was initiated by collecting pathogen culture (sputum, urine and blood samples), empirically broad-spectrum antibiotics administration (Meropenem), along with fluid resuscitation, vasopressor use. E. tarda was confirmed both in blood culture and mNGS (metagenomics next generation sequencing). Thus, the antibiotics were switched to piperacillin-tazobactam according to the susceptibility test that was susceptible to piperacillin-tazobactam and resistant to ampicillin, quinolones and gentamicin. The patient finally recovered and discharged after 18 days of ICU treatment.<br><br>CONCLUSIONS: Empiric antibiotics should be selected with piperacillin-tazobactam and amikacin, and avoid ampicillin, quinolones and gentamicin for suspecting E. tarda infection in southern China. Bacteremia complicated with septic shock caused by E. tarda requires intensive care to improve survival rates.}, }
@article {pmid40119088, year = {2025}, author = {Santos, CA and Morais, MAB and Mandelli, F and Lima, EA and Miyamoto, RY and Higasi, PMR and Araujo, EA and Paixão, DAA and Junior, JM and Motta, ML and Streit, RSA and Morão, LG and Silva, CBC and Wolf, LD and Terrasan, CRF and Bulka, NR and Diogo, JA and Fuzita, FJ and Colombari, FM and Santos, CR and Rodrigues, PT and Silva, DB and Grisel, S and Bernardes, JS and Terrapon, N and Lombard, V and Filho, AJC and Henrissat, B and Bissaro, B and Berrin, JG and Persinoti, GF and Murakami, MT}, title = {Publisher Correction: A metagenomic 'dark matter' enzyme catalyses oxidative cellulose conversion.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-025-08872-9}, pmid = {40119088}, issn = {1476-4687}, }
@article {pmid40118380, year = {2025}, author = {Guo, D and Fan, J and Zhang, X and Chen, S and Du, X}, title = {Next-generation Sequencing assistance in the diagnosis of Active Tuberculosis following Allogeneic Hematopoietic Stem Cell Transplantation: A Case Series.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {}, number = {}, pages = {102683}, doi = {10.1016/j.jiac.2025.102683}, pmid = {40118380}, issn = {1437-7780}, abstract = {Tuberculosis poses a rare but life-threatening complication for patients undergoing hematopoietic stem cell transplantation. In a case series spanning January 2020 to January 2024, we evaluated the application of metagenomic Next-Generation Sequencing in the early diagnosis of tuberculosis in patients following allogeneic hematopoietic stem cell transplantation. We identified 9 cases of post-transplant tuberculosis, predominantly pulmonary, with 1 case of disseminated disease. In early fluid samples from patients with post-transplant active tuberculosis, metagenomic next-generation sequencing detected Mycobacterium tuberculosis complex earlier than conventional tests, enabling rapid diagnosis. In this study, metagenomic next-generation sequencing showed a sensitivity of 66.6% and specificity of 100%, higher than TB-DNA and Xpert (55.6%). Concurrently, among mNGS-positive samples, 4 (44.4%) were from peripheral blood and 3 (33.3%) from bronchoalveolar lavage fluid. The combination of metagenomic Next-Generation sequencing and Xpert may enhance the capacity for detecting Mycobacterium tuberculosis complex in extrapulmonary specimens from post-transplant patients. The time from symptom onset to Next-Generation Sequencing positivity was 2 to 76 days, and from transplantation to TB diagnosis was 30 to 485 days. Despite some fatalities, the majority of patients completed extended anti-tuberculosis treatment and are under regular follow-up, highlighting the value of Next-Generation Sequencing in diagnosing tuberculosis in this high-risk population.}, }
@article {pmid40118224, year = {2025}, author = {Bai, M and Wang, B and Zhao, W and Qiu, H and Su, S and Wang, Y and Qin, Y and Wang, C and Zhao, Z and Gao, Z and Yang, C}, title = {Novel anammox-enhanced A-B wastewater treatment process based on carbon capture concept.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132431}, doi = {10.1016/j.biortech.2025.132431}, pmid = {40118224}, issn = {1873-2976}, abstract = {The high energy consumption and high carbon footprint of sewage treatment are technical shortcomings of the conventional activated sludge process. To address the emergency issue, this research demonstrated the viability of a pre-anammox enhanced A-B process to treat municipal wastewater while achieving an energy-efficient operation. In the proposed A-B process, an anaerobic moving bed biofilm reactor (A-MBBR) functions as the A-stage for COD capture, while a nitrification MBBR functions as the B-stage. The results show that during the 210-days of operation, 83.3 % of the influent COD was converted in the A-stage, and 93.1 % NH4[+]-N removal was achieved, resulting in an effluent NH4[+]-N concentration of 0.9 mg/L. The metagenomic sequencing results show that, in the B-stage MBBR, Nitrosomonas was the main ammonia-oxidizing bacterium (4.9 % relative abundance) and Nitrospira was the main nitrite-oxidizing bacterium (18.0 % relative abundance). In the A-stage MBBR, Thauera was the dominant denitrification bacterium (9.2 % relative abundance) and Candidatus Brocadia was the dominant anammox bacterium. Finally, hdh and hzs were key anammox genes detected in this system. This study clearly demonstrates a novel pre-anammox enhanced A-B process with an energy-efficient operation.}, }
@article {pmid40118220, year = {2025}, author = {Rozera, T and Pasolli, E and Segata, N and Ianiro, G}, title = {Machine learning and artificial intelligence in the multi-omics approach to gut microbiota.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.02.035}, pmid = {40118220}, issn = {1528-0012}, abstract = {The gut microbiome is involved in human health and disease, and its comprehensive understanding is necessary to exploit it as a diagnostic or therapeutic tool. Multi-omics approaches, including metagenomics, metatranscriptomics, metabolomics, and metaproteomics, enable depicting the complexity of the gut microbial ecosystem. However, these tools generate a large data stream, which integration is needed to produce clinically useful readouts but, in turn, might be difficult to carry out with conventional statistical methods. Artificial intelligence and machine learning have been increasingly applied to multi-omics datasets in several conditions associated with microbiome disruption, from chronic disorders to cancer. Such tools show potential for clinical implementation, including the discovery of microbial biomarkers for disease classification or prediction, the prediction of response to specific treatments, the fine-tuning of microbiome-modulating therapies. Here we discuss the state of the art, potential, and limits, of artificial intelligence and machine learning in the multi-omics approach to gut microbiome.}, }
@article {pmid40118219, year = {2025}, author = {Yan, R and Zhang, L and Chen, Y and Zheng, Y and Xu, P and Xu, Z}, title = {Therapeutic potential of gut microbiota modulation in epilepsy: A focus on short-chain fatty acids.}, journal = {Neurobiology of disease}, volume = {}, number = {}, pages = {106880}, doi = {10.1016/j.nbd.2025.106880}, pmid = {40118219}, issn = {1095-953X}, abstract = {According to the criteria established by the International League Against Epilepsy (ILAE), epilepsy is defined as a disorder characterized by at least two unprovoked seizures occurring more than 24 h apart. Its pathogenesis is closely related to various physiological and pathological factors. Advances in high-throughput metagenomic sequencing have increasingly highlighted the role of gut microbiota dysbiosis in epilepsy. Short-chain fatty acids (SCFAs), the major metabolites of the gut microbiota and key regulators of the gut-brain axis, support physiological homeostasis through multiple mechanisms. Recent studies have indicated that SCFAs not only regulate seizures by maintaining intestinal barrier integrity and modulating intestinal immune responses, but also affect the structure and function of the blood-brain barrier (BBB) and regulate neuroinflammation. This review, based on current literatures, explores the relationship between SCFAs and epilepsy, emphasizing how SCFAs affect epilepsy by modulating the intestinal barrier and BBB. In-depth studies on SCFAs may reveal their therapeutic potential and inform the development of gut microbiota-targeted epilepsy treatments.}, }
@article {pmid40117915, year = {2025}, author = {Ghemrawi, M and Ramírez Torres, A and Netherland, M and Wang, Y and Hasan, NA and El-Fahmawi, B and Duncan, G and McCord, B}, title = {Forensic insights from shotgun metagenomics: Tracing microbial exchange during sexual intercourse.}, journal = {Forensic science international. Genetics}, volume = {78}, number = {}, pages = {103266}, doi = {10.1016/j.fsigen.2025.103266}, pmid = {40117915}, issn = {1878-0326}, abstract = {The microbiome is becoming an emerging field of interest within forensic science with high potential for individualization; however, little is known about bacterial species specific to the genital area or their ability to transfer between individuals during sexual contact. In this proof-of-concept study, we investigated microbial transfer dynamics in seven monogamous, heterosexual couples by collecting pre- and post-sexual intercourse samples from their genital areas, including penile, vaginal, and labial locations. Utilizing Shotgun Metagenomic Sequencing, we sequenced the microbial profiles of these samples. Our findings reveal significant transfer from the vaginal microbiome onto the penile microbiome, predominantly originating from the labial genitalia. Moreover, strain analysis unveiled distinct differentiation between the same species of bacteria across individuals, underscoring the potential for microbial forensics to distinguish individuals. This study contributes to our understanding of microbial transfer during sexual contact and highlights the forensic implications of the genital microbiome.}, }
@article {pmid40117911, year = {2025}, author = {Wang, J and Feng, Y and Cheng, H and Qian, K and Wan, B and Liu, S and Liu, Y and Hu, J}, title = {Management strategies and outcomes for fracture-related infection of patellar fractures.}, journal = {Injury}, volume = {56}, number = {4}, pages = {112272}, doi = {10.1016/j.injury.2025.112272}, pmid = {40117911}, issn = {1879-0267}, abstract = {INTRODUCTION: Fracture-related infection (FRI) poses a substantial challenge in orthopaedic trauma surgery, potentially leading to permanent functional impairment or necessitating amputation in patients who are expected to recover fully. Data on the incidence, pathogen detection rates, outcomes, and optimal management strategies for patellar FRI are limited. Therefore, this study aimed to identify the most common pathogens associated with patellar fixation-related infections, evaluate the functional outcome associated with FRI of the patella, and develop a management algorithm for addressing these severe complications.<br><br>METHODS: This retrospective review analyzed a prospectively maintained database to identify all patients with FRI of the patella treated at our institution between January 2015 and August 2023. Data on demographics, fracture characteristics, surgical details, and outcomes were collected. Descriptive statistical analyses were performed using SPSS software.<br><br>RESULTS: Over the 9-year period, 32 cases of patellar fractures complicated by infection following surgical treatment were identified, with complete follow-up data available (mean age, 56.5 &#xb1; 15.8 years). Infection occurred in 13 patients within 2 weeks of fixation and in 19 patients between 2 and 10 weeks postoperatively. Following debridement, nine patients retained their original fixation, eight underwent hardware removal, and 15 underwent hardware replacement. Seven patients developed septic arthritis and were managed with arthroscopic knee lavage. Metagenomic next-generation sequencing demonstrated a sensitivity of 93.8 % (30/32), which was significantly higher than that of traditional microbiological culture (53.1 %; P < 0.01). All surgical incisions achieved primary healing within 2 weeks post-closure with no recurrence of infection, skin necrosis, osteomyelitis, or nonunion. At the final follow-up, all fractures had united, with the B&#xf6;stman patellar fracture functional scores ranging from 24 to 29, resulting in a 100 % excellent/good rate.<br><br>CONCLUSIONS: Comprehensive and multidisciplinary management approaches can achieve successful bone union and favourable long-term outcomes in patients with patellar FRI. However, further validation through large-scale studies is necessary to confirm these findings.}, }
@article {pmid40117769, year = {2025}, author = {Jiang, Z and Fang, W and Jiang, Y and Hu, Y and Dong, Y and Li, P and Shi, L}, title = {Arsenic mobilization by Bathyarchaeia in subsurface sediments at the Jianghan Plain, China.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {138002}, doi = {10.1016/j.jhazmat.2025.138002}, pmid = {40117769}, issn = {1873-3336}, abstract = {As one of the most abundant microorganisms on Earth, Bathyarchaeia with diverse abilities to degrade complex organic carbon play a vital role in the global carbon cycle. However, the role of Bathyarchaeia in arsenic (As) metabolism and their contribution to As mobilization in aquifers remain unclear. In this study, we recovered 15 Bathyarchaeota metagenome-assembled genomes (MAGs) from metagenomes of borehole sediments in the Jianghan Plain (JHP), China. Together with 374 representative Bathyarchaeia MAGs from public databases, six As metabolism genes i.e. arrA, arsR, arsA, arsB, arsC (Trx) and arsM were identified, accounting for 4.4, 47.6, 20.3, 38.3, 37.5 and 49.4 % of total Bathyarchaeia MAGs, respectively. Heterologous expression of multiple arsC and arsM genes of Bathyarchaeia MAGs obtained from JHP sediments validated their abilities for As(V) reduction and As(III) methylation at environmentally relevant As concentration. These results indicate that in addition to providing bioavailable carbon sources for other microbial functional populations, Bathyarchaeia directly participate in As mobilization in the JHP aquifer via As(V) reduction and As(III) methylation. The diversified distribution of arsC and arsM in the class Bathyarchaeia suggests that Bathyarchaeia may contribute to As cycling in other As-rich environments, such as hot spring, saline lakes, marine hydrothermal sediments and soils.}, }
@article {pmid40117176, year = {2025}, author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP}, title = {Healthy microbiome-moving towards functional interpretation.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf015}, pmid = {40117176}, issn = {2047-217X}, support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Metagenome ; Phylogeny ; Dysbiosis/microbiology ; Principal Component Analysis ; COVID-19/virology ; }, abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.<br><br>FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.<br><br>CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).}, }
@article {pmid40116459, year = {2025}, author = {Blakeley-Ruiz, JA and Bartlett, A and McMillan, AS and Awan, A and Walsh, MV and Meyerhoffer, AK and Vintila, S and Maier, JL and Richie, TG and Theriot, CM and Kleiner, M}, title = {Dietary protein source alters gut microbiota composition and function.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf048}, pmid = {40116459}, issn = {1751-7370}, support = {7002782//USDA National Institute of Food and Agriculture, Hatch/ ; P30 DK034987/NH/NIH HHS/United States ; }, abstract = {The source of protein in a person's diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices impact the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determined the effects of seven different sources of dietary protein on the gut microbiota of mice using an integrated metagenomics-metaproteomics approach. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the molecular phenotype of microbiota members because measured proteins indicate the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial proteins involved in the degradation of amino acids and the degradation of glycosylations conjugated to dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes. Egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein sources can change the gut microbiota's metabolism, which could have major implications in the context of gut microbiota mediated diseases.}, }
@article {pmid40116405, year = {2025}, author = {Shekhawat, N}, title = {Precision Medicine for Diagnosis of Microbial Keratitis.}, journal = {International ophthalmology clinics}, volume = {65}, number = {2}, pages = {20-25}, doi = {10.1097/IIO.0000000000000562}, pmid = {40116405}, issn = {1536-9617}, mesh = {Humans ; *Precision Medicine/methods ; *Eye Infections, Bacterial/diagnosis/microbiology ; *Keratitis/diagnosis/microbiology ; Eye Infections, Fungal/diagnosis/microbiology ; Cornea/microbiology ; Bacteria/genetics/isolation &amp; purification ; Proteomics/methods ; }, abstract = {Microbial keratitis (MK) is the leading cause of corneal blindness and can be caused by several species of bacteria, fungi, or parasites. Accurate and timely identification of the causative microbe is critical for initiating targeted antimicrobial and anti-inflammatory treatment and preventing vision loss. MK diagnosis currently relies on corneal culture or microscopy, which have suboptimal yield and can produce inconclusive results. MK requires immediate treatment with empiric antimicrobials, followed by targeted treatment after the microbe is identified. The clinical utility of anti-inflammatory therapy in MK remains controversial and likely differs due to host- and microbe-specific factors. Newer diagnostic techniques such as whole genome sequencing, metagenomic deep sequencing, transcriptomics, and proteomics have the potential to greatly improve timeliness, accuracy, and precision when diagnosing and treating MK. Metagenomic deep sequencing can identify pathogenic microbes with comparable or superior accuracy to traditional microbiology techniques, enabling faster and more accurate diagnosis and initiation of appropriate treatment. Whole genome sequencing of corneal culture isolates has the potential to provide patient-specific insights about microbial phylogenetics, antimicrobial resistance genes, and virulence factors to enable more targeted antimicrobial therapy. Characterization of the host immune response using RNA sequencing or tear proteomics could help inform the use of tailored anti-inflammatory therapies to prevent corneal damage. Although most of these precision medicine approaches are in the research phase, they show the potential to customize MK treatment based on host and microbial factors and improve clinical outcomes.}, }
@article {pmid40115744, year = {2025}, author = {Kimmel, M and Tong, B and Devall, AE and Björvang, RD and Schuppe-Koistinen, I and Engstrand, L and Fransson, E and Skalkidou, A and Hugerth, LW}, title = {Investigating the Microbiome in Relation to Mental Distress Across Two Points During Pregnancy: Data From U.S. and Swedish Cohorts.}, journal = {Biological psychiatry global open science}, volume = {5}, number = {3}, pages = {100453}, pmid = {40115744}, issn = {2667-1743}, abstract = {BACKGROUND: In this study, we aimed to characterize the gut microbiome and its potential functioning in 2 populations at 2 time points during pregnancy in relation to mental distress.<br><br>METHODS: During the second and third trimester, individuals from the United States and Sweden completed the Edinburgh Postnatal Depression Scale and provided fecal samples for whole-genome metagenomics. A total of 832 and 161 samples were sequenced and analyzed from the Swedish cohort and the U.S. cohort, respectively. Multiple characterizations of the microbial community were analyzed in relation to distress measured using the Edinburgh Postnatal Depression Scale. Principal coordinate analysis and distance-based redundancy analysis assessed variation in functional gut-brain modules. For the U.S. cohort, the Trier Social Stress Test was administered 8 weeks postpartum while collecting salivary cortisol.<br><br>RESULTS: Principal coordinate analysis identified 4 sample clusters based on the gut-brain modules distinguished by functions such as short-chain fatty acid synthesis and cortisol degradation. While with distance-based redundancy analysis, mental distress subtypes did not significantly contribute to variation in gut-brain modules (p&#xa0;= .085 for Sweden, p&#xa0;= .23 for the U.S.), a U.S. sample cluster distinguished by lower cortisol degradation from another cluster with higher gut microbial cortisol degradation abundance had significantly higher odds of being associated with depression (p&#xa0;= .024). The U.S. sample cluster with lower gut microbial cortisol degradation abundance also had significantly higher cortisol levels after a postpartum social stressor.<br><br>CONCLUSIONS: Further studies are warranted to investigate the potential for the gut microbiome to serve as biomarkers of gut-brain axis health during pregnancy across disparate populations.}, }
@article {pmid40115680, year = {2025}, author = {Patankar, C and Kulsum, U and Mahajan, S and Kumar, S and Kale, D and Sharma, VK and Nema, S and Biswas, D}, title = {Mapping Viral Landscapes: Genomic Surveillance of Aedes Mosquitoes From Central India.}, journal = {Cureus}, volume = {17}, number = {2}, pages = {e79206}, pmid = {40115680}, issn = {2168-8184}, abstract = {BACKGROUND: Mosquito-borne viral diseases pose a significant impact on human health, with the potential to cause widespread outbreaks of diseases. Monitoring viral genomes in mosquito populations can lead to informed risk assessment and promote early diagnosis. However, a standardized methodology is lacking to decipher circulating viral sequences in mosquito populations collected from human habitats. Our study aims to establish and evaluate a system of viral metagenomic analysis in the Aedes mosquito population.<br><br>METHODS: Mosquitoes were collected using CDC-approved BG-Sentinel version 2 traps (Biogents AG, Regensburg, Germany) and battery-operated vacuum aspirators from different locations in the Bhopal region, India. They were sorted based on genus, gender, location, and collection date. The RNA was extracted from the homogenized mosquito pools and reverse transcribed. Complementary DNA (cDNA) was amplified using sequence-independent, single-prime amplification (SISPA). Further, polymerase chain reaction (PCR) products were sequenced using the Illumina NovaSeq 6000 platform (Illumina, Inc., San Diego, CA). Bioinformatic analysis of the reads was performed using Trimmomatic (Bolger&#xa0;AM, Lohse M, Usadel B (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data (Bioinformatics, btu170) for trimming low-quality raw reads. Later, Kraken2 and Bracken (Johns Hopkins University, Baltimore, MD)&#xa0;were used for the identification of viral sequences.<br><br>RESULTS: The study examined virus diversity and seasonal distribution in mosquito populations collected from 13 sites in Bhopal, India, over 15 months. A total of 31 mosquito pools of female Aedes mosquitoes were analyzed. Metagenomic analysis revealed viruses encompassing plant, animal, insect, fungal, and bacteriophage hosts. The highest mosquito catch was during the post-monsoon period, while virus diversity peaked during the monsoon. Seasonal variations showed a higher frequency and diversity of viruses during the monsoon than during pre- and post-monsoon periods. The findings highlight the importance of temporal and ecological factors in viral surveillance and mosquito-borne disease management.<br><br>CONCLUSIONS: Our findings demonstrate the potential of combining entomological and genomic surveillance for monitoring virus circulation in mosquito populations, which may be implemented as a routine surveillance tool for the timely detection of spikes in viruses with human pathogenic potential and thus inform targeted vector control measures to avert potential outbreaks in the future.}, }
@article {pmid40115125, year = {2025}, author = {Pavloudi, C and Santi, I and Azua, I and Baña, Z and Bastianini, M and Belser, C and Bilbao, J and Bitz-Thorsen, J and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Daguin, C and Díaz de Cerio, O and Exter, K and Fauvelot, C and Frada, MJ and Galand, PE and Garczarek, L and González Fernández, J and Guillou, L and Hablützel, PI and Heynderickx, H and Houbin, C and Kervella, AE and Krystallas, A and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhaes, C and Maidanou, M and Margiotta, F and Montresor, M and Not, F and Paredes, E and Percopo, I and Péru, E and Poulain, J and Præbel, K and Rigaut-Jalabert, F and Romac, S and Stavroulaki, M and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Trano, AC and Wincker, P and Pade, N}, title = {First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e143585}, pmid = {40115125}, issn = {1314-2828}, abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.}, }
@article {pmid40115072, year = {2025}, author = {Li, J and Hu, X and Tao, X and Li, Y and Jiang, W and Zhao, M and Ma, Z and Chen, B and Sheng, S and Tong, J and Zhang, H and Shen, B and Gao, X}, title = {Deconstruct the link between gut microbiota and neurological diseases: application of Mendelian randomization analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1433131}, pmid = {40115072}, issn = {2235-2988}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Nervous System Diseases/genetics/microbiology ; Brain-Gut Axis ; Genome-Wide Association Study ; }, abstract = {BACKGROUND: Recent research on the gut-brain axis has deepened our understanding of the correlation between gut bacteria and the neurological system. The inflammatory response triggered by gut microbiota may be associated with neurodegenerative diseases. Additionally, the impact of gut microbiota on emotional state, known as the "Gut-mood" relationship, could play a role in depression and anxiety disorders.<br><br>RESULTS: This review summarizes recent data on the role of gut-brain axis in the pathophysiology of neuropsychiatric and neurological disorders including epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke. Also, we conducted a Mendelian randomization study on seven neurological disorders (Epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke). MR-Egger and MR-PRESSO tests confirmed the robustness of analysis against horizontal pleiotropy.<br><br>CONCLUSIONS: By comparing the protective and risk factors for neurological disorders found in our research and other researches, we can furtherly determine valuable indicators for disease evolution tracking and potential treatment targets. Future research should explore extensive microbiome genome-wide association study datasets using metagenomics sequencing techniques to deepen our understanding of connections and causality between neurological disorders.}, }
@article {pmid40114670, year = {2025}, author = {Hu, W and Teng, Y and Wang, X and Xu, Y and Sun, Y and Wang, H and Li, Y and Dai, S and Zhong, M and Luo, Y}, title = {Mixotrophic cyanobacteria are critical active diazotrophs in polychlorinated biphenyl-contaminated paddy soil.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae160}, pmid = {40114670}, issn = {2730-6151}, abstract = {Biological nitrogen fixation by diazotrophs is a crucial biogeochemical process in global terrestrial ecosystems, especially in nitrogen-limited, organic-contaminated soils. The metabolic activities of diazotrophs and their ability to supply fixed nitrogen may facilitate the transformation of organic pollutants. However, the active diazotrophic communities in organic-contaminated soils and their potential metabolic functions have received little attention. In the current study, the relationship between biological nitrogen fixation and polychlorinated biphenyl (PCB) metabolism was analyzed in situ in paddy soil contaminated with a representative tetrachlorobiphenyl (PCB52). [15]N-DNA stable isotope probing was combined with high-throughput sequencing to identify active diazotrophs, which were distributed in 14 phyla, predominantly Cyanobacteria (23.40%). Subsequent metagenome binning and functional gene mining revealed that some mixotrophic cyanobacteria (e.g. FACHB-36 and Cylindrospermum) contain essential genes for nitrogen fixation, PCB metabolism, and photosynthesis. The bifunctionality of Cylindrospermum sp. in nitrogen fixation and PCB metabolism was further confirmed by metabolite analyses of Cylindrospermum sp. from a culture collection as a representative species, which showed that Cylindrospermum sp. metabolized PCB and produced 2-chlorobiphenyl and 2,5-dihydroxybenzonic acid. Collectively, these findings indicate that active diazotrophs, particularly mixotrophic cyanobacteria, have important ecological remediation functions and are a promising nature-based in situ remediation solution for organic-contaminated environments.}, }
@article {pmid40114290, year = {2025}, author = {Demina, T and Marttila, H and Pessi, IS and Männistö, MK and Dutilh, BE and Roux, S and Hultman, J}, title = {Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {79}, pmid = {40114290}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Genome, Viral ; *Virome ; *Tundra ; *Phylogeny ; *Metagenome ; Arctic Regions ; Finland ; Bacteriophages/genetics/classification/isolation &amp; purification ; Acidobacteria/genetics/classification/isolation &amp; purification ; Soil ; DNA, Viral/genetics ; }, abstract = {BACKGROUND: Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils.<br><br>RESULTS: Five virus isolates, Tunturi 1-5, were obtained from Arctic tundra soils, Kilpisj&#xe4;rvi, Finland (69&#xb0;N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63-98&#xa0;kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisj&#xe4;rvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisj&#xe4;rvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisj&#xe4;rvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils.<br><br>CONCLUSIONS: This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic. Video Abstract.}, }
@article {pmid40114168, year = {2025}, author = {Wu, Y and Qu, Z and Wu, Z and Zhuang, J and Wang, Y and Wang, Z and Chu, J and Qi, Q and Han, S}, title = {Multiple primary malignancies and gut microbiome.}, journal = {BMC cancer}, volume = {25}, number = {1}, pages = {516}, pmid = {40114168}, issn = {1471-2407}, support = {2022E50008, 2024ZY01056//Zhejiang Provincial Clinical Research Center for CANCER/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Metagenomics/methods ; *Neoplasms, Multiple Primary/microbiology/virology ; Colorectal Neoplasms/microbiology/virology ; Adult ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Enterovirus/isolation &amp; purification/genetics ; Case-Control Studies ; Feces/microbiology/virology ; }, abstract = {BACKGROUND: Multiple primary malignancies (MPM) are two or more independent primary malignancies. Recently, the relationship between microbiome and various tumors has been gradually focused on.<br><br>OBJECTIVE: To describe the relationship between MPM patients (MPMs) and gut microbiome.<br><br>METHODS: A total of 27 MPMs, 30 colorectal cancer patients (CRCs), and 30 healthy individuals were included to obtain metagenomic sequencing data. The knowledge graphs of gut bacteria and enteroviruses were plotted based on metagenomics. Wilcoxon rank-sum test was used to screen the characteristic gut microbiome.<br><br>RESULTS: The knowledge graph of gut microbiome in MPM patients was plotted. A total of 26 different gut bacteria, including Dialister, Fecalibacterium and Mediterraneibacter, were found between MPMs and healthy individuals. Twenty gut bacteria, including Parvimonas, Dialister and Mediterraneibacter, were more abundant in MPM complicated by CRC compared with CRCs. Twenty-one different enterovirus, including Triavirus, Punavirus and Lilyvirus, were screened between MPMs and healthy individuals. Triavirus, Punavirus and Lilyvirus were less abundant in MPM than healthy individuals. The abundance of Triavirus, Punavirus and Lilyvirus in CRC patients were also lower than MPM complicated by CRC patients.<br><br>CONCLUSION: The knowledge graph of gut microbiome in MPM patients was plotted. It may provide basic data support for future research of MPM.}, }
@article {pmid40113957, year = {2025}, author = {Lai, Y and Chen, B and Chen, S and Shen, Y}, title = {Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9579}, pmid = {40113957}, issn = {2045-2322}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Metagenomics/methods ; Female ; Aged ; Middle Aged ; Retrospective Studies ; Adult ; Aged, 80 and over ; Respiratory Tract Infections/microbiology/diagnosis/drug therapy ; Bacteria/genetics/isolation &amp; purification/classification ; Metagenome ; }, abstract = {Pulmonary infections remain a leading cause of infectious disease-related hospitalizations. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool for identifying pathogens responsible for pulmonary infections. However, implementing mNGS in clinical practice presents several challenges. We conducted a retrospective analysis of 97 patients with suspected pulmonary infections who were admitted to our hospital and underwent mNGS alongside conventional microbiologic tests (CMT) over the past three years. We compared the diagnostic efficacy of mNGS versus CMT and assessed the clinical applications and challenges associated with mNGS in managing pulmonary infections. mNGS detected pathogens in 63.9% of cases, outperforming CMT (27.8%) and showing notable improvements in identifying Mycobacterium, fungal species, and rare pathogens. Antibiotic regimens were adjusted for 77.4% of patients with positive mNGS results, with clinical improvement observed in 93.5%. Of the 138 microbial strains initially identified by mNGS as possible pathogens, 65 (47.1%) were reclassified as colonizing organisms upon further clinical evaluation, including bacteria and fungi commonly associated with pulmonary infections. Notably, one patient was diagnosed with aspiration pneumonia due to oral anaerobes, which mNGS had categorized as normal microbial flora. In conclusion, mNGS serves as a valuable diagnostic approach for pulmonary infections, enhancing etiologic precision and informing patient management. Nevertheless, a comprehensive clinical interpretation of mNGS-identified microorganisms is essential to achieve accurate diagnosis.}, }
@article {pmid40113286, year = {2025}, author = {Li, F and Qiu, CS and Wang, CC and Xu, F and Wang, D and Liu, NN and Chen, X and Wang, SP}, title = {[Distribution Characteristics and Influencing Factors of Antibiotic Resistance Genes in Surface Sediments of Regulating Pond in South-to-North Water Transfer Pumping Station].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {3}, pages = {1435-1442}, doi = {10.13227/j.hjkx.202312226}, pmid = {40113286}, issn = {0250-3301}, mesh = {*Geologic Sediments/microbiology ; China ; *Drug Resistance, Microbial/genetics ; Ponds/microbiology ; Genes, Bacterial ; Environmental Monitoring ; Water Supply ; Bacteria/genetics/classification ; Rivers/microbiology ; Water Microbiology ; }, abstract = {As an important facility to ensure the safety of the water supply, the regulating pond of a raw water pumping station in the Tianjin Section of the middle route of the South-to-North Water Transfer Project linked the raw water from the Hanjiang River with the urban water plants. Surface sediment samples from different regions of the regulator pond were collected in summer, autumn, and winter of 2022 and spring of 2023, respectively. Metagenomic sequencing technology was used to analyze the distribution characteristics and influencing factors of antibiotic resistance genes （ARGs）, and the correlation between sediment ARGs and physicochemical indices, microbial community structure, and mobile genetic elements （MGEs） was also analyzed. The results showed that 20 antibiotic resistance types and 921 ARGs subtypes were detected in the surface sediment samples of the regulator pond. The dominant ARGs in the samples at different sampling times and sampling points were multidrug resistance, MLS, tetracycline, and glycopeptides, and the main resistance mechanism was efflux pump. Correlation analysis showed that TN, NO3[-]-N, TP, and OM of sediments were significantly correlated （P<0.05） with various ARGs of the top 20 ARGs. Among the top 20 microbial genera, 19 species were significantly correlated （P<0.05） with ARGs. The MGEs types of conjugate transfer protein, recombinase, and transposase were significantly positively correlated （P<0.05） with the top 20 ARGs.}, }
@article {pmid40113151, year = {2025}, author = {Zhang, W and Wen, L and Xin, Z and Wang, G and Lin, H and Wang, H and Wei, B and Yan, X and Wang, W and Guo, B}, title = {Research on the histopathology of Larimichthys crocea affected by white gill disease and analysis of its bacterial and viral community characteristics.}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {110287}, doi = {10.1016/j.fsi.2025.110287}, pmid = {40113151}, issn = {1095-9947}, abstract = {White gill disease (WGD) is one of the major diseases affecting Larimichthys crocea, although its etiology remains unclear. To investigate the causes of WGD, this study selected WGD-affected Larimichthys crocea (WG) and healthy Larimichthys crocea (NH) from multiple aquaculture regions for pathological analysis and analysis of bacterial and viral community characteristics. The results indicated severe tissue damage and significant inflammatory responses, as evidenced by clinical manifestations and electron microscopy. Two bacterial species, Photobacterium damselae and Vibrio campbellii, were isolated from all lesion tissues. Additionally, 16S full-length sequencing results showed that Photobacterium damselae and Vibrio campbellii dominated in the tissues of Larimichthys crocea, with a combined relative abundance of approximately 90%. There were no significant differences in α-diversity and β-diversity between the NH group and WG group from the three aquaculture regions, and no significant biomarkers were identified. The diversity of DNA and RNA viruses did not show significant differences between the NH and WG groups, although both types of viruses exhibited notable synergistic and antagonistic relationships. Analyses from 16S full-length sequencing, metagenomics, and metatranscriptomics revealed that the related functional genes were primarily enriched in various metabolic pathways, including glycine biosynthesis, membrane transport, and energy metabolism. The metatranscriptomic analysis indicated that the expression levels of genes related to antibiotic resistance, biosynthesis, transport, and degradation processes were significantly downregulated in the WG group. Finally, through PCR, qPCR, and metagenomic sequencing, we were unable to detect iridovirus in Larimichthys crocea, further suggesting that the causes of WGD may differ across aquaculture regions compared to previous reports. This study indicates that the etiology of WGD may involve complex ecological and metabolic mechanisms, rather than being merely the result of a single pathogen infection. This research provides a comprehensive analysis of the microbial communities in WGD-affected Larimichthys crocea from multiple aquaculture regions for the first time, providing a theoretical basis for further elucidating the causes of WGD and developing preventive measures.}, }
@article {pmid40113108, year = {2025}, author = {Ruan, Z and Shi, H and Chang, L and Zhang, J and Fu, M and Li, R and Zeng, D and Yang, Y and Li, R and Ai, L and Wang, Y and Hai, B}, title = {The Diagnostic Efficacy of Metagenomic Next-Generation Sequencing (mNGS) in Pathogen Identification of Pediatric Pneumonia using Bronchoalveolar Lavage Fluid (BALF): A Systematic Review and Meta-Analysis.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107492}, doi = {10.1016/j.micpath.2025.107492}, pmid = {40113108}, issn = {1096-1208}, abstract = {OBJECTIVE: This meta-analysis evaluates and compares the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) with conventional microbiological tests (CMTs) in diagnosing pediatric pneumonia using bronchoalveolar lavage fluid (BALF).<br><br>METHODS: Data were sourced from Embase, Medline (via PubMed), Web of Science, and the Cochrane Library. The pooled positive detection rate (PDR) of pathogens was estimated using fixed-effects or random-effects models. Subgroup analyses explored factors influencing mNGS diagnostic performance. Data analysis was conducted using Review Manager (RevMan) 5.4 and Stata version 16.0.<br><br>RESULTS: The pooled PDR of mNGS was 85.83%, which is higher than the pooled PDR of 49.97% for CMTs. A random-effects model indicated that, compared to CMTs, mNGS has a significantly higher PDR in pediatric pneumonia (OR=3.99, 95%CI: 2.12-7.50, P<0.0001, I[2]=81%). Subgroup analysis indicated that mNGS exhibited greater advantages in the group using the QIAamp kit (OR=5.55, 95% CI: 3.03-10.16, P<0.00001), the group using the Illumina Nextseq platform (OR=4.87, 95% CI: 2.97-7.99, P<0.00001), the DNA-only mNGS group (OR=4.54, 95% CI: 2.73-7.54, P<0.00001), and the non-severe pneumonia group (OR=4.76, 95% CI: 3.51-6.46, P<0.00001). However, when the subgroups were categorized as mixed infections or single-pathogen infections, no statistically significant differences were observed (Mixed: OR=1.77, 95% CI: 0.30-10.56, P=0.53; Single: OR=3.97, 95% CI: 0.42-37.87, P=0.23) CONCLUSION: mNGS demonstrates high diagnostic efficacy in detecting pathogens in BALF from pediatric patients with pneumonia. The diagnostic stability of mNGS is influenced by sample extraction, sequencing platforms, positive interpretation criteria, and disease status. Standardized procedures and technologies can enhance mNGS diagnostic performance.}, }
@article {pmid40112621, year = {2025}, author = {Ma, C and Zhao, Y and Ma, B and Li, X and Li, X and Chen, X}, title = {Co-critical golden-flower fungus (Eurotium repens) contributed to characteristic flavor formation of two Yunnan jinhua teas through jinhua formation during the storage.}, journal = {Food chemistry}, volume = {479}, number = {}, pages = {143765}, doi = {10.1016/j.foodchem.2025.143765}, pmid = {40112621}, issn = {1873-7072}, abstract = {Jinhua formation during the storage (JFDS) was found in two Yunnan teas that were defined as jinhua ripened Pu-erh tea (JRIPT) and jinhua white tea (JWT), respectively. Integrated multi-omics of metagenomics, volatilomics and metabolomics was developed to elucidate JFDS mechanism. Overall, JFDS caused significant differences in characteristic flavor, microbial community structure and volatile organic compounds (VOCs) profile. Among 14 co-critical fungi, Eurotium repens was regarded as the golden-flower fungus for JFDS, and had higher relative abundance in Yunnan jinhua teas over 50 %. Based on 291 VOCs and 83 odor-active compounds, E. repens directly promoted glycoside hydrolysis and carotene degradation to formulate β-linalool, β-ionone and 3,4-dehydro-β-ionone for jinhua fungus aroma of JWT. With Arxula adeninivorans synergy, E. repens activity contributed to Chinese medicine-like smell of JRIPT through sesquiterpenes and methoxybenzenes accumulation. Additionally, E. repens activity in the JFDS accelerated catechins oxidative polymerization, and other flavonoids conversion to enhance mellow taste.}, }
@article {pmid40111891, year = {2025}, author = {Díez-Madueño, K and Montero, I and Fernández-Gosende, M and Martínez-Álvarez, N and Hidalgo-Cantabrana, C and de la Cueva Dobao, P and Coto-Segura, P}, title = {Compositional and Functional Profile of Gut Microbiota in a Cohort of Adult Spanish Patients with Atopic Dermatitis Using Metagenomics: A Cross-Sectional Study.}, journal = {Dermatitis : contact, atopic, occupational, drug}, volume = {}, number = {}, pages = {}, doi = {10.1089/derm.2024.0536}, pmid = {40111891}, issn = {2162-5220}, abstract = {Background: The role of gut dysbiosis in the pathophysiology of atopic dermatitis (AD) through immune system (IS) imbalance is a novel line of investigation currently under discussion. This study aimed to characterize compare the composition and functional profile of the gut microbiota (GM) between adults with AD and healthy individuals. Methods: Observational cross-sectional study, where fecal samples from 70 adults (38 patients and 32 controls) were analyzed using metagenomics and bioinformatics. Results: Differences between the GM of patients with AD and healthy individuals were demonstrated. Reduced microbial diversity was found in subjects with AD. Bacterial species with lower abundance primarily belonged to the families Ruminococcaceae, Akkermansiaceae, and Methanobacteriaceae. Several microbial metabolic pathways were found to be decreased in patients with AD, including amino acid biosynthesis, vitamin biosynthesis, fatty acids and lipids biosynthesis, and energy metabolism. Conclusion: Adults with AD exhibited a distinct GM compared to healthy individuals. Changes were demonstrated both compositionally and functionally. Further investigation is mandatory to elucidate the potential link and causal relationship between gut dysbiosis and AD, which may be crucial for a deeper understanding of the disease's pathophysiology and the development of novel therapeutic approaches.}, }
@article {pmid40111684, year = {2025}, author = {de Barros Santos, HS and Pagnussatti, MEL and Arthur, RA}, title = {Symbiosis Between the Oral Microbiome and the Human Host: Microbial Homeostasis and Stability of the Host.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {31-51}, pmid = {40111684}, issn = {0065-2598}, mesh = {Humans ; *Symbiosis ; *Mouth/microbiology ; *Microbiota/physiology ; *Homeostasis ; *Host Microbial Interactions ; Bacteria/metabolism/genetics/classification ; Metagenomics/methods ; Oral Health ; }, abstract = {The oral cavity presents a highly diverse microbial composition. All the three domains of life, Bacteria, Eukarya, and Archaea, as well as viruses constitute the oral microbiome. Bacteria are among the most abundant microorganisms in the oral cavity, followed by viruses, fungi, and Archaea. These microorganisms tend to live in harmony with each other and with the host by preventing the colonization of oral sites by exogenous microorganisms. Interactions between the host and its microbiota are crucial for keeping ecological stability in the oral cavity and a condition compatible with oral health. This chapter focuses on describing the oral microbiota in healthy individuals based on both targeted and nontargeted genome sequencing methods and the functional activity played by those microorganisms based on metagenomic, metatranscriptomic, metaproteomic, and metabolomic analyses. Additionally, this chapter explores mutualistic and antagonistic microbe-microbe relationships. These interactions are mediated by complex mechanisms like cross-feeding networks, production of bacteriocins and secondary metabolites, synthesis of pH-buffering compounds, and the use of universal signaling molecules. At last, the role played by host-microbe interactions on colonization resistance and immune tolerance will help provide a better understanding about the harmonious and peaceful coexistence among host and microbial cells under oral health-related conditions.}, }
@article {pmid40111141, year = {2025}, author = {Yang, F and Zhang, Y and Qi, B and Chen, L and Lin, F and Wu, J and Gong, S and Cao, L and Zeng, M and Cheng, Q and Jiang, D and Tang, S and He, J and Xu, Z and Li, T and Ni, Z and Li, Y and Huang, X and Pan, C and Liu, R and Lan, Y}, title = {Clinical Manifestations and Prognosis of Patients With Mucormycosis in Intensive Care Units in Western China: A Multi-Center Retrospective Study.}, journal = {Mycoses}, volume = {68}, number = {3}, pages = {e70042}, doi = {10.1111/myc.70042}, pmid = {40111141}, issn = {1439-0507}, support = {2023QN02//Research Fund of Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital/ ; 2025ZNSFSC1542//Sichuan Science and Technology Program/ ; }, mesh = {Humans ; *Mucormycosis/mortality/diagnosis/drug therapy/epidemiology/microbiology ; Female ; Male ; Middle Aged ; Retrospective Studies ; *Intensive Care Units ; China/epidemiology ; Aged ; *Antifungal Agents/therapeutic use ; Adult ; Prognosis ; Critical Illness ; Amphotericin B/therapeutic use ; }, abstract = {BACKGROUND: Mucormycosis is a life-threatening fungal infection with high mortality in critically ill patients. Clinical manifestations and outcomes of mucormycosis in intensive care units (ICUs) remain poorly investigated.<br><br>METHODS: We conducted a multicenter retrospective study including 43 adult patients with confirmed mucormycosis admitted to 14 tertiary ICUs between January 2014 and May 2022. Clinical characteristics, diagnostic approaches, treatment strategies, and outcomes were analysed.<br><br>RESULTS: The mean age was 56.8&#x2009;&#xb1;&#x2009;16.2&#x2009;years, with 16/43 (37.2%) female patients. The 28-day survival rate was 46.5% (20/43). Lung involvement was predominant (29/43, 67.4%), and 29/43 (67.4%) patients received amphotericin B therapy. Survivors showed significantly better treatment response compared to non-survivors (16/20, 80% vs. 4/23, 17.4%, p&#x2009;<&#x2009;0.001). Non-survivors demonstrated significantly higher levels of aspartate aminotransferase, C-reactive protein, and white blood cells, along with lower albumin levels. Metagenomic next-generation sequencing (mNGS) was associated with a shorter time to diagnosis. Multivariate analysis identified age, respiratory failure, time from symptom onset to diagnosis, and antifungal treatment response as independent predictors of 28-day mortality (AUC&#x2009;=&#x2009;0.852).<br><br>CONCLUSION: In critically ill patients with mucormycosis, early diagnosis and prompt targeted therapy are crucial determinants of survival, with our newly developed prediction model providing a practical tool for risk stratification, while mNGS shows promise in expediting diagnosis.}, }
@article {pmid40111052, year = {2025}, author = {Martí, JM and Kok, CR and Thissen, JB and Mulakken, NJ and Avila-Herrera, A and Jaing, CJ and Allen, JE and Be, NA}, title = {Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0123924}, doi = {10.1128/msystems.01239-24}, pmid = {40111052}, issn = {2379-5077}, abstract = {UNLABELLED: Accurate metagenomic classification relies on comprehensive, up-to-date, and validated reference databases. While the NCBI BLAST Nucleotide (nt) database, encompassing a vast collection of sequences from all domains of life, represents an invaluable resource, its massive size-currently exceeding 10[12] nucleotides-and exponential growth pose significant challenges for researchers seeking to maintain current nt-based indices for metagenomic classification. Recognizing that no current nt-based indices exist for the widely used Centrifuge classifier, and the last public version currently available was released in 2018, we addressed this critical gap by leveraging advanced high-performance computing resources. We present new Centrifuge-compatible nt databases, meticulously constructed using a novel pipeline incorporating different quality control measures, including reference decontamination and filtering. These measures demonstrably reduce spurious classifications, as shown through our reanalysis of published metagenomic data where Plasmodium annotations were dramatically reduced using our decontaminated database, highlighting how database quality can significantly impact research conclusions. Through temporal comparisons, we also reveal how our approach minimizes inconsistencies in taxonomic assignments stemming from asynchronous updates between public sequence and taxonomy databases. These discrepancies are particularly evident in taxa such as Listeria monocytogenes and Naegleria fowleri, where classification accuracy varied significantly across database versions. These new databases, made available as pre-built Centrifuge indexes, respond to the need for an open, robust, nt-based pipeline for taxonomic classification in metagenomics. Applications such as environmental metagenomics, forensics, and clinical metagenomics, which require comprehensive taxonomic coverage, will benefit from this resource. Our work highlights the importance of treating reference databases as dynamic entities, subject to ongoing quality control and validation akin to software development best practices. This approach is crucial for ensuring accuracy and reliability of metagenomic analysis, especially as databases continue to expand in size and complexity.<br><br>IMPORTANCE: Accurately identifying the diverse microbes present in a sample, whether from the human gut, a soil sample, or a crime scene, is crucial for fields ranging from medicine to environmental science. Researchers rely on comprehensive DNA databases to match sequenced DNA fragments to known microbial species. However, the widely used NCBI nt database, while vast, poses significant challenges. Its massive size makes it difficult for many researchers to use effectively with taxonomic classifiers, and inconsistencies and contamination within the database can impact the accuracy of microbial identification. This work addresses these challenges by providing cleaned, updated, and validated nt-based databases specifically optimized for the widely used Centrifuge classification tool. This new resource demonstrably reduces errors and improves the reliability of microbial identification across diverse taxonomic groups. Moreover, by providing readily usable indexes, we overcome the size barrier, enabling researchers to leverage the full potential of the nt database for metagenomic analysis. Our findings underscore the need to treat reference databases as dynamic entities, emphasizing continuous quality control and versioning as essential practices for robust and reproducible metagenomics research.}, }
@article {pmid40111022, year = {2025}, author = {Lim, SJ and Rogers, A and Rosario, K and Kerr, M and Garrett, M and Koester, J and Hubbard, K and Breitbart, M}, title = {Diverse ssRNA viruses associated with Karenia brevis harmful algal blooms in southwest Florida.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0109024}, doi = {10.1128/msphere.01090-24}, pmid = {40111022}, issn = {2379-5042}, abstract = {Harmful algal blooms (HABs) caused by the dinoflagellate Karenia brevis frequently occur in the eastern Gulf of Mexico, where they negatively impact the environment, human health, and economy. Very little is known about viruses associated with K. brevis blooms, although viral infection of other HAB-forming phytoplankton species can play an important role in bloom dynamics. We used viral metagenomics to identify viruses in 11 pooled seawater samples collected from southwest Florida, USA, in 2021 during a severe, spatiotemporally dynamic K. brevis bloom. Assembled viral genomes were similar to published genomes from the order Picornavirales, family Marnaviridae, and genera Sogarnavirus, Bacillarnavirus, and Marnavirus. Several of the cultured viruses from these groups infect bloom-forming diatoms (Chaetoceros sp. and Rhizosolenia setigera) and the raphidophyte Heterosigma akashiwo. We also recovered unclassified Riboviria genomes related to a Symbiodinium positive-sense ssRNA virus sequenced from coral dinoflagellate symbionts. Reverse-transcriptase PCR assays were performed to monitor the occurrence of seven representative virus genomes in these samples from 2021 and 43 seawater samples collected during a subsequent, typical bloom between November 2022 and May 2023. Over half of the samples contained multiple viruses, and at least one viral genome was detected in 44 of the 54 samples collected across seasons and years, highlighting the ubiquity of these viruses in this region. Alpha diversity was highest in the summer months and positively correlated with K. brevis cell counts. Multiple regression revealed month and the presence of unclassified Riboviria sequences most similar to dinoflagellate viruses as significant predictors of K. brevis cellular abundance.IMPORTANCEHarmful algal blooms caused by the dinoflagellate Karenia brevis negatively impact the tourism, fisheries, and public health sectors. Anticipated impacts of climate change, nutrient pollution, and ocean acidification may sustain and/or exacerbate K. brevis blooms in the future, underscoring the need for proactive monitoring, communication, and mitigation strategies. This study represents a pioneering effort in monitoring viruses associated with K. brevis blooms. The findings lay the groundwork for studying the effects of environmental drivers on K. brevis blooms and their associated viruses, as well as for exploring the roles of viruses in bloom dynamics and potential applications of viruses as biocontrol agents for K. brevis blooms. Furthermore, the comparison of viral dynamics relative to local and regional bloom dynamics in this study helps inform future monitoring and modeling needs.}, }
@article {pmid40110701, year = {2025}, author = {Liang, H and Li, T and Chen, Y and Wang, J and Aslam, M and Qin, H and Fan, W and Du, H and Kao, SJ and Lin, S}, title = {Urea Amidolyase as an Enzyme for Urea Utilisation in Phytoplankton: Functional Display in Chlamydomonas reinhardtii.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17734}, doi = {10.1111/mec.17734}, pmid = {40110701}, issn = {1365-294X}, support = {42206116//Natural Science Foundation of China/ ; 2024A1515011467&#xff1b;2025A1515010095//Natural Science Foundation of Guangdong Province, China/ ; 2021B1212050025//Science and Technology Plan Projects of Guangdong Province/ ; 2022KCXTD008//Program for University Innovation Team of Guangdong Province/ ; 2024-MRB-00-001//Research on Breeding Technology of Candidate Species for Guangdong Modern Marine Ranching/ ; }, abstract = {Urea is an important source of nitrogen for many phytoplankton with the potential to stimulate harmful algal blooms, but the molecular machinery underpinning urea uptake and assimilation by algae is not fully understood. Urease (URE) is commonly regarded as the responsible enzyme, but urea amidolyase (UAL), albeit known to exist, has hardly been studied. Here, the species distribution, expression patterns and functional roles of UAL are examined. We found a widespread occurrence of UAL across six major phytoplankton lineages, along with evidence of a potential URE-independent evolutionary trajectory and lineage-specific losses. Quantitative analyses based on marine planktonic metagenomes and metatranscriptomes revealed that UAL is as prevalent as URE, but exhibits higher expression levels in phytoplankton than in bacteria, suggesting that UAL plays a crucial role in nitrogen nutrition in marine phytoplankton. Furthermore, using the CRISPR/Cas9 genome editing method and Chlamydomonas reinhardtii as the algal model, we showed that DUR2 in UAL is essential for urea utilisation, as its knockout completely abolishes the ability of algae to grow under urea as the sole nitrogen source. This study unveils an unappreciated mechanism in algae for utilising urea as a nutrient, underscores the need to consider both URE and UAL enzyme systems to model urea utilisation by algae and provides a crucial gene (DUR2) as a potential genetic marker for detecting the contribution of UAL to urea utilisation in phytoplankton.}, }
@article {pmid40110433, year = {2025}, author = {Cheng, C and Zheng, Y and Wang, X and Tao, J and Cheng, D}, title = {Research in etiology of Floppy Kid Syndrome.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1557951}, pmid = {40110433}, issn = {2297-1769}, abstract = {Floppy Kid Syndrome (FKS) is a common and serious disease in goats, with incidence rates ranging from 10 to 50% and mortality rates between 20 and 60%. This study aimed to investigate the etiology of FKS through blood biochemical analysis and metagenomic sequencing. Blood biochemical analysis revealed metabolic disorders in FKS-affected goats, including acidosis and hypoglycemia. Metagenomic analysis showed marked gastric and gut dysbacteriosis, characterized by an increase in pathogenic bacteria such as Escherichia coli and Staphylococcus aureus, alongside a significant reduction in probiotic like Lactobacillus amylovorus. Furthermore, species diversity and richness were notably lower in FKS-affected goats compared to healthy goats. Based on these findings, we infer that FKS is a multifactorial disease caused by gastric and gut dysbacteriosis. The immaturity of the digestive system in newborn goats, combined with environmental stressors (such as sudden changes in weather), leads to gastric and gut dysbacteriosis, with a significant reduction in probiotic and an overgrowth of pathogenic bacteria. The dysbacteriosis, along with the inability to properly digest excessive milk intake, contributes to the accumulation of undigested milk in the digestive tract, creating an environment conducive to pathogenic bacteria growth. The fermentation of milk and the production of excessive lactic acid by pathogenic bacteria are absorbed into the bloodstream, causing acidosis and hypoglycemia. These metabolic disorders, in conjunction with the dysbacteriosis and systemic dysfunction, lead to the onset of FKS. These results underscore the critical role of gastric and gut dysbacteriosis in the pathogenesis of FKS, highlighting the need for targeted preventive and therapeutic strategies.}, }
@article {pmid40109965, year = {2025}, author = {Zou, Z and Tang, F and Qiao, L and Wang, S and Zhang, H}, title = {Integrating sequencing methods with machine learning for antimicrobial susceptibility testing in pediatric infections: current advances and future insights.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1528696}, pmid = {40109965}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) presents a critical challenge in clinical settings, particularly among pediatric patients with life-threatening conditions such as sepsis, meningitis, and neonatal infections. The increasing prevalence of multi- and pan-resistant pathogens is strongly associated with adverse clinical outcomes. Recent technological advances in sequencing methods, including metagenomic next-generation sequencing (mNGS), Oxford Nanopore Technologies (ONT), and targeted sequencing (TS), have significantly enhanced the detection of both pathogens and their associated resistance genes. However, discrepancies between resistance gene detection and antimicrobial susceptibility testing (AST) often hinder the direct clinical application of sequencing results. These inconsistencies may arise from factors such as genetic mutations or variants in resistance genes, differences in the phenotypic expression of resistance, and the influence of environmental conditions on resistance levels, which can lead to variations in the observed resistance patterns. Machine learning (ML) provides a promising solution by integrating large-scale resistance data with sequencing outcomes, enabling more accurate predictions of pathogen drug susceptibility. This review explores the application of sequencing technologies and ML in the context of pediatric infections, with a focus on their potential to track the evolution of resistance genes and predict antibiotic susceptibility. The goal of this review is to promote the incorporation of ML-based predictions into clinical practice, thereby improving the management of AMR in pediatric populations.}, }
@article {pmid40109771, year = {2025}, author = {Chen, HB and Liu, J and Zhang, Y and Huang, H and Wang, LN}, title = {Application of metagenomic next-generation sequencing in the diagnosis of pathogens in patients with diabetes complicated by community-acquired pneumonia.}, journal = {Open life sciences}, volume = {20}, number = {1}, pages = {20221048}, pmid = {40109771}, issn = {2391-5412}, abstract = {To explore the clinical utility and optimal timing of metagenomic next-generation sequencing (mNGS) in diagnosing pathogens in patients with diabetes complicated by community-acquired pneumonia (CAP). The study included 50 hospitalized patients diagnosed with diabetes complicated by CAP who underwent conventional microbiological testing (CMT) and mNGS using bronchoalveolar lavage fluid. Among the 50 cases, 16% presented no respiratory symptoms. There were significant increases in inflammatory markers such as C-reactive protein, erythrocyte sedimentation rate, and interleukin-6, with patchy imaging changes being the most prevalent. The positive rates for pathogen detection by mNGS and CMTs were 78 and 21% (P < 0.05). The mNGS was significantly better than the CMTs in the detection of rare pathogens such as Anaerobes, Chlamydia psittaci, Legionella pneumophila, Mycobacterium bovis, Aspergillus fumigatus, and Pneumocystis japonicus (P < 0.05). After clinical interpretation, 85% (22/26) of viruses, 24% (9/37) of bacteria, and 25% (2/8) of fungi were non-pathogen organisms by mNGS. There was a significant difference in the rates of adjustment in anti-infection treatment strategies based on the pathogen detection results from CMTs and mNGS, which were 2 and 46%, respectively (P < 0.05). We found that mNGS was superior to CMTs in terms of the positive rate of pathogen detection, detecting mixed infection incidence, rare pathogen detection rates, and the adjustment of treatment strategies. However, mNGS results need to be interpreted in the context of the clinic.}, }
@article {pmid40109467, year = {2025}, author = {Han, Y and Shen, S and Fu, J and Ren, Q}, title = {[Mechanisms of Wandai Decoction in Improving Vaginal Flora of Vulvovaginal Candidiasis of the Spleen Deficiency and Excessive Dampness Type: A Study Based on Metagenomics and Metabolomics].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {56}, number = {1}, pages = {68-73}, pmid = {40109467}, issn = {1672-173X}, mesh = {Female ; Humans ; *Vagina/microbiology ; *Candidiasis, Vulvovaginal/drug therapy/microbiology ; *Metabolomics ; *Drugs, Chinese Herbal/therapeutic use/administration &amp; dosage ; *Fluconazole/pharmacology/therapeutic use ; Metagenomics ; Antifungal Agents/therapeutic use ; Adult ; Spleen/metabolism/microbiology ; }, abstract = {OBJECTIVE: To explore the mechanism by which Wandai Decoction prevents and treats vulvovaginal candidiasis (VVC) of the spleen deficiency and excessive dampness type and restores the vaginal flora structure, and to identify the potential metabolic pathways involved using metagenomics and metabolomics.<br><br>METHODS: Twenty VVC patients who met the inclusion criteria were randomly assigned to a Wandai Decoction group and a fluconazole group (n = 10 in each group). Subjects in the fluconazole group were given a single oral dose of 150 mg fluconazole, while those in the Wandai Decoction group took the Wandai Decoction orally for 14 days. The vulvovaginal signs and symptoms (VSS) scores of both patient groups were evaluated before and after treatment. Vaginal secretions were collected before and after treatment. The Illumina sequencing and the liquid chromatography with tandem mass spectrometry (LC-MS/MS) platform were used to conduct metagenomic and metabolomics analyses of the vaginal secretions, respectively.<br><br>RESULTS: The VSS score results showed that the VSS scores of both groups decreased after treatment compared with those before treatment (P < 0.01), and there was no statistically significant difference in the VSS scores between the two groups after treatment. Metagenomics results showed that, after treatment, the vaginal microbial communities in the Wandai Decoction group were of CST &#x2161; and &#x2164; types (predominated by Lactobacillus gasseri and Lactobacillus jensenii), while those in the fluconazole group were Lactobacillus_intestinalis and Streptococcus_sp._oral_ taxon_431. KEGG functional enrichment analysis results showed that, in terms of the cell cycle and meiosis functions of Candida albicans, statistically significant differences between the Wandai Decoction and fluconazole groups were observed (P < 0.05). Metabolomic analysis identified 120 differential metabolites between the two groups after treatment. The results of KEGG metabolic pathway enrichment analysis of differential metabolites showed that the Wandai Decoction might be significantly superior to fluconazole in improving local vaginal metabolic pathways of &#x3b1;-linolenic acid, glycerophospholipid metabolism, pentose and glucuronic acid interconversion, and arachidonic acid.<br><br>CONCLUSION: The Wandai Decoction can improve the vaginal flora of VVC patients. It may be superior to fluconazole in the signaling pathways of the cell cycle and meiosis. The improvement of the vaginal flora by the Wandai Decoction may be associated with its effect on metabolic pathways of glycerophospholipid metabolism, pentose and glucuronic acid interconversion, and others in the vagina.}, }
@article {pmid40109356, year = {2025}, author = {Kantor, RS and Kennedy, LC and Miller, SE and Favere, J and Nelson, KL}, title = {Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community.}, journal = {ACS ES&amp;T engineering}, volume = {5}, number = {3}, pages = {772-781}, pmid = {40109356}, issn = {2690-0645}, abstract = {Potable water reuse has become a key component of water sustainability planning in arid regions. Many advanced water purification facilities use reverse osmosis (RO) as part of treatment, including as a barrier for microorganisms; however, regrowth after RO treatment has been observed. Questions remain about the identity, source, and survival mechanisms of microorganisms in RO permeate, but the extremely low biomass of this water is a limitation for common microbiological methods. Here, we performed high-throughput sequencing on samples collected throughout a potable reuse train, including samples collected by filtering large volumes of RO permeate and biomass collected from RO membranes during an autopsy. We observed a stable, consistent microbial community across three months and in two parallel RO trains. RO permeate samples contained Burkholderiaceae at high relative abundance, including one Aquabacterium sp. that accounted for 29% of the community, on average. Like most other RO permeate microorganisms, this sequence was not seen in upstream samples and we suggest that biofilm growing on unit process infrastructure, rather than active treatment breakthrough, was the primary source. A metagenome-assembled genome corresponding to Aquabacterium sp. from RO permeate was found to lack most sugar-utilization pathways and to be able to consume low molecular weight organic molecules, potentially those that pass through RO.}, }
@article {pmid40108525, year = {2025}, author = {Liu, G and Chen, T and Tian, X and Ai, Y and Chen, Z and Liu, J and Sun, Z}, title = {Brain abscess due to clostridium celerecrescens: first report and literature review.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {386}, pmid = {40108525}, issn = {1471-2334}, support = {82371407//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Brain Abscess/microbiology/diagnostic imaging/drug therapy ; Female ; *Clostridium Infections/microbiology/diagnosis/drug therapy ; *Anti-Bacterial Agents/therapeutic use ; Adolescent ; *Clostridium/isolation &amp; purification/genetics ; Foreign Bodies/complications/surgery ; Debridement ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Brain abscess caused by atypical pathogens presents significant diagnostic and therapeutic challenges. The unusual clinical presentations, coupled with incomplete or inaccurate patient histories, often result in misdiagnosis and inappropriate treatment.<br><br>CASE PRESENTATION: We report a case of a retained intracranial bamboo foreign body resulting in a brain abscess. A female adolescent presented with a newly developed mass on the eyelid. Medical imaging identified a foreign body that had penetrated the frontal lobes via the transorbital route, leading to the formation of a brain abscess. The foreign body was successfully removed through transnasal endoscopy. Inflamed tissue adherent to the foreign body was cultured and analyzed using metagenomic next-generation sequencing (mNGS), which identified Clostridium celerecrescens as the causative pathogen. The patient fully recovered after surgical debridement and two weeks of antibiotic therapy.<br><br>CONCLUSIONS: Infections caused by C. celerecrescens are exceedingly rare in clinical practice. This case highlights the bacterium's ability to adhere to a bamboo foreign body, leading to the formation of a rare brain abscess. mNGS proves to be a valuable diagnostic tool for identifying uncommon infectious agents.}, }
@article {pmid40108202, year = {2025}, author = {Redgwell, TA and Thorsen, J and Petit, MA and Deng, L and Vestergaard, G and Russel, J and Chawes, B and Bønnelykke, K and Bisgaard, H and Nielsen, DS and Sørensen, S and Stokholm, J and Shah, SA}, title = {Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {46}, pmid = {40108202}, issn = {2055-5008}, mesh = {*Gastrointestinal Microbiome ; *Prophages/genetics/physiology ; Humans ; Infant ; *Metagenome ; Virome ; Female ; Feces/microbiology/virology ; Bacteria/genetics/classification/virology ; Bacteroides/genetics/virology ; }, abstract = {Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.}, }
@article {pmid40108151, year = {2025}, author = {Krueger, ME and Boles, JS and Simon, ZD and Alvarez, SD and McFarland, NR and Okun, MS and Zimmermann, EM and Forsmark, CE and Tansey, MG}, title = {Comparative analysis of Parkinson's and inflammatory bowel disease gut microbiomes reveals shared butyrate-producing bacteria depletion.}, journal = {NPJ Parkinson's disease}, volume = {11}, number = {1}, pages = {50}, pmid = {40108151}, issn = {2373-8057}, support = {PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; }, abstract = {Epidemiological studies reveal that inflammatory bowel disease (IBD) is associated with an increased risk of Parkinson's disease (PD). Gut dysbiosis has been documented in both PD and IBD, however it is currently unknown whether gut dysbiosis underlies the epidemiological association between both diseases. To identify shared and distinct features of the PD and IBD microbiome, we recruited 54 PD, 26 IBD, and 16 healthy control individuals and performed the first joint analysis of gut metagenomes. Larger, publicly available PD and IBD metagenomic datasets were also analyzed to validate and extend our findings. Depletions in short-chain fatty acid (SCFA)-producing bacteria, including Roseburia intestinalis, Faecalibacterium prausnitzii, Anaerostipes hadrus, and Eubacterium rectale, as well depletion in SCFA-synthesis pathways were detected across PD and IBD datasets, suggesting that depletion of these microbes in IBD may influence the risk for PD development.}, }
@article {pmid40107220, year = {2025}, author = {Zhang, T and Zhou, S and Cheng, C and Yang, Y and Yang, D and Shi, D and Li, H and Yang, Z and Chen, T and Li, J and Jin, M}, title = {Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban river.}, journal = {Ecotoxicology and environmental safety}, volume = {294}, number = {}, pages = {118063}, doi = {10.1016/j.ecoenv.2025.118063}, pmid = {40107220}, issn = {1090-2414}, abstract = {The microbiological safety of urban rivers that flow through cities is crucial to local public health. However, detailed insights into the key characteristics of pathogens in urban rivers remain limited due to the lack of efficient high-throughput analysis tools. In this study, a comprehensive profiling of potential pathogens, antibiotic-resistant pathogens (ARPs), and multidrug-resistant pathogens (MDRPs) in the Hai River, which runs through the central city of Tianjin, was conducted using metagenomic assembled genome (MAG) analysis. Of the 436 recovered MAGs assigned to 430 species, 110 MAGs were identified as potential pathogens due to the presence of virulence factors (VFs), whereas 19 MAGs containing both antibiotic resistance genes (ARGs) and VFs, were classified as potential ARPs, predominantly belonging to the genera Kluyvera, Enterobacter, and Klebsiella. Notably, nine species of MDRPs, including Enterobacter kobei, Klebsiella pneumoniae, Morganella morganii, Kluyvera intermedia, Aeromonas salmonicida, Rahnella aceris, Hafnia paralvei, the unidentified species Sep. D_bin46, and Vibrio cholerae, exhibited resistance to multidrug, beta-lactam, polymyxin, bacitracin, tetracycline, other peptide antibiotics, macrolide-lincosamide-streptogramin, aminoglycoside, and chloramphenicol. The unknown pathogen Sep. D_bin46, classified under Aeromonas, showed resistance to both carbapenems and polymyxins. The strong co-occurrence of ARGs, VFs, and mobile genetic elements suggests a significant risk of ARGs and VFs transfers among MDRPs with last-resort ARGs (r > 0.8; p < 0.05). Interestingly, the sampling location significantly influenced the presence of pathogens, ARPs, and MDRPs carrying last-resort ARGs in the water. Notably, their abundance was lower downstream of the Hai River compared to upstream. This observation suggests that urban environmental sanitation facilities may be more effective in reducing contaminants as the river flows from upstream to downstream. Nevertheless, the presence of pathogens, ARPs, and MDRPs with last-resort ARGs in the water underscores the ongoing microbiological risks associated with urban surface water.}, }
@article {pmid40107213, year = {2025}, author = {Lu, W and Guo, X and Wu, Y and Sun, S and Wang, Q and Guo, J and Zhao, HP and Lai, CY}, title = {Particulate methane monooxygenase and cytochrome P450-induced reactive oxygen species facilitate 17β-estradiol biodegradation in a methane-fed biofilm.}, journal = {Water research}, volume = {280}, number = {}, pages = {123501}, doi = {10.1016/j.watres.2025.123501}, pmid = {40107213}, issn = {1879-2448}, abstract = {Methane-fed biosystems have shown great potential for degrading various organic micropollutants, yet underlying molecular degradation mechanisms remain largely unexplored. In this study, we uncover the critical role of biogenic reactive oxygen species (ROS) in driving the degradation of 17β-estradiol (E2) within a methane-fed biofilm reactor. Metagenomic analyses confirm that aerobic methanotrophs, specifically Methylococcus and Methylomonas, are responsible for the efficient degradation of E2, achieving a degradation rate of 367.7 ± 8.3 μg/L/d. ROS scavenging in conjunction with enzyme inhibition experiments indicate that particulate methane monooxygenase (pMMO) and cytochrome P450 monooxygenase (CYP450) could generate hydroxyl radicals (•OH), which are the primary ROS involved in E2 degradation. Molecular dynamics simulations suggest that E2 can enter the active catalytic site of pMMO through electrostatic attraction. Four amino acid residues are found to form stable hydrogen bonds with E2, with a high binding free energy, indicating a high affinity for the substrate. Additionally, density functional theory calculations combined with transformation product analysis reveal that •OH targets carbon atoms on the benzene ring and the hydroxyl group attaches to the cyclopentane ring, primarily through hydrogen abstraction and hydroxylation reactions. This work provides critical insights into the mechanisms of E2 biodegradation in methane-fed systems and highlights the potential for optimizing microbial pathways to enhance the degradation of organic micropollutants from contaminated water.}, }
@article {pmid40107211, year = {2025}, author = {Gong, Q and Zeng, W and Hao, X and Wang, Y and Peng, Y}, title = {DNA stable isotope probing and metagenomics reveal temperature responses of sulfur-driven autotrophic partial denitrification coupled with anammox (SPDA) system.}, journal = {Water research}, volume = {280}, number = {}, pages = {123494}, doi = {10.1016/j.watres.2025.123494}, pmid = {40107211}, issn = {1879-2448}, abstract = {The sulfur-driven autotrophic partial denitrification coupled with anammox (SPDA) process showed significant advantages in energy conservation and resource recovery in municipal wastewater treatment. However, its application in regions with seasonal temperature fluctuations and high latitudes is challenged by low temperatures. In this study, the feasibility of the SPDA process for treating low-strength municipal wastewater across a wide temperature range (30-10 °C) was systematically investigated. The results demonstrated that thiosulfate-driven autotrophic partial denitrification maintained an efficient nitrate removal rate of 7.82 mg NO3[-]-N/gVSS/h and a nitrate to nitrite transformation rate of 62.7 % even at temperatures as low as 10 °C. Molecular ecological network and DNA-SIP revealed that dominant sulfur-oxidizing bacteria (SOB) shifted from norank_f_Hydrogenophilaceae and Thiobacillus at higher temperatures (30-20 °C) to Thiobacillus and Sulfurimonas as temperature decreased, thus ensuring the performance of autotrophic partial denitrification and consistent nitrite supply for anammox. Metagenomic analysis showed that the abundance of functional genes related to sulfur conversion increased almost universally, ensuring a stable electron supply for nitrate reduction through sulfur oxidation at low temperatures. The functional genes responsible for nitrate reduction changed from nar genes at higher temperatures to nap genes at lower temperatures, while a decrease in the abundance of hzs and hdh genes corresponding to reduced anammox performance. This study highlights the stable performance of the sulfur-driven autotrophic denitrification at low temperatures and the reliability of coupling with anammox, extending the applicability of SPDA to a broader geographical range.}, }
@article {pmid40107206, year = {2025}, author = {Tang, H and Chen, Y and Tang, X and Wei, M and Hu, J and Zhang, X and Xiang, D and Yang, Q and Han, D}, title = {Corrigendum to "Yield of clinical metagenomics: insights from real-world practice for tissue infections" [eBioMedicine 111(2025), 105536].}, journal = {EBioMedicine}, volume = {114}, number = {}, pages = {105574}, doi = {10.1016/j.ebiom.2025.105574}, pmid = {40107206}, issn = {2352-3964}, }
@article {pmid40107015, year = {2025}, author = {Xia, Z and Luo, G and Gou, LY and Zhang, W and Ji, EG and Li, S and Gao, T and Abi, KM and Yang, F}, title = {Metaviromic and metagenomic study of the pathogens in unexplained pneumonia cases in goats.}, journal = {Veterinary microbiology}, volume = {304}, number = {}, pages = {110469}, doi = {10.1016/j.vetmic.2025.110469}, pmid = {40107015}, issn = {1873-2542}, abstract = {Goats are an economically important livestock species in China. However, the high mortality rate due to pneumonia represents a significant challenge to the development of intensive goat farms. 10 goat lung tissue samples were collected in this study, and all samples exhibited pneumonia of different severity as determined by lung lesion scoring and histopathological examination. Subsequently, this study employed qRT-PCR to measure the relative expression level of pro-inflammatory cytokines in lung tissue, and conducted metaviromic and metagenomic analyses to elucidate the structure and composition of the pulmonary microbiota, the correlation between the abundance of specific microbes and inflammatory factors, and between microbial abundance and the expression of virulence genes. Metaviromic results indicated that Ungulate tetraparvovirus 4 (83.3 %) had the highest relative abundance in the viral composition. Metagenomic data showed that Mycoplasma (28.2 %) and Streptococcus (24.8 %) are the primary dominant genus in goat pneumonia. Notably, a total of 8 pathogens associated with pneumonia in humans or animals were identified across all samples, including Mycoplasma ovipneumoniae, Streptococcus agalactiae, Streptococcus pneumoniae, Escherichia coli, Bordetella hinzii, Bibersteinia trehalosi, Bordetella pertussis, and Pasteurella multocida, with mixed infections with multiple pathogens are very common in this study. Correlation analysis indicates a significant association between the degree of pathogen co-infection and the severity of pulmonary lesions. Furthermore, Pasteurella multocida showed a significant positive correlation with the expression of IL-6 (P< 0.01). The pneumonia samples also revealed a multitude of virulence factors associated with bacterial pathogenicity including those related to biofilm formation, endotoxin production, bacterial invasion and evasion of host immunity. In conclusion, the present study can provide a reference for clinical pathogen diagnosis of unexplained pneumonia in goats.}, }
@article {pmid40105325, year = {2025}, author = {Zhang, H and Lu, T and Guo, S and He, T and Shin, M-K and Luo, C and Tong, J and Zhang, Y}, title = {Rumen microbes affect the somatic cell counts of dairy cows by modulating glutathione metabolism.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0109324}, doi = {10.1128/msystems.01093-24}, pmid = {40105325}, issn = {2379-5077}, abstract = {Healthy mammary glands are essential for high-quality milk production in the dairy industry. The relationship between somatic cell counts (SCCs), rumen fermentation, and microbiota interactions remains unclear. This study integrated physiological indicators, high-throughput 16S rRNA gene sequencing, and metagenomics data analysis to investigate the mechanisms linking rumen microbes and mastitis and to evaluate the changes in milk production and serum cytokine levels in cows with low (L-SCC) and high (H-SCC) somatic cell counts. Compared with the L-SCC group, the H-SCC group exhibited significantly lower lactose and fat contents in milk, reduced rumen fermentation product levels, and increased abundances of Bacteroidetes, Firmicutes, Lachnospiraceae, Prevotella, and Rumiclostridium. Elevated serum levels of IgG2, IgM, IL-1β, IL-6, and TNF-ɑ in the H-SCC group indicated inflammation and rumen microbiota dysbiosis. Functional analysis of microbial communities revealed significant enrichment in pathways related to glutathione metabolism, thyroid hormone synthesis, hypertrophic cardiomyopathy (HCM), the phosphotransferase system (PTS), the P53 signaling pathway, and the Jak-STAT signaling pathway. Correlation network analysis showed that changes in bacterial families, such as Rikenellaceae, Muribaculaceae, and Prevotellaceae, were associated with cytokines, rumen fermentation, and milk quality. The study highlights the interaction between rumen microbiota homeostasis and mammary gland health, indicating that rumen fermentation status influences serum inflammation and milk quality. Modulating rumen fermentation to enhance mammary gland immune function presents a viable strategy for sustainable dairy industry development with long-lived, highly productive cows.IMPORTANCEHigh somatic cell counts (SCCs) are a key biomarker of mastitis and are associated with decreased milk production and significant economic losses in dairy farming. This study systematically examines the relationship between elevated SCCs, rumen microbial dysbiosis, and host inflammatory responses, shedding light on the intricate interplay between microbial ecosystems and host physiology. The findings highlight the potential for microbiota-targeted interventions to reduce inflammation, improve milk composition, and enhance dairy cow productivity. Rather than presuming a direct causative link between SCC-associated dysbiosis and inflammation, this research focuses on their interdependent dynamics, offering a nuanced understanding of the complex biological mechanisms involved. This work advances knowledge of host-microbiota interactions in livestock, providing practical insights for the development of innovative strategies to manage mastitis and improve overall herd health. By adhering to One Health principles, this study underscores the significance of sustainable agricultural practices that prioritize animal welfare, environmental stewardship, and food security. These findings establish a robust foundation for future research into microbiota-driven solutions aimed at enhancing the health and productivity of dairy cattle.}, }
@article {pmid40104686, year = {2025}, author = {Lin, X and Zhang, R and Cui, FQ and Hong, W and Yang, S and Ju, F and Xi, C and Sun, X and Song, L}, title = {Natural-selected plastics biodegradation species and enzymes in landfills.}, journal = {PNAS nexus}, volume = {4}, number = {3}, pages = {pgaf066}, pmid = {40104686}, issn = {2752-6542}, abstract = {Biodegradation is a promising and environmentally friendly strategy for plastic pollution management. Landfills decompose municipal solid waste, including almost 50% of global plastic debris and even some of the oldest synthetic plastics, fostering naturally selected plastic biodegradation. Herein, we present a global collection of plastic biocatalytic enzymes from landfills using metagenomics and machine learning. Metagenomic analysis identified 117 plastic-degrading genes, with 39 incorporated in 22 prokaryotic metagenome-assembled genomes (MAGs). A machine-learning approach predicted 978,107 candidate plastic-degrading genes, 712 of which were encoded respectively by 150 MAGs. Our results highlight landfills as reservoirs of diverse, naturally selected plastic-degrading microbes and enzymes, serving as references and/or models for biocatalysis engineering and in situ bioremediation of plastic pollution.}, }
@article {pmid40104674, year = {2025}, author = {Nawrocki, EP and Petrov, AI and Williams, KP}, title = {Expansion of the tmRNA sequence database and new tools for search and visualization.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {1}, pages = {lqaf019}, pmid = {40104674}, issn = {2631-9268}, mesh = {*RNA, Bacterial/genetics/chemistry ; Databases, Nucleic Acid ; Nucleic Acid Conformation ; Databases, Genetic ; Introns/genetics ; Sequence Analysis, RNA/methods ; }, abstract = {Transfer-messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.}, }
@article {pmid40104595, year = {2025}, author = {Galanis, A and Papadimitriou, K and Moloney, GM}, title = {Editorial: Omics technologies and bioinformatic tools in probiotic research.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1577852}, pmid = {40104595}, issn = {1664-302X}, }
@article {pmid40104149, year = {2025}, author = {Wu, W and Xu, J and Ruan, J and Tian, B and Xuan, N}, title = {Metagenomic next-generation sequencing identifies native valve Aspergillus fumigatus endocarditis with cerebral involvement: a case report.}, journal = {Frontiers in cardiovascular medicine}, volume = {12}, number = {}, pages = {1487543}, pmid = {40104149}, issn = {2297-055X}, abstract = {Aspergillus endocarditis is a rare but highly fatal condition, particularly in immunocompromised patients. This case report describes a 74-year-old male with native valve Aspergillus fumigatus endocarditis and intracranial infection. Diagnosis was complicated by atypical presentation and negative blood cultures, but metagenomic next-generation sequencing (mNGS) enabled rapid identification of the pathogen. This case is notable for being the first to document Aspergillus fumigatus endocarditis with cerebral involvement confirmed by mNGS, highlighting the importance of early diagnosis and advanced diagnostic tools in improving outcomes.}, }
@article {pmid40103993, year = {2025}, author = {Rai, A and Sirotiya, V and Ahirwar, A and Singh, G and Kawatra, R and Sharma, AK and Harish,  and Vinayak, V}, title = {Textile dye removal using diatomite nanocomposites: a metagenomic study in photosynthetic microalgae-assisted microbial fuel cells.}, journal = {RSC advances}, volume = {15}, number = {11}, pages = {8300-8314}, pmid = {40103993}, issn = {2046-2069}, abstract = {In this study, Coomassie brilliant blue (CBB), brilliant green (BG), and rhodamine (Rh) dyes were used to simulate dye-rich wastewater. Adsorption and degradation of these dyes (2 μM, 10 μM, and 30 μM) on diatomite (DE) were evaluated under light (L) and dark (D) conditions. The adsorption of dye-DE composites followed pseudo-second-order kinetics at all concentrations and conditions had R [2] > 0.99, thus showing a good fit. The calculated equilibrium adsorption amount q e,(cal) was coherent with the value of experimental q e,(exp). The poorest adsorption and photocatalysis occurred at 30 μM, prompting the functionalization of dyes with TiO2 and Fe3O4 nanoparticles (NP(s)). The highest dye degradation efficiencies (DGeff) for 30 μM dyes were 86.79% (CBB-DE-Fe3O4, 72 h), 96.10% (BG-DE-TiO2, 52 h), and 81.74% (Rh-DE-TiO2, 48 h), with Rh-DE-TiO2 showing the fastest degradation. Functionalized DE-dye (30 μM) nanocomposites were further tested in a photosynthetic microalgae-assisted microbial fuel cell with dye-simulated wastewater at the anode (PMA-MFC-1 with CBB-DE-Fe3O4, PMA-MFC-2 with BG-DE-TiO2 and PMA-MFC-3 with Rh-DE-TiO2) and Asterarcys sp. GA4 microalgae at the cathode. In dark anode chambers, PMA-MFC-3 achieved the highest DGeff value of Rh dye as 88.23% and a polarization density of 30.06 mW m[-2], outperforming PMA-MFC-2 with BG dye and PMA-MFC-1 with CBB dye. The molecular identifier analysis of microbes in wastewater at the anode showed the dominance of Sphingobacteria and Proteobacteria in PMA-MFC-3 (Rh-DE-TiO2) and COD removal of 61.36%, highlighting its potential for efficient dye degradation and bioelectricity generation. Furthermore, PMA-MFC-3 simultaneously demonstrated a superior microalgal lipid yield of 3.42 μg g[-1] and an algal growth of 8.19 μg g[-1] at the cathode.}, }
@article {pmid40103786, year = {2025}, author = {Wang, KM and Mu, N and Wang, HB}, title = {Intracranial infection in an adult caused by Mycoplasma hominis, diagnosed using mNGS technology: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1560635}, pmid = {40103786}, issn = {2296-858X}, abstract = {Mycoplasma hominis is a rare cause of adult central nervous system infections, posing significant diagnostic challenges due to its fastidious growth requirements and high false-negative rate in conventional cultures. We report a case of Mycoplasma hominis meningoencephalitis in a postpartum female, diagnosed via metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). The patient presented with fever, headache, and progressive neurological deficits following a cesarean section. Neuroimaging revealed a subdural hematoma, and CSF analysis demonstrated an inflammatory response. mNGS identified Mycoplasma hominis, prompting targeted antimicrobial therapy with moxifloxacin and doxycycline, which led to significant clinical improvement. This case underscores the utility of mNGS in detecting rare intracranial infections and highlights the critical role of early pathogen identification in optimizing treatment outcomes.}, }
@article {pmid40103293, year = {2025}, author = {Rasmussen, AN and Tolar, BB and Bargar, JR and Boye, K and Francis, CA}, title = {Metagenome-Assembled Genomes for Oligotrophic Nitrifiers From a Mountainous Gravelbed Floodplain.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70060}, doi = {10.1111/1462-2920.70060}, pmid = {40103293}, issn = {1462-2920}, support = {DE- AC02-76SF00515//SLAC Accelerator Laboratory, U.S. Department of Energy, Biological and Environmental Research/ ; //Watershed Function Science Focus Area/ ; }, mesh = {*Archaea/genetics/classification/metabolism ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Geologic Sediments/microbiology ; *Nitrification ; *Metagenome ; *Ammonia/metabolism ; *Phylogeny ; Rivers/microbiology ; Oxidation-Reduction ; Nitrites/metabolism ; Genome, Bacterial ; }, abstract = {Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidising archaea (AOA) and comammox bacteria from Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, we explore MAGs from potential nitrite-oxidising bacteria (NOB) from the Nitrospirales. AOA diversity in SR is lower than observed in other western US floodplain sediments and Nitrosotalea-like lineages such as the genus TA-20 are the dominant AOA. No ammonia-oxidising bacteria (AOB) MAGs were recovered. Microorganisms from the Palsa-1315 genus (clade B comammox) are the most abundant ammonia-oxidizers in SR floodplain sediments. Established NOB are conspicuously absent; however, we recovered MAGs from uncultured lineages of the NS-4 family (Nitrospirales) and Nitrospiraceae that we propose as putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira NOB lineages based on the genomic content of uncultured Nitrospirales clades. Nitrifier MAGs recovered from SR floodplain sediments harbour genes for using alternative sources of ammonia, such as urea, cyanate, biuret, triuret and nitriles. The SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.}, }
@article {pmid40102971, year = {2025}, author = {Luo, Z and Ou, H and Tan, Z and Jiao, J}, title = {Rumen-protected methionine and lysine supplementation to the low protein diet improves animal growth through modulating colonic microbiome in lambs.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {46}, pmid = {40102971}, issn = {1674-9782}, abstract = {BACKGROUND: Dietary protein level and amino acid (AA) balance are crucial determinants of animal health and productivity. Supplementing rumen-protected AAs in low-protein diets was considered as an efficient strategy to improve the growth performance of ruminants. The colon serves as a crucial conduit for nutrient metabolism during rumen-protected methionine (RPMet) and rumen-protected lysine (RPLys) supplementation, however, it has been challenging to clarify which specific microbiota and their metabolites play a pivotal role in this process. Here, we applied metagenomic and metabolomic approaches to compare the characteristic microbiome and metabolic strategies in the colon of lambs fed a control diet (CON), a low-protein diet (LP) or a LP diet supplemented with RPMet and RPLys (LR).<br><br>RESULTS: The LP treatment decreased the average daily weight gain (ADG) in lambs, while the LR treatment tended to elicit a remission in ADG. The butyrate molar concentration was greater (P&#x2009;<&#x2009;0.05), while acetate molar concentration (P&#x2009;<&#x2009;0.05) was lower for lambs fed the LP and LR diets compared to those fed the CON diet. Moreover, the LP treatment remarkably decreased total AA concentration (P&#x2009;<&#x2009;0.05), while LR treatment showed an improvement in the concentrations of methionine, lysine, leucine, glutamate, and tryptophan. Metagenomic insights proved that the microbial metabolic potentials referring to biosynthesis of volatile fatty acids (VFAs) and AAs in the colon were remarkably altered by three dietary treatments. Metagenomic binning identified distinct microbial markers for the CON group (Alistipes spp., Phocaeicola spp., and Ruminococcus spp.), LP group (Fibrobacter spp., Prevotella spp., Ruminococcus spp., and Escherichia coli), and LR group (Akkermansia muciniphila and RUG099 spp.).<br><br>CONCLUSIONS: Our findings suggest that RPMet and RPLys supplementation to the low-protein diet could enhance the microbial biosynthesis of butyrate and amino acids, enriche the&#xa0;beneficial bacteria in the colon, and&#xa0;thereby improve the growth performance of lambs.}, }
@article {pmid40102641, year = {2025}, author = {Kalvapalle, PB and Staubus, A and Dysart, MJ and Gambill, L and Reyes Gamas, K and Lu, LC and Silberg, JJ and Stadler, LB and Chappell, J}, title = {Information storage across a microbial community using universal RNA barcoding.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40102641}, issn = {1546-1696}, support = {2021-33522-35356//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; 1805901//National Science Foundation (NSF)/ ; 1828869//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2237512//National Science Foundation (NSF)/ ; FWP 78814//U.S. Department of Energy (DOE)/ ; A23-0202-004//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation/ ; }, abstract = {Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.}, }
@article {pmid40102546, year = {2025}, author = {Lechleiter, N and Wedemeyer, J and Schütz, A and Sehl-Ewert, J and Schaufler, K and Homeier-Bachmann, T}, title = {Metagenomic analysis of the faecal microbiota and AMR in roe deer in Western Pomerania.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9288}, pmid = {40102546}, issn = {2045-2322}, mesh = {Animals ; *Deer/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; Escherichia coli/genetics/isolation &amp; purification ; Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; Germany ; Metagenome ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; Anti-Bacterial Agents/pharmacology ; }, abstract = {As an integral part of the global wellbeing, the health of wild animals should be regarded just as important as that of humans and livestock. The investigation of wildlife health, however, is limited by the availability of samples. In an attempt to implement a method with little invasiveness and broad areas of application, shotgun metagenomics were utilised to investigate the faecal microbiome and its antimicrobial resistance genes (AMRG) in roe deer. These genes can facilitate antimicrobial resistances (AMR) in bacteria and are therefore of increasing importance in global health. Accordingly, the abundance in potential vectors like wildlife needs to be assessed. The samples were additionally investigated for ESBL-E. coli, an antibiotic resistant pathogen of global concern, via cultivation. Twenty-seven hunt-harvested animals in Western Pomerania were sampled. This study is the first to our knowledge to describe the faecal microbiome of the European roe deer (Capreolus capreolus), providing insights into the bacterial and archaeal composition. Among the animals, the microbiome was mostly similar and showed a comparable composition to what has been reported in related species, with a ratio of 1.76 between Bacillota and Bacteroidota. The normalised abundance of AMR genes was found to be 0.035 on average, which is similar to other investigations on wild ruminants. Selective cultivation found no ESBL-E. coli in the animals. The prevalence of AMRG in roe deer of Western Pomerania was found to be in line with previous results. The use of shotgun metagenomics allowed for the simultaneous investigation of composition and AMR genes in the faecal microbiome of roe deer, which suggests it as a promising method for the health monitoring of wildlife. This study is the first to describe the prokaryotic assemblage in the faeces of roe deer and its differences to the microbiomes published on other cervids were discussed.}, }
@article {pmid40102379, year = {2025}, author = {Deng, L and Taelman, S and Olm, MR and Toe, LC and Balini, E and Ouédraogo, LO and Bastos-Moreira, Y and Argaw, A and Tesfamariam, K and Sonnenburg, ED and Hanley-Cook, GT and Ouédraogo, M and Ganaba, R and Van Criekinge, W and Huybregts, L and Stock, M and Kolsteren, P and Sonnenburg, JL and Lachat, C and Dailey-Chwalibóg, T}, title = {Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2683}, pmid = {40102379}, issn = {2041-1723}, support = {OPP1175213//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; *Dietary Supplements ; Infant ; Pregnancy ; Adult ; Burkina Faso ; *Carbohydrate Metabolism ; Infant, Newborn ; Feces/microbiology ; Dietary Proteins/metabolism ; Male ; Lactation ; }, abstract = {Balanced energy-protein (BEP) supplementation during pregnancy and lactation can improve birth outcomes and infant growth, with the gut microbiome as a potential mediator. The MISAME-III randomized controlled trial (ClinicalTrial.gov: NCT03533712) assessed the effect of BEP supplementation, provided during pregnancy and the first six months of lactation, on small-for-gestational age prevalence and length-for-age Z-scores at six months in rural Burkina Faso. Nested within MISAME-III, this sub-study examines the impact of BEP supplementation on maternal and infant gut microbiomes and their mediating role in birth outcomes and infant growth. A total of 152 mother-infant dyads (n = 71 intervention, n = 81 control) were included for metagenomic sequencing, with stool samples collected at the second and third trimesters, and at 1-2 and 5-6 months postpartum. BEP supplementation significantly altered maternal gut microbiome diversity, composition, and function, particularly those with immune-modulatory properties. Pathways linked to lipopolysaccharide biosynthesis were depleted and the species Bacteroides fragilis was enriched in BEP-supplemented mothers. Maternal BEP supplementation also accelerated infant microbiome changes and enhanced carbohydrate metabolism. Causal mediation analyses identified specific taxa mediating the effect of BEP on birth outcomes and infant growth. These findings suggest that maternal supplementation modulates gut microbiome composition and influences early-life development in resource-limited settings.}, }
@article {pmid40101714, year = {2025}, author = {Lynn, HM and Gordon, JI}, title = {Sequential co-assembly reduces computational resources and errors in metagenome-assembled genomes.}, journal = {Cell reports methods}, volume = {}, number = {}, pages = {101005}, doi = {10.1016/j.crmeth.2025.101005}, pmid = {40101714}, issn = {2667-2375}, abstract = {Generating metagenome-assembled genomes from DNA shotgun sequencing datasets can demand considerable computational resources. Here, we describe a sequential co-assembly method that reduces the assembly of duplicate reads through successive application of single-node computing tools for read assembly and mapping. Using a simulated mouse microbiome DNA shotgun sequencing dataset, we demonstrated that this approach shortens assembly time, uses less memory than traditional co-assembly, and produces significantly fewer assembly errors. Applying sequential co-assembly to shotgun sequencing reads from (1) a longitudinal study of gut microbiomes from undernourished Bangladeshi children and (2) a 2.3-terabyte dataset generated from gnotobiotic mice colonized with pooled microbiomes from these children that was too large to be handled by a traditional co-assembly approach also demonstrated significant reductions in assembly time and memory requirements. These results suggest that this approach should be useful in resource-constrained settings, including in low- and middle-income countries.}, }
@article {pmid40101514, year = {2025}, author = {Zhang, X and Wu, L and Gu, L and Jiang, Q and He, Z and Qi, Y and Zheng, X and Xu, T}, title = {Dietary areca nut extract supplementation modulates the growth performance and immunity of Jiaji ducks (Cairina moschata).}, journal = {Poultry science}, volume = {104}, number = {5}, pages = {104971}, doi = {10.1016/j.psj.2025.104971}, pmid = {40101514}, issn = {1525-3171}, abstract = {Areca nut extract (ANE) has a variety of pharmacological effects on animals. Here, we investigated the influence of ANE on the slaughter performance and immune function of Jiaji ducks. One hundred and fifty 42-day-old healthy Jiaji ducks were randomly divided into 2 groups (5 replicates of 15 ducks each), named DCK group (control) and DNT group (treatment), respectively. Ducks in the DCK group were fed a basal diet and ducks in the DNT group were fed a basal food supplemented with 0.08 g ANE per kg of basal diet. Additionally, using proteomics, untargeted metabolomics, and metagenomics, we analyzed the impact of ANE on the protein profile of the spleen, the composition of plasma metabolites, and the structure of the cecal microbiota. The results showed that the dietary inclusion of ANE significantly increased the slaughter rate of Jiaji ducks. Proteomic analysis revealed 78 differentially expressed proteins in the spleens of ANE-treated birds, including 54 proteins up-regulated and 24 proteins down-regulated in the DNT group, mainly enriched in cell adhesion molecules and glutathione metabolic pathways. Untargeted metabolomic analysis revealed that 117 serum metabolites were differentially regulated between the ANE and DCK groups; meanwhile, KEGG pathway analysis indicated that these metabolites were mainly involved in arachidonic acid metabolism, phospholipase D signaling pathway and eicosanoids. Furthermore, a metagenomic analysis showed that the genus Methanobrevibacter was significantly downregulated in the ANE supplementation group. Combined, the results of the metagenomic and metabolomic analyses showed that the relative abundance of Prevotella was significantly lower in the ANE group than in the DCK group and that Prevotella was negatively correlated with the levels of the anti-inflammatory compound hydrocinnamic acid and the lipid metabolism regulator ganoderic acid A. This study provides a reference for the application of ANE as a supplement in the diet of Jiaji ducks.}, }
@article {pmid40101486, year = {2025}, author = {Sun, J and Geng, L and Zhou, D and Teng, X and Chen, M}, title = {Gut microbiota participates in polystyrene microplastics-induced defective implantation through impairing uterine receptivity.}, journal = {Journal of environmental management}, volume = {380}, number = {}, pages = {124997}, doi = {10.1016/j.jenvman.2025.124997}, pmid = {40101486}, issn = {1095-8630}, abstract = {Microplastics (MPs) are widespread in global ecosystems and could pose risks to human health. However, crucial information on the impact of MP exposure on female reproductive health remains insufficient. In this study, we constructed an MP-exposure mice model through oral administration of polystyrene microplastics (PS-MPs) and found that it resulted in impaired uterine receptivity and defective implantation. An accumulation of plastic particles was detected in MP mice intestines. Metagenomic sequencing of feces samples indicated a structural and functional alteration of gut microbiota. Alistipes played a prominent role in MP biodegradation, while among the biodegradable functional genes, ACSL made the greatest contribution. Both had a significant increase in MP group, suggesting a potential occurrence of ferroptosis. Ferroptosis, a form of programmed cell death, is closely associated with uterine receptivity impairment and defective implantation. We detected MDA contents and ferroptosis-related proteins, and the results indicated the activation of ferroptosis in the process. Our research is the first to elucidate that exposure to MPs impairs uterine receptivity and results in deficient implantation, while also providing initial evidence that gut microbiota plays a critical role in this process.}, }
@article {pmid40100955, year = {2025}, author = {Davis, BC and Vikesland, PJ and Pruden, A}, title = {Evaluating Quantitative Metagenomics for Environmental Monitoring of Antibiotic Resistance and Establishing Detection Limits.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c08284}, pmid = {40100955}, issn = {1520-5851}, abstract = {Metagenomics holds promise as a comprehensive, nontargeted tool for environmental monitoring. However, one key limitation is that the quantitative capacity of metagenomics is not well-defined. Here, we demonstrated a quantitative metagenomic technique and benchmarked the approach for wastewater-based surveillance of antibiotic resistance genes. To assess the variability of low-abundance oligonucleotide detection across sample matrices, we spiked DNA reference standards (meta sequins) into replicate wastewater DNA extracts at logarithmically decreasing mass-to-mass percentages (m/m%). Meta sequin ladders exhibited strong linearity at input concentrations as low as 2 × 10[-3] m/m% (R[2] > 0.95), with little to no reference length or GC bias. At a mean sequencing depth of 94 Gb, the limits of quantification (LoQ) and detection were calculated to be 1.3 × 10[3] and 1 gene copy per μL DNA extract, respectively. In wastewater influent, activated sludge, and secondary effluent samples, 27.3, 47.7, and 44.3% of detected genes were ≤LoQ, respectively. Volumetric gene concentrations and log removal values were statistically equivalent between quantitative metagenomics and ddPCR for 16S rRNA, intI1, sul1, CTX-M-1, and vanA. The quantitative metagenomics benchmark here is a key step toward establishing metagenomics for high-throughput, nontargeted, and quantitative environmental monitoring.}, }
@article {pmid40100697, year = {2025}, author = {Sun, J and Hirai, M and Takaki, Y and Evans, PN and Nunoura, T and Rinke, C}, title = {Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001351}, pmid = {40100697}, issn = {2057-5858}, mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Metagenome ; Phylogeny ; Pacific Ocean ; Microbiota/genetics ; }, abstract = {Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included Chloroflexota, the most abundant phylum across all samples, whereby the classes Dehalococcoida and Anaerolineae dominated deep-subsurface and most shallow coastal sediments, respectively. Thermoproteota and Asgardarchaeota were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. Tangaroaeota phyl. nov. (former RBG-13-66-14), Ryujiniota phyl. nov. (former UBA6262) and Spongiamicota phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.}, }
@article {pmid40099977, year = {2025}, author = {López-Sánchez, R and Aguilar-Vera, A and Castillo-Ramírez, S}, title = {Metagenome-assembled genomes reveal novel diversity and atypical sources of a superbug.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0010625}, doi = {10.1128/spectrum.00106-25}, pmid = {40099977}, issn = {2165-0497}, abstract = {The genomic epidemiology of Acinetobacter baumannii has been based on culture-dependent whole-genome sequencing. However, this approach neglects sources that are not amenable to microbial culture. Here, we show that metagenome-assembled genomes (MAGs) are useful in appraising the neglected diversity of A. baumannii from unconventional sources. We analyzed 22 MAGs in the context of genomes from the main human international clones and some animal and plant isolates. Given the known ecology of the species, some of these MAGs came from unexpected sources, such as the New York City subway or a kitchen counter. Our global phylogeny, with 240 genomes, demonstrated that although some MAGs were associated with some human international clones, most of them were not and were distantly related to the human clones. Furthermore, we found that these MAGs have antibiotic-resistance genes. Our results show that many MAGs represent novel lineages with some important resistance genes coming from unexpected sources. Our work illustrates a powerful approach to studying the neglected diversity of this superbug from uncommon sources. We anticipate that in the coming years, MAGs will be employed to analyze unconventional sources for other important superbugs.IMPORTANCEThe genomic epidemiology of Acinetobacter baumannii has been based on cultivated bacterial isolates. This disregards A. baumannii diversity from sources not amenable to microbial culture. In this study, we demonstrate that metagenome-assembled genomes (MAGs) are very helpful in assessing the understudied diversity of A. baumannii from atypical sources. Our results show that many MAGs represent novel lineages with important resistance genes coming from unexpected sources. We anticipate that in the coming years, approaches similar to ours will be employed to delve into different sources for other important superbugs.}, }
@article {pmid40099899, year = {2025}, author = {Nakao, R and Yamaguchi, T and Shibasaki, H and Saeki, J and Takahashi, A and Tominaga, R and Abe, K and Akeda, Y and Nakagawa-Nakamura, T and Nishino, T and Ishihara, K and Jinno-Oue, A and Inoue, S}, title = {Assessment of periodontitis vaccine using three different bacterial outer membrane vesicles in canine model.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0103324}, doi = {10.1128/msphere.01033-24}, pmid = {40099899}, issn = {2379-5042}, abstract = {UNLABELLED: Canines frequently develop periodontitis, which is similar and relevant to immunopathology and microbiology of human periodontitis. The aim of this study was to investigate whether bacterial outer membrane vesicle (OMV)-based periodontal vaccines induced humoral immune response in canines from a human vaccine development perspective. Porphyromonas gingivalis (Pg) and Treponema denticola (Td), two major periodontal pathobionts, were chosen as vaccine targets. Intranasal (IN) immunization with Pg OMVs and Td OMVs strongly elicited humoral immune responses against the two respective species in preparative mouse experiments, particularly when adjuvanted with a probiotic Escherichia coli derivative (EcNΔflhD)-derived OMVs. However, in beagles, intranasal immunization with the same Pg/Td/EcNΔflhD OMV vaccine insufficiently elicits humoral immune responses. Nevertheless, the subcutaneous booster with the same OMVs dramatically improved antibody responses in both systemic blood circulation and mucosal sites such as eyes, oral cavity, and upper and lower respiratory tracts. Metagenomic analysis of salivary microbiota revealed that the OMV vaccine might change the microbial composition, while not reducing the number of any periodontal pathobionts at least during the timeframe of the present beagle study. In in vitro Pg growth inhibition assay, serum samples from OMV-immunized beagles significantly inhibited growth of the gingipain-deficient strain but not the gingipain-expressing wild-type strain. Taken together, our data offer the trivalent OMV vaccine strategy by IN-prime/SC-boost regimen, which could elicit robust mucosal immune responses, while suggesting the requirement of revised periodontal vaccine regimen toward achievement of sterilizing immunity in the oral cavity.<br><br>IMPORTANCE: Bacterial outer-membrane vesicles (OMVs) are attractive for use as novel nanoparticle adjuvants, as well as delivery platforms. Periodontal diseases are the most prevalent oral diseases in humans and have serious health and economic burdens, greatly reducing quality of life. The aim of this study is to investigate the humoral immune responses to an OMV-based periodontal disease vaccine in beagles. The vaccine elicited strong mucosal immune responses when administered to beagles by a four-dose heterologous immunization (IN-IN-IN prime and subcutaneous [SC] boost). The OMV vaccine significantly altered the composition of the microbial community in the oral cavity. These findings suggest the utility of the intranasal (IN) prime followed by the SC boost regimen as a rational option to elicit robust humoral immune responses in canines, and most probably in humans as well. We here discuss the outcomes of beagle experiments, the mechanism behind immunological escape of Pg from host immunity, and a rational perspective toward sterilizing immunity in the oral cavity.}, }
@article {pmid40099881, year = {2025}, author = {de Kleine, RH and Carbo, EC and Lexmond, WS and Zhou, XW and de Kroon, A and Mei, H and Bontemps, STH and Hennevelt, R and Gard, L and Sidorov, IA and Boers, SA and van den Heuvel, MC and Buddingh, EP and Kroes, ACM and de Meijer, VE and Schölvinck, EH and von Eije, KJ and Jochems, SP and de Vries, JJC}, title = {Metagenomic and transcriptomic investigation of pediatric acute liver failure cases reveals a common pathway predominated by monocytes.}, journal = {mBio}, volume = {}, number = {}, pages = {e0391324}, doi = {10.1128/mbio.03913-24}, pmid = {40099881}, issn = {2150-7511}, abstract = {UNLABELLED: In 2022, a cluster of severe childhood hepatitis was detected primarily in Europe and North America, leading to a global alert by the World Health Organization. An association with adeno-associated virus 2 (AAV2) in conjunction with human adenoviruses was found. Five percent of the cases progressed to acute liver failure, necessitating transplantation. The mechanism of disease that accounts for fulminant liver failure in these patients remains incompletely described. An upsurge was observed of in the five total cases of acute liver failure that presented to the Dutch national referral center for pediatric liver transplantation in the spring of 2022. An in-depth molecular analysis of the mechanism of pediatric acute liver failure was performed using targeted transcriptomics and metagenomics to identify any virus present in the cases, immune profile haplotypes, and differentially expressed gene groups. Explanted liver tissue and plasma samples (n = 15) were subjected to viral metagenomic and human transcriptomic profiling, targeting >600 inflammatory genes. Liver transcriptomic signatures of transplanted cases were compared with those of pediatric controls from a liver biobank (n = 6). AAV2, adenoviruses, and herpesviruses were detected in liver explant tissue and plasma samples of the cases. Epstein-Barr virus and varicella zoster virus infection with pathognomonic clinical symptomatology preceded liver failure in two respective cases. AAV2 was detected in one-third of control livers. Excessive activation of monocyte pathways was detected in liver explants from cases compared with controls. Remarkably, this signature was comparable for AAV2, adenoviruses, and/or herpesviruses-positive transplant cases. Our multi-omic findings suggest a common transcriptomic profile, with an upregulation of monocyte pathways in the presented transplanted cases, which had similar severe clinical outcomes. In the cohort presented, AAV2 was not exclusively associated with acute liver failure, suggesting that other processes may have contributed to a uniform cascade of irreversible pathology.<br><br>IMPORTANCE: Since the appearance of the cluster of pediatric hepatitis of unknown origin in 2022, several groups have reported an association of adenoviruses and AAV2 in a high number of cases in contrast to controls. The adenoviruses detected were heterogeneous in both species-adenovirus C and F-and sequences. The mechanisms of disease that accounts for fulminant liver failure, occurring in 5% of pediatric hepatitis cases, remain incompletely described. The current study adds to previous data by including pediatric acute liver failure cases during the upsurge, enabling the analyses of inflammation expression profiles in cases with different viruses in relation to pediatric controls. This led to the discovery of transcriptome upregulation of monocyte pathways in liver explants from the cases. This inflammatory transcriptomic signature was comparable for AAV2, adenoviruses, and/or herpesviruses-positive transplant cases.}, }
@article {pmid40099113, year = {2025}, author = {Tomasella, F and Pizzi, C}, title = {MetaComBin: combining abundances and overlaps for binning metagenomics reads.}, journal = {Frontiers in bioinformatics}, volume = {5}, number = {}, pages = {1504728}, pmid = {40099113}, issn = {2673-7647}, abstract = {INTRODUCTION: Metagenomics is the discipline that studies heterogeneous microbial samples extracted directly from their natural environment, for example, from soil, water, or the human body. The detection and quantification of species that populate microbial communities have been the subject of many recent studies based on classification and clustering, motivated by being the first step in more complex pipelines (e.g., for functional analysis, de novo assembly, or comparison of metagenomes). Metagenomics has an impact on both environmental studies and precision medicine; thus, it is crucial to improve the quality of species identification through computational tools.<br><br>METHODS: In this paper, we explore the idea of improving the overall quality of metagenomics binning at the read level by proposing a computational framework that sequentially combines two complementary read-binning approaches: one based on species abundance determination and another one relying on read overlap in order to cluster reads together. We called this approach MetaComBin (metagenomics combined binning).<br><br>RESULTS AND DISCUSSION: The results of our experiments with the MetaComBin approach showed that the combination of two tools, based on different approaches, can improve the clustering quality in realistic conditions where the number of species is not known beforehand.}, }
@article {pmid40098591, year = {2025}, author = {Hernández-Trujillo, PN and Lopez-Barón, CA and Arévalo-Pinzón, G and Trujillo-Güiza, ML and González-Duque, MI and Flórez, AM and Franco, DC and Vanegas, J}, title = {Taxonomic and functional profile of the anorectal microbiota in HIV-positive and HIV-negative men who have sex with men, using a metagenomic approach.}, journal = {HIV medicine}, volume = {}, number = {}, pages = {}, doi = {10.1111/hiv.70014}, pmid = {40098591}, issn = {1468-1293}, support = {2022218//Universidad Antonio Nari&#xf1;o/ ; }, abstract = {INTRODUCTION: The study of bacterial diversity in human samples is crucial for developing biomarkers of health and disease. This research characterized the taxonomic and functional diversity of the anorectal bacterial microbiota in men who hae sex with men (MSM) with HIV compared to men from this group without HIV.<br><br>MATERIALS AND METHODS: In July and August 2023, self-collected anorectal swabs were obtained. DNA was extracted from each sample, and metagenomic sequencing was performed. With the obtained data, alpha and beta diversity, bacterial abundance, differential operational taxonomic units, and functional diversity were determined.<br><br>RESULTS: Initially, 90 samples were collected, with 20 discarded due to having less than 200&#x2009;ng of DNA and 15 due to incomplete sequencing, leaving 55 samples analysed (15 HIV-positive and 40 HIV-negative). No significant differences were found between groups in terms of alpha diversity (Shannon index p&#x2009;=&#x2009;0.45) and beta diversity (PERMANOVA R&#x2009;=&#x2009;-0.03). Prevotella was identified as the most abundant genus in both groups. Twelve genes were found to be more abundant in the anorectal microbiota of the HIV group, which promote bacterial growth, colonization and survival.<br><br>CONCLUSION: Alterations in the anorectal microbiota could influence the pathogenesis of HIV and its complications in this population, underscoring the need to investigate these mechanisms and explore interventions to improve health. Longitudinal studies are needed to analyse changes in the anorectal microbiota during HIV infection and its response to treatment, integrating metagenomic, clinical, and immunological data to better understand the interactions between HIV, the microbiota and host health.}, }
@article {pmid40098558, year = {2025}, author = {Di Rienzi, SC and Danhof, HA and Forshee, MD and Roberts, A and Britton, RA}, title = {Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {6}, pages = {e70408}, doi = {10.1096/fj.202401669R}, pmid = {40098558}, issn = {1530-6860}, support = {T15 LM007093/LM/NLM NIH HHS/United States ; F32 AI136404/AI/NIAID NIH HHS/United States ; //Weston Family Foundation (WFF)/ ; //BioGaia/ ; }, mesh = {*Limosilactobacillus reuteri/metabolism ; *Enteroendocrine Cells/metabolism ; *Enterocytes/metabolism/microbiology ; Humans ; Organoids/metabolism ; Gastrointestinal Hormones/metabolism/genetics ; Gastrointestinal Microbiome ; Animals ; }, abstract = {Intestinal microbes can beneficially impact host physiology, prompting investigations into the therapeutic usage of such microbes in a range of diseases. For example, human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments, including colic, infection, and inflammation, as well as for non-intestinal ailments, including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses, we postulated that L. reuteri may also regulate intestinal hormones to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promote the secretion of enteric hormones, including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta, and identify by metabolomics metabolites potentially mediating these effects on hormones. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.}, }
@article {pmid40098182, year = {2025}, author = {Rodríguez, V and Bartholomäus, A and Liebner, S and Oses, R and Scholten, T and Wagner, D}, title = {Microbial transcriptome patterns highlight increased pedogenesis-related activity in arid soils under simulated humid conditions.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {31}, pmid = {40098182}, issn = {2524-6372}, support = {72200201//BECAS Chile (ANID)/ ; SCHO 739/17//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: In arid and semiarid environments, microbial activity is restricted by low water availability and high evapotranspiration rates, and soil development is limited. Under humid conditions, such limitations can be overcome, accelerating pedogenesis by microbial processes. Our study aims to broaden our understanding of soil development under a climate change scenario toward humid conditions and to identify the microorganisms that help transform initial soils from arid and semiarid sites. We characterized pedogenetic microbial processes and how their gene expression differs between soils from arid and semiarid sites under a sixteen-week climate simulation experiment using metagenomic and metatranscriptomic approaches.<br><br>RESULTS: We found that an intense functional response is triggered under humid climate conditions in the arid site compared to the semiarid site, which showed greater resilience. The arid site undergoes higher transcription of genes involved in soil aggregate formation, phosphorus metabolism, and weathering, potentially adapting the development of arid sites to climate change. Additionally, a transcriptional reconfiguration linked to soil carbon and nitrogen dynamics suggests that soil microorganisms use available organic resources alongside autotrophy in response to increased moisture. Pseudomonadota and Actinomycetota dominated the overall transcriptional profile and specific functions associated with the early stages of soil development in both sites.<br><br>CONCLUSIONS: Our findings highlight the rapid activation of pathways related to pedogenesis under humid conditions in arid sites, potentially driven by their metabolic requirements and environmental stressors, influencing soil development dynamics under global climate change.}, }
@article {pmid40098172, year = {2025}, author = {Raziq, MF and Khan, N and Manzoor, H and Tariq, HMA and Rafiq, M and Rasool, S and Kayani, MUR and Huang, L}, title = {Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {343}, pmid = {40098172}, issn = {1479-5876}, mesh = {Humans ; *Polymorphism, Single Nucleotide/genetics ; *Carcinoma, Non-Small-Cell Lung/genetics/microbiology/drug therapy ; *Computational Biology/methods ; *Gastrointestinal Microbiome/genetics ; *Lung Neoplasms/genetics/drug therapy/microbiology ; *Immunotherapy ; Treatment Outcome ; Male ; Female ; Metagenome/genetics ; }, abstract = {BACKGROUND: The human gut microbiome has emerged as a potential modulator of treatment efficacy for different cancers, including non-small cell lung cancer (NSCLC) patients undergoing immune checkpoint inhibitor (ICI) therapy. In this study, we investigated the association of gut microbial variations with response against ICIs by analyzing the gut metagenomes of NSCLC patients.<br><br>METHODS: Strain identification from the publicly available metagenomes of 87 NSCLC patients, treated with nivolumab and collected at three different timepoints (T0, T1, and T2), was performed using StrainPhlAn3. Variant calling and annotations were performed using Snippy and associations between microbial genes and genomic variations with treatment responses were evaluated using MaAsLin2. Supervised machine learning models were developed to prioritize single nucleotide polymorphisms (SNPs) predictive of treatment response. Structural bioinformatics approaches were employed using MUpro, I-Mutant 2.0, CASTp and PyMOL to access the functional impact of prioritized SNPs on protein stability and active site interactions.<br><br>RESULTS: Our findings revealed the presence of strains for several microbial species (e.g., Lachnospira eligens) exclusively in Responders (R) or Non-responders (NR) (e.g., Parabacteroides distasonis). Variant calling and annotations for the identified strains from R and NR patients highlighted variations in genes (e.g., ftsA, lpdA, and nadB) that were significantly associated with the NR status of patients. Among the developed models, Logistic Regression performed best (accuracy&#x2009;>&#x2009;90% and AUC ROC&#x2009;>&#x2009;95%) in prioritizing SNPs in genes that could distinguish R and NR at T0. These SNPs included Ala168Val (lpdA) in Phocaeicola dorei and Tyr233His (lpdA), Leu330Ser (lpdA), and His233Arg (obgE) in Parabacteroides distasonis. Lastly, structural analyses of these prioritized variants in objE and lpdA revealed their involvement in the substrate binding site and an overall reduction in protein stability. This suggests that these variations might likely disrupt substrate interactions and compromise protein stability, thereby impairing normal protein functionality.<br><br>CONCLUSION: The integration of metagenomics, machine learning, and structural bioinformatics provides a robust framework for understanding the association between gut microbial variations and treatment response, paving the way for personalized therapies for NSCLC in the future. These findings emphasize the potential clinical implications of microbiome-based biomarkers in guiding patient-specific treatment strategies and improving immunotherapy outcomes.}, }
@article {pmid40097931, year = {2025}, author = {Boutin, S and Käding, N and Belheouane, M and Merker, M and Rupp, J and Nurjadi, D}, title = {Towards unraveling antimicrobial resistance dynamics: a longitudinal exploration of rectal swab metagenomes.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {150}, pmid = {40097931}, issn = {1471-2180}, mesh = {Humans ; *Rectum/microbiology ; *Metagenome ; *Metagenomics/methods ; Bacteria/genetics/drug effects/isolation &amp; purification/classification ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Longitudinal Studies ; Male ; Microbial Sensitivity Tests ; Female ; Middle Aged ; Microbiota/genetics/drug effects ; Aged ; Genome, Bacterial/genetics ; Adult ; }, abstract = {The increasing prevalence of antimicrobial resistance (AMR) poses significant challenges in clinical settings. In particular, early screening and detection of colonization by multidrug-resistant organisms (MDROs) in patients at admission is crucial. In this context, the clinical use of metagenomics (mNGS) holds promise for fast and untargeted diagnostic methods. Here, we aimed to evaluate the long-term stability of the rectal microbiome and the diagnostic accuracy of mNGS in comparison to culture and whole-genome sequencing (WGS) of MDROs. We analyzed rectal swabs from 26 patients with two consecutive admissions over a four-year period. The detected antimicrobial resistance genes and assembled metagenomes were compared to those obtained via classical culture-based antimicrobial susceptibility testing and WGS of isolated MDROs. Our results showed that the rectal microbiome is variable during the two timepoints, highlighting the variability in the niche. Nevertheless, we also observed strong co-occurrence of taxa, suggesting that the rectal swab microbiome is also a regulated environment with cooperative biotic interactions. In total, we isolated and sequenced 6 MDROs from 6 patients at individual timepoints. Almost all AMR genes from the genomes of the isolates (median: 100%, range: 84.6-100%) could be detected by mNGS of the rectal swabs at the time of isolation of the MDRO but not at the time of culture negativity. In addition, we detected AMR genes and potentially pathogenic species in patients with negative cultures. In conclusion, our study showed that, in principle, mNGS of rectal swabs can detect clinically relevant AMR profiles. However, the cooccurrence of AMR genes and potentially-pathogenic species does not always correlate with culture-based diagnostic results but rather indicates a potential risk of horizontal AMR gene transfer. However, it is unclear whether the observed discrepancies are due to transient or locally confined colonization of MDROs, limits of detection, or variability of the sampling method and specimens.}, }
@article {pmid40097230, year = {2025}, author = {Nair, SS and Kutty Narayanan, A and Nair, K and Mallick, S and Zackariah, NM and Biswas, L and Praseedom, R and G Nair, BK and Surendran, S}, title = {Microbiota-directed intervention in living donor liver transplant recipients: protocol for a randomised double-blind placebo-controlled trial.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e092984}, doi = {10.1136/bmjopen-2024-092984}, pmid = {40097230}, issn = {2044-6055}, mesh = {Humans ; *Liver Transplantation ; *Living Donors ; Double-Blind Method ; *Synbiotics/administration &amp; dosage ; *Gastrointestinal Microbiome ; Randomized Controlled Trials as Topic ; Acute-On-Chronic Liver Failure/therapy ; Probiotics/therapeutic use ; Adult ; Postoperative Complications/microbiology ; Male ; Female ; }, abstract = {INTRODUCTION: Acute-on-chronic liver failure (ACLF) patients have the highest propensity for post-liver transplantation (LT) infections and mortality. Liver-associated diseases have been one of the primary targets for synbiotic therapy to augment immunity and mitigate infections. However, despite multiple studies showing benefits of synbiotics in liver diseases, data on their use following LT are sparse.<br><br>METHODS AND ANALYSIS: This randomised placebo-controlled study aims to assess the impact of synbiotics in ACLF patients undergoing living donor liver transplantation (LDLT). Following randomisation by computer-generated block number sequence, 3&#x2009;days prior to LDLT, the intervention arm will receive standard medical treatment and synbiotics (VSL#3 a probiotic, and Yogut, prebiotic and probiotic combination) for 6&#x2009;weeks, while the control arm will receive standard medical treatment with a placebo. The patients will be followed up for 6&#x2009;months to study the clinical and biochemical outcomes. The primary objective is to compare the difference in the occurrence of infectious complications between the patients who receive synbiotics versus placebo during the 6-month period following LDLT. The secondary objectives include assessing the qualitative and quantitative change in microbiota with synbiotics and LDLT, adverse reactions due to synbiotics, and post-LT morbidity and mortality. The minimum sample size comes to 71 in each group. The first 50 patients in the study protocol will undergo gut microbiome analysis using 16s metagenomic and nanopore sequencing to analyse the microbial composition before starting synbiotics/placebo and at 6 weeks after LDLT.<br><br>ETHICS AND DISSEMINATION: The study is approved by the Research Ethics Committee of Amrita Institute of Medical Sciences, Kochi, India (IEC-AIMS-2022-GISUR-203) and registered in the Clinical Trial Registry of India (CTRI) CTRI/2022/10/046327. The results of the trial will be disseminated by presentation at national/international conferences and publication in peer-reviewed journals.<br><br>TRIAL REGISTRATION NUMBER: CTRI/2022/10/046327 - Clinical Trial Registry of India.}, }
@article {pmid40096869, year = {2025}, author = {Xing, X and Zhu, J and Li, Z and Zhang, G and Li, W and Tan, H and Xie, B and Yang, Y and Zhao, S and Ding, Y and You, H}, title = {Increasing the light-dark ratio enhances nitrogen removal performance by altering the mechanism in photogranules.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132400}, doi = {10.1016/j.biortech.2025.132400}, pmid = {40096869}, issn = {1873-2976}, abstract = {Photogranules provide a cost-effective solution for treating mariculture wastewater. The impact of light: dark ratios on nitrogen removal needs further study. We tested four photogranular reactors with different light: dark ratios and found that higher ratios increased total inorganic nitrogen (TIN) removal rate, achieved 99 ± 0 % every 48 h at a 5.5 h:0.5 h ratio. Kinetic and metagenomic analyses showed that increased TIN removal was mainly due to a significant transformation in the nitrogen removal mechanism of photogranules. At 5.5 h:0.5 h, diatoms replaced the outer cyanobacteria, causing nitrifying bacteria to disappear via direct and indirect inhibition. In addition, the mechanisms by which photogranules remove nitrate nitrogen are diverse. Adjusting the light: dark ratio could change the nitrogen removal mechanism of photogranules in mariculture wastewater treatment and enhance their nitrogen removal performance. This offered insights into controlling light - related parameters of photogranules for practical engineering applications.}, }
@article {pmid40096540, year = {2025}, author = {Zhang, Q and Li, J and Tuo, J and Liu, S and Liu, Y and Liu, P and Ye, L and Zhang, XX}, title = {Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf051}, pmid = {40096540}, issn = {1751-7370}, abstract = {Bacteria have evolved various antiviral defense systems to protect themselves, but how defense systems respond to the variation of bacteriophages in complex bacterial communities and whether defense systems function effectively in maintaining the stability of bacterial community structure and function remain unknown. Here, we conducted a long-term metagenomic investigation on the composition of bacterial and phage communities of monthly collected activated sludge samples from two full-scale wastewater treatment plants over six years and found that defense systems were widespread in activated sludge, with 91.1% of metagenome-assembled genomes having more than one complete defense system. The stability of the bacterial community was maintained under the fluctuations of the phage community, and defense system abundance and phage abundance were strongly positively correlated; there was a 0-3-month time lag in the responses of defense systems to phage fluctuations. The rapid turnover of CRISPR spacer repertoires further highlighted the dynamic nature of bacterial defense mechanisms. A pan-immunity phenomenon was also observed, with nearly identical metagenome-assembled genomes showing significant differences in defense system composition, which contributed to community stability at the species level. This study provides novel insights into the complexity of phage-bacteria interactions in complex bacterial communities, and reveals the key roles of defense systems in stabilizing bacterial community structure and function.}, }
@article {pmid40095061, year = {2025}, author = {Laiho, JE and Oikarinen, S and Morfopoulou, S and Oikarinen, M and Renner, A and Depledge, D and Ross, MC and Gerling, IC and Breuer, J and Petrosino, JF and Plagnol, V and Pugliese, A and Toniolo, A and Lloyd, RE and Hyöty, H and , }, title = {Detection of enterovirus RNA in pancreas and lymphoid tissues of organ donors with type 1 diabetes.}, journal = {Diabetologia}, volume = {}, number = {}, pages = {}, pmid = {40095061}, issn = {1432-0428}, support = {R01-AI50237//National Institutes of Health, USA/ ; personal grant for JEL//Diabetestutkimuss&#xe4;&#xe4;ti&#xf6;/ ; personal grants for JEL//Yrj&#xf6; Jahnssonin S&#xe4;&#xe4;ti&#xf6;/ ; MO//Yrj&#xf6; Jahnssonin S&#xe4;&#xe4;ti&#xf6;/ ; Grant#2018PG-T1D053//Leona M. and Harry B. Helmsley Charitable Trust/ ; G-2108-04793//Leona M. and Harry B. Helmsley Charitable Trust/ ; 97013//European Foundation for the Study of Diabetes/ ; 25-2012-770//JDRF/United States ; JDRF 25-2012-516//JDRF/United States ; nPOD: 5-SRA-2018-557-Q-R//JDRF/United States ; RRID:SCR_014641//network for Pancreatic Organ donors with Diabetes, nPOD/ ; personal grant for JEL//Pirkanmaan Rahasto/ ; Persistent Virus Infection in Diabetes Network [PE//Seventh Framework Programme/ ; for HH//Sigrid Jus&#xe9;liuksen S&#xe4;&#xe4;ti&#xf6;/ ; 288671//Research Council of Finland/ ; personal grants for JEL//P&#xe4;ivikki ja Sakari Sohlbergin S&#xe4;&#xe4;ti&#xf6;/ ; MO//P&#xe4;ivikki ja Sakari Sohlbergin S&#xe4;&#xe4;ti&#xf6;/ ; }, abstract = {AIMS/HYPOTHESIS: The nPOD-Virus group collaboratively applied innovative technologies to detect and sequence viral RNA in pancreas and other tissues from organ donors with type 1 diabetes. These analyses involved the largest number of pancreas samples collected to date. The aim of the current work was to examine the presence of enterovirus RNA in pancreas and lymphoid tissues of organ donors with and without type 1 diabetes.<br><br>METHODS: We analysed pancreas, spleen, pancreatic lymph nodes and duodenum samples from the following groups: (1) donors with type 1 diabetes (n=71) with (n=35) or without (n=36) insulin-containing islets; (2) donors with single or double islet autoantibody positivity without diabetes (n=22); and (3) autoantibody-negative donors without diabetes (control donors) (n=74). Five research laboratories participated in this collaborative effort using approaches for unbiased discovery of RNA viruses (two RNA-Seq platforms), targeted detection of Enterovirus A-D species using RT-PCR, and tests for virus growth in cell culture.<br><br>RESULTS: Direct RNA-Seq did not detect virus signal in pancreas samples, whereas RT-PCR detected enterovirus RNA confirmed by sequencing in low amounts in pancreas samples in three of the five donor groups: donors with type 1 diabetes with insulin-containing islets, 16% (5/32) being positive; donors with single islet autoantibody positivity, 53% (8/15) being positive; and non-diabetic donors, 8% (4/49) being positive. Detection of enterovirus RNA was significantly more frequent in single islet autoantibody-positive donors compared with donors with type 1 diabetes with insulin-deficient islets (p<0.001) and control (non-diabetic) donors (p=0.004). In some donors, pancreatic lymph nodes were also positive. RT-PCR detected enterovirus RNA also in the spleen of a small number of donors and virus enrichment in susceptible cell lines before RT-PCR resulted in much higher rate in spleen positivity, particularly in donors with type 1 diabetes. Interestingly, the enterovirus strains detected did not cause a typical lytic infection, possibly reflecting their persistence-prone nature.<br><br>CONCLUSIONS/INTERPRETATION: This was the largest coordinated effort to examine the presence of enterovirus RNA in the pancreas of organ donors with type 1 diabetes, using a multitude of assays. These findings are consistent with the notion that donors with type 1 diabetes and donors with islet autoantibodies may carry a low-grade enterovirus infection in the pancreas and lymphoid tissues.}, }
@article {pmid40094563, year = {2025}, author = {Cheng, W and Yi, L and Xu, T and Xie, Y and Zhu, J and Guan, X and Li, Q and Huang, Y and Zhao, Y and Zhao, S}, title = {The stems and leaves of Panax notoginseng reduce the abundance of antibiotic resistance genes by regulating intestinal microbiota in Duzang pigs.}, journal = {Animal biotechnology}, volume = {36}, number = {1}, pages = {2471785}, doi = {10.1080/10495398.2025.2471785}, pmid = {40094563}, issn = {1532-2378}, mesh = {Animals ; *Panax notoginseng/microbiology ; Swine ; *Gastrointestinal Microbiome/drug effects ; *Plant Leaves ; *Plant Stems ; Drug Resistance, Microbial/genetics ; Animal Feed/analysis ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/classification ; Genes, Bacterial/genetics ; Cecum/microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {In order to study the distribution characteristics of intestinal microbiota and antibiotic resistance genes (ARGs) in Duzang pigs after adding stems and leaves of Panax notoginseng to the feed, the characteristics of intestinal microbiota were explored by metagenomic sequencing, and 14 ARGs and 2 integrase genes were detected by qPCR. The results showed that the addition of stems and leaves of P. notoginseng increased the relative abundance of Firmicutes, Lactobacillus and Pediococcus in the cecum of Duzang pigs. A total of 10 ARGs and 2 integrase genes were detected in the cecal contents of pigs. The addition of stems and leaves of P. notoginseng reduced the relative abundance of total ARGs, ermB, tetO and tetW in the cecum of Duzang pigs. The results of network analysis showed that multiple genera were potential hosts of ARGs. The addition of stems and leaves of P. notoginseng may reduce the relative abundance of ARGs by reducing the relative abundance of genera such as Corynebacterium and Flavonifractor, thereby reducing the risk of ARGs spread. This study provides a theoretical basis for the rational use of stems and leaves of P. notoginseng to control ARGs.}, }
@article {pmid40094561, year = {2025}, author = {Gai, Y and Liu, S and Zhang, Z and Wei, J and Wang, H and Liu, L and Bai, Q and Qin, Q and Zhao, C and Zhang, S and Xiang, N and Zhang, X}, title = {Integrative Approaches to Soybean Resilience, Productivity, and Utility: A Review of Genomics, Computational Modeling, and Economic Viability.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/plants14050671}, pmid = {40094561}, issn = {2223-7747}, abstract = {Soybean is a vital crop globally and a key source of food, feed, and biofuel. With advancements in high-throughput technologies, soybeans have become a key target for genetic improvement. This comprehensive review explores advances in multi-omics, artificial intelligence, and economic sustainability to enhance soybean resilience and productivity. Genomics revolution, including marker-assisted selection (MAS), genomic selection (GS), genome-wide association studies (GWAS), QTL mapping, GBS, and CRISPR-Cas9, metagenomics, and metabolomics have boosted the growth and development by creating stress-resilient soybean varieties. The artificial intelligence (AI) and machine learning approaches are improving genetic trait discovery associated with nutritional quality, stresses, and adaptation of soybeans. Additionally, AI-driven technologies like IoT-based disease detection and deep learning are revolutionizing soybean monitoring, early disease identification, yield prediction, disease prevention, and precision farming. Additionally, the economic viability and environmental sustainability of soybean-derived biofuels are critically evaluated, focusing on trade-offs and policy implications. Finally, the potential impact of climate change on soybean growth and productivity is explored through predictive modeling and adaptive strategies. Thus, this study highlights the transformative potential of multidisciplinary approaches in advancing soybean resilience and global utility.}, }
@article {pmid40094559, year = {2025}, author = {Gao, S and Wei, G and Chang, Y and Yin, Y and Wei, Q and Shi, Y}, title = {Multiomic Analysis of Environmental Effects and Nitrogen Use Efficiency of Two Potato Varieties Under High Nitrogen Conditions.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/plants14050633}, pmid = {40094559}, issn = {2223-7747}, support = {CARS-09&#xff1b;2022ZXJ06B01&#xff1b;JD2023GJ01-09&#xff1b;LH2021C027//China Agriculture Research Systems&#xff1b;Heilongjiang Province Scientific and Technological Project&#xff1b;Key R&amp;D projects of Heilongjiang Province in 2023&#xff1b;Natural Science Foundation of Heilongjiang Province/ ; }, abstract = {Potato (Solanum tuberosum L.) has high nutritional value and strong adaptability and plays an extremely important role in global food security. Excessive use of nitrogen (N) fertilizer in potato production has increased costs and environmental pollution. In this study, the N use efficiency (NUE) of two potato varieties (DXY and DN310) was determined under high nitrogen conditions. The N use efficiency of DXY was relatively high. The differences between the rhizosphere microbial population groups of the two varieties were determined using the metagenomic sequencing method. The genes related to N efficiency were jointly identified using transcriptome and metabolome analyses. Significant difference was observed between the two varieties of microorganisms, leading to different rhizosphere microorganisms. Compared with DN310, the roots of DXY retained more available N and generated less NO. Additionally, DXY exhibited relatively low disease susceptibility. Combined transcriptome and metabolome analyses indicated that the differentially expressed metabolites in the two different varieties under high N conditions were mainly enriched in amino acid metabolism and sugar metabolism pathways. Using weighted gene co-expression network analysis, two genes associated with N fertilizer response were identified: PGSC0003DMG400025888 and PGSC0003DMG400017276. This study provided valuable insights into breeding potato varieties with high N efficiency.}, }
@article {pmid40094201, year = {2025}, author = {Masaadeh, AH and Eletrebi, M and Parajuli, B and De Jager, N and Bosch, DE}, title = {Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2479774}, doi = {10.1080/19490976.2025.2479774}, pmid = {40094201}, issn = {1949-0984}, mesh = {Humans ; *Dysbiosis/microbiology ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; *Disease Progression ; *Colorectal Neoplasms/microbiology/pathology ; *Bacteria/classification/isolation &amp; purification/genetics ; Inflammatory Bowel Diseases/microbiology/pathology/complications ; Colitis-Associated Neoplasms/microbiology/pathology ; Adult ; RNA, Ribosomal, 16S/genetics ; Colitis/microbiology/pathology ; Metagenomics ; Intestinal Mucosa/microbiology/pathology ; }, abstract = {Dysbiosis and pathobionts contribute to inflammation and the risk of colitis-associated carcinoma (CAC) in animal models, but their roles in humans with this uncommon disease are unknown. We identified microbiome differences in human CAC compared with longstanding inflammatory bowel disease (IBD) and sporadic colorectal carcinoma (CRC). Twenty-four CAC resections were matched with CRC and IBD controls. Methods included histopathology, 16S rDNA metagenomics, and pathobiont-specific qPCR. Beta diversity differed by diagnosis (PERMANOVA p = 0.007). The distinguishing taxa included Akkermansia enriched in CRC, and Bacteroides spp. enriched in IBD. The non-neoplastic mucosae presented distinct beta diversity (p = 0.005), but the CAC/CRC tumor microbiomes were similar (p = 0.7). Within metastases and margins, Enterobacteriaceae were enriched in CAC, and Bacteroidales in CRC. Pathobiont-specific qPCR confirmed a greater frequency of pks+ E. coli and enterotoxigenic Bacteroides fragilis in CAC than IBD. High alpha diversity was associated with active inflammation, advanced cancer stage, and shorter overall survival (log-rank p = 0.008). Mucosal microbiomes distinguish CAC from longstanding IBD, implicating pathobionts as markers for disease progression. Integrating our findings with prior animal model research, pathobionts promote carcinogenesis in IBD patients through genotoxicity and host cell signaling.}, }
@article {pmid40093613, year = {2025}, author = {Huang, X and Yuan, T and Huang, Y and Qazi, IH and Liu, J}, title = {Analysis of causal pathogens of mulberry bacterial blight in samples collected from eight provinces of China using culturomics and metagenomic sequencing methods.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1517050}, pmid = {40093613}, issn = {1664-462X}, abstract = {Mulberry bacterial blight (MBB) is a complex and one of the devastating diseases of mulberry that causes serious reduction in the yield and quality of mulberry. In recent years, the transformation of sericulture industry, mulberry production system, and increasing seedling trade have resulted in the spread of MBB to different parts of China, posing a major economic threat to the farmers and industry. This study investigated the occurrence of MBB in eight provinces of China during years 2023 and 2024. The MBB disease samples were collected and the composition of the MBB pathogenic microbiome was analyzed by combining culturomics and metagenomic sequencing methods. A total of 498 bacterial strains were isolated and identified through culturomics, and then 109 suspected pathogen strains were preliminarily screened based on metagenomic sequencing data. Finally, 10 pathogens including, Pseudomonas syringae, P. fulva, P. fluorescens, Pantoea ananatis, Pectobacterium parvum, P. carotovorum, Flavobacterium fluviale, Citrobacter portucalensis, Klebsiella grimontii, Stenotrophomonas maltophilia, were identified through Koch's postulates. Based on the distribution pattern of pathogens and the changes in the microbiome community of mulberry following infection with P. syringae, we infer that P. syringae, and P. fulva are important pathogens of MBB. In addition, based on the analysis of meteorological data, different bacteria showed adaptability to different environments, leading to differences in the pathogens of MBB under different climate conditions and latitudes. The data presented herein provides a foundation for understanding the occurrence, spatial distribution and pathogenic mechanism of MBB and its major pathogens.}, }
@article {pmid40093185, year = {2025}, author = {France, MT and Chaudry, I and Rutt, L and Quain, M and Shirtliff, B and McComb, E and Maros, A and Alizadeh, M and Hussain, FA and Elovitz, MA and Relman, DA and Rahman, A and Brotman, RM and Price, J and Kassaro, M and Holm, JB and Ma, B and Ravel, J}, title = {VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.04.641479}, pmid = {40093185}, issn = {2692-8205}, abstract = {Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. This study expands our understanding of the function and ecology of the vaginal microbiome using VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 revealed novel insights, including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2,500 metagenomes and 4,000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.}, }
@article {pmid40092793, year = {2025}, author = {Abakumov, S and Ruppeka-Rupeika, E and Chen, X and Bouwens, A and Leen, V and Dedecker, P and Hofkens, J}, title = {DeepMAP: Deep CNN Classifiers Applied to Optical Mapping for Fast and Precise Species-Level Metagenomic Analysis.}, journal = {ACS omega}, volume = {10}, number = {9}, pages = {9224-9232}, pmid = {40092793}, issn = {2470-1343}, abstract = {DNA optical mapping is a powerful technique commonly used for structural variant calling and genome assembly verification. Despite being inherently high-throughput, the method has not yet been applied to highly complex settings such as species identification in microbiome analysis due to the lack of alignment algorithms that can both assign large numbers of reads in minutes and handle large database size. In this work, we present a novel genomic classification pipeline based on deep convolutional neural networks for optical mapping data (DeepMAP), which can perform fast and accurate assignment of individual optical maps to their respective genomes. We furthermore achieve a superior performance of DeepMAP in the presence of evolutionary divergent sequences, making it robust to the presence of unknown strains within metagenomic samples. We evaluate DeepMAP on genomic DNA extracted from bacterial mixtures, reaching species-level resolution with true positive rates of around 75% and a false positive rate of less than 1%, with measured classification speeds significantly outpacing those of previously developed approaches for high-density optical mapping data alignment.}, }
@article {pmid40092035, year = {2025}, author = {Li, S and Liu, Y and Yang, X and Yang, Y and Peng, J and Xu, Y and Wei, J}, title = {Spatiotemporal composition and diversity of endophyte communities in Dracaena cambodiana on Hainan Island.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1540669}, pmid = {40092035}, issn = {1664-302X}, abstract = {INTRODUCTION: Dracaena cambodiana produces a red resin known as Dragon's blood, which is used worldwide in traditional medicine and as a dye. The role of endophytes in the resin-formation process remains underexplored. Understanding the endophyte communities and their functional roles in resin production could enable the development of efficient induction techniques for resin production.<br><br>METHODS: In this study, ITS and metagenomic sequencing analyzed endophyte communities' characteristics and functional traits in different tissues and D. cambodiana across multiple wild populations on Hainan Island.<br><br>RESULTS: We identified distinct fungal genera that were dominant in different tissues. Following injury, we observed significant changes in the expression of endophytic fungal genes. These changes indicated that metabolic pathways associated with resin metabolism, sucrose metabolism, signal transduction, and phenylalanine metabolism were likely involved in resin formation. Additionally, several glycosylation gene families were upregulated in the post-injury endophytic communities, which suggests a role in flavonoid transport and the reduction of autotoxic effects.<br><br>DISCUSSION: Our results suggest that endophytes play a vital role in the resin-formation process of D. cambodiana. Isolating specific endophytes or using synthetic communities could potentially improve resin yields and avoid pathogenic fungi, ensuring safety. The findings from this study provide a theoretical basis for the development of high-efficiency resin induction techniques by targeting the dynamic changes in endophyte communities across tissues, regions, and resin formation stages.}, }
@article {pmid40091996, year = {2025}, author = {Chandra Nayak, S and Latha, PB and Kandanattu, B and Pympallil, U and Kumar, A and Kumar Banga, H}, title = {The Oral Microbiome and Systemic Health: Bridging the Gap Between Dentistry and Medicine.}, journal = {Cureus}, volume = {17}, number = {2}, pages = {e78918}, pmid = {40091996}, issn = {2168-8184}, abstract = {The oral microbiome, consisting of a mixture of bacteria, fungi, and viruses, is an important contributor to oral and systemic health. Microbial balance disruptions are associated with oral pathologies like dental caries and periodontitis as well as systemic diseases such as cardiovascular diseases, adverse pregnancy outcomes, and respiratory diseases. This review explores the mechanistic pathways linking oral dysbiosis to systemic inflammation, endothelial dysfunction, and immune modulation. The roles of key microbial species in health and disease are analyzed, with an emphasis on how hematogenous dissemination leads to systemic pathologies through inflammatory signaling. Also, advances in high throughput sequencing are discussed, as well as microbial diversity and its implications for diagnostics and therapeutics. The review highlights the potential of oral microbiota-targeted interventions to mitigate systemic diseases through dentistry and medicine integration, by throwing light on interdisciplinary strategies. Future work should focus on the evaluation of the mechanisms by which the oral microbiome plays a role in systemic diseases through the integration of multi-omics approaches such as metagenomics, transcriptomics, and metabolomics. Furthermore, clinical trials need to be designed in a way to evaluate the efficacy of microbiome-targeted therapies in the prevention of cardiovascular diseases, adverse pregnancy outcomes, and autoimmune disorders.}, }
@article {pmid40091534, year = {2025}, author = {Lu, YM and Lu, JQ and Zhao, Q and Chen, J and Xiong, JB}, title = {Pathogenic mechanisms of Enterocytozoon hepatopenaei through the parasite-gut microbiome-shrimp (Litopenaeus vannamei) physiology axis.}, journal = {Zoological research}, volume = {46}, number = {2}, pages = {401-413}, doi = {10.24272/j.issn.2095-8137.2024.411}, pmid = {40091534}, issn = {2095-8137}, mesh = {Animals ; *Penaeidae/microbiology ; *Gastrointestinal Microbiome/physiology ; *Enterocytozoon/physiology/genetics ; Host-Parasite Interactions ; }, abstract = {The progressive impact of Enterocytozoon hepatopenaei (EHP) infection on gut microbial function in Litopenaeus vannamei remains poorly understood beyond static comparisons between healthy and infected individuals. To close this knowledge gap, metagenomic sequencing was used to characterize the gut microbiomes of normal, long, medium, and short-sized adult shrimp categorized by increasing severity of infection. EHP infection suppressed digestive activity while inducing immune responses compared with healthy shrimp. Increasing infection severity was associated with a gradual decline in gut α-diversity and an expansion of potential pathogens and virulence factors (VFs). In addition, dysbiosis in gut microbiota composition and function, as well as reduced network stability among differential species, intensified with infection severity. Accordingly, we identified 24 EHP-discriminatory species that contributed an overall 83.3% accuracy in diagnosing infection severity without false negatives. Functional pathway analysis revealed significant suppression of metabolic, degradative, and biosynthetic processes in EHP-infected shrimp compared with healthy controls. Among them, map00630 glyoxylate and dicarboxylate metabolism and map00280 valine, leucine and isoleucine degradation were consistently depleted in infected individuals, thereby impairing their digestive function and anti-inflammatory responses. Additionally, EHP infection diversified VFs directly affecting shrimp gut microbiome. These findings support a conceptual model linking EHP pathogenesis to the parasite-gut microbiome-shrimp physiology axis.}, }
@article {pmid40091365, year = {2025}, author = {Norgan, AP and Enninga, EAL and Fedyshyn, B and Wolf, M and Goldstein, JA and Shanes, ED}, title = {Enterovirus Placentitis is an Underrecognized Cause of Placental Pathology.}, journal = {The American journal of surgical pathology}, volume = {}, number = {}, pages = {}, doi = {10.1097/PAS.0000000000002378}, pmid = {40091365}, issn = {1532-0979}, abstract = {The placenta is susceptible to infection by a number of viral pathogens, including severe acute respiratory syndrome coronavirus 2, which is associated with poor fetal outcomes. The histologic pattern of injury, termed severe acute respiratory syndrome coronavirus 2 placentitis, is characterized by a triad of increased perivillous fibrin deposition, intervillous histiocytes, and trophoblast necrosis. While the etiology of massive perivillous fibrin deposition (MPVFD) is mostly unknown, previous case reports of MPVFD in association with maternal Enterovirus (ENT) suggest that a subset of these cases are a consequence of undiagnosed viral infection. We evaluated 46 placentas collected between 2011 and 2022 with a diagnosis of MPVFD (n = 41) or chronic histiocytic intervillositis (CHI; n = 4). Combining methods of pan-viral metagenomic sequencing and targeted viral PCR, we detected Enterovirus DNA in 8 of 45 (18%) MPVFD and/or CHI cases. Seven of these positive cases were from MPVFD, and 1 was associated with a CHI diagnosis. Enterovirus A species (n = 7) were commonly identified, whereas one case had Enterovirus B. Histologic evaluation of these cases, including immunohistochemical staining for CD68, demonstrated increased intervillous histiocytes in Enterovirus-positive MPVFD cases in comparison with Enterovirus-negative, as well as evidence of trophoblast necrosis. Thus, we favor the terminology Enterovirus placentitis to describe this pathology. Overall, these findings suggest that Enterovirus is an underrecognized etiology of histologic MPVFD and, possibly, CHI. Further study to evaluate the recurrence risk of Enterovirus placentitis in comparison to MPVFD may help inform future fertility planning in patients with these diagnoses.}, }
@article {pmid40091083, year = {2025}, author = {Honda, H and Suzuki, T and Kitajima, M and Kondo, NI and Miyata, K and Utsumi, S and Yamada, M}, title = {The new era shaped by environmental genome monitoring - symposium of the japanese environmental mutagen and genome society (JEMS), 2024.}, journal = {Genes and environment : the official journal of the Japanese Environmental Mutagen Society}, volume = {47}, number = {1}, pages = {6}, pmid = {40091083}, issn = {1880-7046}, abstract = {The symposium "The New Era Shaped by Environmental Genome Monitoring," held in December 2024 by the Japanese Environmental Mutagen and Genome Society (JEMS), aimed to explore the interdisciplinary collaborations that are essential for the development of new scopes in environmental genome monitoring. This event highlighted the necessity of integrating mutagenicity research with ecological assessments to enhance public health and biodiversity conservation. Presentations focused on the evolving landscape of environmental genomics, including metagenomic analyses for antibiotic resistance, viral genomic surveillance in wastewater, and innovations in noninvasive biodiversity and stress monitoring through environmental DNA and RNA. This report summarizes the key discussions and presentations from the symposium, underscoring the critical role of environmental genome monitoring in shaping future safety research.}, }
@article {pmid40090954, year = {2025}, author = {Lund, D and Parras-Moltó, M and Inda-Díaz, JS and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E}, title = {Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2595}, pmid = {40090954}, issn = {2041-1723}, support = {2018-02835//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2018-05771//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2019-03482//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2022-00945//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Humans ; *Phylogeny ; Wastewater/microbiology ; Genome, Bacterial ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Microbiota/genetics/drug effects ; Genes, Bacterial ; Metagenome ; Drug Resistance, Bacterial/genetics ; }, abstract = {The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in ~1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.}, }
@article {pmid40090735, year = {2025}, author = {Yabuki, A and Fujii, C and Yazaki, E and Tame, A and Mizuno, K and Obayashi, Y and Takao, Y}, title = {Massive RNA Editing in Ascetosporean Mitochondria.}, journal = {Microbes and environments}, volume = {40}, number = {1}, pages = {}, doi = {10.1264/jsme2.ME24070}, pmid = {40090735}, issn = {1347-4405}, mesh = {*RNA Editing ; *Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; High-Throughput Nucleotide Sequencing ; Eukaryota/genetics/classification ; Phylogeny ; Adenosine Deaminase/genetics/metabolism ; }, abstract = {Ascetosporeans are parasitic protists of invertebrates. A deep sequencing ana-lysis of species within the orders Mikrocytida, Paramyxida, and Haplosporida using metagenomic approaches revealed that their mitochondria were functionally reduced and their organellar genomes were lacking. Ascetosporeans belonging to the order Paradinida have not been sequenced, and the nature of their mitochondria remains unclear. We herein established two cultures of Paradinida and conducted DNA and RNA sequencing ana-lyses. The results obtained indicate that mitochondrial function in paradinids was not reduced and their organellar genomes were retained. In contrast, their mitochondrial genomes were involved in massive A-to-I and C-to-U substitution types of RNA editing. All edits in protein-coding genes were nonsynonymous substitutions, and likely had a restorative function against negative mutations. Furthermore, we detected possible sequences of DYW type of pentatricopeptide repeat (PPR-DYW) protein and a homologue of adenosine deaminase acting on RNA (ADAR-like), which are key enzymes for C-to-U and A-to-I substitutions, respectively. An immunofluorescence ana-lysis showed that ADAR-like of paradinids may specifically localize within mitochondria. These results expand our knowledge of the diversity and complexity of organellar RNA editing phenomena.}, }
@article {pmid40090521, year = {2025}, author = {Kitaya, S and Horiba, K and Kabata, T and Iyobe, T and Hashino, M and Yamazaki, H and Takahashi, Y and Zaimoku, Y and Oshima, M and Kanamori, H}, title = {The contribution of metagenomic next-generation sequencing to a diagnosis of gas-producing Fusobacterium-induced septic hip arthritis: A case report.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {}, number = {}, pages = {102681}, doi = {10.1016/j.jiac.2025.102681}, pmid = {40090521}, issn = {1437-7780}, abstract = {Pyogenic arthritis with gas gangrene triggered by intra-articular steroid injections can occasionally result in fatal complications. Clostridium perfringens is typically the causative pathogen, with infections caused by Fusobacterium sp. being relatively rare. Fusobacterium sp. are known to cause pyogenic infections, but due to their extreme sensitivity to oxygen, they can be difficult to detect with traditional culture methods. Recently, metagenomic next-generation sequencing (mNGS) has gained attention as an alternative diagnostic tool to traditional culture, enabling rapid identification of causative pathogens in infectious diseases, including pyogenic arthritis. Its use is illustrated in the following case report, which demonstrates the diagnostic utility of mNGS in pyogenic arthritis with gas gangrene triggered by an intra-articular steroid injection. Using mNGS as a complement to conventional culture testing allows for a more precise narrowing-down of causative pathogens, enabling targeted therapy and improving patient outcomes. This approach may also help reduce the use of broad-spectrum antibiotics and prevent the emergence of antibiotic-resistant bacteria.}, }
@article {pmid40090450, year = {2025}, author = {Wu, H and Chen, S and Deng, Y and Shen, J and Xu, Y and Wen, T and Yuan, J and Shen, Q and Xue, C}, title = {Dynamics of antibiotic resistance genes and the bacterial community after stress from a single Dazomet fumigation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126048}, doi = {10.1016/j.envpol.2025.126048}, pmid = {40090450}, issn = {1873-6424}, abstract = {Although chemical fumigants are widely applied in agriculture to control soil-borne diseases, their influence on soil antibiotic resistance genes (ARGs) remains poorly understood. This study employed metagenomic sequencing to investigate the dynamic response and recovery processes of soil bacterial communities and ARGs after the end of fumigation with Dazomet. The results revealed that the effects of Dazomet were both phased and recoverable. Initially, no significant shifts in bacterial community diversity were observed; however, by day 10 of recovery (Dazomet10), diversity had decreased by 3.1%. By contrast, ARG levels surged by 17.3% and 10.9% on days 10 and 20 (Dazomet20), respectively, before reverting to the baseline by day 50 (Dazomet50). These patterns were corroborated by qPCR data, which showed a 90.8% reduction in 16S rRNA gene abundance, alongside a 4.17- to 4.38-fold increase in the relative abundance of ARGs at Dazomet10 and Dazomet20. Approximately 63% of the variation in ARGs was attributed to bacterial community composition and mobile genetic elements (MGEs). Combined with community analysis and host-tracking analysis, it was found that Streptomyces and Nocardioides were identified as key ARGs hosts. Overall, the microbial communities and resistome required at least 50 days after the end of fumigation to recover to their pre-fumigation state. This study sheds light on the dynamic interactions between bacterial communities and ARGs during recovery from Dazomet fumigation and underscores the critical need for the rational use of fumigants in agricultural practices.}, }
@article {pmid40090148, year = {2025}, author = {Dong, KY and Yang, CX and Pang, JL and Chang, RR and Chen, KY and Yao, W and Huang, BC and Jin, RC}, title = {Antibiotics shape the core microbial community distribution between floc and biofilm in an endogenous partial denitrification system: Insight from metabolic pathway.}, journal = {Water research}, volume = {280}, number = {}, pages = {123491}, doi = {10.1016/j.watres.2025.123491}, pmid = {40090148}, issn = {1879-2448}, abstract = {The response mechanism of microorganisms in partial denitrification (PD) system under antibiotic stress, particularly microbial energy metabolism and electron transfer, remain inadequately understood. This knowledge gap hinders the establishment of ecological links between microbial dynamics and macro-level reactor performance. To address this, moving bed biofilm reactors were employed to investigate the dynamic changes of microbial community and metabolism under sulfadiazine (SDZ) and ciprofloxacin (CIP) stress. Results showed that dosing 2 mg/L SDZ or CIP accelerated nitrite accumulation, achieving this milestone 15 days earlier than in the control group. At the end of the operational phase, nitrate removal efficiencies reached 90.3 ± 18.3 % (Control), 83.5 ± 16.2 % (SDZ-treated) and 93.9 ± 12.4 % (CIP-treated), with nitrate-to nitrite-transformation rates of 61.3 ± 12.7 %, 65.6 ± 13.1 % and 58.0 ± 21.2 %, respectively. The abundances of energy supply related genes, i.e., sucC and PK were higher in the CIP-treated group, while those in the other two groups were similar. The promoted tricarboxylic acid cycle and glycolysis led to NADH and ATP accumulation, accelerating nitrogen metabolism and benefiting early nitrite accumulation in the antibiotic-stressed system. More importantly, increasing antibiotics concentration from 2 mg/L to 4 mg/L induced selective migration of Thauera from floc to biofilm (abundance in floc reduced to < 2.01 %). Metagenomic sequencing indicated that the higher abundance of narGHI in biofilms, compared to flocs, was crucial for maintaining stable PD performance under antibiotic stress. The electron transport related genes, such as IDH1, DLD and DLAT, were more abundant in biofilms than in flocs after SDZ and CIP addition. These findings provide a theoretical basis for understanding the response mechanism of PD consortia to antibiotic.}, }
@article {pmid40090144, year = {2025}, author = {Deng, B and Ren, Z and Li, Q and Zhang, Z and Xu, C and Wang, P and Zhao, H and Yuan, Q}, title = {Black soldier fly larvae mediate Zinc and Chromium transformation through the ZnuCBA and citric acid cycle system.}, journal = {Water research}, volume = {280}, number = {}, pages = {123483}, doi = {10.1016/j.watres.2025.123483}, pmid = {40090144}, issn = {1879-2448}, abstract = {Intestinal microbiota and metal regulatory proteins (MRPs) underlie the transformation of heavy metals (HMs) by the black soldier fly larvae (BSFL), but the mechanisms involved are still not fully defined. Here, using 16S rRNA and metagenomics-assisted tracing, we found that zinc (Zn) and chromium (Cr) stress led to enrichment of Proteobacteria in the BSFL intestine. Support of Proteobacteria also led to increased levels of the Zn transporter proteins ZnuC/B/A and the Zn efflux proteins zntR/A. Meanwhile, the genes MltE, CitT, and SLT, which mediate the citric acid cycle, were also significantly up-regulated and involved in the cellular uptake of Cr. Although Zn and Cr stress affected the expression of antibiotic resistance genes and pathogenic genes, the BSFL intestine tended to form stable microbial communities (MCs) to transform HMs through a mechanism driven by ZupT and chrA. In addition, the expression of SCARB1 and LdcA was significantly down-regulated by acute HMs stimulation, but BSFL were still able to complete the life cycle. Therefore, we determined the protective role of MCs and MRPs on BSFL during the transformation of HMs.}, }
@article {pmid40089680, year = {2025}, author = {Wang, S and Niu, W and Lv, T and Xie, K}, title = {Traceability of septic shock caused by phocaeicola vulgatus: a rare case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {364}, pmid = {40089680}, issn = {1471-2334}, mesh = {Humans ; *Shock, Septic/microbiology ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Phocaeicola vulgatus (P.vulgatus) is a member of Bacteroides fragilis Group(BFG). Septic shock caused by P.vulgatus has not been reported yet. In recent years, BFG have attracted much clinical attention. BFG are the commensal microbiota residing in human mucosal sites, most notably the gut, that provide several benefits to healthy hosts. Yet BFG can cause devastating infections when they gain access to normally sterile body compartments following trauma, surgery, or mucosal barrier disruption.<br><br>CASE PRESENTATION: We report a case of septic shock event in a middle-aged male who underwent surgical intervention for a gallbladder mass incidentally detected during routine abdominal CT screening. P.vulgatus was isolated and cultured from blood sample and abdominal drainage fluid after surgery. We further performed the Metagenomic Next-Generation Sequencing (mNGS) with pathological slices of colon and hepatobiliary tissue, and result of mNGS also showed P.vulgatus. The patient was treated with comprehensive therapies and had a good outcome.<br><br>CONCLUSION: To the best of our knowledge, septic shock secondary to P.vulgatus infection originating from non-gastrointestinal area represents an rare clinical condition. We realized that research on BFG should not only focus on its positive effects on the intestine, but also on its potential pathogenicity, including intra-abdominal infections, abscesses, and bloodstream infection.}, }
@article {pmid40089034, year = {2025}, author = {Zhang, Z and Liu, Y and Yang, X and Luo, Q and Huang, W and Zhao, Z}, title = {Impacts of hydraulic retention time on organic removal in treating liquor wastewater via algal-bacterial granular sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132394}, doi = {10.1016/j.biortech.2025.132394}, pmid = {40089034}, issn = {1873-2976}, abstract = {This study optimized hydraulic retention time (HRT) to improve p-cresol and chemical oxygen demand (COD) removal and promote algal-bacterial granular sludge (ABGS) formation in Chinese fermented liquor wastewater treatment. At an HRT of 4 h, no granules formed in the sequential batch reactor, and after 30 days, the removal efficiencies were low for both COD (58.5 %) and p-cresol (21.6 %). In contrast, compact granules developed at HRT 8 and 12 h. The HRT of 8 h achieved the highest removal efficiencies (COD: 96.0 %, p-cresol: 91.3 %), outperforming the HRT of 12 h (COD: 95.1 %, p-cresol: 82.7 %). Microbial analysis identified Rhodobacteraceae and Pseudomonas as key p-cresol degraders. Metagenomic analysis revealed a higher abundance of benzoate degradation genes at an HRT of 8 h compared to 12 h, with Acidovorax predominantly contributing at 8 h and Hydrogenophaga at 12 h. These findings provide insights into the optimization of liquor wastewater treatment.}, }
@article {pmid40088533, year = {2025}, author = {Kim, HR and Kim, SH and Le, HD and Kim, JK and Her, M}, title = {The complete genome sequence of quail coronavirus identified in disease surveillance on quail farms in South Korea.}, journal = {Poultry science}, volume = {104}, number = {5}, pages = {105007}, doi = {10.1016/j.psj.2025.105007}, pmid = {40088533}, issn = {1525-3171}, abstract = {Avian carcasses collected from 103 flocks on 14 quail farms in Korea between 2022 and 2023 were diagnosed with viral diseases (22 flocks), bacterial disease (58 flocks), parasitic diseases (28 flocks) and non-infectious diseases (60 flocks). The only viral disease identified was viral enteritis in quails that showed pathological lesions in duodenum and appeared to be caused by quail coronavirus (QcoV) through viral metagenomics and RT-PCR assay. Two complete genomes of QCoV from samples diagnosed as viral enteritis were obtained using amplicon-based whole genome sequencing. The two QcoVs were gammacoronavirus, but were distinct from other avian coronaviruses. The spike genes of QCoV have 86.2 ∼ 87.1 % identity with that of American turkey coronavirus, but other gene sequences of QcoV was found to be similar to those of Korean infectious bronchitis virus. Genetic analysis based on the complete genomic sequences found QCoVs had a genetic structure similar to avian coronaviruses, yet it seems to be a unique pathogen specific to quail. This is the first report about the complete genome and genetic analysis of QCoV and the result of disease surveillance in quail in South Korea.}, }
@article {pmid40087960, year = {2025}, author = {Sabba, F and Farmer, M and Dunlap, P and Qin, C and Kozak, J and Barnard, J and Wells, G and Downing, L}, title = {Unlocking the potential of sidestream EBPR: exploring the coexistence of PAO, GAO and DGAO for effective phosphorus and nitrogen removal.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {91}, number = {5}, pages = {469-481}, pmid = {40087960}, issn = {0273-1223}, mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Waste Disposal, Fluid/methods ; Bioreactors ; Denitrification ; Anaerobiosis ; Glycogen/metabolism ; Water Pollutants, Chemical/metabolism ; }, abstract = {Wastewater treatment facilities use enhanced biological phosphorus removal (EBPR) to meet discharge quality limits. However, the EBPR process can experience upsets due to a lack of influent carbon or inadequate anaerobic zones. By using a sidestream EBPR (S2EBPR) process, carbon can be generated internally through fermentation processes and a higher anaerobic mass fraction can be attained in smaller volumes. This study investigates nutrient removal and microbial community trends in a full-scale S2EBPR demonstration at the Calumet Water Reclamation Plant. The study aims to improve a process model of the system by better representing the activity of glycogen-accumulating organisms (GAO) and potential competitors of phosphorus-accumulating organisms (PAO), which were found in high abundance in this study. Modifying anaerobic hydrolysis, GAO glycogen storage and ORP activity parameters resulted in model prediction improvements of approximately 5% for nitrate and nitrite and 10-60% for phosphorus. The study also uses shotgun metagenomic sequencing to profile denitrification pathways of PAO and GAO. It shows that denitrifying GAO may contribute to nitric oxide reduction to a greater degree than denitrifying PAO. This study improves process modeling predictions for S2EBPR and highlights the potential role of denitrifying PAO and GAO in combined phosphorus and nitrogen removal in S2EBPR.}, }
@article {pmid40087791, year = {2025}, author = {Centeno-Delphia, RE and Glidden, N and Long, E and Ellis, A and Hoffman, S and Mosier, K and Ulloa, N and Cheng, JJ and Davidson, JL and Mohan, S and Kamel, M and Szasz, JI and Schoonmaker, J and Koziol, J and Boerman, JP and Ault, A and Verma, MS and Johnson, TA}, title = {Nasal pathobiont abundance is a moderate feedlot-dependent indicator of bovine respiratory disease in beef cattle.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {27}, pmid = {40087791}, issn = {2524-4671}, support = {2020-68014-31302//National Institute of Food and Agriculture/ ; 2018-006//Purdue University's Colleges of Agriculture and Engineering Collaborative Projects Program/ ; }, abstract = {BACKGROUND: Bovine respiratory disease (BRD) poses a persistent challenge in the beef cattle industry, impacting both animal health and economic aspects. Several risk factors make an animal susceptible to BRD, including bacteria such as Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Despite efforts to characterize and quantify these bacteria in the nasal cavity for disease diagnosis, more research is needed to understand if there is a pathobiont abundance threshold for clinical signs of respiratory disease, and if the results are similar across feedlots. This study aims to compare the nasal microbiome community diversity and composition, along with the abundance of four bacterial pathogens and associated serotypes, in apparently healthy and BRD-affected beef cattle. Nasal swabs were collected from four beef feedlots across the US, covering the years 2019 to 2022. The study included post-weaned beef cattle with diverse housing conditions.<br><br>RESULTS: Quantification of BRD-associated pathogens effectively distinguished BRD-affected from apparently healthy beef cattle, surpassing the efficacy of 16S rRNA gene sequencing of the nasal microbiome community. Specifically, H. somni, M. bovis, and M. haemolytica had higher abundance in the BRD-affected group. Utilizing the abundance of these pathobionts and analyzing their combined abundance with machine learning models resulted in an accuracy of approximately 63% for sample classification into disease status. Moreover, there were no significant differences in nasal microbiome diversity (alpha and beta) between BRD-affected and apparently healthy cattle; instead, differences were detected between feedlots.<br><br>CONCLUSIONS: Notably, this study sheds light on the beef cattle nasal microbiome community composition, revealing specific differences between BRD-affected and apparently healthy cattle. Pathobiont abundance was increased in some, but not all farms. Nonetheless, more research is needed to determine if these differences are consistent across other studies. Additionally, future research should consider bacterial-viral interactions in the beef nasal metagenome.}, }
@article {pmid40087775, year = {2025}, author = {Duret, M and Wallner, A and Besaury, L and Aziz, A}, title = {Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {30}, pmid = {40087775}, issn = {2524-6372}, support = {1564//French National Research Agency through the PRIMA-MiDiVine project/ ; 1564//French National Research Agency through the PRIMA-MiDiVine project/ ; 1564//French National Research Agency through the PRIMA-MiDiVine project/ ; }, abstract = {BACKGROUND: Plant health depends on beneficial interactions between the roots and their microbiomes. Despite recent progress on the role of the grapevine microbiome, the taxonomic identity and functional traits of microbial taxa specific to healthy or Plasmopara viticola-diseased plants, as well as to the susceptible or resistant cultivar are unknown. Using metabarcoding and shotgun metagenomics sequencing, we investigated the effect of downy mildew on the root-associated microbiome (rhizospheric soil, rhizoplane and endosphere) of 41B-grafted susceptible cultivar (Chardonnay) and resistant interspecific hybrid (Voltis) at flowering and veraison stages. The impact of conventional treatment on the rhizomicrobiome assembly of Chardonnay was also evaluated.<br><br>RESULTS: Analyses revealed a core bacteriome shared between both susceptible and resistant cultivars. This also highlighted common functional traits between the rhizosphere and rhizoplane bacteriomes in both cultivars. A dysbiosis state was also evidenced by a loss of beneficial communities in the rhizosphere of the P. viticola-infected cultivar. Microbial genome assemblies showed functional differences between healthy and diseased plants, with a loss of Pseudomonas and Phyllobacterium taxa at veraison. This state was mainly characterized by a loss of genes involved in polyamine transport and metabolism in the susceptible cultivar. It was also marked by an increase in population evenness and total bacterial diversity, and the presence of pathogenic species in susceptible plants.<br><br>CONCLUSIONS: This study reveals distinct and overlapping bacterial communities and functional genes in the rhizospheric soil, rhizoplane and root endosphere of both susceptible and resistant grapevine cultivars to downy mildew. Microbial diversity and abundant taxa of grapevine roots are influenced by downy mildew and cultivar susceptibility. Common bacterial functions are shared among rhizocompartments of susceptible and resistant cultivars, revealing a dysbiosis state and functional signatures related to plant immunity, especially in the infected-susceptible plants.}, }
@article {pmid40087699, year = {2025}, author = {Gu, D and Liu, J and Wang, J and Yi, Y and Chu, Y and Gao, R and Liu, H and She, J and Lu, B}, title = {Integrating DNA and RNA sequencing for enhanced pathogen detection in respiratory infections.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {325}, pmid = {40087699}, issn = {1479-5876}, support = {L222073//Beijing Natural Science Foundation/ ; CFH, 2024-1-4063//Alpha Foundation for the Improvement of Mine Safety and Health/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; }, mesh = {Humans ; *Respiratory Tract Infections/microbiology/diagnosis/virology ; Male ; Female ; Sequence Analysis, RNA/methods ; Middle Aged ; High-Throughput Nucleotide Sequencing/methods ; Adult ; Sequence Analysis, DNA/methods ; Aged ; Reproducibility of Results ; Retrospective Studies ; Young Adult ; Metagenomics/methods ; Adolescent ; }, abstract = {BACKGROUND: The clinical value of shotgun metagenomic next-generation sequencing (mNGS) in improving the detection rates of respiratory pathogens is well-established. However, mNGS is complex and expensive. This study designed and evaluated the performance of targeted NGS (tNGS) in diagnosing respiratory infections.<br><br>METHODS: We retrospectively included samples from 281 patients with lower respiratory tract infections to establish thresholds of pathogens. Subsequently, target pathogens were selected and a probe hybridization system was established. The performance and clinical manifestations of tNGS for 306 pathogens were evaluated using clinical and simulated samples.<br><br>RESULTS: The tNGS method took 16&#xa0;h with sequencing data sizes of 5&#xa0;M reads. The limit-of-detection of tNGS was 100-200 CFU/mL, respectively. Bioinformatics simulation confirmed the method's high specificity and robustness. In 281 patients of clinical validation cohort, tNGS exhibited a sensitivity of 97.73% and specificity of 75.41% compared to the composite reference standard, which notably surpasses those of culture-based and conventional microbiological methods (CMT). In detecting bacterial and viral infection, tNGS demonstrated superior sensitivity relative to CMT. Notably, 61.40% of target viruses were subtype-resolved with the initial establishment of reliable typing cutoffs, with the subtyping results being completely consistent with the PCR results. tNGS allowed for concurrent identification of antimicrobial resistance (AMR) markers and viral subtyping. 80.56% of AMR markers identified by tNGS were consistent with antimicrobial susceptibility testing.<br><br>CONCLUSION: This research established the robust performance of our tailored tNGS assay in the simultaneous detection of DNA and RNA pathogens, underscoring its prospective suitability for widespread use in clinical diagnostics.}, }
@article {pmid40087607, year = {2025}, author = {Meng, B and Liu, H and Wu, Q and Qu, L and Mao, C and Yang, F and Lan, T and Fang, J and Hu, Z and Fang, Y}, title = {Antimicrobial strategies of lower respiratory tract infections in immunocompromised patients based on metagenomic next-generation sequencing: a retrospective study.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {360}, pmid = {40087607}, issn = {1471-2334}, support = {2020-55//Wuhan Young and Middle-aged Medical Backbone Talent Project 2020/ ; ZZ20231693//Young Talent Project of General Hospital of Center Theater/ ; JCZRYB202500657//Natural Science Foundation of Hubei Province/ ; }, mesh = {Humans ; *Immunocompromised Host ; *High-Throughput Nucleotide Sequencing ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Metagenomics/methods ; *Respiratory Tract Infections/drug therapy/microbiology ; Aged ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Adult ; Bacteria/genetics/drug effects/isolation &amp; purification/classification ; }, abstract = {BACKGROUND: Immunocompromised patients with Lower Respiratory Tract Infections (LRTI) frequently encounter a diverse range of pathogenic infections, characterized by rapid disease progression and significant mortality rates due to reckless or excessive utilization of antibiotics. Therefore, it is crucial to promptly and accurately identify the causative microorganisms for pathogen diagnosis and clinical decision-making. The objective of this study is to evaluate the clinical applicability of metagenomic next-generation sequencing (mNGS) in the diagnosis and management of LRTI, as well as its impact on empirical antibacterial therapy for patients with varying immune statuses.<br><br>METHODS: We conducted a comparative analysis of positivity rate, detection accuracy, pathogen spectrum, duration of treatment (DOT), and antibiotic management in a cohort of 283 patients diagnosed with lower respiratory tract infections.<br><br>RESULTS: The positive detection rate was higher in mNGS compared to conventional culture in both immunocompetent group (89.92% vs. 28.57%, P&#x2009;<&#x2009;0.001) and immunocompromised group (84.44% vs. 33.33%, P&#x2009;<&#x2009;0.001). The antibiotic escalation in the immunocompromised group was more frequent than that in the immunocompetent group (49.00% vs. 31.00%, P&#x2009;=&#x2009;0.018), but no difference was observed for antibiotic de-escalation (20.00% vs. 15.00%, P&#x2009;=&#x2009;0.458).<br><br>CONCLUSIONS: The application of mNGS can significantly enhance the pathogen detection rate and optimize antimicrobial drug management in immunocompromised patients with LRTI.}, }
@article {pmid40087598, year = {2025}, author = {Lu, S and Li, H and Ma, C and Li, X}, title = {Systemic and localized infections in humans caused by Paenibacillus: a case report and literature review.}, journal = {BMC ophthalmology}, volume = {25}, number = {1}, pages = {133}, pmid = {40087598}, issn = {1471-2415}, support = {LHGJ20220370//Joint Construction Project of Henan Medical Science and Technology/ ; LHGJ20220370//Joint Construction Project of Henan Medical Science and Technology/ ; 232300420237//Natural Science Foundation of Henan/ ; 232300420237//Natural Science Foundation of Henan/ ; }, mesh = {Humans ; Male ; Adult ; *Eye Infections, Bacterial/diagnosis/microbiology/drug therapy ; *Paenibacillus/isolation &amp; purification ; *Gram-Positive Bacterial Infections/diagnosis/microbiology/drug therapy ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: As opportunistic pathogens, Paenibacillus organisms rarely induce human infections. This research paper details the clinical manifestations, treatment, and prognosis of an intraocular infection caused by Paenibacillus in a 43-year-old male patient.<br><br>CASE PRESENTATION: In this case, the patient initially presented with persistent ocular redness and a sensation of foreign bodies following trauma surgery. Upon admission, we performed intraocular fluid metagenomic next generation sequencing (mNGS) testing and systemic blood sampling for infection-related assessments. The results revealed a localized ocular infection with Paenibacillus organisms. Consequently, the patient received daily levofloxacin injections (500&#xa0;mg) and clindamycin (300&#xa0;mg) for systemic anti-infective therapy, along with subconjunctival injections of gentamicin (2 WIU) and dexamethasone (5&#xa0;mg) for topical application. The infection was effectively managed, and their ocular symptoms showed improvement during the treatment course.<br><br>CONCLUSIONS: We conducted a comprehensive review of previously reported cases involving Bacillus-like organisms causing human infections, exploring mechanisms, diagnostic approaches, and treatment strategies.}, }
@article {pmid40087549, year = {2025}, author = {Wang, X and Shang, Y and Xing, Y and Chen, Y and Wu, X and Zhang, H}, title = {Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {142}, pmid = {40087549}, issn = {1471-2180}, support = {2022KJ177//the Youth Innovation Team in Colleges and Universities of Shandong Province/ ; 32001228//the National Natural Science Foundation of China/ ; 32270444//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Virulence Factors/genetics ; *Wolves/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/enzymology ; Dogs ; *Foxes/microbiology ; Animals, Zoo/microbiology ; Animals, Wild/microbiology ; Carbohydrate Metabolism ; Metagenomics ; }, abstract = {Species in the family Canidae occupy different spatial ecological niches, and some (e.g., wolf) can be kept in zoos. The gut microbiome may differ among various wild and captive canids. Therefore, we compared the gut microbiomes of wild canids (wolf, red fox, and corsac fox) in the Hulun Lake area, captive wolves, and domestic dogs in different regions using metagenomic data. A random forest analysis revealed significant enrichment for bacterial species producing short-chain fatty acids and the thermogenesis pathway (ko04714) in the gut microbiome of wild wolf, potentially providing sufficient energy for adaptation to a wide range of spatial ecological niches. The significantly enriched bacterial species and functional pathways in the gut microbiome of corsac foxes were related to physiological stability and adaptation to arid environments. Alpha diversity of carbohydrate-active enzymes in the gut microbiome was higher in the red fox than in the corsac fox and wild wolf, which may be related to the abundance of plant seeds (containing carbohydrates) in their diets (red foxes inhabit seed-rich willow bosk habitats). However, the influence of host genetic factors cannot be excluded, and further experimental studies are needed to verify the study results. In addition, captive environments drove similarity in carbohydrate-active enzymes (CAZymes) and virulence factors (VFs) in the gut microbiomes of captive wolf and domestic dog, and increased the diversity of CAZymes and VFs in the gut microbiome of captive wolf. Increased VFs diversity may increase the pathogenic potential of the gut microbiome in captive wolves. Therefore, it is necessary to continue monitoring the health status of captive wolves and develop appropriate management strategies.}, }
@article {pmid40087199, year = {2025}, author = {Zhang, Y and Xu, S and Xu, Y}, title = {Clinical Analyses of 4 Cases of Microsporidial Keratoconjunctivitis.}, journal = {Acta parasitologica}, volume = {70}, number = {2}, pages = {71}, pmid = {40087199}, issn = {1896-1851}, mesh = {Humans ; *Keratoconjunctivitis/microbiology/drug therapy/diagnosis ; Male ; Adult ; Female ; Middle Aged ; China ; Microsporidiosis/diagnosis/drug therapy/microbiology ; Encephalitozoon/isolation &amp; purification/genetics ; Antifungal Agents/therapeutic use ; Eye Infections, Fungal/drug therapy/microbiology/diagnosis ; Encephalitozoonosis/drug therapy/diagnosis ; }, abstract = {OBJECTIVE: To report four cases of microsporidial keratoconjunctivitis (MKC) from The Affiliated Eye Hospital of Nanjing Medical University (from May 2023 to October 2024) and to aid ophthalmologists in diagnosing and treating MKC, as MKC has been increasingly reported in Asian healthy individuals but not much in Mainland China.<br><br>METHODS: Four patients with MKC were studied. Demographic information, symptoms, and clinical data were collected. Diagnosis involved ophthalmic examinations, corneal scraping microscopy (including Giemsa staining, modified Ziehl-Neelsen staining, Calcofour white staining), bacterial and fungal cultures, and metagenomic next-generation sequencing (mNGS). Treatment included various topical medications like polyhexamethylene biguanide (PHMB), fluconazole, tacrolimus, sodium hyaluronate, and systemic medication such as albendazole.<br><br>RESULTS: Three cases were caused by Encephalitozoon hellem proved by mNGS. Patients had symptoms like eye redness, swelling, pain, foreign body sensation, and vision loss. Risk factors included improper contact lens - wearing habits, contact with birds, or exposure to potentially contaminated environments. All patients showed improvements after treatment, with 3 cases cured and 1 case improved.<br><br>CONCLUSION: MKC is a unilateral, acute, non-purulent ocular surface infectious disease. Clinicians should be more aware of it. Diagnosis depends on recognizing clinical signs, exploring risk factors, and laboratory tests. There is no consensus on treatment, but combined topical and systemic anti-protozoal drugs showed good results. Further large-scale validation is needed. Relevant departments should strengthen water source management, and patients should pay attention to personal hygiene.}, }
@article {pmid40087044, year = {2025}, author = {Chen, B and Li, Y and Li, Z and Hu, X and Zhen, H and Chen, H and Nie, C and Hou, Y and Zhu, S and Xiao, L and Li, T}, title = {Vitamin E ameliorates blood cholesterol level and alters gut microbiota composition: A randomized controlled trial.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {}, number = {}, pages = {103964}, doi = {10.1016/j.numecd.2025.103964}, pmid = {40087044}, issn = {1590-3729}, abstract = {BACKGROUND AND AIMS: Antioxidants, including vitamin E (VE) and grape seed extract (GSE), as anti-aging supplementation have been widely used to improve human health. The gut microbiota plays a crucial role in health and affects the treatment effect of various interventions. However, the role of gut microbiota in VE remains unclear. This study aimed to assess the longitudinal impact of VE treatment on body health and the gut microbiota.<br><br>METHODS AND RESULTS: A randomized controlled trial was conducted with 90 healthy individuals. The participants were randomly assigned to three groups: a treatment group receiving VE, another antioxidant treatment group receiving GSE, and a control group receiving a placebo. We found that VE ameliorated blood cholesterol levels by reducing the levels of low-density lipoprotein cholesterol (LDL-C) in healthy volunteers. After the intervention, there was an increase in the relative abundance of short-chain fatty acid (SCFA)-producing bacteria and bile acid metabolizers. Specifically, the abundances of Lachnospira sp. and Faecalibacterium spp. increased in the VE. Interestingly, the gut microbiota of poor responders harbored a greater proportion of disease-associated bacterial species.<br><br>CONCLUSIONS: VE could promote health by lowering LDL-C, partly and indirectly by affecting gut bacteria with the ability to produce SCFAs or metabolize bile acids.<br><br>The clinical trial was registered on August 28, 2021. Registration number was ChiCTR2100050567 (https://www.chictr.org.cn).}, }
@article {pmid40086988, year = {2025}, author = {Peng, Q and Quan, L and Zheng, H and Li, J and Xie, G}, title = {Analyzing the contribution of top-down and bottom-up methods to the construction of synthetic microbial communities in Jiuyao.}, journal = {Food microbiology}, volume = {129}, number = {}, pages = {104759}, doi = {10.1016/j.fm.2025.104759}, pmid = {40086988}, issn = {1095-9998}, mesh = {*Fermentation ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Food Microbiology ; Fermented Foods/microbiology ; Metagenomics ; Fungi/genetics/classification/metabolism/isolation &amp; purification ; Saccharomyces cerevisiae/genetics/metabolism ; Taste ; }, abstract = {The construction of synthetic microbial communities is a crucial strategy for improving the stability of microbial populations and the quality of fermented foods. Jiuyao, an essential saccharification and fermentation starter in Huangjiu production, was the focus of this study. Using metagenomics combined with culture-dependent methods, we identified 11 microbial species involved in Huangjiu fermentation. Through metagenomic analysis and simulated fermentation, Rhizopus delemar, Rhizopus microspores, Rhizopus stolonife, Rhizopus azygosporus, Saccharomycopsis fibuligera, Saccharomyces cerevisiae, Wickerhamomyces anomalus and Pediococcus pentosaceus were determined to be the core microbial species driving the Jiuyao fermentation process. A synthetic microbial community was constructed based on these species, successfully reproducing the flavor and sensory qualities of Huangjiu while enhancing fermentation efficiency. This study provides valuable insights into the functional roles of Jiuyao-associated microbes and offers a framework for improving microbial community stability and fermentation quality in Huangjiu production.}, }
@article {pmid40086981, year = {2025}, author = {Kothe, CI and Renault, P}, title = {Metagenomic driven isolation of poorly culturable species in food.}, journal = {Food microbiology}, volume = {129}, number = {}, pages = {104722}, doi = {10.1016/j.fm.2025.104722}, pmid = {40086981}, issn = {1095-9998}, mesh = {*Metagenomics ; *Cheese/microbiology ; *Food Microbiology ; *Bacteria/isolation &amp; purification/classification/genetics ; Microbiota ; Metagenome ; Phylogeny ; }, abstract = {Although isolating microorganisms from food microbiota may appear less challenging than from the gut or environmental sources, recovering all representative species from food remains a difficult task. Here, we showed by metagenomic analysis that several abundant species had escaped isolation in a previous study of ten cheeses, including several previously uncharacterized species. This highlights the ongoing challenge of achieving a comprehensive recovery of microbes from food. To address this gap, we designed a novel strategy integrating metagenomics-based probes targeting the species of interest, coupled with an incremental culturing approach using pooled samples. As proof of concept, we applied this strategy to two cheeses containing species that were not isolated in our previous study, with the objective of isolating all species present at levels above 2% and, in particular, potential novel food species. Through this approach, we successfully performed the targeted isolation of two Psychrobacter and two Vibrio species from the first cheese, and four Halomonas and two Pseudoalteromonas species from the second one. Notably, P. undina and V. litoralis represented, as far as we know, the first cheese isolates characterized for these species. However, we were unable to isolate a novel species of Pseudoalteromonas, with no characterized representative to date, and Marinomonas foliarum, previously isolated from marine environment. Using metagenome-assembled genomes (MAGs) and metagenomic analysis, we discussed the possible reasons for their non-recovery. Finally, this strategy offers a promising approach for isolating a set of strains representative of the microbial diversity present in food ecosystems. These isolates can serve as a basis for investigating their roles in the communities, their impact on product development, safety implications and their potential in the development of starter cultures.}, }
@article {pmid40086705, year = {2025}, author = {Ma, G and Chai, Y and Tye, KD and Xie, H and Meng, L and Tang, X and Luo, H and Xiao, X}, title = {Predictive analysis of the impact of probiotic administration during pregnancy on the functional pathways of the gut microbiome in healthy infants based on 16S rRNA gene sequencing.}, journal = {Gene}, volume = {}, number = {}, pages = {149414}, doi = {10.1016/j.gene.2025.149414}, pmid = {40086705}, issn = {1879-0038}, abstract = {Maternal probiotic supplementation altered the microbial composition in infants' gut, yet its effect on the functional pathways of the microbiota remains unclear. This study aimed to explore the potential impact of maternal probiotic intake on the predicted functional pathways of the gut microbiome in healthy infants. A total of 24 pregnant women were randomly allocated to either the control group or the probiotic group. The women in the probiotic group began receiving probiotics at the 32nd week of pregnancy and continued until delivery. Meconium and fecal samples were collected from infants at birth, as well as on the 3rd day, 14th day, and 6th month after birth. The functional characteristics of the microbial community were inferred using 16S rRNA gene analysis, processed with PICRUSt software, and cross-referenced with the KEGG database. The probiotic group had lower levels of Actinobacteria and Bacteroidetes, while Bifidobacterium growth was notably increased in the infant gut microbiota. At day 0 postpartum, the control group exhibited higher levels of Prevotellaceae compared to the probiotic group (P < 0.05). However, no significant differences were found by day 3. At day 14, the control group exhibited higher levels of Bacteroidaceae and Bacteroides, while Bacteroides_thetaiotaomicron was more abundant in the probiotic group (P < 0.05). By 6 months, the control group showed a higher abundance of Firmicutes (P < 0.05). On day 0 postpartum, maternal probiotic consumption increased the Environmental information processing pathway at KEGG Level 1, and increased Energy metabolism, Metabolism of cofactors and vitamins, and Cell growth and death pathways at KEGG Level 2. It also increased Histidine metabolism, One carbon pool by folate, and Folate biosynthesis at KEGG Level 3. No changes were observed in the infant gut microbiota's functional metabolic pathways at 3 days postpartum. At 14 days postpartum, probiotics reduced Lipid metabolism pathways at KEGG Level 2 and the Citrate cycle at KEGG Level 3. At 6 months postpartum, probiotics decreased Carbohydrate metabolism pathways at KEGG Level 2. Our findings suggest that probiotic supplementation during pregnancy affects the functional metabolism of the gut microbiota in healthy infants. This, in turn, may influence the development of the infant's immune system, metabolism, and overall health by modifying the gut microbial environment.}, }
@article {pmid40086585, year = {2025}, author = {Rawat, N and Sivanesan, S and Kanade, GS and Bafana, A}, title = {Interaction of environmental fluoride exposure and gut microbes: potential implication in the development of fluorosis in human subjects.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {}, number = {}, pages = {115388}, doi = {10.1016/j.fct.2025.115388}, pmid = {40086585}, issn = {1873-6351}, abstract = {Fluoride exposure primarily occurs through contaminated water and leads to fluorosis, which is a global health concern. After ingestion, fluoride is absorbed via gastrointestinal tract, where it interacts with the gut microbiota. While animal studies have explored fluoride's effects on gut microbiota, no human studies have yet been conducted. Most research emphasizes metagenomic diversity, neglecting isolation and characterization of pure cultures for further applications. Additionally, the association between gut microbiota with fluorosis outcomes in fluoride-exposed populations is unexplored. This study characterizes and compares the cultivable gut microbiota in the fluoride-exposed population with (symptomatic, group II) or without (asymptomatic, group I) signs of skeletal fluorosis along with unexposed control (group III). Group I displayed higher abundance of Firmicutes (58.58%), group II had predominance of Proteobacteria (61.25%) while group III showed similar abundance of Proteobacteria (50.38%) and Firmicutes (49.51%). On analyzing short-chain fatty acid (SCFA) profiles, group I isolates produced higher isobutyric acid (1.31 ± 0.9 mM) than group II (0.71 ± 0.35 mM), while group II produced more isovaleric acid (0.8 ± 0.41 mM) than group I (0.61 ± 0.08 mM) (p < 0.05). These findings suggest that gut microbiota and SCFAs alteration may influence bone metabolism, affecting the fluorosis progression.}, }
@article {pmid40086354, year = {2025}, author = {Can Yilmaz, E and Barnes, MA}, title = {Comparative study of rates of environmental DNA (eDNA) accumulation and degradation in water and sediment from model plant (Egeria densa) and animal (Daphnia magna) species.}, journal = {The Science of the total environment}, volume = {971}, number = {}, pages = {179057}, doi = {10.1016/j.scitotenv.2025.179057}, pmid = {40086354}, issn = {1879-1026}, abstract = {Understanding of the ecology of environmental DNA (eDNA)-its origin, state, transport, and fate- is critical for interpreting the results of eDNA applications ranging from single-species presence/absence monitoring to whole-community analysis via metabarcoding and metagenomics. Accumulation and degradation of eDNA can be most accurately measured by conducting systematic manipulative experiments under controlled conditions. We compared eDNA accumulation and degradation in a laboratory setting for two different taxa (Daphnia magna and Egeria densa) across two different substrates (water and sediment). In accumulation experiments, both D. magna and E. densa showed increased eDNA levels in both water and sediment over 24 h. Daphnia magna eDNA concentrations were twice as high in sediment compared to water, whereas E. densa eDNA remained consistent between the two substrates. Degradation kinetic models were applied to our data for the two model organisms to characterize eDNA decay rates, inadvertently introducing an additional nutrient treatment with three different levels. The degradation of D. magna and E. densa eDNA varied based on nutrient concentrations and substrate types, with different models providing the best fit for different scenarios. Overall, we have demonstrated the importance of taxonomic, sample type, and environmental differences in eDNA ecological processes such as accumulation and degradation. These and similar processes require further study to enhance the interpretation of eDNA results in both research and management contexts.}, }
@article {pmid40086306, year = {2025}, author = {Russo, A and D'Alessandro, A and Di Paola, M and Cerasuolo, B and Renzi, S and Meriggi, N and Conti, L and Costa, J and Pogni, R and Martellini, T and Cincinelli, A and Ugolini, A and Cavalieri, D}, title = {On the role of bacterial gut microbiota from supralittoral amphipod Talitrus saltator (Montagu, 1808) in bioplastic degradation.}, journal = {The Science of the total environment}, volume = {972}, number = {}, pages = {179109}, doi = {10.1016/j.scitotenv.2025.179109}, pmid = {40086306}, issn = {1879-1026}, abstract = {Despite the promise of a reduced environmental impact, bioplastics are subjected to dispersion and accumulation similarly to traditional plastics, especially in marine and coastal environments. The environmental impact of bioplastics is attracting increasing attention due to the growing market demand. The ability of the supralittoral amphipod Talitrus saltator to ingest and survive on pristine starch-based bioplastic has already been assessed. However, the involvement of the gut microbiota of this key coastal species in making bioplastics a dietary supplement, remains unknown. In this study, we investigated the modification of T. saltator gut microbiota following bioplastic ingestion and the effect of this change on the modification of their chemical composition. Groups of adult amphipods were fed with: 1 - two different kinds of starch-based bioplastic; 2 - a 50 %/50 % chitosan-starch mixture; and 3 - paper and dry-fish-food. Freshly collected, unfed individuals were used as control group. Faecal pellets from the amphipods were collected and characterized using ATR-FTIR spectroscopy. DNA was extracted from gut samples for metagenomic analysis. Spectroscopic investigation suggested a partial digestion of polysaccharide components in the experimental polymeric materials. The analysis of the gut microbiota revealed that bioplastic feeding induced modification of sandhopper's gut microbial communities, shifting the abundance of specific microbial genera already present in the gut, towards bacterial genera associated with plastic/bioplastic degradation, especially in groups fed with starch-based bioplastics. Overall, our results highlight the involvement of T. saltator's gut microbiota in bioplastic modification, providing new insights into the potential role of microbial consortia associated to sandhoppers in bioplastic management.}, }
@article {pmid40086246, year = {2025}, author = {Han, NN and Yang, JH and Wu, GG and Yang, JH and Jin, JA and Fan, NS and Jin, RC}, title = {Differential size-dependent response patterns and antibiotic resistance development mechanism in anammox consortia.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137886}, doi = {10.1016/j.jhazmat.2025.137886}, pmid = {40086246}, issn = {1873-3336}, abstract = {Antibiotic resistance is a global threat to human and animal health. Anaerobic ammonia oxidation (anammox) is an efficient and innovative wastewater treatment technology, which can be served as a promising approach to teat antibiotic wastewater. This study systematically investigated effects of sulfamethazine on the performance, microbial community dynamics and the resistome in anammox systems inoculated with different-sized granular sludge. The activity and performance of small (< 0.5 mm) anammox granules were more susceptible to sulfamethazine stress than those of medium (0.5-1.0 mm) and large (1.0-2.0 mm) granules. Sulfamethazine addition greatly increased the diversity and abundance of mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs). Based on the metagenomic analysis, the horizontal transfer of ARGs in the anammox system was upregulated through bacterial oxidative stress, pili synthesis and type IV secretion system. In addition, two strains of sulfamethazine-resistant bacteria (Pseudomonas asiatica sp. nov. and Pseudomonas shirazica sp. nov.) were isolated from the anammox system. Their whole genome sequencing results showed that the most abundant plasmid was pkF7158B, which mediated the horizontal transfer of two main multidrug resistance genes (cpxR and mexB). This work provides a holistic insight into microbial heterogeneity of different-sized anammox granular sludge and their evolution and resistance development mechanism.}, }
@article {pmid40086153, year = {2025}, author = {Huang, JN and Liu, ZQ and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ}, title = {Stocking filter-feeder in fed fish aquaculture pond: Unexpected Aggravation of nitrous oxide emission.}, journal = {Water research}, volume = {280}, number = {}, pages = {123475}, doi = {10.1016/j.watres.2025.123475}, pmid = {40086153}, issn = {1879-2448}, abstract = {Intensive farming of fed fish could produce large amounts of uneaten feed and feces, potentially leading to increased nitrous oxide (N2O) emissions. Filter-feeding fish can ingest residual feed and feces, but it is unclear whether introducing them into fed fish farming ponds could reduce N2O emissions. This study employed monoculture of fed largemouth bass (Micropterus salmoides, LB) and polyculture of LB with filter-feeding silver carp (Hypophthalmichthys molitrix, SC) at density ratios of 18:1, 9:1 and 4.5:1 to compare the N2O emission characteristics. The results showed that silver carp could indeed feed on largemouth bass feces, and isotope mixing model indicated that feces was the second largest contributor to the food of silver carp, reaching 14.75 %-15.56 %. However, polyculture of the two species did not or even increased N2O emission flux at water-air interface and its release potential in sediment. Increased mineralization, nitrification and denitrification rates were observed in polyculture systems, particularly at high stocking densities of silver carp. Also, the higher NH4[+] accumulation were found across sediment-water interface within polyculture systems. Metagenome revealed that polyculture disturbed the microbial community structure and increased the abundance of Burkholderiales and Steroidobacteraceae. Moreover, polyculture increased the abundance of nitrogen-cycling functional genes, including gdhA, hao, nirB and norB, potentially contributing to the elevated N2O emissions. Structural equation model highlighted that polyculture of largemouth bass and silver carp could drive N2O emissions, mainly through increased sedimental NH4[+] concentration and microbial activity. These findings indicate that the introduction of extractive filter-feeding fish into fed fish farming ponds could not reduce N2O emissions, implying the need for optimized management strategies to balance aquaculture productivity with environmental sustainability.}, }
@article {pmid40085365, year = {2025}, author = {Makarani, N and Kaushal, RS}, title = {Advances in actinobacteria-based bioremediation: mechanistic insights, genetic regulation, and emerging technologies.}, journal = {Biodegradation}, volume = {36}, number = {2}, pages = {24}, pmid = {40085365}, issn = {1572-9729}, mesh = {*Biodegradation, Environmental ; *Actinobacteria/metabolism/genetics ; *Metals, Heavy/metabolism ; }, abstract = {Untreated wastewater from sewage, industries, and agriculture contaminates ecosystems due to rapid population growth and industrialization. It introduces hazardous pollutants, including pesticides, polycyclic aromatic hydrocarbons (PAHs), and heavy metals, which pose serious health risks such as cancer, lung disorders, and kidney damage, threatening both environmental and human well-being. Using microorganisms for bioremediation is thought to be safer and more effective. Compared to other approaches, bioremediation is the most effective way to absorb heavy metals. Due to the high cost and unreliability of traditional remediation techniques, such as chemical and physical treatments, interest in bioremediation as an environmentally benign substitute has grown. Through the use of microorganisms, bioremediation successfully removes heavy metals and breaks down organic contaminants from contaminated circumstances. Actinobacteria are unique among these microbes because of their flexibility in metabolism and capacity to endure severe environments. They create secondary metabolites, such as enzymes, that help break down a variety of pollutants. Actinobacteria also produce siderophores and extracellular polymeric substances (EPS), which aid in trapping organic contaminants and immobilizing heavy metals. This review explores the diverse applications of actinobacteria in bioremediation, with a focus on their mechanisms for breaking down and neutralizing pollutants. We highlighted the advancements in bioremediation strategies, including the use of mixed microbial cultures, biosurfactants, nanoparticles and immobilized cell technologies which enhance the efficiency and sustainability of pollutant removal. The integration of omics technologies such as metagenomics, meta-transcriptomics, and meta-proteomics provides deeper insights into the genetic and metabolic pathways involved in bioremediation, suggesting the way for the development of genetically optimized strains with enhanced degradation capabilities. By leveraging these emerging technologies and microbial strategies, actinobacteria-mediated bioremediation presents a highly promising approach for mitigating environmental pollution. Ongoing research and technological advancements in this field can further enhance the scalability and applicability of bioremediation techniques, offering sustainable solutions for restoring contaminated ecosystems and protecting human health.}, }
@article {pmid40085274, year = {2025}, author = {Rono, JK and Zhang, Q and He, Y and Wang, S and Lyu, Y and Yang, ZM and Feng, Z}, title = {Biochemical characterization of a bilfunctional endoglucanase/glucomannanase derived from mountain soil.}, journal = {Biotechnology letters}, volume = {47}, number = {2}, pages = {33}, pmid = {40085274}, issn = {1573-6776}, support = {32370089//National Natural Science Foundation of China/ ; }, mesh = {*Soil Microbiology ; *Enzyme Stability ; *Cellulase/genetics/metabolism/chemistry ; *Mannans/metabolism ; Hydrogen-Ion Concentration ; Substrate Specificity ; *Recombinant Proteins/genetics/metabolism/chemistry/isolation &amp; purification ; Temperature ; Escherichia coli/genetics ; Carboxymethylcellulose Sodium/metabolism ; Metagenome/genetics ; Kinetics ; Hydrolysis ; Cloning, Molecular ; }, abstract = {Metagenomics is increasingly recognized as a vital technique for exploring uncultured microorganisms, with one key application being the discovery of novel enzymes for industrial use. This study identified an endoglucanase gene from soil metagenome, termed ZFEG1801, which was expressed in E. coli BL21, purified, and characterized for its biochemical properties. The 72.8 kDa recombinant protein exhibited hydrolytic activity against sodium carboxymethyl cellulose (CMC) and konjac glucomannan (KG), with activities of 12.1 U/mg and 42.1 U/mg, respectively. The enzyme displayed optimal activity at pH 5 for CMC and pH 6 for KG, with broad pH stability ranging from 5 to 9. The optimal temperature was 40 °C, and it remained thermally stable between 20 and 40 °C, retaining over 60% of its activity. The enzyme activity remained stable in the presence of most metal ions; however, CMCase activity was inhibited by Cu[2+], while glucomannanase activity was inhibited by Mn[2+], Fe[3+], and Ca[2+]. The catalytic efficiency towards both substrates was reduced by addition of SDS, DMSO, ethanol, isopropanol and acetonitrile. The Vmax and Km of the purified recombinant enzyme were 106.4 μmol/L/min and 4.9 mg/mL for CMC, and 833.3 μmol/L/min and 11.1 mg/mL for KG, respectively. The dual catalytic properties of ZFEG1801, broad pH stability and resistance to additives, demonstrate its potential for use in various biomass degradation processes.}, }
@article {pmid40084919, year = {2025}, author = {Baalbaki, N and Slob, EMA and Kazer, SW and I Abdel-Aziz, M and Bogaard, HJ and Golebski, K and Maitland-van der Zee, AH}, title = {The Omics Landscape of Long COVID-A Comprehensive Systematic Review to Advance Biomarker, Target and Drug Discovery.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.16526}, pmid = {40084919}, issn = {1398-9995}, support = {//Health~Holland/ ; }, abstract = {An estimated 10% of coronavirus disease (COVID-19) survivors suffer from persisting symptoms referred to as long COVID (LC), a condition for which approved treatment options are still lacking. This systematic review (PROSPERO: CRD42024499281) aimed to explore the pathophysiological mechanisms underlying LC and potential treatable traits across symptom-based phenotypes. We included studies with primary data, written in English, focusing on omics analyses of human samples from LC patients with persistent symptoms of at least 3 months. Our search in PubMed and Embase, conducted on January 8, 2024, identified 642 studies, of which 29 met the inclusion criteria after full-text assessment. The risk of bias was evaluated using the Joanna Briggs Institute appraisal tool. The synthesis of omics data, including genomics, transcriptomics, proteomics, metabolomics, and metagenomics, revealed common findings associated with fatigue, cardiovascular, pulmonary, neurological, and gastrointestinal phenotypes. Key findings included mitochondrial dysfunction, dysregulated microRNAs associated with pulmonary dysfunction, tissue impairment, blood-brain barrier disruption, coagulopathy, vascular dysfunction, microbiome disturbances, microbial-derived metabolite production and persistent inflammation. Limitations include cross-study heterogeneity and variability in sampling methods. Our review emphasizes the complexity of LC and the need for further longitudinal omics-integrated studies to advance the development of biomarkers and targeted treatments.}, }
@article {pmid40084893, year = {2025}, author = {Yuan, S and Wu, Y and Balcazar, JL and Wang, D and Zhu, D and Ye, M and Sun, M and Hu, F}, title = {Expanding the potential soil carbon sink: unraveling carbon sequestration accessory genes in vermicompost phages.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0029625}, doi = {10.1128/aem.00296-25}, pmid = {40084893}, issn = {1098-5336}, abstract = {The compost microbiome is important in regulating soil carbon sequestration. However, there is limited information concerning phage communities and phage-encoded auxiliary metabolic genes (AMGs) in compost-applied soils. We combined metagenomics and meta-viromes to explore the potential role of bacterial and phage communities in carbon sequestration in the compost microbiome. The experiment comprised swine manure compost (SW) and vermicompost (VE) applied to the soil along with a control treatment (CK). The bacterial community richness decreased after swine manure application and increased after vermicomposting compared to the control treatment. The phage community in the vermicompost-applied soil was dominated (63.1%) by temperate phages. In comparison, the communities of the swine manure compost-applied soil (92.7%) and control treatments (75.4%) were dominated by virulent phages. Phage-encoded carbon sequestration AMGs were detected in all three treatments, with significant enrichment in the vermicompost-applied soil. The average carbon sequestration potential (the coverage ratio of phage AMGs:total genes) of phage AMGs (aceF, GT11, and GT6) in the vermicompost-applied soil (65.18%) was greater than in the swine manure-applied (0) and control soils (50.21%). The results highlight the role of phage-encoded AMGs in improving soil carbon sequestration in vermicompost-applied soil. The findings provide new avenues for increasing soil carbon sequestration.IMPORTANCEThe phage-bacteria interactions have a significant impact on the global carbon cycle. Soil microbial carbon sequestration is a process in combination withcarbon sequestration genes and growth activity. This is the first study aimed at understanding the carbon sequestration potential of phage communities in vermicompost. The results of this study provide variations in carbon sequestration genes in vermicompost microbial communities, and some novel phage auxiliary metabolic genes were revealed to assist bacterial communities to increase soil carbon sequestration potential. Our results highlight the importance of phages in soil carbon sequestration from the perspective of phage-bacterial community interactions.}, }
@article {pmid40084890, year = {2025}, author = {Sarkar, P and Beebe, M and Bhandari, G and Wielinski, J and Lowry, GV and Gulliver, D}, title = {Novel anaerobic selenium oxyanion reducers native to FGD wastewater for enhanced selenium removal.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0122224}, doi = {10.1128/aem.01222-24}, pmid = {40084890}, issn = {1098-5336}, abstract = {Biological treatment is a recognized approach for removing selenate and selenite oxyanions present in flue gas desulfurization (FGD) wastewater. However, the knowledge of the specific microbial species or communities responsible for reducing water-soluble selenium oxyanions to insoluble elemental selenium remains limited. In addition, the selenium oxyanion reduction genes and pathways have yet to be understood in these wastewaters. This study characterizes selenium oxyanion-reducing bacteria (SeRB) native to FGD wastewater, and the resulting elemental selenium particles formed. By selecting native SeRB microbes in a defined media, a novel resolution of these organisms has been achieved. This research identifies previously unrecognized selenium oxyanion-reducing capabilities in Anaerosolibacter, alongside predominant SeRB from Mesobacillus and Tepidibacillus genera. This work encompasses both 16S and metagenomic techniques to recover novel metagenome-assembled genomes, distinct to this environment. The biogenic selenium produced by these organisms was predominantly of elemental selenium, either amorphous or with a hexagonal structure. This study identifies the SeRB present in FGD wastewater and characterizes their selenium products, offering crucial insights to enhance the efficiency of biological treatment strategies and the potential of selenium recovery from this industrial waste.IMPORTANCEThis is the first report on the culturability and recovery of taxonomic and metabolic information of the anaerobic selenium oxyanion-reducing bacteria (SeRB) in flue gas desulfurization (FGD) wastewater. Selenium is a regulated contaminant in FGD wastewater found on average to be 3,130 µg/L that must be removed to meet EPA discharge limits of 16 µg/L (D. B. Gingerich, E. Grol, and M. S. Mauter, Environ Sci Water Res Technol 4:909-925, 2018, https://doi.org/10.1039/C8EW00264A; also see U.S. EPA EPA-821-R-20-001, 2020). Better understanding of anaerobic SeRB and the microbial community in FGD wastewater is needed to harness their full potential for the bioremediation and recovery of selenium from FGD wastewater. Optimizing the biotreatment strategies for these wastewaters promises to yield cleaner and healthier waterways and ecosystems, even as the United States undergoes a shift in its energy landscape.}, }
@article {pmid40084855, year = {2025}, author = {Brock, ML and Tavares-Reager, JF and Dong, J and Larkin, AA and Lam, T and Pineda, N and Olivares, CI and Mackey, KRM and Martiny, AC}, title = {Bacterial response to the 2021 Orange County, California, oil spill was episodic but subtle relative to natural fluctuations.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0226724}, doi = {10.1128/spectrum.02267-24}, pmid = {40084855}, issn = {2165-0497}, abstract = {An oil spill began in October 2021 off the coast of Orange County, California, releasing 24,696 gallons of crude oil into coastal environments. Although oil spills, such as this one, are recurrent accidents along the California coast, no prior studies have been performed to examine the severity of the local bacterial response. A coastal 10-year time series of short-read metagenomes located within the impacted area allowed us to quantify the magnitude and duration of the disturbance relative to natural fluctuations. We found that the largest change in bacterial beta-diversity occurred at the end of October. The change in taxonomic beta-diversity corresponded with an increase in the sulfur-oxidizing clade Candidatus Thioglobus, an increase in the total relative abundance of potential hydrocarbon-degrading bacteria, and an anomalous decline in the picocyanobacteria Synechococcus. Similarly, changes in function were related to anomalous declines in photosynthetic pathways and anomalous increases in sulfur metabolism pathways as well as aromatic degradation pathways. There was a lagged response in taxonomy and function to peaks in total PAHs. One week after peaks in total PAH concentrations, the largest shifts in taxonomy were observed, and 1 week after the taxonomy shifts were observed, unique functional changes were seen. This response pattern was observed twice during our sampling period, corresponding with the combined effect of resuspended PAHs and increased nutrient concentrations due to physical transport events. Thus, the impact of the spill on bacterial communities was temporally extended and demonstrates the need for continued monitoring for longer than 3 months after initial oil exposure.IMPORTANCEOil spills are common occurrences in waterways, releasing contaminants into the aquatic environment that persist for long periods of time. Bacterial communities are rapid responders to environmental disturbances, such as oil spills. Within bacterial communities, some members will be susceptible to the disturbance caused by crude oil components and will decline in abundance, whereas others will be opportunistic and will be able to use crude oil components for their metabolism. In many cases, when an oil spill occurs, it is difficult to assess the oil spill's impact because no samples were collected prior to the accident. Here, we examined the bacterial response to the 2021 Orange County oil spill using a 10-year time series that lies within the impacted area. The results presented here are significant because (i) susceptible and opportunistic taxa to oil spills within the coastal California environment are identified and (ii) the magnitude and duration of the in situ bacterial response is quantified for the first time.}, }
@article {pmid40083791, year = {2025}, author = {, }, title = {Erratum: Integrative analysis of intestinal flora and untargeted metabolomics in attention-deficit/hyperactivity disorder.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1576969}, doi = {10.3389/fmicb.2025.1576969}, pmid = {40083791}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1452423.].}, }
@article {pmid40083784, year = {2025}, author = {Yang, D and Wuyunsiqin,  and YanNiu,  and Hashentuya,  and Tana,  and Anna,  and Ma, M and Zhao, W and Menggenduxi,  and Wang, M}, title = {Traditional Mongolian Medicine Qiqirigan-8 alleviates non-alcoholic fatty liver disease via restoring gut microbiota and metabolism.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1517082}, pmid = {40083784}, issn = {1664-302X}, abstract = {BACKGROUND: Mongolian Medicine Qiqirigan-8 (MMQ-8) is a traditional Mongolian medicine formula used to treat fatty liver disease. However, the material basis and in vivo metabolic process of the therapeutic effect of MMQ-8 on non-alcoholic fatty liver disease (NAFLD) remain unclear.<br><br>METHODS: The chemical composition of MMQ-8 was determined using Ultra-high-performance liquid chromatography-quadrupole Exactive Mass spectrometry analysis (UHPLC-QE-MS). C57BL/6J mice were fed a choline-deficient diet for 12 weeks to induce a NAFLD model. Hematoxylin and Eosin (H&amp;E)-staining, combined with serum biochemical indexes, was used to observe liver appearance and characterize the pathological changes and functions of the liver. HE staining and Alcian Blue-Phosphoric Acid Schiff (AB-PAS) staining of the colon, along with ZO-1 immunofluorescence expression in the colon were used to reveal the effect of MMQ-8 on the disruption of the intestinal epithelial mucosal barrier in the NAFLD. The expression of intestinal tight junction genes was analyzed by qRT-PCR to observe the protective effect of MMQ-8 against intestinal epithelial mucosal barrier disruption. Fecal metagenomics and serum non-targeted metabolomics were used to reveal the effects of MMQ-8 on the gut microbiota and metabolism in mice with NAFLD. Finally, we emphasize the interaction between gut microbiota and metabolites through Spearman correlation coefficient analysis.<br><br>RESULTS: Mongolian Medicine Qiqirigan-8 contains 17 active ingredients, which can reduce hepatic steatosis and lobular inflammation in mice with NAFLD, and have protective effects against liver injury. MMQ-8 reduced the infiltration of inflammatory cells in the colon epithelium of model mice while restoring the number of goblet cells. MMQ-8 significantly enhanced ZO-1 protein expression in the colon, as well as the mRNA expression of both ZO-1 and Occludin. Fecal metagenomics results showed that MMQ-8 reduced the Bacillota/Bacteroidota ratio in NAFLD mice. Increased the abundance of beneficial bacteria such as Porphyromonadaceae, Prevotella, and Bacteroidota. and suppressed the abundance of dysfunctional bacteria, such as Bacillota, Acetatifactor, and Erysipelotrichaceae. Furthermore, metabolomics studies revealed that MMQ-8 intervention significantly regulated the expression of metabolites related to glutathione metabolism, butyric acid metabolism, sphingolipid metabolism, and glycerophospholipid metabolism in NAFLD mice compared to the model group. These metabolic pathways play key roles in NAFLD. According to Spearman's correlation coefficient analysis, up-regulation of Porphyromonadaceae, Prevotella, and Bacteroidota after MMQ-8 intervention was negatively correlated with LPC levels in glycerophospholipid metabolic pathways, while positively correlated with PC levels. In contrast, the relationship between Bacillota and Acetatifactor, which were down-regulated after MMQ-8 intervention, was the opposite. In addition, the up-regulation of Porphyromonadaceae, Prevotella, and Bacteroidota after MMQ-8 intervention was positively correlated with fumaric acid, 2-oxoglutaric acid, adenosine, and L-glutathione levels, while those down-regulated after MMQ-8 intervention were positively correlated with the levels of Bacillota, Acetatifactor were negatively correlated with all the above metabolites. Thus, glutathione metabolism, butyric acid metabolism, sphingolipid metabolism, glycerophospholipid metabolism and gut microbial ecosystem are tightly intertwined in this process.<br><br>CONCLUSION: In summary, these findings indicate that MMQ-8 has a synergistic anti-NAFLD effect through its multi-component, multi-target, gut microbiota-modulating and multi metabolic pathway characteristics. The host's regulation of specific gut microbiota and involvement in multiple metabolic pathways may be one of the important mechanisms by which MMQ-8 exerts its therapeutic effects on NAFLD. It is worth noting that metabolic pathways such as glutathione metabolism, butyric acid metabolism, sphingolipid metabolism, glycerophospholipid metabolism, and the gut microbiota ecosystem are closely intertwined in this process.}, }
@article {pmid40083550, year = {2025}, author = {Ng, HY and Liao, Y and Cheung, CL and Zhang, R and Chan, KH and Seto, WK and Leung, WK and Hung, IFN and Lam, TTY and Cheung, KS}, title = {Gut microbiota is associated with persistence of longer-term BNT162b2 vaccine immunogenicity.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1534787}, pmid = {40083550}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; Middle Aged ; Adult ; *BNT162 Vaccine/immunology ; *SARS-CoV-2/immunology ; *COVID-19/immunology ; Antibodies, Neutralizing/blood/immunology ; Immunogenicity, Vaccine ; Prospective Studies ; Antibodies, Viral/blood/immunology ; Hong Kong ; Feces/microbiology ; }, abstract = {INTRODUCTION: BNT162b2 immunogenicity wanes with time and we investigated association between gut microbiota and longer-term immunogenicity.<br><br>METHODS: This cohort study prospectively recruited adult BNT162b2 two-dose recipients from three vaccination centers in Hong Kong. Blood samples were collected at baseline and day 180 after first dose, and tested for neutralizing antibodies (NAb) against receptor-binding domain (RBD) of wild type SARS-CoV-2 virus using chemiluminescence immunoassay. Shotgun DNA metagenomic sequencing was performed to characterize baseline stool microbiome. Baseline metabolites were measured by gas and liquid chromatography-tandem mass spectrometry (GC-MS/MS and LC-MS/MS). Primary outcome was persistent high NAb response (defined as top 25% of NAb level) at day 180. Putative bacterial species and metabolic pathways were identified using linear discriminant analysis [LDA] effect size analysis. Multivariable logistic regression adjusting for clinical factors was used to derive adjusted odds ratio (aOR) of outcome with bacterial species and metabolites.<br><br>RESULTS: Of 242 subjects (median age: 50.2 years [IQR:42.5-55.6]; male:85 [35.1%]), 61 (25.2%) were high-responders while 33 (13.6%) were extreme-high responders (defined as NAb&#x2265;200AU/mL). None had COVID-19 at end of study. Ruminococcus bicirculans (log10LDA score=3.65), Parasutterella excrementihominis (score=2.82) and Streptococcus salivarius (score=2.31) were enriched in high-responders, while Bacteroides thetaiotaomicron was enriched in low-responders (score=-3.70). On multivariable analysis, bacterial species (R. bicirculans-aOR: 1.87, 95% CI: 1.02-3.51; P. excrementihominis-aOR: 2.2, 95% CI: 1.18-4.18; S. salivarius-aOR: 2.09, 95% CI: 1.13-3.94) but not clinical factors associated with high response. R. bicirculans positively correlated with most metabolic pathways enriched in high-responders, including superpathway of L-cysteine biosynthesis (score=2.25) and L-isoleucine biosynthesis I pathway (score=2.16) known to benefit immune system. Baseline serum butyrate (aOR:10.00, 95% CI:1.81-107.2) and isoleucine (aOR:1.17, 95% CI:1.04-1.35) significantly associated with extreme-high vaccine response.<br><br>CONCLUSION: Certain gut bacterial species, metabolic pathways and metabolites associate with longer-term COVID-19 vaccine immunogenicity.}, }
@article {pmid40083506, year = {2025}, author = {Zhou, Y and Ren, D and Chen, Y and Wen, S and Zhang, Y and Song, F and Yang, M and Eisenhut, M and O'Rourke, J and Li, Y and Gui, S}, title = {Presepsin, procalcitonin, interleukin-6, and high-sensitivity C-reactive protein for predicting bacterial DNAaemia among patients with sepsis.}, journal = {Journal of thoracic disease}, volume = {17}, number = {2}, pages = {991-1001}, pmid = {40083506}, issn = {2072-1439}, abstract = {BACKGROUND: Anti-infective therapy against pathogens is the key to treatment of sepsis. Metagenomic next-generation sequencing (mNGS) has higher sensitivity than blood culture. The aim of this study was to use mNGS to identify DNAaemia of pathogens and to assess the diagnostic accuracy of presepsin (PSEP), procalcitonin (PCT), interleukin-6 (IL-6), and high-sensitivity C-reactive protein (hsCRP) in differentiating between bacterial and nonbacterial infections in patients with sepsis.<br><br>METHODS: This retrospective study included patients with sepsis from November 2020 to September 2022 in the Shenzhen Second People's Hospital. Blood samples were sent for blood culture and mNGS when the patients were diagnosed with sepsis. Plasma PSEP, PCT, and IL-6 levels were measured using whole blood specimens that were collected and analyzed after a diagnosis of sepsis. Area under the receiver operating characteristic curve (AUC) was used to evaluate the accuracy of PSEP, PCT, IL-6, and hsCRP for prediction of bacterial DNAaemia detected by mNGS in patients with sepsis.<br><br>RESULTS: This study included 230 patients with sepsis. The bacterial DNAaemia rate was 53.0% [Gram-positive DNAaemia (GPD), Gram-negative DNAaemia (GND), and fungi DNAaemia rate was 18.2%, 37.8%, and 10.9%, respectively]. Among GND, Klebsiella was the most common, followed by Escherichia coli; meanwhile, the GPD were mainly Enterococcus, and Aspergillus was identified in 5 patients with sepsis. The PSEP median values were significantly higher in GND than in non-GND [GND: 1,291 pg/mL, interquartile range (IQR) 456-3,502 pg/mL; non-GND: 707 pg/mL, IQR 332-2,417 pg/mL; P=0.035]. There was no significant difference in PSEP values between GPD and non-GPD groups, or between fungi DNAaemia and non-fungi DNAaemia groups. Receiver operating characteristics analysis indicated that the best cutoff values for PSEP, PCT, IL-6, and hsCRP were 869 pg/mL, 1.14 ng/mL, 85.5 pg/mL, and hsCRP 96.2 mg/L, respectively. Logistic regression indicated that PSEP, PCT, IL-6, and hsCRP had significant predictive value for GND in patients with sepsis. The levels of PCT and IL-6 were different between patients with GPD and those with non-GPD. Only PCT levels differed significantly between fungal DNAaemia and nonfungal DNAaemia.<br><br>CONCLUSIONS: Bacterial-DNAaemia was detected in half of the patients with sepsis. PSEP, PCT, IL-6, and hsCRP demonstrated significant predictive value for GND, PCT and IL-6 levels demonstrated significant predictive value for GPD. Meanwhile, only PCT demonstrated significant predictive value for fungal DNAaemia.}, }
@article {pmid40083031, year = {2025}, author = {Wang, H and Li, Y and You, J and Feng, N and Wang, D and Su, Y and Feng, X}, title = {Diurnal oscillations of amino acids dynamically associate with microbiota and resistome in the colon of pigs.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {26}, pmid = {40083031}, issn = {2524-4671}, support = {2023YFD1301304//National Key R&amp;D Program of China/ ; 32072688//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Nutrients are one of the key determinants of gut microbiota variation. However, the intricate associations between the amino acid (AA) profile and the dynamic fluctuations in the gut microbiota and resistome remain incompletely elucidated. Herein, we investigated the temporal dynamics of AA profile and gut microbiota in the colon of pigs over a 24-hour period, and further explored the dynamic interrelationships among AA profile, microbiota, and resistome using metagenomics and metabolomics approaches.<br><br>RESULTS: JTK_circle analysis revealed that both the AA profile and the gut microbiota exhibited rhythmic fluctuations. With respect to the feed intake, all AAs except L-homoserine (PAdj = 0.553) demonstrated significant fluctuations. Over 50% of Lactobacillaceae, Ruminococcaceae, Clostridiaceae, and Eubacteriaceae species reached their peaks during T15&#x2009;&#x223c;&#x2009;T21 when 50% of Lachnospiraceae species experienced a trough. The eLSA results showed that most AAs positively correlated with Prevotellaceae species but negatively correlated with Lactobacillaceae and Lachnospiraceae species. Moreover, most of the AAs negatively correlated with the mobile genetic elements Tn916 and istA group but positively correlated with plasmids. Further partial least squares structural equation model analysis indicated that AAs affected the antibiotic resistance gene dynamics through mobile genetic elements and the gut microbiota.<br><br>CONCLUSIONS: Taken together, the AA profile and the gut microbiota exhibit robust fluctuations over a day. The AA profile can affect the gut microbiota and resistome in a direct or indirect manner. These findings may provide new insights into a potential strategy for manipulating the gut microbiota and resistome.}, }
@article {pmid40082992, year = {2025}, author = {Edminster, SY and Rebbe, RW and Khatchadourian, C and Hurth, KM and Mathew, AJ and Huss-Bawab, J and Shiroishi, MS and Clark, D and Norgan, AP and Butler-Wu, SM and Hiniker, A}, title = {The role of plasma metagenomic sequencing in identification of Balamuthia mandrillaris encephalitis.}, journal = {Acta neuropathologica communications}, volume = {13}, number = {1}, pages = {60}, pmid = {40082992}, issn = {2051-5960}, mesh = {Humans ; Female ; *Balamuthia mandrillaris/genetics/isolation &amp; purification ; Middle Aged ; *Amebiasis/diagnosis/cerebrospinal fluid ; *Metagenomics/methods ; Encephalitis/diagnosis/parasitology/cerebrospinal fluid ; High-Throughput Nucleotide Sequencing ; Infectious Encephalitis/diagnosis/cerebrospinal fluid ; Central Nervous System Protozoal Infections/diagnosis/parasitology ; Brain/pathology/parasitology ; }, abstract = {Balamuthia mandrillaris is a rare, free-living amoeba (FLA) that causes granulomatous amoebic encephalitis, a disease with close to 90% mortality. The geographical ranges of many FLA are expanding, potentially increasing human exposure to B. mandrillaris. Here, we report a case of a 58-year-old woman with progressive neurological symptoms, ultimately diagnosed postmortem with B. mandrillaris encephalitis through plasma metagenomic next-generation sequencing (mNGS) despite negative results on both cerebrospinal fluid (CSF) mNGS and CSF PCR testing. Histologic analysis and real-time PCR (qPCR) studies on postmortem brain tissue confirmed B. mandrillaris infection with significant vascular clustering of trophozoites. Retrospective analysis of CSF mNGS data demonstrated subthreshold reads for B. mandrillaris, emphasizing the challenges of interpreting low-level pathogen signals. A systematic review of 159 published B. mandrillaris cases revealed only two reports of B. mandrillaris diagnosed using plasma mNGS, both of which also had diagnostic CSF studies. This case demonstrates the diagnostic challenges of B. mandrillaris infections, highlights its vascular tropism, and suggests that plasma mNGS may warrant evaluation as a diagnostic tool for B. mandrillaris.}, }
@article {pmid40082612, year = {2025}, author = {Đokić, J and Dinić, M and Soković Bajić, S and Bisenić, A and Mitrović, H and Jakovljević, S and Radojević, D and Brdarić, E and Lukić, J and Živković, M and Tolinački, M and Terzić-Vidojević, A and Golić, N}, title = {High-throughput workflow for cultivation and characterization of gut microbiota strains with anti-inflammatory properties and metabolite signature associated with gut-brain communication.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8741}, pmid = {40082612}, issn = {2045-2322}, support = {Grant IDEAS No. 7744507, NextGenBiotics//Science Fund of the Republic of Serbia/ ; Grant No. 451-03-66/2024-03/200042//Ministry of Science, Technological Development and Innovations of the Republic of Serbia/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Brain-Gut Axis ; Anti-Inflammatory Agents/metabolism/pharmacology ; Workflow ; Bacteria/metabolism/classification/genetics ; Brain/metabolism ; Probiotics ; Metagenome ; }, abstract = {The gut microbiota is deeply interconnected with the brain, a phenomenon often referred to as the gut-brain axis. Dysfunction in the microbiota-gut-brain axis can cause various neurological and psychiatric disorders associated with chronic inflammation and gut microbiota dysbiosis. Therefore, cultivation of anaerobic human gut microbiota strains, and characterization of their safety status and immunomodulatory potential could contribute to deciphering the molecular mechanisms underlying the microbiota-gut-brain communication and revealed their biotherapeutic potential. However, poor cultivability of gut microbiota members, makes research into their physiological role challenging. Hence, we report a high-throughput workflow based on targeted cultivation linked to metagenome sequencing, combined with the bioinformatic search for gut members with anti-inflammatory properties which produce the most important microbial metabolites that affect brain function. With this approach, we isolated 147 bacterial strains, and 41 were characterized for their immunomodulatory status with 12 strains showing immunosuppressive features with ability of producing brain important metabolites. Through this workflow we established the best growing conditions essential for cultivation, archiving, phenotyping, and characterization of anaerobic gut bacteria important for microbiota-gut-brain-axis research, and characterized the safety and probiotic potential of 7 extremely oxygen-sensitive strains.}, }
@article {pmid40082593, year = {2025}, author = {Cardona, ST and Rahman, ASMZ and Novomisky Nechcoff, J}, title = {Innovative perspectives on the discovery of small molecule antibiotics.}, journal = {npj antimicrobials and resistance}, volume = {3}, number = {1}, pages = {19}, pmid = {40082593}, issn = {2731-8745}, support = {169121//Canadian Institutes of Health Research (CIHR)/ ; }, abstract = {Antibiotics are essential to modern medicine, but multidrug-resistant (MDR) bacterial infections threaten their efficacy. Resistance evolution shortens antibiotic lifespans, limiting investment returns and slowing new approvals. Consequently, the WHO defines four innovation criteria: new chemical class, target, mode of action (MoA), and lack of cross-resistance. This review explores innovative discovery approaches, including AI-driven screening, metagenomics, and target-based strategies, to develop novel antibiotics that meet these criteria and combat MDR infections.}, }
@article {pmid40082238, year = {2025}, author = {Yong-Chun, R and Yi-Qing, Z and Hai-Wang, Z and Jie, Z and Jin-Nan, D and Xiao-Jing, Z and Ming-Hui, LI}, title = {Metagenomic Next-Generation Sequencing-Assisted Diagnosis of Japanese Spotted Fever: Report of One Case.}, journal = {Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae}, volume = {47}, number = {1}, pages = {146-149}, doi = {10.3881/j.issn.1000-503X.15997}, pmid = {40082238}, issn = {1000-503X}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Rickettsia/genetics/isolation &amp; purification ; *Metagenomics/methods ; Spotted Fever Group Rickettsiosis/diagnosis/microbiology ; Male ; Doxycycline/therapeutic use ; }, abstract = {Japanese spotted fever(JSF)is an infectious disease caused by Rickettsia japonica,with nonspecific clinical symptoms and a high risk of misdiagnosis.We reported a case of JSF,in which Rickettsia japonica was detected in blood cells by metagenomic next-generation sequencing.The patient recovered after treatment with doxycycline.This report provides a reference for the clinical diagnosis and treatment of JSF.}, }
@article {pmid40082172, year = {2025}, author = {Wang, ZJ and Zhang, J and Shi, YY}, title = {Successful Oral Isavuconazole Monotherapy for Invasive Pulmonary Mucormycosis in Kidney Transplant Recipients: Case Reports and Literature Review.}, journal = {Transplantation proceedings}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.transproceed.2025.02.047}, pmid = {40082172}, issn = {1873-2623}, abstract = {This study represents 2 cases of kidney transplant recipients (KTRs) with invasive pulmonary Rhizopus infection, successfully treated with oral isavuconazole monotherapy without lobectomy. The rapid detection via mNGS of bronchoalveolar lavage fluid enabled early diagnosis and timely intervention, resulting in complete recovery and stable graft function. The literature review revealed a 16.7% mortality rate among 13 cases, with a higher mortality rate of 66.7% among patients receiving antifungal treatment without surgical intervention. Our findings underscore the efficacy of isavuconazole as a first-line monotherapy, characterized by lower nephrotoxicity and fewer interactions with immunosuppressants, and emphasize the crucial role of metagenome next-generation sequencing (mNGS) in early diagnosis of invasive mucormycosis in high-risk population.}, }
@article {pmid40082024, year = {2025}, author = {Yin, F and Ge, T and Zalucki, MP and Xiao, Y and Peng, Z and Li, Z}, title = {Gut symbionts affect Plutella xylostella (L.) susceptibility to chlorantraniliprole.}, journal = {Pesticide biochemistry and physiology}, volume = {209}, number = {}, pages = {106327}, doi = {10.1016/j.pestbp.2025.106327}, pmid = {40082024}, issn = {1095-9939}, mesh = {Animals ; *ortho-Aminobenzoates/pharmacology ; *Moths/drug effects/microbiology ; *Insecticides/pharmacology ; *Insecticide Resistance/genetics ; *Gastrointestinal Microbiome/drug effects ; *Symbiosis ; Bacteria/drug effects/genetics/metabolism ; Larva/drug effects/microbiology ; }, abstract = {Plutella xylostella, a globally economically important pest of cruciferous crops, has varying degrees of resistance to almost all insecticides. Insect gut microbiotas have a variety of physiological functions, and recent studies have shown that they have some potential connection with insecticide resistance. Here, we use metagenomics to analyze the differences in gut microbiota among 5 different populations of P. xylostella resistant to chlorantraniliprole. Differential gene expression was enriched in various metabolic pathways including carbohydrate metabolism, amino acid metabolism, energy metabolism, metabolism of cofactors and vitamins, nucleotide metabolism and so on. Proteobacteria was the dominate phyla, and the relative abundance of common dominant genera in the treated group (CL, Bt, and BtCL) was higher than that in susceptible controls. We successfully isolated 15 species of bacteria, in which the Enterobacter hormaechei was associated with enhanced insecticide resistance. The population we isolated can metabolize chlorantraniliprole in vitro, with a metabolic rate of 34.8 % within 4 days. Our work advances understanding of the evolution of insecticide resistance and lays a foundation for the further exploration of symbiotic microbial associations of lepidopteran insects and their ecological consequences.}, }
@article {pmid40082000, year = {2025}, author = {Massaro, CA and Meade, S and Lemarié, FL and Kaur, G and Bressler, B and Rosenfeld, G and Leung, Y and Williams, AJ and Lunken, G}, title = {Gut microbiome predictors of advanced therapy response in Crohn's disease: protocol for the OPTIMIST prospective, longitudinal, observational pilot study in Canada.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e094280}, doi = {10.1136/bmjopen-2024-094280}, pmid = {40082000}, issn = {2044-6055}, mesh = {Humans ; *Crohn Disease/microbiology/therapy ; *Gastrointestinal Microbiome ; Pilot Projects ; Prospective Studies ; Longitudinal Studies ; Observational Studies as Topic ; Feces/microbiology ; British Columbia/epidemiology ; Canada ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis, is characterised by chronic and relapsing inflammation of the gastrointestinal tract, leading to significant morbidity and reduced quality of life. The global rise in IBD incidence is driven by a complex interplay of genetic, environmental, dietary and microbiome-related factors. Despite advancements in treatment, such as biologics, response rates remain variable, highlighting the need for personalised approaches. Recent research suggests that specific microbiome signatures may serve as biomarkers for predicting therapeutic efficacy, offering a potential tool for optimising treatment strategies in CD. The aim of the Optimising IBD Patient Treatment with Integrated Microbiome Investigation for Specialised Therapeutics (OPTIMIST) study is to evaluate microbiome profiles across various sample types in a Canadian CD cohort starting or already on advanced therapy, with the goal of developing predictive models for personalised therapeutics.<br><br>METHODS AND ANALYSIS: This study is a two-phase, longitudinal, prospective observational pilot study conducted in British Columbia, Canada, involving both CD patients and non-IBD controls. Phase 1 focuses on baseline microbiome differences across participant cohorts through cross-sectional analysis. Phase 2 follows participants over 12 months to assess microbiome changes and their association with treatment response. Stool samples, intestinal biopsies from the left colon, right colon and ileum, as well as mucosal wash samples from the proximal part of the distal colon, will undergo metagenomics, metaproteomics and metabolomics analyses to explore compositional and functional differences. Data will be analysed using alpha and beta diversity metrics, differential abundance analyses and multivariate analyses to identify microbiome-based predictors of therapeutic response.<br><br>ETHICS AND DISSEMINATION: Ethical approval was received by the Research Ethics Board (REB) of University of British Columbia-Providence Healthcare (UBC-PHC) with a REB number H23-02927. All amendments to the protocol are reported and adapted based on the requirements of the REB. The results of this study will be submitted to peer-reviewed journals and will be communicated in editorials/articles by the IBD Centre of BC and BC Children's Hospital Research Institute.<br><br>TRIAL REGISTRATION NUMBER: NCT06453720.<br><br>PROTOCOL VERSION: 2024-06-21, version 3.0.}, }
@article {pmid40081757, year = {2025}, author = {Armengaud, J}, title = {The dawn of the revolution that will allow us to precisely describe how microbiomes function.}, journal = {Journal of proteomics}, volume = {}, number = {}, pages = {105430}, doi = {10.1016/j.jprot.2025.105430}, pmid = {40081757}, issn = {1876-7737}, abstract = {The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others - is known as the microbiota. A holobiont, in turn, refers to an integrated ecological unit where microbial communities function and interact with their host, thus is a more integrative concept. To understand the processes involved, the diversity of microorganisms present must be identified and their molecular components quantified, especially proteins. Indeed, proteins - through their roles as catalytic units, structural components, and signaling molecules - are the main drivers of biological processes. Metagenomics has significantly expanded what we know about the genetic material present in microbiota, revealing their functional potential; metabolomics delivers an overall snapshot of the metabolites produced by the community. But metaproteomics offers a complementary approach to explore microbiome and holobiont functionality by focusing on the active proteins and functional pathways from each taxon. Significant recent advances in high-resolution tandem mass spectrometry have greatly expanded the catalog of peptide sequences accessible in each sample, creating the conditions for unprecedented taxonomical profiling, while also providing more accurate biomass quantification, more detailed protein characterization, and a greater capacity to monitor abundance and distinguish host biomarkers. By integrating artificial intelligence into the metaproteomics pipeline, extended datasets can now be efficiently mined to gain a more comprehensive functional view of complex biological systems, paving the way for next-generation metaproteomics. In this perspective, I discuss the transformative potential of this methodology. We are on the cusp of a remarkable omic revolution that promises to uncover the intricate workings of microbiomes by producing a vast array of new knowledge with multiple applications. SIGNIFICANCE: Metaproteomics provides a powerful lens to investigate microbiome and holobiont functionality by identifying and quantifying active proteins and functional pathways within each taxon. Recent breakthroughs in high-resolution tandem mass spectrometry have dramatically expanded the repertoire of peptide sequences detectable per sample. This progress enables unprecedented taxonomic resolution for microbial identification, more precise biomass quantification, comprehensive protein characterization, abundance monitoring, and the unique identification of host biomarkers. In this commentary, I delve into the distinctive features that make metaproteomics a transformative tool. I discuss the recent advancements in tandem mass spectrometry and argue that the primary challenge in analyzing complex samples is shifting from data acquisition to data interpretation. With the integration of artificial intelligence, I believe next-generation metaproteomics is poised to become the next Big Thing in microbiome research, unlocking profound insights into microbial functionality and ecosystem dynamics.}, }
@article {pmid40081368, year = {2025}, author = {Dai, R and Zhang, J and Liu, F and Xu, H and Qian, JM and Cheskis, S and Liu, W and Wang, B and Zhu, H and Pronk, LJU and Medema, MH and de Jonge, R and Pieterse, CMJ and Levy, A and Schlaeppi, K and Bai, Y}, title = {Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.02.013}, pmid = {40081368}, issn = {1097-4172}, abstract = {Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.}, }
@article {pmid40081359, year = {2025}, author = {Ali, MJ}, title = {Metagenomic Profile of the Lacrimal Sac Microbial Communities in Congenital Nasolacrimal Duct Obstruction: The Lacriome Paper 7.}, journal = {Ophthalmic plastic and reconstructive surgery}, volume = {}, number = {}, pages = {}, doi = {10.1097/IOP.0000000000002931}, pmid = {40081359}, issn = {1537-2677}, abstract = {PURPOSE: To study the metagenomics of microbes isolated from the lacrimal sacs of patients with congenital nasolacrimal duct obstruction (CNLDO).<br><br>METHODS: A prospective study was performed on 10 consecutive lacrimal sac samples obtained for the metagenomic analysis from the patients with CNLDO who underwent endoscopic dacryocystorhinostomy at a tertiary care dacryology service. Immediately after a full-length lacrimal sac marsupialization, the samples were collected and transported on ice to the laboratory. A whole shotgun metagenome sequencing was performed on the Illumina platform following DNA extraction and library preparation. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in the SqueezeMeta pipeline, and the functional annotation was performed using the MetaCerberus, v1.3.1.<br><br>RESULTS: The taxonomic hit distribution across the samples showed that bacteria were the most common isolates, followed by fungi and viruses. The major bacterial phyla identified across the samples of CNLDO were proteobacteria, firmicutes, actinobacteria, and bacteroidetes. The prevalent organisms include Haemophilus influenzae, Streptococcus pneumoniae, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Staphylococcus aureus, and Ochrobactrum anthropi, among others. The predominant fungal species identified include Botrytis cinerea, Aspergillus oryzae, and Fusarium fujikuroi. Several species of pandoravirus were the common viruses recognized.<br><br>CONCLUSIONS: This is the first whole metagenome sequencing of the lacrimal sac contents from patients with CNLDO, which showed that the sacs harbored diverse microbial communities of bacteria, fungi, and viruses. Further work is needed to decipher the polymicrobial interactions and their relationship with CNLDO.}, }
@article {pmid40081035, year = {2025}, author = {Qv, M and Dai, D and Wu, Q and Wang, W and Li, L and Zhu, L}, title = {Metagenomic insight into the horizontal transfer mechanism of fluoroquinolone antibiotic resistance genes mediated by mobile genetic element in microalgae-bacteria consortia.}, journal = {Journal of environmental management}, volume = {380}, number = {}, pages = {124946}, doi = {10.1016/j.jenvman.2025.124946}, pmid = {40081035}, issn = {1095-8630}, abstract = {Antibiotics could accumulate in the environment with the discharge of wastewater from families, hospitals and livestock farms, which intensifies the spread of resistance genes around the world. Although microalgae-bacteria consortia (MBC) can efficiently remove antibiotics, the horizontal transfer mechanism of antibiotics resistance genes in MBC is still rarely reported. In this study, the removal efficiency of ofloxacin, norfloxacin and enrofloxacin by MBC under different antibiotic concentrations was investigated, while resistance genes in the MBC were identified and the mechanism of horizontal transfer was disclosed. The results showed that norfloxacin removal efficiency (up to 56.35 %) surpassed that of ofloxacin and enrofloxacin. The abundance of the fluoroquinolone resistance gene QnrS8 was the highest at 1331. The horizontal transfer of resistance gene QnrS8 and QnrS11 were mainly mediated by transposons. Fluoroquinolones increased the abundance of Brevundimonas (<0.10 % up to 9.63 %) and Bosea (0.96 % up to 17.67 %) involved in antibiotic removal. Arthrobacter and Acidovorax might be potential hosts which carried fluoroquinolone resistance genes. Structural equation model indicated that the key factor influencing the fluoroquinolone resistance genes abundance in MBC was transposons. These findings drew an insightful understanding of MBC application for fluoroquinolone antibiotics removal and the horizontal transfer mechanism of fluoroquinolone resistance genes.}, }
@article {pmid40080648, year = {2025}, author = {Starcevic, A and Figueredo, RTA and Naldoni, J and Corrêa, LL and Okamura, B and Adriano, EA and Long, PF}, title = {Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa).}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf014}, pmid = {40080648}, issn = {2047-217X}, support = {2019/17427-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 307485/2023-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*DNA Methylation ; *Myxozoa/genetics ; Animals ; *Cytosine/metabolism ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; }, abstract = {Oxford-Nanopore PromethION sequencing is a PCR-free method that retains epigenetic markers and provides direct quantitative information about DNA methylation. Using this long-read sequencing technology, we successfully assembled 5 myxozoan genomes free from discernible host DNA contamination, surpassing previous studies in both quality and completeness. Genome assembly revealed DNA methylation patterns within myxozoan genomes, particularly in GC-rich regions within gene bodies. The findings not only refute the notion of myxozoans lacking DNA methylation capability but also offer a new perspective on gene regulation in these parasites. The high-quality genome assemblies lay a solid foundation for future research on myxozoans, including new strategies to control these commercially significant fish pathogens.}, }
@article {pmid40080343, year = {2025}, author = {Birkeland, KW and Mostert, L and Claas, ECJ and Aamot, HV and Demuyser, T}, title = {The added value of metagenomic next-generation sequencing in central nervous system infections: a systematic review of case reports.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {40080343}, issn = {1439-0973}, abstract = {BACKGROUND: The diversity of pathogens causing central nervous system (CNS) infections presents a diagnostic challenge. Patient demographics and geographical location affect the likelihood of certain pathogens causing infection. Current diagnostic methods rely on labour-intensive cultivation or targeted detection. Metagenomic next-generation sequencing (mNGS) is a promising tool for detecting pathogens in CNS infections, offering an unbiased approach. To enhance our understanding of patient demographics and the range of pathogens identified through mNGS, we conducted a systematic review of case reports.<br><br>METHODS: The PubMed database was searched in March 2024. Case reports on CNS infections and mNGS published from January 2014 through February 2024 were included based on predefined criteria.<br><br>RESULTS: The search yielded 649 articles, of which 76 were included, encompassing 104 patients. Most patients were male (75%), the median age was 31,5 years [0-75] and 28% were immunocompromised. The most common diagnosis was encephalitis (36%), followed by meningitis (23%) and meningoencephalitis (22%). 53 unique pathogens were identified, comprising 27 different viruses, 19 bacteria, 5 parasites, and 2 fungi. Syndromic encephalitis/meningitis panels would only have detected four of the viruses and five of the bacteria. Additionally, 14 of the bacterial species are considered slow-growing or fastidious and could be challenging to detect by culture.<br><br>CONCLUSION: The application of mNGS in diagnosing CNS infections reveals the diversity of pathogens responsible for these severe infections, thereby improving diagnostics and facilitating targeted treatment. While case reports may be subjected to bias, they provide valuable insights into the use of mNGS in this clinical context.}, }
@article {pmid40079640, year = {2025}, author = {Passos, GS and Pellegrinetti, TA and Fiore, MF}, title = {Metagenome-assembled bacterial genomes from long accurate reads associated with Capilliphycus salinus ALCB114379.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0080724}, doi = {10.1128/mra.00807-24}, pmid = {40079640}, issn = {2576-098X}, abstract = {We report the complete genome sequences of five bacteria associated with the marine cyanobacterium Capilliphycus salinus ALCB114379 of the phylum Pseudomonadota. This genetic diversity offers insights into the cyanosphere, shedding light on potential relationships between these microorganisms and their cyanobacterial hosts.}, }
@article {pmid40078981, year = {2024}, author = {Hu, T and Cheng, Y and Wan, J and Liu, Y and Zhuang, Y and Zhou, M and Zhang, X and Tan, X and Deng, A and Zhang, M and Wang, P and Li, X and Zong, J and Cheng, L and Kang, M}, title = {Q fever diagnosed using metagenomic next-generation sequencing in Guangdong Province, China.}, journal = {Biosafety and health}, volume = {6}, number = {6}, pages = {337-340}, pmid = {40078981}, issn = {2590-0536}, abstract = {Q fever is a zoonotic disease caused by infection with Coxiella burnetii (C. burnetii). Due to its atypical symptoms and the absence of specific detection methods, Q fever is underdiagnosed commonly. Herein, we report a case of Q fever confirmed by metagenomic next-generation sequencing (mNGS) in March 2024 in Guangdong Province, China. The patient initially experienced fever and was admitted to hospital six days later. Despite a series of laboratory tests conducted at the hospital, the pathogen remained undetermined. Ten days after admission, mNGS revealed that the patient was infected with C. burnetii. The patient subsequently underwent treatment with doxycycline and recovered well. Epidemiological investigation revealed that the patient had been exposed to sheep infected with C. burnetii without any protective measures in Jiangxi Province, China. Based on the comprehensive results of mNGS, exposure history, clinical manifestations and treatment response, the patient was confirmed as a Q fever case. As a neglected and underestimated illness, Q fever necessitates an elevation in awareness among medical staff and the public. The public should be encouraged to take personal protective measures when exposed to livestock. Further research is needed to explore the rational application of mNGS in the diagnosis of uncommon and unknown diseases.}, }
@article {pmid40078947, year = {2024}, author = {Fan, Q and Jiang, M and Zhang, J and Tang, G and Gao, M and Wen, Y and Deng, X and Dai, J and Lai, H and Qian, P and Lin, Y and He, R and Li, L and Li, Y and Li, Z and Liu, X and Li, Y and Yu, N and Lan, Y and Hu, F and Li, F}, title = {Prevalence of bacteria, fungi, and virus coinfections with SARS-CoV-2 Omicron variant among patients with severe COVID-19 in Guangzhou, China, winter 2022.}, journal = {Biosafety and health}, volume = {6}, number = {2}, pages = {92-97}, pmid = {40078947}, issn = {2590-0536}, abstract = {The status of coinfection during the national outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.5.2 or BF.7 in China in the winter of 2022, which is suspected to contribute substantially to the overloaded severe cases, needs to be investigated. We analyzed the coinfection status of 385 severe patients infected with the Omicron variant in Guangzhou using metagenomic sequencing. We found that 317 (82.3 %) patients were coinfected with at least one additional pathogen(s), including bacteria (58.7 %), fungi (27.1 %) and viruses (73.5 %). Pseudomonas aeruginosa (P. aeruginosa) (24.2 %), Staphylococcus aureus (S. aureus) (14.0 %), and Klebsiella pneumoniae (K. pneumonia) (13.4 %) ranked as the top three coinfected bacteria. Aspergillus fumigatus (A. fumigatus) (39.5 %), Pneumocystis jirovecii (P. jirovecii) (24.4 %) and Canidia albicans (C. albicans) (22.1 %) were the top three coinfected fungi. Epstein-Barr virus (EBV) (63.1 %), Human herpesvirus 7 (HHV-7) (34.8 %), and Herpes simplex virus 1 (HSV-1) (32.6 %) were the top three coinfected viruses. Of note, the detection of multiple coinfections of potential pathogenic bacteria, fungi, and viruses, despite lacking consistent patterns, highlighted a complicated synergistic contribution to disease severity. Our study presents the most comprehensive spectrum of bacterial, fungal, and viral coinfections in Omicron-associated severe coronavirus disease 2019 (COVID-19), implying that the coinfection of conditional pathogens might synergistically deteriorate the Omicron infection outcomes.}, }
@article {pmid40078943, year = {2024}, author = {Wang, Y and Qu, M and Bi, Y and Liu, WJ and Ma, S and Wan, B and Hu, Y and Zhu, B and Zhang, G and Gao, GF}, title = {The multi-kingdom microbiome catalog of the chicken gastrointestinal tract.}, journal = {Biosafety and health}, volume = {6}, number = {2}, pages = {101-115}, doi = {10.1016/j.bsheal.2024.02.006}, pmid = {40078943}, issn = {2590-0536}, abstract = {Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs. Despite recent significant advances in gut microbiome studies, a comprehensive study of chicken gut bacterial, archaeal, and viral genomes remains unavailable. In this study, we constructed a chicken multi-kingdom microbiome catalog (CMKMC), including 18,201 bacterial, 225 archaeal, and 33,411 viral genomes, and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes (MAGs) from ten countries. We found that 812 and 240 MAGs in our dataset were putative novel species and genera, respectively, far beyond what was previously reported. The newly unclassified MAGs were predominant in Phyla Firmicutes_A (n = 263), followed by Firmicutes (n = 126), Bacteroidota (n = 121), and Proteobacteria (n = 87). Most of the classified species-level viral operational taxonomic units belong to Caudovirales. Approximately, 63.24 % of chicken gut viromes are predicted to infect two or more hosts, including complete circular viruses. Moreover, we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by viruses. Together, our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date, functional insights into the chicken gastrointestinal tract microbiota, and paves the way for microbial interventions for better chicken health and productivity.}, }
@article {pmid40078550, year = {2025}, author = {Wang, G and Haenelt, S and Corrêa, FB and da Rocha, UN and Musat, F and Zhang, J and Müller, JA and Musat, N}, title = {Riverine antibiotic resistome along an anthropogenic gradient.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1516033}, doi = {10.3389/fmicb.2025.1516033}, pmid = {40078550}, issn = {1664-302X}, abstract = {The introduction of antibiotic-resistant bacteria into riverine systems through the discharge of wastewater treatment plant (WWTP) effluent and agricultural waste poses significant health risks. Even when not pathogenic, these bacteria can act as reservoirs for antibiotic resistance genes (ARGs), transferring them to pathogens that infect humans and animals. In this study, we used fluorescence in situ hybridization, qPCR, and metagenomics to investigate how anthropogenic activities affect microbial abundance and the resistome along the Holtemme River, a small river in Germany, from near-pristine to human-impacted sites. Our results showed higher bacterial abundance, a greater absolute and relative abundance of ARGs, and a more diverse ARG profile at the impacted sites. Overall, the ARG profiles at these sites reflected antibiotic usage in Germany, with genes conferring resistance to drug classes such as beta-lactams, aminoglycosides, folate biosynthesis inhibitors, and tetracyclines. There were also variations in the ARG profiles of the impacted sites. Notably, there was a high abundance of the oxacillin resistance gene OXA-4 at the downstream site in the river. In the metagenome assembly, this gene was associated with a contig homologous to small plasmids previously identified in members of the Thiotrichaceae. The likely in-situ host of the putative plasmid was a close relative of Thiolinea (also known as Thiothrix) eikelboomii, a prominent member of WWTP microbiomes worldwide. Our results show that the effluent from WWTPs can introduce bacteria into the environment that act as shuttle systems for clinically relevant ARG.}, }
@article {pmid40078542, year = {2025}, author = {Zhang, C and Liu, Z and Yu, H and Shen, Y and Lu, L and Kong, F and Sun, W and Wei, X and Jin, L and Ge, L and Zeng, B}, title = {Dynamic changes in the gut microbiota of SPF Bama piglets during breast and formula feeding.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1537286}, doi = {10.3389/fmicb.2025.1537286}, pmid = {40078542}, issn = {1664-302X}, abstract = {The gut microbiota plays a crucial role in the growth performance, health status, and welfare of pigs. Breast milk is a key factor in the colonization of gut microbiota and the overall health of newborn piglets. With advancements in breeding technology, formula milk has been widely adopted as a substitute for breast milk. This study aims to investigate the effects of sow feeding (natural breastfeeding) and formula milk feeding on the gut microbiota of specific pathogen-free (SPF) Bama pigs. Using metagenomic sequencing technology, we analyzed 114 fecal samples to uncover the impacts of different feeding methods on gut microbial diversity, dominant microbial populations, metabolic functions, carbohydrate-active enzymes (CAZymes), and antibiotic resistance genes (ARGs). The results revealed significant differences in the structure and function of gut microbiota between the breast milk (BM) group and the formula milk (FM) group at day 21. The BM group exhibited higher gut microbial diversity compared to the FM group, along with more extensive metabolic functions at both the gene and species levels. Notably, the FM group demonstrated higher activity in galactose metabolism and glycan metabolism, particularly at day 21. Additionally, the FM group showed significantly higher levels of ARGs against glycopeptide antibiotics at days 21 and 28 compared to the BM group. This study also found that breastfeeding and formula feeding differentially regulate the metabolic activity of gut microbiota and the expression of related enzymes, which may have long-term effects on nutrient absorption and disease resistance in pigs. These findings provide new insights into how different feeding methods shape the gut microbiota of pigs and offer a scientific basis for optimizing feeding strategies and improving breeding efficiency.}, }
@article {pmid40078316, year = {2025}, author = {Zhao, C and Escalante, C and Jacobson, AL and Balkcom, KS and Conner, KN and Martin, KM}, title = {Metatranscriptomic and metagenomic analyses of cotton aphids (Aphis gossypii) collected from cotton fields in Alabama, USA.}, journal = {Frontiers in insect science}, volume = {5}, number = {}, pages = {1461588}, doi = {10.3389/finsc.2025.1461588}, pmid = {40078316}, issn = {2673-8600}, }
@article {pmid40077957, year = {2025}, author = {Ma, Z and Wen, X and Zhang, Y and Ai, Z and Zhao, X and Dong, N and Dou, X and Shan, A}, title = {Thymol Alleviates Colitis by Modulating Intestinal Barrier Damage, Gut Microbiota, and Amino Acid Metabolic Pathways.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c10406}, pmid = {40077957}, issn = {1520-5118}, abstract = {Thymol (THY) is a phenolic monoterpene compound that has garnered attention due to its various biological properties, including antioxidant, anti-inflammatory, and immune-regulatory effects. The purpose of this study was to determine the therapeutic and protective effects of THY in colitic mice, with a particular focus on the mechanisms involving gut microbiota. The results showed that early intervention with THY (40 and 80 mg/kg) not only alleviated the clinical symptoms and colonic damage in mice with dextran sodium sulfate (DSS)-induced colitis but also suppressed the colonic production of inflammatory cytokines (IL-1β, IL-6, and IL-18) and enhanced the expression of mucins (MUC1 and MUC2) and trefoil factor family 3 (TFF3), thereby improving the integrity of the intestinal epithelial barrier. In addition, THY altered the composition of the gut microbiota in colitis mice by increasing the abundance of Bacteroides and reducing the abundance of Proteobacteria. Fecal microbial transplantation (FMT) results demonstrated that FM from THY donor mice significantly improved symptoms of inflammatory bowel disease (IBD), confirming the crucial role of the gut microbiota. Metagenomic and untargeted metabolomic studies found that the characteristic microbiota of THY is Prevotellaceae, and THY significantly upregulated the amino acid metabolic pathways related to arginine and proline metabolism, arginine biosynthesis, and glycerophospholipid metabolism. In summary, THY holds significant potential as a functional additive to enhance host intestinal activity.}, }
@article {pmid40077671, year = {2025}, author = {Gao, Y and Borjihan, Q and Zhang, W and Li, L and Wang, D and Bai, L and Zhu, S and Chen, Y}, title = {Complex Probiotics Ameliorate Fecal Microbiota Transplantation-Induced IBS in Mice via Gut Microbiota and Metabolite Modulation.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/nu17050801}, pmid = {40077671}, issn = {2072-6643}, support = {2022-Science and Technology Xing Meng-Quality improvement-02//the Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; 2022-Science and Technology Xing Meng-Quality improvement-02//the Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Irritable Bowel Syndrome/therapy/microbiology ; *Fecal Microbiota Transplantation ; *Probiotics/pharmacology ; Mice ; *Feces/microbiology ; *Disease Models, Animal ; Mice, Inbred C57BL ; Male ; Dysbiosis/therapy ; Serotonin/metabolism ; Serotonin Plasma Membrane Transport Proteins/metabolism ; Acetic Acid ; Constipation/therapy/microbiology/metabolism ; Butyric Acid/metabolism ; Tryptophan/metabolism ; }, abstract = {Background/Objectives: Irritable bowel syndrome (IBS) is a highly prevalent functional gastrointestinal disorder. Emerging evidence implicates gut microbiota dysbiosis in IBS pathogenesis, and probiotic interventions targeting microbial modulation hold therapeutic promise. Methods: this study used fecal microbiota transplantation to establish a mouse model of IBS before evaluating the effects of the complex probiotic by using metagenomics and targeted metabolomics to explore the potential mechanism. Results: After 14 days, the probiotic relieved constipation, reduced inflammation and intestinal permeability, lowered 5-HT levels and increased serotonin transporter (SERT) expression in tissues. Metagenomic analysis showed a reduced inflammation-related species abundance. It also decreased fecal butyric acid, acetic acid and tryptophan levels in IBS mice. Conclusions: The probiotic complex effectively alleviated IBS symptoms in mice by modulating gut microbiota and fecal metabolites, providing insights for future IBS research and treatment.}, }
@article {pmid40077516, year = {2025}, author = {Li, W and Xu, M and Liu, Y and Zhang, S and Wang, J and Zhang, Z and Xiao, G and Wang, R and Zhang, J and Xue, H}, title = {Lactiplantibacillus plantarum GOLDGUT-HNU082 Alleviates CUMS-Induced Depressive-like Behaviors in Mice by Modulating the Gut Microbiota and Neurotransmitter Levels.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/foods14050813}, pmid = {40077516}, issn = {2304-8158}, support = {No. 32222066//National Natural Science Foundation of China/ ; THAITS-4//Earmarked Fund for Tropical High-efficiency Agricultural Industry Technology System of Hainan University/ ; }, abstract = {Emerging evidence links depressive disorders to the gut microbiota via the gut-brain axis. Probiotics, which are microorganisms that modulate the gut microbiota, have shown promising results in alleviating depression and are increasingly recognized as functional food components with potential health benefits. This study examines the effects of Lactiplantibacillus plantarum GOLDGUT-HNU082 (Lp082), a probiotic strain with potential applications in functional foods, on chronic unpredictable mild stress (CUMS)-induced depression in mice. Behavioral tests, measurements of the neurotransmitters and inflammatory cytokines in the serum and colon tissue, and the metagenomic sequencing of the gut microbiota were used to investigate potential mechanisms. The results demonstrated that Lp082 significantly alleviated depressive-like behaviors in CUMS mice, restored the balance of key neurotransmitters like serotonin (5-HT), reduced the levels of inflammatory cytokines like TNF-α, and enhanced brain neuroplasticity by promoting hippocampal neurogenesis. Additionally, Lp082 altered the composition of the gut microbiota in CUMS mice and promoted the growth of Bifidobacterium, improving metabolic pathways related to neurotransmitter synthesis. These findings indicate that Lp082, as a potential functional food ingredient, alleviates depressive-like behaviors in mice by reshaping the gut microbiota, offering new insights into the use of probiotics in functional foods for mental health management.}, }
@article {pmid40077458, year = {2025}, author = {Jing, Y and Wang, Z and Cheng, W and Fan, H and Zheng, K and Zheng, Y and Wu, L}, title = {Structure Characterization and Treatment Effect of Zingiber officinale Polysaccharide on Dextran Sulfate Sodium-Induced Ulcerative Colitis.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/foods14050753}, pmid = {40077458}, issn = {2304-8158}, support = {HBCT2023080201, HBCT2023080205//the Innovation Team of Hebei Province Modern Agricultural Industry Technology System/ ; H2024423098//the Hebei Natural Science Foundation/ ; 2024107//the Science and Technology Program of Hebei Administration of Traditional Chinese Medicine/ ; }, abstract = {BACKGROUND: Ulcerative colitis (UC) is on the rise all over the world. Zingiber officinale polysaccharide (ZOP-1) has good anti-inflammatory and antioxidant effects, but the therapeutic effect and mechanism of ZOP-1 on UC are still unclear.<br><br>METHODS: ZOP-1 obtained by water extraction and alcohol precipitation was analyzed by methylation and NMR. At the same time, the mechanism of ZOP-1 in the treatment of UC was clarified by hematoxylin-eosin (HE) staining, metagenomics, immunohistochemistry, and protein blot (Wb).<br><br>RESULTS: ZOP-1 was the structure of the by &#x2192;4,6)-&#x3b2;-Glcp-1&#x2192; and &#x2192;3,6)-&#x3b1;-Galp-(1&#x2192; constitute the main chain, there were two branched chain by &#x2192;4)-&#x3b2;-Glcp(1&#x2192;, and &#x3b1;-Araf(1&#x2192; as the end group. ZOP-1 significantly improved the shortening and thickening of the colon, changed the index of immune organs, inhibited the production of inflammatory factors in mice with ulcerative colitis, changed the intestinal flora of mice, increased the content of short-chain fatty acids (SCFAs) in the intestine, and controlled the TLR4/NF-&#x3ba;B/MAPK signaling pathway, thus preventing and treating DSS-induced ulcerative colitis in mice.<br><br>CONCLUSIONS: ZOP-1 alleviated UC by controlling the expression of cytokines, thereby reducing intestinal inflammation and oxidative stress, enhancing intestinal integrity, modulating intestinal flora, and regulating the levels of SCFAs.}, }
@article {pmid40076957, year = {2025}, author = {Kumagai, K and Ishikawa, S and Iino, M and Edamatsu, K and Okuyama, N and Yusa, K and Shimizu, Y and Aoki, R and Masuda, C and Ohashi, Y and Horie, A and Hoshi, K and Hamada, Y}, title = {Characterization of Salivary Microbiota in Japanese Patients with Oral Cancer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052339}, pmid = {40076957}, issn = {1422-0067}, support = {JP 22K10113//JSPS KAKENHI Grant-in-Aid for Scientific Research (C)/ ; }, mesh = {Humans ; *Saliva/microbiology ; Male ; Female ; *Microbiota/genetics ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; *Mouth Neoplasms/microbiology ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Japan ; Case-Control Studies ; Adult ; Metagenomics/methods ; East Asian People ; }, abstract = {This study aimed to characterize salivary microbiota in patients with oral cancer using 16S rRNA amplicon sequencing. DNA was extracted from saliva samples of 23 patients with oral cancer and 95 age-matched controls. A metagenomic analysis was performed using 16S rRNA amplicon sequencing. Patients with oral cancer exhibited lower α-diversity, as indicated by the Chao-1 index, compared to the control group, and significant differences in β-diversity were observed between the two groups. At the genus level, 25 bacterial species such as Lautropia, Megasphaera, Lactobacillus, Kingella, Gemella, Staphylococcus, and Propionibacterium were identified in patients with oral cancer, with more than half being Gram-positive facultative anaerobes or anaerobes. The reduced bacterial diversity in saliva of patients with oral cancer suggests dysbiosis during oral carcinogenesis may contribute to changes in bacterial distribution within the oral cavity.}, }
@article {pmid40076673, year = {2025}, author = {Velazquez-Meza, ME and Galarde-López, M and Cornejo-Juárez, P and Bobadilla-Del-Valle, M and Godoy-Lozano, E and Aguilar-Vera, E and Carrillo-Quiroz, BA and Ponce de León-Garduño, A and Velazquez Acosta, C and Alpuche-Aranda, CM}, title = {Bacterial Communities and Resistance and Virulence Genes in Hospital and Community Wastewater: Metagenomic Analysis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052051}, pmid = {40076673}, issn = {1422-0067}, support = {682339//CONAHCYT, M&#xe9;xico/ ; }, mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Virulence Factors/genetics ; *Drug Resistance, Bacterial/genetics ; Hospitals ; Bacteria/genetics/pathogenicity ; Metagenome ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence/genetics ; Genes, Bacterial ; Humans ; Microbiota/genetics ; }, abstract = {Metagenomic studies have made it possible to deepen the analysis of the abundance of bacterial populations that carry resistance and virulence determinants in the wastewater environment. In this study, a longitudinal collection of samples of community and hospital wastewater from August 2021 to September 2022 was obtained. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize the bacterial abundance, antimicrobial resistance genes (ARGs), plasmids, and virulence factor genes (VFGs) contained in the wastewater. The microbial composition of the community and hospital wastewater showed that the most abundant bacterial phyla detected in all samples were: Proteobacteria, Bacteroides, Firmicutes, Campylobacterota, and Actinobacteria. Seasonal differences in the relative abundances of species, ARGs, plasmids, and VFGs were observed. In this study, a total of 270 ARGs were detected, and it was found that the absolute abundance of ARGs only showed a 39% reduction in the treated wastewater. Furthermore, the ARGs detected in this study were found to encode resistance to antibiotics of the last choice. Our results showed that plasmids carrying resistance genes were more abundant in raw wastewater, and 60% more abundant in hospital wastewater compared to community wastewater. Several of the VFGs detected in this study encode for adhesion, motility, and biofilm formation, which likely allows bacteria to remain and persist in the wastewater environment and survive WWTP treatment systems, thus managing to escape into the environment via treated wastewater.}, }
@article {pmid40076252, year = {2025}, author = {Gao, Y and Xu, Y and Dong, Z and Guo, Y and Luo, J and Wang, F and Yan, L and Zou, X}, title = {Endophytic Fungal Diversity and Its Interaction Mechanism with Medicinal Plants.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {5}, pages = {}, doi = {10.3390/molecules30051028}, pmid = {40076252}, issn = {1420-3049}, support = {BS0050//Heilongjiang Province Postdoctoral Research Fund/ ; LH2022H001//Heilongjiang Natural Science Foundation Joint Guidance Project/ ; ZYW2023-073//Heilongjiang Province Traditional Chinese Medicine Research Project/ ; GZ20210110//Key Research and Development Guidance Project of Heilongjiang Province/ ; }, mesh = {*Plants, Medicinal/microbiology/chemistry ; *Endophytes/metabolism ; *Fungi/metabolism ; Biodiversity ; Metabolomics/methods ; Metagenomics/methods ; Proteomics/methods ; }, abstract = {This paper reviewed the diversity of endophytic fungi and their interactions with medicinal plants, along with the research methodologies utilized to investigate these interactions. It mainly includes the diversity of endophytic fungi, as well as distribution diversity, species diversity, and the diversity of their metabolites and functions, including antibacterial, anti-inflammatory, anti-tumor, insecticidal, antioxidant capabilities, and so on. The research methodologies employed to investigate the interactions between endophytic fungi and medicinal plants are categorized into metagenomics, transcriptomics, metatranscriptomics, proteomics, and metabolomics. Furthermore, this study anticipates the potential applications of secondary metabolites derived from endophytic fungi in both medicine and agriculture.}, }
@article {pmid40076036, year = {2025}, author = {Bai, X and Gu, Y and Li, D and Li, M}, title = {Gut Metagenome Reveals the Microbiome Signatures in Tibetan and Black Pigs.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/ani15050753}, pmid = {40076036}, issn = {2076-2615}, support = {National Key R &amp; D Program of China (2020YFA0509500 and 2023YFD1301302)//Mingzhou Li/ ; the Biological Breeding-Major Projects in National Science and Technology (2023ZD0404404)//Mingzhou Li/ ; the Sichuan Science and Technology Program (2021ZDZX0008 and 2021YFYZ0009)//Mingzhou Li/ ; the National Natural Science Foundation of China (32421005, 32225046 and 32494802)//Mingzhou Li/ ; }, abstract = {The harsh conditions of the Qinghai-Tibet Plateau pose significant physiological challenges to local fauna, often resulting in gastrointestinal disorders. However, Tibetan pigs have exhibited remarkable adaptability to the high-altitude stress of the Tibetan Plateau, a phenomenon that remains not fully understood in terms of their gastrointestinal microbiota. This study collected 57 gastrointestinal tract samples from Tibetan pigs (n = 6) and plain black pigs (n = 6) with comparable genetic backgrounds. Samples from the stomach, jejunum, cecum, colon, and rectum, underwent comprehensive metagenomic analysis to elucidate the gut microbiota-related adaptive mechanisms in Tibetan pigs to the extreme high-altitude environment. A predominance of Pseudomonadota was observed within gut microbiome of Tibetan pigs. Significant differences in the microbial composition were also identified across the tested gastrointestinal segments, with 18 genera and 141 species exhibiting differential abundance. Genera such as Bifidobacterium, Megasphaera, Fusobacterium, and Mitsuokella were significantly more abundant in Tibetan pigs than in their lowland counterparts, suggesting specialized adaptations. Network analysis found greater complexity and modularity in the microbiota of Tibetan pigs compared to black pigs, indicating enhanced ecological stability and adaptability. Functional analysis revealed that the Tibetan pig microbiota was particularly enriched with bacterial species involved in metabolic pathways for propionate and butyrate, key short-chain fatty acids that support energy provision under low-oxygen conditions. The enzymatic profiles of Tibetan pigs, characterized by elevated levels of 4-hydroxybutyrate dehydrogenase and glutaconyl-CoA decarboxylase, highlighted a robust fatty acid metabolism and enhanced tricarboxylic acid cycle activity. In contrast, the gut microbiome of plain black pigs showed a reliance on the succinate pathway, with a reduced butyrate metabolism and lower metabolic flexibility. Taken together, these results demonstrate the crucial role of the gastrointestinal microbiota in the adaptation of Tibetan pigs to high-altitude environments by optimizing carbohydrate metabolism and short-chain fatty acid production for efficient energy utilization. This study not only highlights the metabolic benefits conferred by the gut microbiota of Tibetan pigs in extreme environments, but also advances our understanding of the adaptive gastrointestinal mechanisms in plateau-dwelling animals. These insights lay the foundation for exploring metabolic interventions to support health and performance in high-altitude conditions.}, }
@article {pmid40075266, year = {2025}, author = {Cao, H and Xu, J and Wang, H and Yi, W and Yang, D and Yang, J and Sun, J and Wang, Y and Zhang, F and Yan, J and Li, D}, title = {Fecal microbiota transplantation mitigates postdieting weight regain in mice by modulating the gut-liver axis.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {135}, pmid = {40075266}, issn = {1471-2180}, support = {2023YFF1104305//National Key Research and Development Program of China/ ; 2022YFF1100601//National Key Research and Development Program of China/ ; K2023004//Key Research project of Health Commission of Jiangsu Province/ ; M2021055//Key Research project of Health Commission of Jiangsu Province/ ; Y2021001//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; K20221026//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; CXTD2021003//Key discipline construction program of Wuxi Commission of Health/ ; KX-23-B050//Soft Science Project of Wuxi Science and Technology Association/ ; KX-23-C196//Soft Science Project of Wuxi Science and Technology Association/ ; YJZ202305//Medical research projects in research-oriented hospitals of Affiliated Hospital of Jiangnan University/ ; HB2023062//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023063//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023061//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; LCYJ202347//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202310//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202322//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202303//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; BK20210468//Natural Science Foundation of Jiangsu Province/ ; BK20210060//Natural Science Foundation of Jiangsu Province/ ; 82370809//National Natural Science Foundation of China/ ; 32101033//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Mice ; *Weight Gain ; *Liver/metabolism ; Male ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Mice, Inbred C57BL ; Feces/microbiology ; Dysbiosis/therapy/microbiology ; Fatty Acids, Volatile/metabolism ; Lipid Metabolism ; }, abstract = {BACKGROUND: Dysbiosis of the microbiome is strongly associated with weight rebound after dieting. However, the interactions between the host and microbiome and their relevance to the pathogenesis of post-diet weight rebound remain unclear.<br><br>PURPOSE: This study aimed to evaluate the effects of fecal microbiota transplantation (FMT) on post-diet weight regain and to investigate the underlying mechanisms by which FMT inhibits weight regain.<br><br>METHODS: FMT was administered once daily to mice for 5 weeks. Gas chromatography tandem mass spectrometry was employed to analyze short-chain fatty acid levels in serum, ultrahigh-performance liquid chromatography tandem mass spectrometry was utilized for analyzing hepatic lipid metabolites, and shotgun metagenomic sequencing was applied to examine the intestinal microbiome.<br><br>RESULTS: FMT reduced weight regain and prevented lipid accumulation in both liver and adipose tissue while also improving glucose intolerance in mice. Furthermore, FMT increased the abundance of Enterorhabdus caecimuris and decreased the abundances of Burkholderiales, Sutterellaceae, Turicimonas muris, Bacteroides stercorirosoris, and Acetivibrio ethanolgignens within the gut microbiota. Additionally, elevated propionic acid levels and significant alterations in hepatic lipid metabolites were observed following FMT administration.<br><br>CONCLUSIONS: Our findings demonstrate that FMT effectively mitigates post-diet weight regain and associated complications. These effects are mediated through interactions between the gut microbiota and the liver via the gut-propionic acid-liver axis.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40075219, year = {2025}, author = {Sun, Y and Huang, S and Li, M and Yang, Y and Ma, J and Xie, R and Wang, J and Zhao, Q and Qin, S and He, L and Jiang, J and Zhao, Q and Jin, G and Liu, X and Huang, H and Yang, Y and Wei, J and Liu, W and Wang, B and Yang, R and Su, X and Cao, H}, title = {Maternal high-fat diet disrupts intestinal mucus barrier of offspring by regulating gut immune receptor LRRC19.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {420}, pmid = {40075219}, issn = {2399-3642}, support = {82270574//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82070545//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82400632//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81970488//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Female ; Mice ; *Intestinal Mucosa/metabolism/immunology/microbiology ; Mice, Inbred C57BL ; Pregnancy ; Mice, Knockout ; Male ; Interleukin-22 ; Receptors, Immunologic/metabolism/genetics ; }, abstract = {Maternal high fat diet (MHFD) increased colitis susceptibility in adulthood. However, the mechanism remains unclear. We sought to explore whether novel gut immune receptor leucine-rich repeat C19 (LRRC19) contributed to the impaired mucus barrier of offspring exposed to MHFD via gut immune response and microbiota. The results showed that MHFD significantly impaired the intestinal mucus barrier of offspring, and up-regulated the expression of LRRC19. Lrrc19 deletion alleviated the mucus barrier disruption. Mechanistically, metagenome sequencing revealed that the MHFD-induced gut microbiota alteration was partly restored in Lrrc19[-/-] offspring. Muc2-associated bacteria were decreased in the MHFD group, such as Akkermansia_muciniphila_CAG_154, which increased in the Lrrc19-deficient offspring. Moreover, Lrrc19[-/-] offspring had a higher rate of indole-3-acetic acid (IAA)-producing bacterium, such as Lactobacillus reuteri. A targeted metabolomics analysis revealed that IAA emerged as the top candidate that might mediate the protective effects. IAA was found to improve the mucus barrier function by increasing the ratio of interleukin-22 (IL-22)[+] ILC3 cells in an aryl hydrocarbon receptor (AhR)-dependent manner. These results suggest that MHFD disrupts the intestinal mucus barrier of offspring through regulating gut immune receptor LRRC19 and inducing an imbalance of gut microbiota and microbiota-derived metabolites.}, }
@article {pmid40074067, year = {2025}, author = {Pragasam, AK and Maurya, S and Jain, K and Pal, S and Raja, C and Yadav, R and Kumar, S and Purohit, A and Pradhan, D and Kajal, K and Talukdar, D and Singh, AN and Verma, J and Jana, P and Rawat, S and Kshetrapal, P and Krishna, A and Kumar, S and Bansal, VK and Das, B and Srikanth, CV and Garg, PK}, title = {Invasive Salmonella Typhimurium Colonizes Gallbladder and Contributes to Gallbladder Carcinogenesis through Activation of Host Epigenetic Modulator KDM6B.}, journal = {Cancer letters}, volume = {}, number = {}, pages = {217621}, doi = {10.1016/j.canlet.2025.217621}, pmid = {40074067}, issn = {1872-7980}, abstract = {Gallbladder stones alone do not explain the risk of gallbladder cancer (GBC) as the sole etiological factor. Chronic microbial infection, particularly Salmonella, has been implicated in GB carcinogenesis, but its causative role and the underlying mechanisms are largely unknown. We studied gut and gallbladder tissue microbiome through targeted metagenomics to identify pathogenic bacteria in GBC. Virulence and pathogenicity of identified Salmonella Typhimurium from GBC tissue were studied after culture by whole genome sequencing, phylogenetic analysis, mutational profiling, and pangenome analysis. Mechanistic studies for GBC carcinogenesis were carried out in a mouse model of gallstones and chronic Salmonella infection, a cellular model using GBC (NOZ) cell lines, and a xenograft tumor model. We found an increased abundance of Salmonella in the gut microbiome of patients with GBC and culturable S. Typhimurium from the gallbladder cancer tissue. Comparative genomics of S. Typhimurium isolated from the GBC tissue showed a high invasive index. S. Typhimurium isolates harbored horizontally acquired virulence functions in their accessory genome. Chronic S. Typhimurium infection caused chronic inflammation, pre-malignant changes, and tumor-promoting mechanisms in the mouse model with gallbladder stones with activation of the epigenetic modulator KDM6B both in the mouse model and human GBC. Inhibition of KDM6B reduced engrafted tumor size in SCID mice. Of the differentially regulated genes in human GBC tissue, ADAMTSL5, CX3CR1, and SPSB4 were also significantly dysregulated in NOZ cells infected with Salmonella. Chronic Salmonella infection contributes to gallbladder carcinogenesis through a host epigenetic mechanism involving KDM6B.}, }
@article {pmid40073489, year = {2025}, author = {Han, NN and Wang, XP and Jin, JA and Li, WH and Yang, WY and Fan, NS and Jin, RC}, title = {Underrated risk of antibiotic resistance genes dissemination mediated by bioaerosols released from anaerobic biological wastewater treatment system.}, journal = {Water research}, volume = {279}, number = {}, pages = {123463}, doi = {10.1016/j.watres.2025.123463}, pmid = {40073489}, issn = {1879-2448}, abstract = {Antibiotic resistance has been recognized as one of the most prevalent public health problems. The bioaerosol-mediated spread of antibiotic resistance genes (ARGs) is an important but underrated pathway. Therefore, this work investigated the comprehensive resistome and pathogen-induced risk in bioaerosols released from anaerobic ammonium oxidation (anammox) process under antibiotic stress. The results showed that the bioaerosol oxidation potential increased by 2.7 times after the addition of sulfamethoxazole (SMX) into the anammox system. Based on the metagenomic analyses, abundant ARGs were enriched in bioaerosols, especially novA, olec, msbA and patA. There were many antibiotic resistance contigs carrying at least two mobile genetic elements (MGEs) in bioaerosols. Compared to the control, SMX caused the significant increase in ARGs proportion in plasmids from 11.4 % to 19.4 %. Similarly, the abundance of the type IV secretion system protein encoding genes (mtrA and mtrB) increased by 30.2 % and 31.5 %, respectively, which was conducive to gene transfer between bacteria. In addition, SMX stress induced the reactive oxygen species (ROS) production and the upregulation of genes related to membrane protein and DNA replication, further facilitating ARGs transfer. The co-occurrence networks showed that Aquamicrobium and Microbacterium probably were the hosts of most ARGs. Notably, four abundant human pathogens were detected in bioaerosols from the anammox system, which raised concerns on the health risk of resistant bioaerosol diffusion. These findings reveal the potential of horizontal gene transfer through bioaerosols and provide a guidance for systematically assessing the risk of environmental antibiotic resistance and relevant pathogens.}, }
@article {pmid40072902, year = {2025}, author = {Varsani, A and Custer, JM and Cobb, IN and Harding, C and Collins, CL and Suazo, C and Schreck, J and Fontenele, RS and Stainton, D and Dayaram, A and Goldstein, S and Kazlauskas, D and Kraberger, S and Krupovic, M}, title = {Bacilladnaviridae: refined taxonomy and new insights into the biology and evolution of diatom-infecting DNA viruses.}, journal = {The Journal of general virology}, volume = {106}, number = {3}, pages = {}, doi = {10.1099/jgv.0.002084}, pmid = {40072902}, issn = {1465-2099}, mesh = {*Diatoms/virology/genetics ; *Phylogeny ; *Genome, Viral ; *DNA Viruses/genetics/classification ; New Zealand ; Metagenomics ; Animals ; Evolution, Molecular ; DNA, Viral/genetics ; Capsid Proteins/genetics ; }, abstract = {Bacilladnaviruses are single-stranded DNA viruses that infect diatoms that, so far, have been primarily identified in marine organisms and environments. Using a viral metagenomics approach, we discovered 13 novel bacilladnaviruses originating from samples of mud-flat snail (Amphibola crenata; n=3 genomes) and benthic sediments (n=10 genomes) collected from the Avon-Heathcote Estuary in New Zealand. Comparative genomics and phylogenetic analysis of the new bacilladnavirus sequences in the context of the previously classified members of the family helped refine and further expand the Bacilladnaviridae taxonomy. Here, based on the replication-associated protein phylogeny and pairwise identities, we established 4 new genera - Aberdnavirus, Keisodnavirus, Puahadnavirus and Seawadnavirus - and 13 new species within the family. Comparison of the bacilladnavirus capsid protein sequences suggests that the positively charged N-terminal region (R-arm) is required for encapsidation of the larger genomes, whereas the smaller bacilladnavirus genomes can be packaged in the absence of the R-arm subdomain. Furthermore, analysis of the bacilladnavirus genomes revealed that members of three genera encode a highly derived variant of a phospholipase A1, which is predicted to be involved in the lysis of the infected diatoms and/or facilitates the entry of the virions into the host cells. Collectively, our results allow refining of the taxonomy of bacilladnaviruses and provide new insights into the biology and evolution of this understudied group of diatom viruses.}, }
@article {pmid40078515, year = {2023}, author = {Li, Z and Wu, C and Tang, LA and Liang, Y and A, R and Huang, D and Ning, C and Wang, W and Tan, W}, title = {mNGS-based dynamic pathogen monitoring for accurate diagnosis and treatment of severe pneumonia caused by fungal infections.}, journal = {Biosafety and health}, volume = {5}, number = {3}, pages = {138-143}, doi = {10.1016/j.bsheal.2023.04.004}, pmid = {40078515}, issn = {2590-0536}, abstract = {Metagenomic next-generation sequencing (mNGS) has been widely applied to identify pathogens associated with infectious diseases. However, limited studies have explored the use of mNGS-based dynamic pathogen monitoring in intensive care unit patients with severe pneumonia. Here, we present a clinical case of an 86-year-old male patient with severe pneumonia caused by a fungal infection. During the clinical treatment, four mNGS analyses were performed within two consecutive weeks. Various respiratory fungal pathogens, including Candida orthopsilosis, Candida albicans, and Aspergillus fumigatus were detected by mNGS of bronchoalveolar lavage fluid (BALF). Based on conventional pathogen identification and clinical symptoms, the patient was diagnosed with severe pneumonia caused by a fungal infection. The abundance of fungal species decreased gradually in response to antifungal and empirical therapies, and the fungal infections were effectively controlled. In summary, our results demonstrated that mNGS could effectively identify pathogens in patients with severe pneumonia. Additionally, dynamic pathogen monitoring based on mNGS could assist in the precise diagnosis of complex infections and may facilitate rapid induction of the most appropriate therapy.}, }
@article {pmid40072675, year = {2025}, author = {Verma, N and Chavan, N and Aulakh, KS and Sharma, A and Shouche, Y and Ramana, VV}, title = {Temporal Dynamics of Microbial Community Composition and Antimicrobial Resistance in a Mass Gathering Setting Using Culturomics and Metagenomic Approaches.}, journal = {Journal of epidemiology and global health}, volume = {15}, number = {1}, pages = {41}, pmid = {40072675}, issn = {2210-6014}, support = {OLP-805//CSIR - Institute of Microbial Technology/ ; GAP-233//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Humans ; India/epidemiology ; *Metagenomics/methods ; Microbiota/drug effects ; Bacteria/drug effects/genetics/isolation &amp; purification/classification ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is one of the major global concerns in the current scenario. Mass-gathering events in fast-developing and densely populated areas may contribute to antibiotic resistance. Despite meticulous planning and infrastructure development, the effect of mass gatherings on microbial ecosystems and antibiotic resistance must be investigated. This study used culture and metagenome-based methods to investigate and compare the bacterial diversity, AMR profile &amp; mechanism of resistance for bacteria in water samples collected from the mass gathering event (2019 Prayagraj Kumbh Mela in Uttar Pradesh, India) with the control samples, collected during no mass gathering.<br><br>METHODS: This study analyzed the water samples collected from a mass gathering event held in February 2019. Water samples collected in this study were grouped into "Test" (mass gathering event) and "Control" (no mass gathering event) groups. This study involved methods including culturomics, antibiotyping, phenotypic &amp; genotypic identification methods, and metagenomics.<br><br>RESULTS: There is a significant variation observed in the evenness and richness of bacterial diversity and MDR profile, expressed in terms of the relative abundance of the bacterial species between test and control samples. Out of the total multi-drug resistant (MDR) strains identified in the Prayagraj sample, the majority were derived from the test sample. A pathway-based analysis of MDR strains revealed the highest levels of acquired resistance were related to the inhibition of cell wall synthesis primarily in Pseudomonas spp., followed by resistance to protein synthesis and nucleic acid synthesis pathways. Additionally, the overall resistance profile of the test sample demonstrated a significantly elevated resistome for beta-lactams, particularly in the Pseudomonas spp. Additionally, several ESBL (Extended-spectrum beta-lactamase)-associated gene variants were identified. The test sample showed a two-fold increase in the prevalence and diversity of common beta-lactam gene variants in addition to the presence of unique variants. Using the metagenomics approach, we investigated the mechanism of antibiotic resistance, and it revealed a dominant trend in antibiotic efflux and inactivation pathways within both the test and control samples. Overall, the bacterial diversity, abundance (including AMR strains of human origin), and ARGs were relatively higher in the Test sample compared to the control sample which was collected 3 months after the mass gathering event.<br><br>CONCLUSION: Our study found significant variations in microbial communities, MDR strains, and ARGs due to environmental and human influences. Pseudomonas spp. was the most abundant MDR strain, primarily resistant to cell wall synthesis inhibitors. The test sample showed an increased resistome for beta-lactams, while the control sample had reduced bacterial species, ARGs, and MDR strains linked to human microflora. This shift could be due to the re-establishment of native bacterial communities in the Ganges River which may be attributed to its bacteriophage activity, biomolecules, and inherent antimicrobial properties. The study highlights the need for surveillance, monitoring AMR emergence to develop new strategies to combat it.}, }
@article {pmid40072088, year = {2025}, author = {Świdnicka-Siergiejko, A and Daniluk, J and Miniewska, K and Daniluk, U and Guzińska-Ustymowicz, K and Pryczynicz, A and Dąbrowska, M and Rusak, M and Ciborowski, M and Dąbrowski, A}, title = {Inflammatory Stimuli and Fecal Microbiota Transplantation Accelerate Pancreatic Carcinogenesis in Transgenic Mice, Accompanied by Changes in the Microbiota Composition.}, journal = {Cells}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/cells14050361}, pmid = {40072088}, issn = {2073-4409}, support = {No NCN 2017/27/B/NZ5/02904//National Science Center/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation ; *Mice, Transgenic ; *Pancreatic Neoplasms/microbiology/genetics/pathology ; Mice ; *Inflammation/pathology/microbiology ; *Gastrointestinal Microbiome/genetics ; *Carcinoma, Pancreatic Ductal/microbiology/genetics/pathology ; Carcinogenesis/genetics/pathology ; Feces/microbiology ; Proto-Oncogene Proteins p21(ras)/genetics ; Pancreas/pathology ; }, abstract = {An association between gut microbiota and the development of pancreatic ductal adenocarcinoma (PDAC) has been previously described. To better understand the bacterial microbiota changes accompanying PDAC promotion and progression stimulated by inflammation and fecal microbiota transplantation (FMT), we investigated stool and pancreatic microbiota by 16s RNA-based metagenomic analysis in mice with inducible acinar transgenic expressions of KrasG12D, and age- and sex-matched control mice that were exposed to inflammatory stimuli and fecal microbiota obtained from mice with PDAC. Time- and inflammatory-dependent stool and pancreatic bacterial composition alterations and stool alpha microbiota diversity reduction were observed only in mice with a Kras mutation that developed advanced pancreatic changes. Stool Actinobacteriota abundance and pancreatic Actinobacteriota and Bifidobacterium abundances increased. In contrast, stool abundance of Firmicutes, Verrucomicrobiota, Spirochaetota, Desulfobacterota, Butyricicoccus, Roseburia, Lachnospiraceae A2, Lachnospiraceae unclassified, and Oscillospiraceae unclassified decreased, and pancreatic detection of Alloprevotella and Oscillospiraceae uncultured was not observed. Furthermore, FMT accelerated tumorigenesis, gradually decreased the stool alpha diversity, and changed the pancreatic and stool microbial composition in mice with a Kras mutation. Specifically, the abundance of Actinobacteriota, Bifidobacterium and Faecalibaculum increased, while the abundance of genera such as Lachnospiraceace A2 and ASF356, Desulfovibrionaceace uncultured, and Roseburia has decreased. In conclusion, pancreatic carcinogenesis in the presence of an oncogenic Kras mutation stimulated by chronic inflammation and FMT dynamically changes the stool and pancreas microbiota. In particular, a decrease in stool microbiota diversity and abundance of bacteria known to be involved in short-fatty acids production were observed. PDAC mouse model can be used for further research on microbiota-PDAC interactions and towards more personalized and effective cancer therapies.}, }
@article {pmid40072031, year = {2025}, author = {Huang, YJ}, title = {The Microbiome in Asthma Heterogeneity: The Role of Multi-Omic Investigations.}, journal = {Immunological reviews}, volume = {330}, number = {1}, pages = {e70015}, doi = {10.1111/imr.70015}, pmid = {40072031}, issn = {1600-065X}, support = {U01TR004066/TR/NCATS NIH HHS/United States ; 75N92024D00012-0-759202400001-1/HL/NHLBI NIH HHS/United States ; }, mesh = {*Asthma/microbiology/immunology/etiology ; Humans ; *Microbiota/immunology ; Animals ; Biomarkers ; Genomics/methods ; Proteomics ; Metabolomics/methods ; Disease Susceptibility ; Metagenomics/methods ; Multiomics ; }, abstract = {Asthma is one of the most prevalent and extensively studied chronic respiratory conditions, yet the heterogeneity of asthma remains biologically puzzling. Established factors like exogenous exposures and treatment adherence contribute to variability in asthma risk and clinical outcomes. It is also clear that the endogenous factors of genetics and immune system response patterns play key roles in asthma. Despite significant existing knowledge in the above, divergent clinical trajectories and outcomes are still observed, even among individuals with similar risk profiles, biomarkers, and optimal medical management. This suggests uncaptured biological interactions that contribute to asthma's heterogeneity, for which the role of host microbiota has lately attracted much research attention. This review will highlight recent evidence in this area, focusing on bedside-to-bench investigations that have leveraged omic technologies to uncover microbiome links to asthma outcomes and immunobiology. Studies centered on the respiratory system and the use of multi-omics are noted in particular. These represent a new generation of reverse-translational investigations revealing potential functional crosstalk in host microbiomes that may drive phenotypic heterogeneity in chronic diseases like asthma. Multi-omic data offer a wide lens into ecosystem interactions within a host. This informs new hypotheses and experimental work to elucidate mechanistic pathways for unresolved asthma endotypes. Further incorporation of multi-omics into patient-centered investigations can yield new insights that hopefully lead to even more precise, microbiome-informed strategies to reduce asthma burden.}, }
@article {pmid40071918, year = {2025}, author = {Foysal, MJ and Neilan, BA and Timms, V}, title = {The impact of anthropogenic activities on antimicrobial and heavy metal resistance in aquatic environments.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0231724}, doi = {10.1128/aem.02317-24}, pmid = {40071918}, issn = {1098-5336}, abstract = {UNLABELLED: This study investigated the prevalence and co-occurrence of antimicrobial (AMR) and metal resistance (MR) in aquatic environments with different human impacts. Metagenomes from pristine, rural and urban sites in Australia were analyzed with AMR ++ and customized binning pipelines. AMR was present in all environments, while MR was mainly in rural and urban samples. AMR gene diversity was higher in rural and urban sites, exhibiting resistance to more antibiotic classes (n = 10) than the pristine site (n = 4). Metal and multicompound resistance was more frequent in rural (14%) compared to urban samples (5%). Pristine samples lacked multidrug and multicompound resistance and had lower resistance to aminoglycosides and the MLS group. Multiresistance was evidenced by copper and aminocoumarin resistance in rural samples and aminoglycoside and mercury resistance in Pseudomonas in all environments. These findings highlight the impact of human activities on AMR and MR spread, emphasizing the need for environmental monitoring and management.<br><br>IMPORTANCE: Antimicrobial resistance (AMR) and metal resistance (MR) are critical global health concerns exacerbated by anthropogenic activities. The intricate mechanism underlying the interaction among anthropogenic activities, microbial communities, and resistance remains enigmatic. We developed novel bioinformatic pipelines to unveil this interaction in three aquatic environments. Our findings demonstrate the presence of specific bacterial communities that drive AMR and MR in rural and urban environments. This study underscores the significance of proper agricultural practices, comprehensive monitoring, and management strategies to reduce anthropogenic impacts on environmental resistance.}, }
@article {pmid40071515, year = {2025}, author = {Medina, JS and Zhang, S and Narayanasamy, S and Wang, C and Al-Gashgari, B and Hong, PY}, title = {Metagenomic Insights in Antimicrobial Resistance Threats in Sludge from Aerobic and Anaerobic Membrane Bioreactors.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c10879}, pmid = {40071515}, issn = {1520-5851}, abstract = {Sludge is a biohazardous solid waste that is produced during wastewater treatment. It contains antibiotic resistance genes (ARGs) that pose significant antimicrobial resistance (AMR) threats. Herein, aerobic and anaerobic membrane bioreactors (AeMBRs and AnMBRs, respectively) were compared in terms of the volume of waste sludge generated by them, the presence of ARGs in the sludge, and the potential for horizontal gene transfer (HGT) events using metagenomics to determine which treatment process can better address AMR concerns associated with the generation of waste sludge. The estimated abundance of ARGs in the suspended sludge generated by the AnMBR per treated volume is, on average, 5-55 times lower than that of sludge generated by the AeMBR. Additionally, the ratio of potential HGT in the two independent runs was lower in the anaerobic sludge (0.6 and 0.9) compared with that in the aerobic sludge (2.4 and 1.6). The AnMBR sludge exhibited reduced HGT of ARGs involving potential opportunistic pathogens (0.09) compared with the AeMBR sludge (0.27). Conversely, the AeMBR sludge displayed higher diversity and more transfer events, encompassing genes that confer resistance to quinolones, rifamycin, multidrug, aminoglycosides, and tetracycline. A significant portion of these ARGs were transferred to Burkholderia sp. By contrast, the AnMBR showed a lower abundance of mobile genetic elements associated with conjugation and exhibited less favorable conditions for natural transformation. Our findings suggest that the risk of potential HGT to opportunistic pathogens is greater in the AeMBR sludge than in AnMBR sludge.}, }
@article {pmid40071205, year = {2025}, author = {Park, J and Park, T}, title = {Composite quantile regression approach to batch effect correction in microbiome data.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1484183}, doi = {10.3389/fmicb.2025.1484183}, pmid = {40071205}, issn = {1664-302X}, abstract = {BACKGROUND: Batch effects refer to data variations that arise from non-biological factors such as experimental conditions, equipment, and external factors. These effects are considered significant issues in the analysis of biological data since they can compromise data consistency and distort actual biological differences, which can severely skew the results of downstream analyses.<br><br>METHOD: In this study, we introduce a new approach that comprehensively addresses two types of batch effects: "systematic batch effects" which are consistent across all samples in a batch, and "nonsystematic batch effects" which vary depending on the variability of operational taxonomic units (OTUs) within each sample in the same batch. To address systematic batch effects, we apply a negative binomial regression model and correct for consistent batch influences by excluding fixed batch effects. Additionally, to handle nonsystematic batch effects, we employ composite quantile regression. By adjusting the distribution of OTUs to be similar based on a reference batch selected using the Kruskal-Walis test method, we consider the variability at the OTU level.<br><br>RESULTS: The performance of the model is evaluated and compared with existing methods using PERMANOVA R-squared values, Principal Coordinates Analysis (PCoA) plots and Average Silhouette Coefficient calculated with diverse distance-based metrics. The model is applied to three real microbiome datasets: Metagenomic urine control data, Human Immunodeficiency Virus Re-analysis Consortium data, and Men and Women Offering Understanding of Throat HPV study data. The results demonstrate that the model effectively corrects for batch effects across all datasets.}, }
@article {pmid40070462, year = {2025}, author = {Amevor, FK and Uyanga, VA and Wu, L and Xu, D and Shu, G and Wang, Y and Zhao, X}, title = {Enhancing poultry health and productivity through the liver-gut axis with integrated nutritional and immunological approaches: a mini-review.}, journal = {Frontiers in physiology}, volume = {16}, number = {}, pages = {1537099}, doi = {10.3389/fphys.2025.1537099}, pmid = {40070462}, issn = {1664-042X}, abstract = {The liver-gut axis plays a central role in maintaining the health and productivity of poultry. In addition, the liver-gut axis serves as a key regulator of digestion, metabolism, immunity, and detoxification. The gut, with its diverse microbiota, is the primary site for nutrient absorption and immune modulation, while the liver metabolizes nutrients, detoxifies harmful substances, and acts as a frontline defense against pathogens translocated from the gut. Disruptions in this interconnected system, including gut dysbiosis or liver inflammation, can lead to compromised immunity and reduced productivity. This mini-review explores integrated nutritional and immunological strategies aimed at optimizing the liver-gut axis to enhance poultry performance. Nutritional interventions, such as the use of flavonoids, vitamins, amino acids, micronutrients, probiotics, prebiotics, and synbiotics, have demonstrated their potential to support liver and gut health. Dietary components such as phytogenic additives, fiber, and fatty acids further contribute to immune modulation and systemic health. Immunological approaches, such as beta-glucans and in ovo stimulation, and molecular approaches, including advanced genetic techniques, offer additional avenues for improving disease resistance and organ function. Despite notable advancements, challenges including antibiotic resistance, environmental stressors, and implementation costs persist. Emerging technologies like metagenomics, metabolomics, and precision breeding offer innovative solutions to enhance liver-gut interactions. This review underscores recent advancements in understanding the liver-gut axis and calls for holistic strategies to improve sustainable poultry production. Future research should integrate these approaches to enhance resilience, productivity, and sustainability in the poultry industry.}, }
@article {pmid40069804, year = {2025}, author = {Ye, X and Sahana, G and Lund, MS and Li, B and Cai, Z}, title = {Network analyses unraveled the complex interactions in the rumen microbiota associated with methane emission in dairy cattle.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {24}, pmid = {40069804}, issn = {2524-4671}, abstract = {BACKGROUND: Methane emissions from livestock, particularly from dairy cattle, represent a significant source of greenhouse gas, contributing to the global climate crisis. Understanding the complex interactions within the rumen microbiota that influence methane emissions is crucial for developing effective mitigation strategies.<br><br>RESULTS: This study employed Weighted Gene Co-expression Network Analysis to investigate the complex interactions within the rumen microbiota that influence methane emissions. By integrating extensive rumen microbiota sequencing data with precise methane emission measurements in 750 Holstein dairy cattle, our research identified distinct microbial communities and their associations with methane production. Key findings revealed that the blue module from network analysis was significantly correlated (0.45) with methane emissions. In this module, taxa included the genera Prevotella and Methanobrevibactor, along with species such as Prevotella brevis, Prevotella ruminicola, Prevotella baroniae, Prevotella bryantii, Lachnobacterium bovis, and Methanomassiliicoccus luminyensis are the key components to drive the complex networks. However, the absence of metagenomics sequencing is difficult to reveal the deeper taxa level and functional profiles.<br><br>CONCLUSIONS: The application of Weighted Gene Co-expression Network Analysis provided a comprehensive understanding of the microbiota-methane emission relationship, serving as an innovative approach for microbiota-phenotype association studies in cattle. Our findings underscore the importance of microbiota-trait and microbiota-microbiota associations related to methane emission in dairy cattle, contributing to a systematic understanding of methane production in cattle. This research offers key information on microbial management for mitigating environmental impact on the cattle population.}, }
@article {pmid40069605, year = {2025}, author = {Zhang, H and Wang, Y and Luo, Z and Zhang, B and Lan, X and Xu, L and Li, X and Huang, Z and Bai, J and Hu, D}, title = {Gut microbiome reveals the trophic variation and significant adaption of three sympatric forest-dwelling ungulates on the eastern Qinghai-Xizang Plateau.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {128}, pmid = {40069605}, issn = {1471-2180}, support = {YC-20018//Zhangzhou Pientzehuang Pharmaceutical Co., Ltd./ ; 2023I0046//Supported by Science and Technology Planning Project of Fujian Province, China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; China ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Phylogeny ; Forests ; Metagenomics ; Sympatry ; Adaptation, Physiological ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Ruminants/microbiology ; }, abstract = {BACKGROUND: The gut microbiome of herbivorous mammals regulates numerous physiological processes, including digestion and energy metabolism. The complex stomach architecture of ruminants, in conjunction with the metabolic capabilities of their microbiota, confers a considerable adaptive advantage to these animals. Nevertheless, a significant gap persists in comparative studies on the variations in the gut microbiome among sympatric ruminants and their potential adaptive implications. Accordingly, in this study, 16S rRNA gene sequencing and metagenomic approaches were used to analyse the composition and functional attributes of the gut microbiome of sympatric Moschus chrysogaster, Capricornis sumatraensis, and Cervus albirostris inhabiting the eastern periphery of the Qinghai-Xizang Plateau.<br><br>RESULTS: The gut microbiome of C. albirostris exhibited a higher diversity than that of M. chrysogaster and C. sumatraensis, whereas those of M. chrysogaster and C. sumatraensis were similar. Although species-specific variations existed among the three mammalian microbiomes, the microbiomes of C. albirostris and C. sumatraensis were more similar, whereas that of M. chrysogaster was markedly distinct. Metagenomic analysis revealed a pattern of functional convergence in the gut microbiome of the three species, with the gut microbiome of C. albirostris exhibiting a pronounced emphasis on carbohydrate metabolism, significantly surpassing that of M. chrysogaster and C. sumatraensis. Compared to the other two species, the gut microbiome of C. sumatraensis presented significantly elevated levels of amino acids and energy metabolism, whereas that of M. chrysogaster presented an increased capacity for 3-hydroxyacyl- [acyl carrier protein]-dehydratase production.<br><br>CONCLUSION: These findings suggest that the gut microbiome of sympatric M. chrysogaster, C. sumatraensis, and C. albirostris tend to converge. Metabolic variations within their gut microbiome may result in differential food resource utilisation, potentially indicating significant nutritional and ecological trait characteristics for stable coexistence.}, }
@article {pmid40069560, year = {2025}, author = {Breselge, S and Skibinska, I and Yin, X and Brennan, L and Kilcawley, K and Cotter, PD}, title = {The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {415}, pmid = {40069560}, issn = {2399-3642}, support = {818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; SFI/12/RC/2273_P2//Science Foundation Ireland (SFI)/ ; USIRL-2019-1//Science Foundation Ireland (SFI)/ ; SFI/16/RC/3835//Department of Agriculture, Food and the Marine (DAFM)/ ; TC/2018/0025//Enterprise Ireland/ ; }, mesh = {*Fermentation ; *Kefir/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; Bacteria/metabolism/genetics/classification ; Metabolomics/methods ; Food Microbiology ; Water/metabolism ; Multiomics ; }, abstract = {Water kefir (WK) is an artisanal fermented beverage made from sugary water, optional fruits and WK grains. WK grains can be reused to start new fermentations. Here we investigate the microbial composition and function of 69 WK grains and their ferments by shotgun metagenomics. A subset of samples was subjected to metabolomic, including volatilomic, analysis. The impact of different fermentation practices on microbial composition and fermentation characteristics was analysed and it was noted that, for example, the common practice of drying water kefir grains significantly reduces microbial diversity and negatively impacts subsequent grain growth. Metagenomic analysis allowed the detection of 96 species within WK, the definition of core genera and the detection of different community states after 48 h of fermentation. A total of 485 bacterial metagenome assembled genomes were obtained and 18 putatively novel species were predicted. Metabolite and volatile analysis show associations between key species with flavour compounds. We show the complex microbial composition of WK and links between fermentation practices, microbes and the fermented product. The results can be used as a foundation for the selection of species for large scale WK production with desired flavour profiles and to guide the regulatory framework for commercial WK production.}, }
@article {pmid40068786, year = {2025}, author = {Wang, L and Zhao, G and Guo, W and Li, Y and Chen, J and Niu, L}, title = {Microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary responding to tidal fluctuation.}, journal = {Environmental research}, volume = {274}, number = {}, pages = {121363}, doi = {10.1016/j.envres.2025.121363}, pmid = {40068786}, issn = {1096-0953}, abstract = {Tidal fluctuation disturbances and amplified anthropogenic activities are defining characteristics of the intertidal zones of mountainous river estuaries. The accumulation and degradation of organic matter and nutrients in the sediments result in a complex element migration and transformation dynamics. Nonetheless, microbial transformation of dissolved organic sulfur (DOS) in the intertidal sediments upon tidal fluctuation remains poorly understood. Here, by taking a representative small mountainous river estuary in southeast China as an example, we synthesize evidence describing the composition of dissolved organic matter (DOM), microbial community structure and metabolic functions in sediments of variable depths (0-80 cm) at both high and low tide via FT-ICR-MS and metagenomic approach. Labile DOM, e.g., aliphatic and proteins were more inclined to be enriched in shallow sediments (0-30 cm). Upon tidal inundation, Thaumarchaeota was verified to facilitate the accumulation of recalcitrant organic matter through the mevalonate pathway, elevating the proportion of carboxyl-rich alicyclic molecules (CRAMs) and lignins in sediments. Whereas during ebb period, the microbial production of DOS through assimilated sulfate reduction (ASR) was signally intensified, contributing to the accumulation of sulfur-containing organic matter in deeper sediments. Based on the associations between Kyoto encyclopedia of Genes and Genomes modules and DOM formulas, cobalamin biosynthesis, ASR, and cysteine biosynthesis were observed positively correlated with the accumulation of sulfur-containing organic matter. Microbial community exhibited obvious taxonomic and functional variations between flood and ebb states. Nitrososphaerta in shallow sediments (0∼30 cm) was beneficial for the production of nitrogen-containing organic matter, while Bathyarchaeota and Chloroflexota in deep sediments (70-80 cm) predominantly governed the mineralization of organic matter. We firstly provided metagenomic evidence for the microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary, which will be key to predicting coastal carbon storage and offer an important scientific basis for formulating intertidal ecosystem management and restoration strategies.}, }
@article {pmid40068396, year = {2025}, author = {Guo, M and Wu, Y and Huang, H and Li, S and Zhao, L and Cao, J and Wang, C}, title = {Revealing the critical role of rare bacterial communities in shaping antibiotic resistance genes in saline soils through metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137848}, doi = {10.1016/j.jhazmat.2025.137848}, pmid = {40068396}, issn = {1873-3336}, abstract = {Salinity is considered one of the basic abiotic factors influencing the diversity and distribution of antibiotic resistance genes (ARGs) in soils, yet little is known about the distribution and driving factors of ARGs in naturally saline soils. In this study, metagenomic analysis was conducted to explore the intricate dynamics among soil salinity, microbial community structure and ARGs propagation, with a particular focus on the key contribution of rare potential-hosts of ARGs in light and heavy saline soils. The findings revealed that salinity was significantly negatively correlated with the abundance of ARGs, light saline soils hosted a greater abundance of ARGs than high saline soils, with particularly significant enrichment in genes conferring resistance to multidrug, vancomycin, bacitracin and tetracenomycin C. Proteobacteria and Actinobacteria were identified as primary hosts for ARGs. Notably, rare potential hosts of ARGs play a crucial role in shaping the abundance of ARGs despite their low relative abundance (0.85 %), significantly influencing the relative abundance of ARGs in light and heavy saline soils. The average degree of rare potential-hosts of ARGs was found to be higher in light saline soils (average degree = 45.729 and 25.923 in light and heavy saline soils, respectively), and there was stronger interaction connected between microorganisms (edges = 35,760 and 20,259 in light and heavy saline soils, respectively). Also, microbial community niche width and niche overlap of rare potential-hosts of ARGs in light saline soils were significantly greater than that in heavy saline soils. This work emphasizes the importance of bacterial communities of rare potential-hosts of ARGs on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.}, }
@article {pmid40068378, year = {2025}, author = {Weng, YT and Huang, CK and Cheng, A and Ruan, SY and Wang, JT}, title = {Next-generation sequencing for rapid etiologic diagnosis of acute respiratory distress syndrome: A case of life-threatening leptospirosis.}, journal = {Journal of infection and public health}, volume = {18}, number = {6}, pages = {102727}, doi = {10.1016/j.jiph.2025.102727}, pmid = {40068378}, issn = {1876-035X}, abstract = {Leptospirosis is a zoonotic infection with public health implications and diverse clinical presentations, ranging from mild symptoms to severe, life-threatening disease. In critical cases, it can cause multiorgan failure and death. Diagnosis is typically based on clinical suspicion and confirmed by laboratory testing. However, in acute, life-threatening cases, obtaining a history of exposure and recognizing early symptoms may be challenging. Traditional diagnostic methods for identifying causative pathogens are time-consuming and limited. Next-generation sequencing (NGS) has emerged as a novel diagnostic tool that identifies pathogens using DNA or RNA from bodily fluids, offering more timely, unbiased results, especially for fastidious or non-culturable organisms.}, }
@article {pmid40068343, year = {2025}, author = {Almarhabi, H and Sarhan, A and Alharbi, A and Al-Amri, A and Ahamed, MF and Hala, S}, title = {Multifocal osteolytic lesions as an initial presentation of mycobacterium riyadhense: Case report and literature review.}, journal = {Journal of infection and public health}, volume = {18}, number = {5}, pages = {102741}, doi = {10.1016/j.jiph.2025.102741}, pmid = {40068343}, issn = {1876-035X}, abstract = {Mycobacterium riyadhense is a newly discovered, slow-growing nontuberculous mycobacterium with an emerging global distribution. We report a case of multifocal osteolytic lesions as the first sign of infection in a previously healthy 39-year-old female. M. riyadhense was detected in this case using next-generation metagenomic sequencing after it failed to be identified with conventional methods. The patient received 12 months of therapy with isoniazid, rifampin, and ethambutol, with the addition of moxifloxacin and clarithromycin in the first four months, and had a full return to health with no detectable disease at the last follow-up.}, }
@article {pmid40068342, year = {2025}, author = {Song, R and Lv, B and He, Z and Li, H and Wang, H}, title = {Rhizosphere metabolite dynamics in continuous cropping of vineyards: Impact on microflora diversity and co-occurrence networks.}, journal = {Microbiological research}, volume = {296}, number = {}, pages = {128134}, doi = {10.1016/j.micres.2025.128134}, pmid = {40068342}, issn = {1618-0623}, abstract = {The metabolism of the crop rhizosphere affects microflora diversity and nutrient cycling. However, understanding rhizosphere metabolism in suitable crops within arid desert environments and its impact on microflora interactions remains limited. Through metagenomic and non-targeted metabolomic sequencing of rhizosphere soils from one uncultivated land and four vineyards with cropping years of 5, 10, 15 and 20 years, the critical importance of rhizosphere metabolites in maintaining bacterial and fungal diversity was elucidated. The results revealed that Nocardioides, Streptomyces, and Solirubrobacter were the relatively abundant bacterial genera in rhizosphere soils, while Rhizophagus, Glomus, and Pseudogymnoascus were the relatively abundant fungal genera. The composition of rhizosphere metabolic changed significantly during the continuous cropping of grapevines. Dimethylglycine, Formononetin, and Dehydroepiandrosterone were the most important metabolites. Enrichment analysis revealed significant involvement of metabolic pathways such as biosynthesis of amino acids, unsaturated fatty acids, and linoleic acid metabolism. Procrustes analysis highlighted stronger correlations between rhizosphere metabolites and bacterial community compared to those of fungal community. This suggests distinct responses of microflora to crop-released chemical elements across different soil habitats. Co-occurrence network analysis demonstrated complex associations between rhizosphere metabolites and soil microflora, the positive correlations between rhizosphere metabolites and microflora networks predominated over negative correlations. Partial least squares path model indicated that the effect of cropping years on rhizosphere metabolites was greater than that on bacterial microflora diversity. Futhermore, pH, total phosphorus, and alkali-hydrolyzed nitrogen were the key environmental factors affecting rhizosphere metabolites and microbial diversity. These results deepen our valuable insights into the complex biological processes that rhizosphere metabolites influence on microorganisms, and provide strong support for maintaining microbial diversity in farmland soils in arid regions.}, }
@article {pmid40068284, year = {2025}, author = {Corbera-Rubio, F and Boersma, AS and de Vet, W and Pabst, M and van der Wielen, PWJJ and van Kessel, MAHJ and van Loosdrecht, MCM and van Halem, D and Lücker, S and Laureni, M}, title = {Biological methane removal by groundwater trickling biofiltration for emissions reduction.}, journal = {Water research}, volume = {279}, number = {}, pages = {123450}, doi = {10.1016/j.watres.2025.123450}, pmid = {40068284}, issn = {1879-2448}, abstract = {Methane removal is an essential step in drinking water production from methane-rich groundwaters. Conventional aeration-based stripping results in significant direct methane emissions, contributing up to one-third of a treatment plant's total carbon footprint. To address this, a full-scale trickling filter was operated for biological methane oxidation upstream of a submerged sand filter, and its performance was compared to a conventional aeration-submerged sand filtration set-up. Full-scale data were combined with ex-situ batch assays and metagenome-resolved metaproteomics to quantify the individual contribution of the main (a)biotic processes and characterize the enriched microbial communities. Both treatment setups fully removed methane, iron, ammonium, and manganese, yet the underlying mechanisms differed significantly. Methane was completely removed from the effluent after trickling filtration, with stripping and biological oxidation each accounting for half of the removal, thereby halving overall methane emissions. Methane-oxidizing bacteria not only outcompeted nitrifiers in the trickling filter, but also likely contributed directly to ammonia oxidation. In contrast to the submerged filter preceded by methane stripping, signatures of biological iron oxidation were almost completely absent in the trickling filter, suggesting that the presence of methane directly or indirectly promotes chemical iron oxidation. All systems had similar ex-situ manganese oxidation capacities, yet removal occurred only in the submerged filters but not the trickling filter. Ultimately, our results demonstrate that trickling filtration is effective in promoting biological methane oxidation at comparable produced drinking water quality, highlighting its potential for advancing sustainable drinking water production.}, }
@article {pmid40067770, year = {2025}, author = {Dominguez, EG and McDonald, BR and Zhang, H and Stephens, MD and Dietmann, EC and Nedden, M and Byington, N and Thompson, S and Junak, M and Pepperell, CS and Kisat, MT}, title = {Enrichment of Microbial DNA in Plasma to Improve Pathogen Detection in Sepsis: A Pilot Study.}, journal = {Clinical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/clinchem/hvaf011}, pmid = {40067770}, issn = {1530-8561}, support = {//the American Association for Surgery of Trauma Research and Education Fund Trauma Critical Care Scholarship/ ; K08GM148858/GF/NIH HHS/United States ; R01-AI113287//NIH/NIAID/ ; }, abstract = {BACKGROUND: Diagnosis of sepsis and timely identification of pathogens in critically ill patients remains challenging. Plasma metagenomic sequencing to detect microbial cell-free DNA (mDNA) has shown promise, but low abundance of mDNA in plasma limits sensitivity and necessitates high sequencing depth. mDNA is shorter and more fragmented than human cell-free DNA. Here, we evaluated whether combining single-stranded DNA (ssDNA) sequencing library preparation and size selection can enrich mDNA and improve pathogen detection.<br><br>METHODS: We prospectively enrolled 48 trauma patients and collected daily blood samples during the first 10 days of intensive care unit (ICU) admission. For patients with culture-proven infections, we extracted plasma DNA, prepared double-stranded DNA (dsDNA) and ssDNA sequencing libraries, and applied size selection to exclude fragments >110&#x2005;bp. Following sequencing, we performed taxonomic classification, and evaluated differences in mDNA fractions and in sensitivity for pathogen detection (compared to background noise).<br><br>RESULTS: We analyzed 46 plasma samples from 5 patients who developed culture-proven infections, including 17 samples coincident with positive microbial cultures. Size-selected ssDNA libraries showed the total mDNA fraction 204-fold higher on average than conventional dsDNA libraries (P < 0.0001). However, for pathogen-specific DNA (at the genus level), the highest sensitivity was observed in size-selected dsDNA (82%), compared to dsDNA (41%), ssDNA (71%), and size-selected ssDNA (35%) library preparations.<br><br>CONCLUSIONS: Our results demonstrate that combining ssDNA library preparation together with fragment size selection improves mDNA yield, potentially reducing sequencing requirements. However, at the genus level, this combination also increases background noise, which limits sensitivity for pathogen detection.}, }
@article {pmid40067020, year = {2025}, author = {Kaminsky, LM and Burghardt, L and Bell, TH}, title = {Evolving a plant-beneficial bacterium in soil vs. nutrient-rich liquid culture has contrasting effects on in-soil fitness.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0208524}, doi = {10.1128/aem.02085-24}, pmid = {40067020}, issn = {1098-5336}, abstract = {UNLABELLED: Inoculation of plant-beneficial microbes into agricultural soils can improve crop growth, but such outcomes depend on microbial survival. Here, we assessed how exposure to prior environmental conditions impacts microbial in-soil fitness, particularly focusing on incubation in liquid culture as an unavoidable phase of inoculant production and on pre-incubation in target soils as a potential method to improve performance. We conducted experimental evolution on a phosphorus-solubilizing bacterial species, Priestia megaterium, in (i) soil only, (ii) liquid media only, and (iii) soil followed by liquid media, using population metagenomic sequencing to track mutations over time. Several typical in vitro evolutionary phenomena were observed in liquid media-incubated populations, including clonal interference, genetic hitchhiking, and mutation parallelism between replicate populations, particularly in the sporulation transcription factor spo0A. Liquid media-incubated populations also developed a clear fitness reduction in soil compared to the ancestral isolate. However, soil-incubated populations grew slowly, experienced far fewer generations despite longer absolute time, and accumulated minimal mutational changes. Correspondingly, soil-incubated populations did not display improved survival compared to the ancestral isolate in their target soils, though there did appear to be minor fitness reductions in unfamiliar soil. This work demonstrates that adaptation to liquid media and/or a native soil can impact bacterial fitness in new soil and that bacterial evolution in more complex real-world habitats does not closely resemble bacterial evolution in liquid media.<br><br>IMPORTANCE: Innovative solutions are needed to address emerging challenges in agriculture while reducing its environmental footprint. Management of soil microbiomes could contribute to this effort, as plant growth-promoting microorganisms provide key ecosystem services that support crops. Yet, inoculating beneficial microbes into farm soils yields unreliable results. We require a greater knowledge of the ecology of these taxa to improve their functioning in sustainable agroecosystems. In this report, we demonstrate that exposure to laboratory media and lingering adaptation to another soil can negatively impact the in-soil survival of a phosphorus-solubilizing bacterial species. We go further to highlight the underlying mutations that give rise to these patterns. These insights can be leveraged to improve our understanding of how soil-dwelling beneficial microorganisms adapt to different evolutionary pressures.}, }
@article {pmid40066816, year = {2025}, author = {Karchmer, AW and Kaufman, NJ and Park, SY and Modi, RM and Abdul-Azim, A and van den Berg, P and Matos, JD and Kramer, DB and Zimetbaum, PJ}, title = {Quantitative Microbial Cell-Free DNA Sequencing from Plasma: A Potential Biomarker for the Diagnosis of Staphylococcal Infection of Cardiac Implantable Electronic Devices.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf113}, pmid = {40066816}, issn = {1537-6591}, abstract = {BACKGROUND: Staphylococcus aureus bacteremia in patients with cardiac implantable electronic devices (CIED) is often associated with infective endocarditis (CIED-IE). The CIED-IE diagnosis is syndromic. Diagnostic uncertainty is common. Frequently, these patients are classified possible CIED-IE, resulting in guideline non-compliant treatment and heterogeneous outcomes. Improved outcomes require accurate diagnoses. In these patients, we evaluated whether metagenomic sequencing of microbial cell-free DNA (mcfDNA) in serial plasma specimens could improve diagnostic precision.<br><br>METHODS: We studied 16 patients with staphylococcal bacteremia who were classified definite or possible CIED-IE and recommended for device removal, if there was a positive blood culture within 7 days and no concurrent deep infection. Plasma specimens obtained at consent, before extraction, and during 96 hours after extraction underwent metagenomic sequencing and quantification of staphylococcal mcfDNA.<br><br>RESULTS: In 10 of 11 definite CIED-IE patients, mcfDNA persisted during antibiotic therapy for prolonged durations (median 11 days, IQR 7.5 days [7.5,15]). In these cases, mcfDNA concentration in plasma obtained early after lead extraction increased significantly and thereafter decreased rapidly. In 5 cases of possible CIED-IE, mcfDNA was undetectable after 6 days (IQR 2 days [5.5,7.5]) of antibiotic therapy and remained undetectable after CIED extraction. These mcfDNA patterns differ significantly (p=0.001), suggesting two distinct patient populations: one with definite CIED-IE and one without lead infection.<br><br>CONCLUSIONS: If confirmed, these mcfDNA patterns can serve as biomarkers, together with clinical features, to improve precision in diagnosing or rejecting S. aureus CIED-IE. Strategically timed mcfDNA testing before and after CIED extraction may aid in planning therapy.}, }
@article {pmid40066307, year = {2025}, author = {Ci, X and Zhang, J and Lu, J and Qi, X and Ma, Y and Liu, W and Shi, J}, title = {Clinical characteristics of varicella-zoster virus central nervous system infection in 108 unimmunocompromised patients.}, journal = {Frontiers in neurology}, volume = {16}, number = {}, pages = {1554954}, pmid = {40066307}, issn = {1664-2295}, abstract = {BACKGROUND: Varicella-zoster virus (VZV) central nervous system infection is typically observed in immunocompromised patients, and there is a lack of studies involving large samples of non-immunocompromised individuals. In this study, we retrospectively analyzed 108 non-immunocompromised patients diagnosed with VZV central nervous system infection.<br><br>METHODS: This retrospective study was conducted in the Department of Neurology, Affiliated Nanjing Brain Hospital, Nanjing Medical University, China. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) revealed a positive result for VZV with a sequence number greater than 3, leading to a clinical diagnosis of VZV central nervous system infection. We analyzed the patients' age, gender, clinical manifestations, blood routine, erythrocyte sedimentation rate (ESR), CSF examination, magnetic resonance imaging (MRI), electroencephalogram (EEG), and Activities of Daily Living (ADL) scale scores (Barthel Index) on the day of admission and 3&#x202f;month post-discharge.<br><br>RESULTS: The study involved 108 patients, average age was 47.58&#x202f;&#xb1;&#x202f;2.91&#x202f;years old (16 to 80), 33 were female (30.60%) and 75 were male (69.40%). Clinical manifestations were fever (63.9%), headache (88.9%), nausea (50%), vomiting (27.8%), fatigue (50%), dizziness (25.0%), herpes zoster (47.2%), chickenpox (0.9%), peripheral facial paralysis (19.4%), encephalopathy (5.6%), and myelitis (2.8%). The average white blood cell (WBC) count was 7.40&#x202f;&#xb1;&#x202f;0.48*10[9]/l, the average CRP was 6.58&#x202f;&#xb1;&#x202f;0.69&#x202f;mg/L, and the average ESR was 7.79&#x202f;&#xb1;&#x202f;0.53&#x202f;mm/h. 28.1% of patients exhibited elevated lumbar puncture pressure, the average lumbar puncture pressure was 155.41&#x202f;&#xb1;&#x202f;2.38&#x202f;mmH2O; the average CSF WBC count was 196.60&#x202f;&#xb1;&#x202f;3.98*10^6/l, the average CSF protein was 1.35&#x202f;&#xb1;&#x202f;0.03&#x202f;g/L, the average CSF glucose was 3.41&#x202f;&#xb1;&#x202f;0.03&#x202f;mmoL/L, the average CSF chloride was 116.62&#x202f;&#xb1;&#x202f;0.15&#x202f;mmoL/L, the average CSF IgG index was 0.66&#x202f;&#xb1;&#x202f;0.01, the average mNGS examination of VZV sequence count was 626.25&#x202f;&#xb1;&#x202f;5402.17. Head MRI scans revealed no new lesions; three patients' spinal cord MRI displayed short-segment, non-transverse, and non-continuous patchy long T1 and long T2 signals in the thoracic or cervical spinal cord. On the first day of admission, 41.7% of the patients achieved ADL score of 100 points, 19.4% scored between 41 and 99 points, and 38.9% of the patients scored less than 40 points. All patients received intravenous infusions of acyclovir with low-dose corticosteroids. An outpatient review conducted 3&#x202f;months after discharge indicated 98.15% of the patients recovered well without any sequelae.<br><br>CONCLUSION: VZV encephalitis in immunocompetent individuals typically presents with mild clinical symptoms and has a favorable prognosis. VZV should be considered the common pathogen in the management of patients without immunocompeted condition with encephalitis.}, }
@article {pmid40066275, year = {2025}, author = {Negrete-Méndez, H and Valencia-Toxqui, G and Sepúlveda-Robles, OA and Ríos-Castro, E and Hurtado-Cortés, JC and Flores, V and Cázares, A and Kameyama, L and Martínez-Peñafiel, E and Fernández-Ramírez, F}, title = {Genomic and proteomic analyses of Nus-dependent non-lambdoid phages reveal a novel coliphage group prevalent in gut: mEpimmI.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1480411}, pmid = {40066275}, issn = {1664-302X}, abstract = {INTRODUCTION: Nus-dependent Mexican Escherichia coli phages (mEp) were previously isolated from clinical samples of human feces. Approximately 50% corresponded to non-lambdoid temperate phages integrating a single immunity group, namely immunity I (mEpimmI), and these were as prevalent as the lambdoid phages identified in such collection.<br><br>METHODS: In this work, we present the structural and functional characterization of six representative mEpimmI phages (mEp010, mEp013, mEp021, mEp044, mEp515, and mEp554). In addition, we searched for homologous phages and prophages in the GenBank sequence database, and performed extensive phylogenetic analyses on the compiled genomes.<br><br>RESULTS: A biological feature-based characterization of these phages was carried out, focusing on proteins relevant to phage biological activities. This included mass spectrometry analysis of mEp021 virion structural proteins, and a series of infection assays to characterize the function of the main repressor protein and the lipoproteins associated with superinfection-exclusion; to identify the main host receptor proteins recognized by these phages and the prophage insertion sites within the host genome, which were associated with specific integrase sequence-types present in the viral genomes. Further, we compiled 42 complete homologous genomes corresponding to 38 prophages from E. coli strains and 4 phages from metagenomes, displaying a wide geographical distribution. Intergenomic distance analyses revealed that these phages differ from previously established phage clades, and whole-proteome similarity analyses yielded a cohesive and monophyletic branch, when compared to >5,600 phages with dsDNA genomes.<br><br>DISCUSSION: According to current taxonomic criteria, our results are consistent with a novel family demarcation, and the studied genomes correspond to 9 genera and 45 distinct species. Further, we identified 50 core genes displaying high synteny among the mEpimmI genomes, and these genes were found arranged in functional clusters. Furthermore, a biological feature-based characterization of these phages was carried out, with experiments focusing on proteins relevant to phage biological activities, revealing common traits as well as diversity within the group. With the integration of all these experimental and bioinformatics findings, our results indicate that the mEpimmI phages constitute a novel branch of Caudoviricetes distinct to other known siphovirus, contributing to the current knowledge on the diversity of phages infecting Escherichia coli.}, }
@article {pmid40065594, year = {2025}, author = {Sun, Y and Yu, YT and Castillo, XO and Anderson, R and Wang, M and Sun, Q and Tallmadge, R and Sams, K and Reboul, G and Zehr, J and Brown, J and Wang, X and Marra, N and Stanhope, B and Grenier, J and Pusterla, N and Divers, T and Mittel, L and Goodman, LB}, title = {Investigation of the Blood Microbiome in Horses With Fever of Unknown Origin.}, journal = {Veterinary medicine and science}, volume = {11}, number = {2}, pages = {e70272}, doi = {10.1002/vms3.70272}, pmid = {40065594}, issn = {2053-1095}, support = {//Harry M. Zweig Memorial Fund for Equine Research/ ; 1U18FD006993//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; 1U18FD006716//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; W81XWH-22-1-0891//Department of Defense/ ; }, mesh = {Horses ; Animals ; *Horse Diseases/microbiology/virology/blood/epidemiology ; Case-Control Studies ; *Fever of Unknown Origin/veterinary/microbiology/etiology ; Microbiota ; Male ; Female ; }, abstract = {BACKGROUND: Fever of unknown origin (FUO) without a respiratory component is a frequent clinical presentation in horses. Multiple pathogens, both tick-borne and enteric, can be involved as etiologic agents. An additional potential mechanism is intestinal barrier dysfunction.<br><br>OBJECTIVES: This case-control study aimed to detect and associate microbial taxa in blood with disease state.<br><br>STUDY DESIGN: Areas known for a high prevalence of tick-borne diseases in humans were chosen to survey horses with FUO, which was defined as fever of 101.5&#xb0;F or higher with no signs of respiratory illness or other recognisable diseases. Blood samples and clinical parameters were obtained from 52 FUO cases and also from matched controls from the same farms. An additional 23 febrile horses without matched controls were included.<br><br>METHODS: Broadly targeted polymerase chain reaction (PCR) amplification directed at conserved sequence regions of bacterial 16S rRNA, parasite 18S rRNA, coronavirus RdRp and parvovirus NS1 was performed, followed by deep sequencing. To control for contamination and identify taxa unique to the cases, metagenomic sequences from the controls were subtracted from those of the cases, and additional targeted molecular testing was performed. Sera were also tested for antibodies to equine coronavirus.<br><br>RESULTS: Over 60% of cases had intestinal microbial DNA circulating in the blood. Nineteen percent of cases were attributed to infection with Anaplasma phagocytophilum, of which two were subtyped as human-associated strains. A novel Erythroparvovirus was detected in two cases and two controls. Serum titres for equine coronavirus were elevated in some cases but not statistically different overall between the cases and controls.<br><br>MAIN LIMITATIONS: Not all pathogens are expected to circulate in blood, which was the sole focus of this study.<br><br>CONCLUSIONS: The presence of commensal gut microbes in blood of equine FUO cases is consistent with a compromised intestinal barrier, which is highlighted as a direction for future study.}, }
@article {pmid40064809, year = {2025}, author = {Ouarabi, L and Taminiau, B and Daube, G and Barache, N and Bendali, F and Drider, D and Lucau-Danila, A}, title = {Insights into fungal diversity and dynamics of vaginal mycobiota.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {40064809}, issn = {1678-4405}, support = {Alibiotech CPER/FEDER 2016-2021//R&#xe9;gion Hauts-de-France/ ; }, abstract = {Although less studied than its bacterial counterpart, the fungal component of the vaginal microbiota plays a critical role in maintaining vaginal homeostasis. Most research on the composition of the vaginal mycobiota has focused on pathological conditions, with relatively few studies involving healthy women. To gain comprehensive insights into the vaginal mycobiota of Algerian women in two different age groups, we performed a targeted metagenomic analysis using ITS2 region sequencing data from 14 vaginal samples collected from healthy women in reproductive and postmenopausal stages. A single dominant fungal species per individual was observed in both young and postmenopausal women, with differences in fungal community composition between the two groups being related to hormone levels. Our results show that Candida and Saccharomyces were the dominant genera in both young and postmenopausal women. Notably, the postmenopausal group had twice as many species, along with the presence of uncommon taxa such as Dipodascus and Fusarium, indicating greater taxonomic diversity. These findings suggest that menopause is associated with increased microbial variability, likely due to hormonal changes that disrupt the vaginal environment. This study paves the way for more extensive analyses involving diverse age groups and ethnic backgrounds.}, }
@article {pmid40064789, year = {2025}, author = {Wang, H and Ma, H and Yan, H and Pei, Z and Zhao, J and Zhang, H and Zhang, Z and Lu, W}, title = {Study on the Effect of Bifidobacterium adolescentis CCFM1066 on Exercise Performance, Gut Microbiota, and Its Metabolites in Mice.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40064789}, issn = {1867-1314}, support = {32172212, 32394052//National Natural Science Foundation of China/ ; 2022YFF1100403//National Key Research and Development Program of China/ ; WMCC202403//Cohort and Clinical Research Program of Wuxi Medical Center, Nanjing Medical University/ ; }, abstract = {Prolonged high-intensity exercise consumes significant energy, leading to fatigue and decreased performance. This study explores the effects of Bifidobacterium adolescentis CCFM1066 on exercise performance, gut microbiota, and its metabolites in mice. The results of the mouse experiments showed the mice which were intervened by Bifidobacterium adolescentis CCFM1066 have a significant increase in exercise performance, including forceful swimming time, fatigue baton turning time, and forelimb grip strength. Through metagenomic sequencing and differential metabolites, analysis indicated that the intervention of CCFM1066 increased Lachnospiraceae bacterium, Parabacteroides goldsteinii, Bacteroides xylanisolvens, and Bifidobacterium adolescentis and altered the key metabolic pathways including protein digestion and absorption and biosynthesis of amino acids. Supplementation with CCFM1066 modulates the production of short-chain fatty acids (SCFAs) and fatty acid amides (FAAs) by gut microbiota, decreasing levels of lactic acid (LA), blood urea nitrogen (BUN), lactate dehydrogenase (LDH), and creatine kinase (CK) while increasing muscle and hepatic glycogen content, thus reducing central nervous system fatigue and thereby improving exercise endurance and performance. These findings provide new insights into nutritional interventions for sports performance.}, }
@article {pmid40064739, year = {2025}, author = {Thakur, SS and González, SS and Suravajhala, P and Jain, SK and Yadav, S and Narayan, KS and Esack, E and Kuzyakov, Y and Ratnasari, A}, title = {Metagenomic insights of microbial functions under conventional and conservation agriculture.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {3}, pages = {100}, pmid = {40064739}, issn = {1573-0972}, support = {Grant ID: 3203/SKMCCC/EPCO/2021//Environmental Planning &amp; Coordination Organisation (EPCO), Ministry of Environment, Government of Madhya Pradesh, India/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Metagenomics ; *Agriculture ; *Archaea/genetics/classification ; *Soil/chemistry ; Metagenome ; Phylogeny ; Biodiversity ; Carbon/metabolism ; Nitrogen/metabolism ; }, abstract = {Agricultural practices such as conventional (CN) and conservation agriculture (CA) influence the composition and structure of soil microorganisms. We used short reads and genome-resolved metagenomic-based dual sequencing approaches to create a profile of bacterial and archaeal communities in hyperthermic Typic Haplustepts soil after seven years of CA and CN. The most differences in the physico-chemical and biological properties of soil were higher pH, organics carbon, available nitrogen and microbial biomass contents, activities of dehydrogenase, β-glucosidase, and arylsulfatase, found in CA soil. The dominant bacterial taxa under both management types were Pseudomonadota (46-48%), Acidobacteriota (12-13%), Planctomycetota (8-10%), Bacteroidota (7-8%), and Actinomycetota (6-7%). Nitrososphaerota (1.1-1.5%) was the predominant archaeal phyla in CA and CN soils. The alpha diversity was 1.5 times higher in CA compared to CN soils. Fourteen high-quality (HQ) metagenomic-assembled genomes (MAGs) were recovered from both groups. Four HQ metagenome-assembled genomes (MAGs) from the Pseudomonadota phylum were exclusively recovered from the CA soil. The dominance of this phylum in the CA soil might be correlated with its nutrient richness, as certain classes of Pseudomonadota, such as Alpha, Beta-, Gamma-, and Deltaproteobacteria, are known to be copiotrophic. Copiotrophic organisms thrive in nutrient-rich environments, which could explain their prevalence in the CA soil. CAZyme gene analysis showed that Glycoside Hydrolases (GH) and GlycosylTransferases (GT) classes are dominant in the CA group, possibly due to higher substrate availability from the application of crop residues, which provide a rich source of complex carbohydrates. Several biogeochemical gene families related to C1 compounds, hydrogen, oxygen, and sulfur metabolism were enriched in CA soils, suggesting these practices may contribute to a soil environment with increased organic matter content, microbial diversity, and nutrient availability. Overall, CA practices seemed to improve soil health by supporting soil microbial communities abundance.}, }
@article {pmid40064231, year = {2025}, author = {Jia, Y and Huang, D and Lan, X and Sun, X and Lin, W and Sun, W and Wang, Y}, title = {Community structure and metabolic potentials of keystone taxa and their associated bacteriophages within rice root endophytic microbiome in response to metal(loid)s contamination.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126028}, doi = {10.1016/j.envpol.2025.126028}, pmid = {40064231}, issn = {1873-6424}, abstract = {Heavy metal (HM) contamination of agricultural products is of global environmental concern as it directly threatened the food safety. Plant-associated microbiome, particularly endophytic microbiome, hold the potential for mitigating HM stress as well as promoting plant growth. The metabolic potentials of the endophytes, especially those under the HM stresses, have not been well addressed. Rice, a major staple food worldwide, is more vulnerable to HM contamination compared to other crops and therefore requires special attentions. Therefore, this study selected rice as the target plants. Geochemical analysis and amplicon sequencing were combined to characterize the rice root endophytic bacterial communities and identify keystone taxa in two HM-contaminated rice fields. Metagenomic analysis was employed to investigate the metabolic potentials of these keystone taxa. Burkholderiales and Rhizobiales were identified as predominant keystone taxa. The metagenome-assembled genome (MAG)s associated with these keystone populations suggested that they possessed diverse genetic potentials related to metal resistance and transformation (e.g., As resistance and cycling, V reduction, Cr efflux and reduction), and plant growth promotion (nitrogen fixation, phosphate solubilization, oxidative stress resistance, indole-3-acetic acid, and siderophore production). Moreover, bacteriophages encoding auxiliary metabolism genes (AMGs) associated with the HM resistance as well as nitrogen and phosphate acquisition were identified, suggesting that these phages may contribute to these crucial biogeochemical processes within rice roots. The current findings revealed the beneficial roles of rice endophytic keystone taxa and their associated bacteriophages within HM-contaminated rice root endophytic microbiome, which may provide valuable insights on future applications of employing root microbiome for safety management of agriculture productions.}, }
@article {pmid40064141, year = {2025}, author = {She, Y and Wu, L and Qi, X and Sun, S and Li, Z}, title = {Aging behaviors intensify the impacts of microplastics on nitrate bioreduction-driven nitrogen cycling in freshwater sediments.}, journal = {Water research}, volume = {279}, number = {}, pages = {123448}, doi = {10.1016/j.watres.2025.123448}, pmid = {40064141}, issn = {1879-2448}, abstract = {Microplastics (MPs) inevitably undergo aging processes in natural environments; however, how aging behaviors influence the interactions between MPs exposures and nitrate bioreduction in freshwater sediments remains poorly understood. Here, we explored the distinct impacts of virgin and aged MPs (polystyrene (PS) and polylactic acid (PLA)) on nitrate bioreduction processes in lake sediments through a long-term microcosm experiment utilizing the [15]N isotope tracing technique and molecular analysis. Compared to virgin MPs, aged PLA significantly increased the rates of denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) (p < 0.05), facilitating sediment nitrogen loss, while aged PS only significantly improved the rates of DNRA by 272-297 % and contributed to nitrogen retention in sediments. Metagenomic sequencing demonstrated that a more significant enrichment of functional genes responsible for nitrate bioreduction pathways occurred with aged MPs exposures than with virgin MPs. By combining analyses of MPs aging traits and the key drivers of nitrate bioreduction, we revealed that aging behaviors directly regulated sediment nutrient status (e.g., DOC/NOx[-] ratio) and microbiological properties (from genes to bacteria), thereby further determining the activity of nitrate bioreduction. This work provides new insights into the impacts of aged MPs on sediment nitrate reduction and highlights the role of MPs aging in future assessments of long-term MPs pollution in freshwater ecosystems.}, }
@article {pmid40063888, year = {2025}, author = {Saraphol, B and Hinthong, W and Chienwichai, P and Pumipuntu, N and Reamtong, O and Srisook, T and Premsuriya, J}, title = {Analysis of the fecal microbiome and metabolome in dairy cows with different body condition scores.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0319461}, pmid = {40063888}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Feces/microbiology ; *Metabolome ; Female ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Holstein Friesian is the most popular breed of dairy cows worldwide due to its exceptional milk production capabilities. In dairy cow management, the body condition score (BCS) is a useful tool, serving as a reliable indicator of a cow's nutritional status and overall health. It is determined via a subjective visual and tactile assessment of fat cover and muscle mass. A low BCS is associated with decreased milk production and fertility. While genetic and nutritional factors have previously been associated with BCS, their effects are often moderate. In this study, we compared the fecal microbiome and the untargeted fecal metabolome of normal (BCS ≥ 3, n = 16) and thin (BCS < 3, n = 16) Holstein Friesian dairy cows. The 16S rRNA gene-based metagenomic analysis revealed that thin cows had significantly higher levels of Clostridiaceae, Erysipelotrichales, Erysipelotrichaceae, and Turicibacter, while normal cows had higher levels of Clostridiales_vadinBB60_group, UCG-010, Bacteroidaceae, Ruminococcaceae, Paludibacteraceae, Alistipes, and Bacteroides. The fecal metabolomic analysis showed that key signaling pathways, including the mechanistic target of rapamycin (mTOR), phosphatidylinositol 3-kinase (PI3K)-Akt, and AMP-activated protein kinase (AMPK) pathways, were enriched in thin cows. In addition, a significant correlation was observed between differential microbial taxa and metabolites. Notably, Clostridiaceae and Erysipelotrichaceae species are linked to inflammation, infectious diseases, and conditions such as ruminal acidosis. Additionally, the mTOR, PI3K-Akt, and AMPK pathways are known to be activated by both nutrient deficiencies and inflammation. We propose that, in addition to genetic and nutritional factors, gut microbiome dysbiosis may contribute to subclinical health conditions, such as chronic inflammation and acidosis, which indirectly affect the cow's BCS. These findings are guiding our ongoing research on the underlying health conditions in thin cows to better understand the role that the gut microbiome plays in the regulation of the body condition.}, }
@article {pmid40063675, year = {2025}, author = {Chavarria, X and Park, HS and Oh, S and Kang, D and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY}, title = {Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001365}, pmid = {40063675}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Supervised Machine Learning ; *Diabetes Mellitus, Type 1/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Adult ; Bacteria/genetics/classification/isolation &amp; purification ; Metagenome ; Support Vector Machine ; Aged ; Algorithms ; }, abstract = {Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic data from a volunteer citizen science initiative to investigate microbial markers associated with diabetes status (positive or negative) and type (type 1 or type 2 diabetes mellitus) using supervised machine learning (ML) models. The diversity of the microbiome varied according to diabetes status and type. Differential microbial signatures between diabetes types and negative group revealed an increased presence of Brucellaceae, Ruminococcaceae, Clostridiaceae, Micrococcaceae, Barnesiellaceae and Fusobacteriaceae in subjects with diabetes type 1, and Veillonellaceae, Streptococcaceae and the order Gammaproteobacteria in subjects with diabetes type 2. The decision tree, elastic net, random forest (RF) and support vector machine with radial kernel ML algorithms were trained to screen and type diabetes based on microbial profiles of 76 subjects with type 1 diabetes, 366 subjects with type 2 diabetes and 250 subjects without diabetes. Using the 1000 most variable features, tree-based models were the highest-performing algorithms. The RF screening models achieved the best performance, with an average area under the receiver operating characteristic curve (AUC) of 0.76, although all models lacked sensitivity. Reducing the dataset to 500 features produced an AUC of 0.77 with sensitivity increasing by 74% from 0.46 to 0.80. Model performance improved for the classification of negative-status and type 2 diabetes. Diabetes type models performed best with 500 features, but the metric performed poorly across all model iterations. ML has the potential to facilitate early diagnosis of diabetes based on microbial profiles of the gut microbiome.}, }
@article {pmid40063348, year = {2025}, author = {Koul, M and Kaushik, S and Singh, K and Sharma, D}, title = {VITALdb: to select the best viroinformatics tools for a desired virus or application.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf084}, pmid = {40063348}, issn = {1477-4054}, support = {BT/2014-15/Plan/P-955//MHRD/ ; R.11013/51/2021-GIA/HR//DHR/ ; }, mesh = {Humans ; *Computational Biology/methods ; Antiviral Agents/therapeutic use ; COVID-19/virology/epidemiology ; SARS-CoV-2/genetics ; Viruses/genetics/classification ; Virus Diseases/virology ; Algorithms ; Software ; }, abstract = {The recent pandemics of viral diseases, COVID-19/mpox (humans) and lumpy skin disease (cattle), have kept us glued to viral research. These pandemics along with the recent human metapneumovirus outbreak have exposed the urgency for early diagnosis of viral infections, vaccine development, and discovery of novel antiviral drugs and therapeutics. To support this, there is an armamentarium of virus-specific computational tools that are currently available. VITALdb (VIroinformatics Tools and ALgorithms database) is a resource of ~360 viroinformatics tools encompassing all major viruses (SARS-CoV-2, influenza virus, human immunodeficiency virus, papillomavirus, herpes simplex virus, hepatitis virus, dengue virus, Ebola virus, Zika virus, etc.) and several diverse applications [structural and functional annotation, antiviral peptides development, subspecies characterization, recognition of viral recombination, inhibitors identification, phylogenetic analysis, virus-host prediction, viral metagenomics, detection of mutation(s), primer designing, etc.]. Resources, tools, and other utilities mentioned in this article will not only facilitate further developments in the realm of viroinformatics but also provide tremendous fillip to translate fundamental knowledge into applied research. Most importantly, VITALdb is an inevitable tool for selecting the best tool(s) to carry out a desired task and hence will prove to be a vital database (VITALdb) for the scientific community. Database URL: https://compbio.iitr.ac.in/vitaldb.}, }
@article {pmid40062866, year = {2025}, author = {Ingle, DJ and Walsh, CJ and Samuel, GR and Wick, RR and Davidovich, N and Fiocchi, E and Judd, LM and Elliman, J and Owens, L and Stinear, TP and Basso, A and Pretto, T and Newton, HJ}, title = {The complete genome sequence of the crayfish pathogen Candidatus Paracoxiella cheracis n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0100224}, doi = {10.1128/msphere.01002-24}, pmid = {40062866}, issn = {2379-5042}, abstract = {The Coxiellaceae bacterial family, within the order Legionellales, is defined by a collection of poorly characterized obligate intracellular bacteria. The zoonotic pathogen and causative agent of human Q fever, Coxiella burnetii, represents the best-characterized member of this family. Coxiellaceae establish replicative niches within diverse host cells and rely on their host for survival, making them challenging to isolate and cultivate within a laboratory setting. Here, we describe a new genus within the Coxiellaceae family that has been previously shown to infect economically significant freshwater crayfish. Using culture-independent long-read metagenomics, we reconstructed the complete genome of this novel organism and demonstrate that the species previously referred to as Candidatus Coxiella cheraxi represents a novel genus within this family, herein denoted Candidatus Paracoxiella cheracis. Interestingly, we demonstrate that Candidatus P. cheracis encodes a complete, putatively functional Dot/Icm type 4 secretion system that likely mediates the intracellular success of this pathogen. In silico analysis defined a unique repertoire of Dot/Icm effector proteins and highlighted homologs of several important C. burnetii effectors, including a homolog of CpeB that was demonstrated to be a Dot/Icm substrate in C. burnetii.IMPORTANCEUsing long-read sequencing technology, we have uncovered the full genome sequence of Candidatus Paracoxiella cheracis, a pathogen of economic importance in aquaculture. Analysis of this sequence has revealed new insights into this novel member of the Coxiellaceae family, demonstrating that it represents a new genus within this poorly characterized family of intracellular organisms. Importantly, the genome sequence reveals invaluable information that will support diagnostics and potentially both preventative and treatment strategies within crayfish breeding facilities. Candidatus P. cheracis also represents a new member of Dot/Icm pathogens that rely on this system to establish an intracellular niche. Candidatus P. cheracis possesses a unique cohort of putative Dot/Icm substrates that constitute a collection of new eukaryotic cell biology-manipulating effector proteins.}, }
@article {pmid40062856, year = {2025}, author = {Kralj, JG and Servetas, SL and Forry, SP and Hunter, ME and Dootz, JN and Jackson, SA}, title = {Analytical assessment of metagenomic workflows for pathogen detection with NIST RM 8376 and two sample matrices.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0280624}, doi = {10.1128/spectrum.02806-24}, pmid = {40062856}, issn = {2165-0497}, abstract = {We assessed the analytical performance of metagenomic workflows using NIST Reference Material (RM) 8376 DNA from bacterial pathogens spiked into two simulated clinical samples: cerebrospinal fluid (CSF) and stool. Sequencing and taxonomic classification were used to generate signals for each sample and taxa of interest and to estimate the limit of detection (LOD), the linearity of response, and linear dynamic range. We found that the LODs for taxa spiked into CSF ranged from approximately 100 to 300 copy/mL, with a linearity of 0.96 to 0.99. For stool, the LODs ranged from 10 to 221 kcopy/mL, with a linearity of 0.99 to 1.01. Furthermore, discriminating different E. coli strains proved to be workflow-dependent as only one classifier:database combination of the three tested showed the ability to differentiate the two pathogenic and commensal strains. Surprisingly, when we compared the linear response of the same taxa in the two different sample types, we found those functions to be the same, despite large differences in LODs. This suggests that the "agnostic diagnostic" theory for metagenomics (i.e., any organism can be identified because DNA is the measurand) may apply to different target organisms and different sample types. Because we are using RMs, we were able to generate quantitative analytical performance metrics for each workflow and sample set, enabling relatively rapid workflow screening before employing clinical samples. This makes these RMs a useful tool that will generate data needed to support the translation of metagenomics into regulated use.IMPORTANCEAssessing the analytical performance of metagenomic workflows, especially when developing clinical diagnostics, is foundational for ensuring that the measurements underlying a diagnosis are supported by rigorous characterization. To facilitate the translation of metagenomics into clinical practice, workflows must be tested using control samples designed to probe the analytical limitations (e.g., limit of detection). Spike-ins allow developers to generate fit-for-purpose control samples for initial workflow assessments and inform decisions about further development. However, clinical sample types include a wide range of compositions and concentrations, each presenting different detection challenges. In this work, we demonstrate how spike-ins elucidate workflow performance in two highly dissimilar sample types (stool and CSF), and we provide evidence that detection of individual organisms is unaffected by background sample composition, making detection sample-agnostic within a workflow. These demonstrations and performance insights will facilitate the translation of the technology to the clinic.}, }
@article {pmid40062854, year = {2025}, author = {Zhang, F and Luan, J and Suo, L and Wang, H and Zhao, Y and Sun, T and Ni, Y and Cao, H and Zou, X and Liu, B}, title = {Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0263924}, doi = {10.1128/spectrum.02639-24}, pmid = {40062854}, issn = {2165-0497}, abstract = {UNLABELLED: Emerging evidence suggests that altered gut microbiota is linked to community-acquired pneumonia (CAP), but the potential mechanisms by which gut microbiota and its metabolites contribute to the development of CAP remain unclear. Fecal samples from 32 CAP patients and 36 healthy controls were analyzed through metagenomic sequencing and metabolomic profiling. The gut microbiota composition in CAP patients showed significant differences and lower diversity compared to healthy controls. Genera involved in short-chain fatty acid (SCFA) production, such as Faecalibacterium, Ruminococcus, and Eubacterium, as well as species like Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, Prevotella copri, and Ruminococcus bromii, were significantly depleted in CAP patients. Bacterial co-occurrence network analysis revealed an over-representation of pro-inflammatory bacteria, which contributed to the core gut microbiome in CAP patients. Metabolomic analysis of fecal samples identified a distinct metabolic profile, with a notable increase in arachidonic acid, but a decrease in secondary bile acids, such as deoxycholic acid, lithocholic acid, and ursodeoxycholic acid, compared to healthy controls. Spearman correlation analysis between differential microbiota and bile acids showed that Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, and Prevotella copri were positively correlated with ursocholic acid, lithocholic acid, and ursodeoxycholic acid, respectively. Our results suggest that the reduction in secondary bile acids, insufficient production of SCFAs, and an overabundance of pro-inflammatory bacteria may contribute to metabolic inflammation in the body. These factors could play a key role in the pathogenesis of CAP, driven by gut microbiota alterations.<br><br>IMPORTANCE: This study presents a comprehensive metagenomic and metabolomic analysis of fecal samples from community-acquired pneumonia (CAP) patients, identifying key characteristics, such as decreased secondary bile acids, imbalanced short-chain fatty acid production, and increased pro-inflammatory bacteria. These findings provide valuable insights into the mechanisms linking gut microbiota alterations to CAP pathogenesis and suggest that targeting the gut microbiota could be a promising strategy for intervening in CAP.}, }
@article {pmid40062772, year = {2025}, author = {Connolly, JP and Kelly, L}, title = {The physical biogeography of Fusobacterium nucleatum in health and disease.}, journal = {mBio}, volume = {}, number = {}, pages = {e0298924}, doi = {10.1128/mbio.02989-24}, pmid = {40062772}, issn = {2150-7511}, abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.<br><br>IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.}, }
@article {pmid40062294, year = {2025}, author = {Kuzudisli, C and Bakir-Gungor, B and Qaqish, B and Yousef, M}, title = {RCE-IFE: recursive cluster elimination with intra-cluster feature elimination.}, journal = {PeerJ. Computer science}, volume = {11}, number = {}, pages = {e2528}, pmid = {40062294}, issn = {2376-5992}, abstract = {The computational and interpretational difficulties caused by the ever-increasing dimensionality of biological data generated by new technologies pose a significant challenge. Feature selection (FS) methods aim to reduce the dimension, and feature grouping has emerged as a foundation for FS techniques that seek to detect strong correlations among features and identify irrelevant features. In this work, we propose the Recursive Cluster Elimination with Intra-Cluster Feature Elimination (RCE-IFE) method that utilizes feature grouping and iterates grouping and elimination steps in a supervised context. We assess dimensionality reduction and discriminatory capabilities of RCE-IFE on various high-dimensional datasets from different biological domains. For a set of gene expression, microRNA (miRNA) expression, and methylation datasets, the performance of RCE-IFE is comparatively evaluated with RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE. On average, RCE-IFE attains an area under the curve (AUC) of 0.85 among tested expression datasets with the fewest features and the shortest running time, while RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE achieve similar AUCs of 0.84 and 0.83, respectively. RCE-IFE and SVM-RCE yield AUCs of 0.79 and 0.68, respectively when averaged over seven different metagenomics datasets, with RCE-IFE significantly reducing feature subsets. Furthermore, RCE-IFE surpasses several state-of-the-art FS methods, such as Minimum Redundancy Maximum Relevance (MRMR), Fast Correlation-Based Filter (FCBF), Information Gain (IG), Conditional Mutual Information Maximization (CMIM), SelectKBest (SKB), and eXtreme Gradient Boosting (XGBoost), obtaining an average AUC of 0.76 on five gene expression datasets. Compared with a similar tool, Multi-stage, RCE-IFE gives a similar average accuracy rate of 89.27% using fewer features on four cancer-related datasets. The comparability of RCE-IFE is also verified with other biological domain knowledge-based Grouping-Scoring-Modeling (G-S-M) tools, including mirGediNET, 3Mint, and miRcorrNet. Additionally, the biological relevance of the selected features by RCE-IFE is evaluated. The proposed method also exhibits high consistency in terms of the selected features across multiple runs. Our experimental findings imply that RCE-IFE provides robust classifier performance and significantly reduces feature size while maintaining feature relevance and consistency.}, }
@article {pmid40061332, year = {2025}, author = {Moore, CM and Secor, EA and Fairbanks-Mahnke, A and Everman, JL and Elhawary, JR and Witonsky, JI and Pruesse, E and Chang, CH and Contreras, MG and Eng, C and Canales, K and Rosado, T and Hu, D and Huntsman, S and Jackson, ND and Li, Y and Lopez, N and Valentin, AM and Medina, V and Montanez-Lopez, CA and Morin, A and Nieves, NA and Oh, SS and Otero, RA and Colon, R and Rodriguez, L and Sajuthi, SP and Salazar, S and Serrano, G and Morales, EV and Vazquez, G and Morales, NV and Williams, BJM and Zhang, P and Sheppard, D and Rodriguez Santana, JR and Seibold, MA}, title = {Independent and interactive effects of viral species on risk for lower respiratory tract illnesses in early life.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.25.25322678}, pmid = {40061332}, abstract = {IMPORTANCE: All children experience upper respiratory tract illnesses (URI) caused by viral infections. However, some of these illnesses progress to the lower airways. Although studies have found infection with certain viral species are more likely to trigger lower respiratory illnesses (LRIs), a comprehensive analysis of viruses underlying early-life LRIs is lacking.<br><br>OBJECTIVE: Determine the incidence of URIs, mild and severe LRIs (mLRI, sLRI) during the first 2 years of life and the association between viral respiratory pathogens and odds of LRIs versus URIs in Puerto Rican children, a population at high risk for respiratory disease.<br><br>Healthy mother-infant pairs were enrolled in the Puerto Rican Infant Metagenomic and Epidemiologic Study of Respiratory Outcomes birth cohort, in Caguas, Puerto Rico. Infants (n=2,061) were surveilled for respiratory illnesses during the first two years of life (March 2020 to April 2024). Nasal swabs from a subset of 1,363 illnesses from 774 participants were screened for 21 pathogens.<br><br>EXPOSURES: Infection with respiratory pathogens.<br><br>MAIN OUTCOMES AND MEASURES: URI, mLRI, and sLRI in the first two years of life.<br><br>RESULTS: RSV infections occurred in 23% of sLRIs and were associated with dramatically increased odds of sLRI vs URI (OR=9.28; 95% CI, 5.43-15.85). Metapneumovirus, parainfluenza, and non-SARS-CoV-2 coronavirus infections also increased odds of sLRIs. SARS-CoV-2 was associated with lower risk of sLRIs vs. URIs (OR=0.33; 95% CI, 0.16-0.68). Though rhinovirus (43%) and bocavirus (16.1%) were commonly detected in sLRIs, neither was associated with increased sLRI risk. Infection with multiple viral species (i.e. co-infection) occurred in one-third of sLRIs and was associated with 2.92-fold greater odds of sLRI (95% CI, 2.05-4.16) compared to single viral species infections. Rhinovirus-bocavirus was the most common co-infection (32.4%), and interaction between these viral infections was associated with increased sLRI risk (OR=2.21; 95% CI, 1.20-4.09) relative to illnesses that were negative for rhinovirus and bocavirus.<br><br>CONCLUSIONS AND RELEVANCE: A diversity of viral pathogens drive early-life sLRIs. Some viral pathogens (e.g. RSV and metapneumovirus) have intrinsic propensity to cause sLRIs, whereas many sLRIs are caused by viruses whose lower airway pathogenicity is dependent on other factors, including co-infection.<br><br>KEY POINTS: Question: How do common respiratory viruses differ in their prevalence and risk of causing severe lower respiratory illnesses (LRIs) during early childhood?Findings: RSV, metapneumovirus, and parainfluenza are independent risk factors for early childhood severe LRIs. While rhinovirus and bocavirus infections alone do not increase the risk of severe LRIs, these two viruses significantly elevate risk when they occur as co-infections.Meaning: Our findings highlight significant variability in viruses that drive severe early-life LRIs. Some viral species appear to inherently predispose individuals to lower airway disease, while for others, the development of disease likely depends on co-infections and/or host susceptibility.}, }
@article {pmid40060957, year = {2025}, author = {Zhao, JH and Li, WJ and Jiao, J and Wang, MX and Zhang, XM and Yin, JY and Hu, WZ and Song, Q and Liu, J}, title = {Treatment of a rare and severe infection of central nervous system by Angiostrongylus cantonensis: A case report.}, journal = {World journal of radiology}, volume = {17}, number = {2}, pages = {105059}, pmid = {40060957}, issn = {1949-8470}, abstract = {BACKGROUND: Angiostrongylus cantonensis-induced acute parasitic infection is a rare food-borne disease in clinical practice. Lack of its specific laboratory markers and subsequent difficulty in detecting pathogens cause high misdiagnosis and missed diagnosis rates.<br><br>CASE SUMMARY: A 20-year-old male developed persistent neck and back pain after consuming raw snail meat, followed by urinary retention and low fever. After admission, the patient was misdiagnosed as viral infection and Mycobacterium tuberculosis in central nervous system. After detection of Angiostrongylus cantonensis in blood and cerebrospinal fluid by metagenomics next generation sequencing, albendazole was administered with ceftriaxone and methylprednisolone treatment simultaneously. With effective antiparasitic treatment, the patient weaned from mechanical ventilation successfully and transferred out of intensive care unit for hyperbaric oxygen and rehabilitation treatment.<br><br>CONCLUSION: This case highlights the diagnostic challenges of Angiostrongylus cantonensis infection and the importance of advanced sequencing techniques in identifying rare pathogens.}, }
@article {pmid40060808, year = {2025}, author = {Gao, B and Shi, X and Zhao, M and Ren, F and Xu, W and Gao, N and Shan, J and Shen, W}, title = {Mixture Effects of Polystyrene Microplastics on the Gut Microbiota in C57BL/6 Mice.}, journal = {ACS omega}, volume = {10}, number = {8}, pages = {7597-7608}, pmid = {40060808}, issn = {2470-1343}, abstract = {Microplastics are plastic particles with sizes of less than 5 mm. The ubiquity of microplastics in the environment has raised serious public health concerns. Microplastics could disturb the composition of the gut microbiota due to both chemical composition and physical interactions, which might further influence the metabolism and immune function of the host. However, most of the exposure studies chose microplastics of specific sizes. In the natural environment, living organisms are exposed to a mixture of microplastics of various sizes. In this study, male C57BL/6 mice were exposed to polystyrene (PS) microplastics with different sizes, including microplastics with diameters of 0.05-0.1 μm (PS0.1 group, 100 ppb), 9-10 μm (PS10 group, 100 ppb), and microplastic mixtures of both 0.05-0.1 and 9-10 μm (PSMix group) at a total concentration of 100 ppb (50 ppb for each size). Mixture effects of microplastics were investigated on the composition of bacteria and fungi as well as functional metagenome and microbial genes encoding antibiotic resistance and virulence factors. We found that some bacteria, fungi, and microbial metabolic pathways were only altered in the PSMix group, not in the PS0.1 or PS10 group, suggesting the toxic effects of the microplastic mixture on the composition of fungi and bacteria, and the functional metagenome is different from the effects of microplastics at specific sizes. Meanwhile, altered genes encoding antibiotic resistance and virulence factors in the PSMix group were shared with the PS0.1 and PS10 groups, possibly due to functional redundancy. Our findings help improve the understanding of the toxic effects of the microplastic mixture on the gut microbiome.}, }
@article {pmid40060671, year = {2025}, author = {Trunfio, M and Scutari, R and Fox, V and Vuaran, E and Dastgheyb, RM and Fini, V and Granaglia, A and Balbo, F and Tortarolo, D and Bonora, S and Perno, CF and Di Perri, G and Alteri, C and Calcagno, A}, title = {The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.28.640732}, pmid = {40060671}, issn = {2692-8205}, abstract = {UNLABELLED: Despite effective HIV suppression, neuroinflammation and neurocognitive issues are prevalent in people with HIV (PWH) yet poorly understood. HIV infection alters the human virome, and virome perturbations have been linked to neurocognitive issues in people without HIV. Once thought to be sterile, the cerebrospinal fluid (CSF) hosts a recently discovered virome, presenting an unexplored avenue for understanding brain and mental health in PWH. This cross-sectional study analyzed 85 CSF samples (74 from PWH on suppressive antiretroviral therapy, and 11 from controls without HIV, CWH) through shotgun metagenomics for DNA/RNA viruses. Taxonomic composition (reads and contigs), α and β diversity, and relative abundance (RA) of prokaryotic (PV), human eukaryotic (hEV), and non-human eukaryotic viruses (nhEV) were evaluated in relation to HIV infection, markers of neuroinflammation and neurodegeneration, cognitive functions, and depressive symptoms. Sensitivity analyses and post-hoc cluster analysis on the RA of viral groups and blood-brain barrier permeability were also performed. Of 46 read-positive CSF samples, 93.5% contained PV sequences, 47.8% hEV, and 45.6% nhEV. Alpha diversity was lower in PWH versus CWH, although p>0.05. At β diversity analysis, HIV status explained 3.3% of the variation in viral composition (p=0.016). Contigs retained 13 samples positive for 8 hEV, 2 nhEV, and 6 PV. Higher RA of PV was correlated with higher CSF S100β (p=0.002) and β-Amyloid 1-42 fragment (βA-42, p=0.026), while higher RA of nhEV with poorer cognitive performance (p=0.022). Conversely, higher RA of hEV correlated with better cognition (p=0.003) and lower βA-42 (p=0.012). Sensitivity analyses in virome-positive samples only confirmed these findings. Three CSF clusters were identified and showed differences in astrocytosis, βA-42, tau protein, and cognitive functions. Participants with hEV-enriched CSF showed better cognitive performance compared to those with virus-devoid and nhEV-enriched CSF (models'p<0.05). This study provides the first comprehensive description of the CSF virome in PWH, revealing associations with neuroinflammation and cognition. These findings highlight the potential involvement of the CSF virome in brain health and inform about its composition, origin, and potential clinical implications in people with and without HIV.<br><br>AUTHOR SUMMARY: HIV can affect brain health and mental well-being, even in people on successful antiretroviral therapy. The reasons behind this are still unclear. HIV also influences the communities of microbes and viruses living in the human body, and recent research suggests that the human virome, the collection of all viruses within the body, may play a role in cognitive functions, mood, and brain health. For a long time, scientists believed that the cerebrospinal fluid (CSF), which surrounds the brain, was sterile, while robust evidence has shown that the CSF hosts its own unique virome. Via advanced genetic sequencing (shotgun metagenomics), we analyzed the CSF virome in people with and without HIV looking for possible links to neuroinflammation, cognitive performance, and depression. We found that while HIV infection does affect the composition of CSF viral communities, there were no remarkable differences in the CSF virome of individuals with and without HIV. Most viral sequences appeared to come outside the brain. A higher abundance of non-human viral sequences, such as viruses of bacteria, plants, fungi, and animals, was associated with neuroinflammation and poorer cognitive performance. On the other hand, a higher abundance of human viruses correlated with better cognitive function and healthier signature of neuromarkers. These findings provide new insights into the presence and characteristics of the human CSF virome and how it might influence brain health. They also suggest new potential mechanisms of HIV-associated neuropathology.}, }
@article {pmid40060627, year = {2025}, author = {Rodriguez-Rodriguez, L and Pfister, J and Schuck, L and Martin, AE and Mercado-Santiago, LM and Tagliabracci, VS and Forsberg, KJ}, title = {Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.28.640651}, pmid = {40060627}, issn = {2692-8205}, abstract = {To prevent phage infection, bacteria have developed an arsenal of antiphage defense systems. Using functional metagenomic selections, we identified new examples of these systems from human fecal, human oral, and grassland soil microbiomes. Our antiphage selections in Escherichia coli revealed over 200 putative defenses from 14 diverse bacterial phyla, highlighting the broad phylogenetic interoperability of these systems. Many defense systems were unrecognizable based on sequence or predicted structure, so could only be identified via functional assays. In mechanistic studies, we show that some defense systems encode nucleases that only degrade covalently modified phage DNA, but which accommodate diverse chemical modifications. We also identify outer membrane proteins that prevent phage adsorption and a set of previously unknown defense systems with diverse antiphage profiles and modalities. Most defenses acted against at least two phages, indicating that broadly acting systems are widely distributed among non-model bacteria.}, }
@article {pmid40060500, year = {2025}, author = {Depuydt, L and Ahmed, OY and Fostier, J and Langmead, B and Gagie, T}, title = {Run-length compressed metagenomic read classification with SMEM-finding and tagging.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.25.640119}, pmid = {40060500}, issn = {2692-8205}, abstract = {Metagenomic read classification is a fundamental task in computational biology, yet it remains challenging due to the scale, diversity, and complexity of sequencing datasets. We propose a novel, lossless, run-length compressed index that enables efficient multi-class metagenomic classification in O (r) space, based on the move structure. Our method identifies all super-maximal exact matches (SMEMs) of length at least L between a read and the reference dataset and associates each SMEM with one class identifier using a sampled tag array. A consensus algorithm then compacts these SMEMs with their class identifier into a single classification per read. We are the first to perform run-length compressed read classification based on full SMEMs instead of semi-SMEMs. We evaluate our approach on both long and short reads in two conceptually distinct datasets: a large bacterial pan-genome with few metagenomic classes and a smaller 16S rRNA gene database spanning thousands of genera or classes. Our method consistently outperforms SPUMONI 2 in accuracy and runtime, with only a modest memory overhead. Compared to Cliffy, we demonstrate better memory efficiency while achieving superior accuracy on the simpler dataset and comparable performance on the more complex one. Overall, our implementation carefully balances accuracy, runtime, and memory usage, offering a versatile solution for metagenomic classification across diverse datasets. The open-source C++11 implementation is available at https://github.com/biointec/tagger under the AGPL-3.0 license.}, }
@article {pmid40060387, year = {2025}, author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA}, title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.03.592475}, pmid = {40060387}, issn = {2692-8205}, abstract = {Decline in ovarian function with age not only affects fertility but is also linked to a higher risk of age-related diseases in women (e.g . osteoporosis, dementia). Intriguingly, earlier menopause is linked to shorter lifespan; however, the underlying molecular mechanisms of ovarian aging are not well understood. Recent evidence suggests the gut microbiota may influence ovarian health. In this study, we characterized ovarian aging associated microbial profiles in mice and investigated the effect of the gut microbiome from young and estropausal female mice on ovarian health through fecal microbiota transplantation. We demonstrate that the ovarian transcriptome can be broadly remodeled after heterochronic microbiota transplantation, with a reduction in inflammation-related gene expression and trends consistent with transcriptional rejuvenation. Consistently, these mice exhibited enhanced ovarian health and increased fertility. Using metagenomics-based causal mediation analyses and serum untargeted metabolomics, we identified candidate microbial species and metabolites that may contribute to the observed effects of fecal microbiota transplantation. Our findings reveal a direct link between the gut microbiota and ovarian health.}, }
@article {pmid40060187, year = {2025}, author = {Cao, J and Ma, Y and Fu, J and Wang, Z and Zhao, Y and Zhong, N and Zhao, P}, title = {Bacillus atrophaeus DX-9 biocontrol against potato common scab involves significant changes in the soil microbiome and metabolome.}, journal = {aBIOTECH}, volume = {6}, number = {1}, pages = {33-49}, pmid = {40060187}, issn = {2662-1738}, abstract = {UNLABELLED: Potato common scab (CS) is a worldwide disease, caused by Streptomyces spp., and its presence reduces the market value of potatoes. A nontoxic and potentially effective approach in many control strategies is the use of antagonistic microbes as biocontrol agents. In this study, Bacillus atrophaeus DX-9 was isolated and assessed for its ability to protect against CS. Through integrated metagenomic and metabolomic analyses, changes in the soil microbial community structure and soil properties were analyzed to understand the effects of Bacillus atrophaeus DX-9 on CS. These studies revealed that DX-9 inoculation could significantly decrease CS disease rate, disease index, and the number of CS pathogens, along with an increase in soil N and P content. Our metagenomic assays identified 102 phyla and 1154 genera, and DX-9 inoculation increased the relative abundances of the phyla Pseudomonadota, Chloroflexota and Gemmatimonadota. Additionally, an increase in the relative abundance of genera, such as Bradyrhizobium, Agrobacterium, and Nitrobacter, were significantly and positively correlated with soil N and P. Metabolomic analysis revealed that DX-9 inoculation significantly increased the soil levels of phytolaccoside A, 7,8-dihydropteroic acid, novobiocin, and azafrin. These compounds were enriched in microbe pathway metabolites, including xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and metabolism of cofactors and vitamins. In summary, the use of Bacillus atrophaeus DX-9 against potato CS offers an alternative biocontrol method that can improve both soil microbial community and properties. This study provides insight into the potential mechanisms by which microbial inoculants can control CS disease.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-025-00199-3.}, }
@article {pmid40060112, year = {2024}, author = {Wei, B and Xu, Q and Kong, J and Su, X and Chen, K and Wang, H}, title = {Metagenomics-based study of rhizospheric microorganisms of Poa alpigena L. in Qinghai Lake, Ganzi River Plateau.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1518637}, pmid = {40060112}, issn = {1664-462X}, abstract = {INTRODUCTION: Poa alpigena Lindm., a dominant forage grass on the Tibetan Plateau, plays a critical role in livestock production and grassland restoration. This study investigates the rhizospheric and non-rhizospheric soil microorganisms of Poa alpigena L. in the Ganzi River area of the Qinghai Lake basin using metagenomic sequencing to understand their diversity and potential ecological functions.<br><br>METHODS: Soil samples were collected from rhizospheric and non-rhizospheric areas of Poa alpigena L. using the S-type five-point sampling method. DNA was extracted, and metagenomic sequencing was performed using the BGISEQ-500 platform. Alpha and Beta diversity analyses were conducted, and LEfSe analysis was used to identify differentially abundant microbial taxa and metabolic pathways.<br><br>RESULTS: A total of 5,681 microbial species across 1,606 genera, 521 families, 61 phyla, and 246 orders were identified. Non-rhizospheric soils exhibited higher species richness than rhizospheric soils. Proteobacteria was the most abundant phylum in both soil types. Rhizospheric soils showed significant enrichment in pathways related to antibiotic biosynthesis, carbon metabolism, and methane metabolism, while non-rhizospheric soils were enriched in quorum sensing and drug-metabolizing pathways.<br><br>DISCUSSION: The findings highlight the selective influence of Poa alpigena L. on soil microbial communities and their potential role in mitigating methane emissions. The study provides a foundation for understanding the ecological functions of soil microorganisms in alpine meadows and supports sustainable grassland management practices.}, }
@article {pmid40059905, year = {2025}, author = {Su, Z and Gu, AZ and Wen, D and Li, F and Huang, B and Mu, Q and Chen, L}, title = {Rapid identification of antibiotic resistance gene hosts by prescreening ARG-like reads.}, journal = {Environmental science and ecotechnology}, volume = {23}, number = {}, pages = {100502}, pmid = {40059905}, issn = {2666-4984}, abstract = {Effective risk assessment and control of environmental antibiotic resistance depend on comprehensive information about antibiotic resistance genes (ARGs) and their microbial hosts. Advances in sequencing technologies and bioinformatics have enabled the identification of ARG hosts using metagenome-assembled contigs and genomes. However, these approaches often suffer from information loss and require extensive computational resources. Here we introduce a bioinformatic strategy that identifies ARG hosts by prescreening ARG-like reads (ALRs) directly from total metagenomic datasets. This ALR-based method offers several advantages: (1) it enables the detection of low-abundance ARG hosts with higher accuracy in complex environments; (2) it establishes a direct relationship between the abundance of ARGs and their hosts; and (3) it reduces computation time by approximately 44-96% compared to strategies relying on assembled contigs and genomes. We applied our ALR-based strategy alongside two traditional methods to investigate a typical human-impacted environment. The results were consistent across all methods, revealing that ARGs are predominantly carried by Gammaproteobacteria and Bacilli, and their distribution patterns may indicate the impact of wastewater discharge on coastal resistome. Our strategy provides rapid and accurate identification of antibiotic-resistant bacteria, offering valuable insights for the high-throughput surveillance of environmental antibiotic resistance. This study further expands our knowledge of ARG-related risk management in future.}, }
@article {pmid40059755, year = {2025}, author = {Munk, P and Brinch, C and Aarestrup, FM}, title = {Resistance genes are not like chemical pollutants and surveillance of them should reflect that.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-3}, doi = {10.1080/17460913.2025.2476880}, pmid = {40059755}, issn = {1746-0921}, }
@article {pmid40059174, year = {2025}, author = {Jin, X and Cheng, AG and Chanin, RB and Yu, FB and Dimas, A and Jasper, M and Weakley, A and Yan, J and Bhatt, AS and Pollard, KS}, title = {Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {71}, pmid = {40059174}, issn = {2049-2618}, support = {1563159//National Science Foundation/ ; HL160862/HL/NHLBI NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; *Bacterial Adhesion/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Animals ; Metagenome ; Mice ; Promoter Regions, Genetic ; Intestines/microbiology ; }, abstract = {BACKGROUND: Bacteria use invertible genetic elements known as invertons to generate heterogeneity among a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes associated with cell surface modifications, suggesting key roles in modulating dynamic processes such as surface adhesion and intestinal colonization. However, comprehensive testing of this hypothesis across complex bacterial communities like the human gut microbiome remains challenging. Metagenomic sequencing holds promise for detecting inversions without isolation and culturing, but ambiguity in read alignment limits the accuracy of the resulting inverton predictions.<br><br>RESULTS: Here, we developed a customized bioinformatic workflow-PhaseFinderDC-to identify and track invertons in metagenomic data. Applying this method to a defined yet complex gut community (hCom2) across different growth environments over time using both in vitro and in vivo metagenomic samples, we detected invertons in most hCom2 strains. These include invertons whose orientation probabilities change over time and are statistically associated with environmental conditions. We used motif enrichment to identify putative inverton promoters and predict genes regulated by inverton flipping during intestinal colonization and surface adhesion. Analysis of inverton-proximal genes also revealed candidate invertases that may regulate flipping of specific invertons.<br><br>CONCLUSIONS: Collectively, these findings suggest that surface adhesion and intestinal colonization in complex gut communities directly modulate inverton dynamics, offering new insights into the genetic mechanisms underlying these processes. Video Abstract.}, }
@article {pmid40058902, year = {2025}, author = {Revelo-Romo, DM and Hurtado Gutiérrez, NH and Hidalgo Troya, A and Amaya-Gómez, CV and Flórez-Martínez, DH and Overmann, J and Villegas Torres, MF and González Barrios, AF}, title = {Omics approaches to explore the coffee fermentation microecosystem and its effects on cup quality.}, journal = {Food research international (Ottawa, Ont.)}, volume = {206}, number = {}, pages = {116035}, doi = {10.1016/j.foodres.2025.116035}, pmid = {40058902}, issn = {1873-7145}, mesh = {*Fermentation ; *Coffee/microbiology ; *Coffea/microbiology/chemistry/metabolism ; Microbiota ; Metagenomics/methods ; Seeds/microbiology/metabolism ; Food Handling/methods ; }, abstract = {The cultivation and postharvest processing of coffee constitute the basis of the subsistence and traditional culture for rural family-owned farms, as well as for the economic success of commercial enterprises in many coffee-producing countries worldwide. The quality of the final beverage is determined by a multitude of variables. A key post-harvest factor is the spontaneous fermentation of the coffee beans, conducted directly on the farm, to remove the mucilage that firmly adheres to the beans. The effect of this fermentation step on the aromatic profile of the coffee is not yet sufficiently understood. All of the above have drawn the attention of researchers on the application of various omics approaches to elucidate fermentation processes in more detail. These approaches have been used to study the fermentation of Arabica (Coffea arabica) beans, as this species is economically most important worldwide. It is known that Arabica mild coffee is obtained through the wet method, which involves fermenting depulped coffee beans using various strategies and then washing the fermented coffee with clean water. In contrast, the fermentation of Canephora coffee beans has been much less studied using omics technologies. This review highlights the trends and future research in coffee fermentation based on a scientometric analysis, supplemented by a traditional systematic literature review. It highlights the composition of the coffee fermentation microbiome, as elucidated by metagenomics applications, in light of several factors that can influence its structure. Additionally, it considers the metabolites associated with microbial metabolism that can influence the chemical composition of coffee beans and, consequently, the cup quality. In this way, this review evidences the promising path in understanding microbial functions in coffee fermentation and in particular in the development of microbial inocula and in the refinement of fermentation processes to improve coffee quality.}, }
@article {pmid40058900, year = {2025}, author = {Wang, X and Li, Q and Li, W and Cai, G and Wu, D and Xie, G and Lu, J}, title = {Metagenomics unveils the roles of microbes in the metabolic network of purine formation during Huangjiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {206}, number = {}, pages = {116031}, doi = {10.1016/j.foodres.2025.116031}, pmid = {40058900}, issn = {1873-7145}, mesh = {*Fermentation ; *Purines/metabolism ; *Metagenomics ; Metabolic Networks and Pathways ; Bacteria/metabolism/genetics/classification ; Microbiota/physiology ; Fermented Foods/microbiology ; }, abstract = {Purine is a major factor contributing to the development of hyperuricemia and gout, and it is found in large quantities in Huangjiu as free bases. Purine production in Huangjiu is strongly associated with microbial metabolism. However, to the best of our knowledge the microorganisms responsible for and the mechanisms of purine formation during Huangjiu fermentation are yet to be evaluated. Herein, changes in purine levels during Huangjiu fermentation were analyzed. Further, the microbes responsible for purine production were identified and their gene abundance was studied. Results revealed that adenine, guanine, hypoxanthine, and xanthine are produced during Huangjiu fermentation. The total purines content on day 0 (27.99 mg/L) was found to be considerably lower than that produced on day 24 (122.15 mg/L) during Huangjiu fermentation. Metagenomics showed that the composition of the microbial community fluctuates sharply during five fermentation periods of Huangjiu, with the microbial community richness and diversity being the most prominent on day 3. At the genus level, Klebsiella, Lactobacillus, Staphylococcus, Saccharopolyspora, and Saccharomyces were abundant during Huangjiu fermentation and were involved in purine metabolism. Relationships between the dominant microorganisms and key enzyme genes of the purine pathways were also established based on the Kyoto Encyclopedia of Genes and Genomes database. Correlation analysis showed that Lactobacillus and Saccharomyces were the main genera involved in purine formation. Saccharomyces cerevisiae, Lactobacillus paralimentarius, and Lactiplantibacillus plantarum were involved in purine formation during Huangjiu fermentation. Overall, this study improves our understanding of the purine formation mechanism during Huangjiu fermentation and provides valuable insights into the regulation of purine formation by microorganisms.}, }
@article {pmid40058503, year = {2025}, author = {Chang, Z and Deng, J and Zhang, J and Wu, H and Wu, Y and Bin, L and Li, D and Liu, J and Yu, R and Lin, H and An, L and Sun, B}, title = {Rapid and Accurate Diagnosis of Urinary Tract Infections Using Targeted Next-Generation Sequencing: A Multicenter Comparative Study with Metagenomic Sequencing and Traditional Culture Methods.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106459}, doi = {10.1016/j.jinf.2025.106459}, pmid = {40058503}, issn = {1532-2742}, abstract = {BACKGROUND: Urinary tract infections (UTIs) rank among the most prevalent bacterial infections globally. Traditional urine culture methods have significant limitations in detection time and sensitivity, prompting the need to evaluate targeted next-generation sequencing (tNGS) as a potential diagnostic tool.<br><br>METHODS: The study included a discovery cohort of 400 suspected UTI patients (202 analyzed) and a validation cohort of 200 patients (110 analyzed). The study assessed detection time, concordance rates, ability to identify polymicrobial infections, and antibiotic resistance genes (ARGs). Both clear and turbid urine samples were evaluated across different clinical settings.<br><br>RESULTS: In the discovery cohort, tNGS demonstrated 96.5% concordance with culture-positive samples, while showing superior specificity in culture-negative specimens (53.1% vs 28.1% for mNGS). Detection time for tNGS (12.89h) was notably shorter than mNGS (17.38h) and traditional culture (61.48h). tNGS exhibited remarkable capability in identifying polymicrobial infections (55.4% of samples), significantly outperforming both mNGS (27.7%) and traditional culture methods, which failed to detect any co-infections. The method showed particular strength in detecting fastidious organisms like Ureaplasma parvum and fungal species such as Candida tropicalis. For antibiotic resistance prediction, tNGS detected more ARGs (52.67% vs 41.22% for mNGS) and achieved 100% sensitivity for vancomycin and methicillin resistance in Gram-positive pathogens. The validation cohort confirmed tNGS's robust performance, maintaining high concordance rates for both culture-positive (90.00%) and culture-negative samples (55.00%), demonstrating consistent reliability across different clinical settings CONCLUSIONS: tNGS demonstrates advantages in rapid and accurate UTI diagnosis, particularly in detecting polymicrobial infections and analyzing antibiotic resistance genes. It shows promise as an effective complementary tool for UTI diagnostics.}, }
@article {pmid40058443, year = {2025}, author = {Zhou, Y and Li, MY and Li, CY and Sheng, YJ and Ye, QT and Chen, RY and Zhou, KY and Zhang, Y and Shen, LF and Shou, D}, title = {Effective mechanism of polysaccharides from Erxian herbal pair in promoting bone repair in traumatic osteomyelitis by activating osteoblast GPR41 and inhibiting the MEK/ERK/MAPK signalling axis.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {141858}, doi = {10.1016/j.ijbiomac.2025.141858}, pmid = {40058443}, issn = {1879-0003}, abstract = {Polysaccharides are the key components of natural products; however, their effects on bone repair haven't been fully evaluated. This study aimed to assess the efficacy and mechanism of polysaccharides in promoting bone repair. The Erxian herb pair polysaccharide (EHP) was isolated and purified using water extraction (1:20 (w/v); 100 ± 2 °C; 5 h) and alcohol precipitation (80 ± 2 %). A traumatic osteomyelitis (TO) rat model was established using lipopolysaccharide (LPS). The gut microbiota was analysed through intestinal flora and metagenomic sequencing. The results revealed that the yields of crude polysaccharide and purified polysaccharide EHP were 3.73 ± 0.34 % and 0.48 ± 0.06 %, respectively. The total sugar content of EHP was 83.53 ± 0.16 %. The EHP, with a molecular weight of 31.964 kDa, was primarily composed of mannose, rhamnose, glucose, galactose, and arabinose. In vivo experiments demonstrated that EHP intervention (300 mg/kg/day) significantly augmented bone density and enhanced the activity of alkaline phosphatase (ALP) (P < 0.01). EHP upregulated the abundance of probiotics and increased the production of butyric acid (P < 0.05). In vitro experiments revealed that butyric acid (500-1000 μM) enhanced osteoblast activity and inhibited the expression of mitogen-activated protein kinase kinase (MEK) and extracellular signal-regulated kinase (ERK) (P < 0.01). These findings indicate that polysaccharides may represent a promising therapeutic agent for bone-healing.}, }
@article {pmid40058279, year = {2025}, author = {Chen, H and Zeng, Z and Lal, R and Wu, J and Chen, J and Li, M and Cao, L and Liu, X and Zhang, R and Gong, C}, title = {Acetic acid production from corn straw via enzymatic degradation using putative acetyl esterase from the metagenome assembled genome.}, journal = {Enzyme and microbial technology}, volume = {187}, number = {}, pages = {110619}, doi = {10.1016/j.enzmictec.2025.110619}, pmid = {40058279}, issn = {1879-0909}, abstract = {Acetic acid production from corn straw by enzyme catalysis shows its application value in food industry. In this study, a gene encoding for a putative acetyl esterase derived from Sphingobacterium soilsilvae Em02 was discovered in metagenome assembled genome. The gene was expressed in Escherichia coli BL21 to obtain enzyme with a molecular mass of 38.8 kDa. P-Nitrophenyl acetate was used as a substrate to determine the enzyme activity. The enzyme demonstrated optimal activity under conditions of 40 °C and a neutral pH of 7.0. Under optimal conditions, 17.58 mg of acetic acid was obtained using the enzyme from 50 mg corn straw pretreated with amylase. The acetyl esterase derived from Sphingobacterium soilsilvae Em02, demonstrates significant potential for biotechnological applications, particularly in biomass degradation.}, }
@article {pmid40058278, year = {2025}, author = {Neri, LCM and Guðmundsson, H and Meurrens, G and Robert, A and Fridjonsson, OH and Hreggvidsson, GO and Adalsteinsson, BT}, title = {Identification and characterization of endo-xylanases from families GH10 and GH11 sourced from marine thermal environments.}, journal = {Enzyme and microbial technology}, volume = {187}, number = {}, pages = {110592}, doi = {10.1016/j.enzmictec.2025.110592}, pmid = {40058278}, issn = {1879-0909}, abstract = {Seaweed biomass is an underutilized resource that is rich in polysaccharides, including xylan. Seaweed polysaccharides could be used as a feedstock in industrial microbiology and and for production of prebiotic oligosaccharides and rare monosaccharides - processes that would benefit from the availability of robust enzymes that break down the seaweed polysaccharides. The present study aimed to identify genes encoding endo-xylanases in bacterial genomes and metagenomes sourced from marine thermal environments, and to characterize the respective enzymes. Twelve endo-xylanases were studied which displayed 59 % median maximal sequence similarity to characterized GH10 or GH11 enzymes. Overall, most of the enzymes functioned optimally at high temperatures, in the presence of salt, and at circumneutral pH. Eight enzymes functioned optimally at temperatures of 50°C or higher, and in the most extreme cases at 85°C to 95°C. Six enzymes retained activity after three-hour incubation at 60°C or higher. Ten enzymes displayed improved catalytic function in the presence of salt, and several retained high catalytic function at 10 % NaCl concentration. All the enzymes hydrolyzed xylan from diverse sources, including crude biomass. The study contributes to an increased understanding of the structural diversity of xylanases; it expands the availability of thermostable xylanases of marine origin; and contributes to increased valorization of seaweed biomass.}, }
@article {pmid40058228, year = {2025}, author = {Tromas, N and Simon, DF and Fortin, N and Hernández-Zamora, M and Pereira, A and Mazza, A and Pacheco, SM and Levesque, MJ and Martínez-Jerónimo, L and Antuna-González, P and Munoz, G and Shapiro, BJ and Sauvé, S and Martínez-Jerónimo, F}, title = {Metagenomic insights into cyanotoxin dynamics in a Mexican subtropical lake.}, journal = {Chemosphere}, volume = {376}, number = {}, pages = {144285}, doi = {10.1016/j.chemosphere.2025.144285}, pmid = {40058228}, issn = {1879-1298}, abstract = {Valle de Bravo is a vital water supply for part of the metropolitan area of the Valle de Mexico megacity, providing 30% of Mexico City's water demand. This water body has experienced an acceleration in its trophic status, going from oligotrophic to eutrophic in just a few years. This temperate lake (at a tropical latitude) is in a persistent bloom dominated by a variety of co-occurring cyanobacteria, many of which have toxigenic potential based on microscopic identification, that makes it difficult or even impractical to identify the cyanotoxin producers. To unravel this complexity and directly identify the toxigenic genera, we showed that integrating classical approaches with metagenomic is required. We first characterized, from genes to metagenomes assembled genomes, the toxigenic Cyanobacteria. We found that Microcystis was the most dominant cyanobacterial genus and the sole carrier of the mcy operon, making it the only microcystin producer. We then quantified twenty-one different cyanopeptides, including twelve microcystin congeners using a high-performance liquid chromatography-high-resolution. Nine microcystins (MCs) and the emerging cyanotoxin anabaenopeptin-A and -B were found at varying concentrations throughout the year, with MC-LA being the most common and abundant. Our findings, constrained by our sampling strategy, indicate that conventional cyanotoxin biomarkers (e.g., toxin mcy genes) were not consistently reliable indicators of cyanotoxin concentrations in this freshwater system. In this study, we followed the dynamics of the cyanobacterial community and the associated cyanopeptides with unprecedented resolution. Our results have implications for better management of toxic blooms in this freshwater system, which supplies drinking water to more than 7 million people in the megalopolis of Valle de México.}, }
@article {pmid40058051, year = {2025}, author = {Castellano-Hinojosa, A and Gallardo-Altamirano, MJ and Pozo, C and González-Martínez, A and González-López, J and Marshall, IPG}, title = {Salinity levels influence treatment performance and the activity of electroactive microorganisms in a microbial fuel cell system for wastewater treatment.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124858}, doi = {10.1016/j.jenvman.2025.124858}, pmid = {40058051}, issn = {1095-8630}, abstract = {There is growing interest in developing effective treatment technologies to mitigate the environmental impact of saline wastewater while also potentially recovering valuable resources from it. However, it remains largely unknown how different salinity levels impact treatment performance, energy generation, and the diversity and composition of electroactive microorganisms in MFCs treating real effluents such as urban wastewater. This study explores the impact of three salinity levels (3.5, 7, and 15 g/L NaCl) on current production, organic removal rates, and bacterial community dynamics in a continuous-flow microbial fuel cell (MFC) fed with urban wastewater. Using metagenomics and metatranscriptomics, we explored variations in the abundance and expression of extracellular electron transfer (EET) genes and those involved in other general metabolisms. We found that low salinity (3.5 g/L NaCl) enhanced both current production and organic removal efficiency compared to higher salinity levels. This improvement was linked to an increased abundance and activity of electroactive microorganisms, particularly taxa within the Ignavibacteria class, which possess genes coding for outer membrane cytochromes and porin cytochromes. Additionally, salinity influenced general metabolic genes and microbial community composition, with higher salinity levels limiting bacterial growth and diversity. This research provides valuable insights into the interplay between salinity stress and microbial adaptation, contributing to the optimization of MFC technologies for enhanced environmental and bioengineering applications.}, }
@article {pmid40057978, year = {2025}, author = {Jeevannavar, A and Florenza, J and Divne, AM and Tamminen, M and Bertilsson, S}, title = {Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf046}, pmid = {40057978}, issn = {1751-7370}, abstract = {Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as down-regulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.}, }
@article {pmid40057571, year = {2025}, author = {Adams, SE and Cawley, AK and Arnold, D and Hoptroff, MJ and Slomka, V and Matheson, JR and Marriott, RE and Gemmell, MR and Marsh, PD}, title = {A randomised, double-blind clinical study into the effect of zinc citrate trihydrate toothpaste on oral plaque microbiome ecology and function.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8136}, pmid = {40057571}, issn = {2045-2322}, mesh = {Humans ; *Toothpastes/pharmacology/therapeutic use ; *Dental Plaque/microbiology ; Male ; Female ; Adult ; *Microbiota/drug effects ; Double-Blind Method ; Middle Aged ; Zinc Compounds/pharmacology/therapeutic use/administration &amp; dosage ; Young Adult ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; }, abstract = {The oral microbiome is a diverse community of microbes residing on all oral surfaces. A balanced oral microbiome is associated with good oral health, and disruption can result in imbalance associated with diseases including gingivitis and dental caries. It is important, therefore, to understand how daily use of oral hygiene products impacts the microbiome. Composition and activity of dental plaque microbiome from 115 participants was analysed after brushing with one of two toothpastes, one containing zinc citrate trihydrate and the other a control toothpaste, in a parallel design. Each participant brushed twice daily for 6-weeks, with samples collected at baseline, 2 and 6-weeks. Metataxonomic analysis demonstrated changes in bacterial communities with use of the zinc toothpaste compared to the control product at community and species level. Increases at the species level were observed for taxa from the genus Veillonella with decrease in a taxon from the genus Fusobacterium for the zinc toothpaste. Analysis of microbiome function based on predicted metagenomic and metatranscriptomic analysis show that use of the zinc toothpaste is associated with an in-vivo reduction in glycolysis, consistent with the mode of action of zinc and, increases in processes linked to gum-health (lysine biosynthesis), and to whole-body health (nitrate reduction). Our findings provide the first understanding of the beneficial modulation of microbiome composition and function by zinc-containing toothpaste in-vivo for oral care benefits.}, }
@article {pmid40057258, year = {2025}, author = {Ragone, P and Parodi, C and Tomasini, N and Ramos, F and Uncos, A and Brandán, CP}, title = {The interplay between Trypanosoma cruzi and the microbiome of Triatoma infestans: Implications for the host's immune response.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107577}, doi = {10.1016/j.actatropica.2025.107577}, pmid = {40057258}, issn = {1873-6254}, abstract = {The infection dynamics of Trypanosoma cruzi is shaped by the parasite's genetics and interactions with host and vector factors. While most studies in the area use axenic parasite cultures devoid of insect fecal components, this study is focused on the immune response and the parasite loads generated after the interaction of T. cruzi with feces from Triatoma infestans in a murine model. First, using metagenomics, we analyzed the microbiota of infected and uninfected feces. Illumina sequencing of the 16S rRNA gene (V3-V4 region) revealed a predominance of the genus Arsenophonus in infected feces and of Enterococcus in uninfected ones. C57BL/6J mice inoculated with T. cruzi infected feces, displayed distinct immune responses compared to those inoculated with culture-derived metacyclic trypomastigotes alone, with lower levels of pro-inflammatory cytokines (IFN-ɣ, TNF-α) and higher amounts of IL-10, suggesting a regulatory response. Besides, total anti-T. cruzi IgG levels remained similar among groups, but IgG1 and IgG2c were reduced in the T. cruzi infected feces group, indicating a balanced Th1/Th2 response. Notably, mice inoculated with T. cruzi infected feces demonstrated significantly reduced blood and muscle parasite loads, potentially limiting inflammation and parasite dissemination. These findings highlight the possible role of vector fecal microbiota in shaping immune responses and influencing disease outcomes during natural T. cruzi infections.}, }
@article {pmid40057163, year = {2025}, author = {Leonard, AFC and Higgins, SL and Hui, M and Gaze, WH}, title = {Investigating landscape-scale variables impacting human exposure to antibiotic resistant bacteria using a targeted metagenome approach.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126015}, doi = {10.1016/j.envpol.2025.126015}, pmid = {40057163}, issn = {1873-6424}, abstract = {Research has shown that exposure to coastal waters containing antibiotic resistant bacteria (ARB) is associated with higher likelihood of gut colonisation by ARB. The aim was to identify landscape-scale processes contributing to the spread of ARB in Hong Kong's coastal waters and to estimate the scale of bathers' exposure to ARB. Twelve recreational water locations were sampled in 2017 for Escherichia coli. A targeted metagenomic approach was used to quantify the abundance and diversity of antibiotic resistance genes (ARGs) harboured by viable E. coli. Data on environmental variables related to ARB distribution in the environment were modelled to identify processes driving the abundance and diversity of ARG-bearing E. coli in coastal waters. These data were combined with data about Hong Kong residents' use of blue space to quantify human exposure to E. coli borne ARG. Several meteorological variables, like rainfall and temperature, were associated with E. coli-borne ARG profiles. Yet when rigorous statistical methods were applied, these relationships were not significant. Meropenem-resistant bacteria were also isolated from samples, most of which were taken from western beaches. Additionally, there was some evidence of elevated abundances of several ARGs, including blaCTX-M, in western beaches. The average E. coli harboured 6.09 ARGs. Over 1.16 million exposure events occurred in 2017 that involved ingestion of E. coli harbouring at least one ARG. This study used robust methods to quantify and explain the abundance and diversity of ARB in Hong Kong's coastal waters. We detected elevated levels of several E. coli-borne ARGs and meropenem-resistant pathogens at western beaches, indicating an influence of the Pearl River on Hong Kong's water quality. Despite updates to wastewater treatment in Hong Kong, recreational use of natural surface waters remains a significant risk of exposure to ARB capable of human gut colonisation.}, }
@article {pmid40056814, year = {2025}, author = {Yasemi, M and Jalali, A and Asadzadeh, M and Komijani, M}, title = {Organophosphate pesticides and their potential in the change of microbial population and frequency of antibiotic resistance genes in aquatic environments.}, journal = {Chemosphere}, volume = {376}, number = {}, pages = {144296}, doi = {10.1016/j.chemosphere.2025.144296}, pmid = {40056814}, issn = {1879-1298}, abstract = {Heavy metals (HMs) and pesticides disrupt aquatic biodiversity and microbial communities, contributing to antibiotic resistance via cross-resistance and co-selection mechanisms. This study investigates the relationship between organophosphorus pesticides (OPs), HMs, microbial diversity, and antibiotic resistance genes (ARGs) in eight lakes and wetlands. Microbial communities were analyzed via metagenomics methods, and data were processed using CLC Genomics Workbench 22. ARGs, including tetA, tetB, qnrA, qnrS, CIT, Fox, KPC, CTX-M1, DHA, GES, OXA, IMP, VEB, NDM1, SHV, TEM, CTX-M, PER, and MOX, were identified through polymerase chain reaction (PCR). Element concentrations and pesticide were quantified using inductively coupled plasma mass spectrometry and gas chromatography-mass spectrometry, respectively. The results indicate that environmental elements and pesticides significantly influence microbial diversity. Proteobacteria (Gamma, Beta, Alpha) dominate over other bacteria in all locations. β-Lactamase resistance genes have a significant positive correlations with the concentrations of boron, iron, lithium, magnesium, sodium, and phosphorus (P-value<0.05). Positive correlations between phosphorus, iron, and beta-lactamase genes suggest that higher concentrations of these elements may increase resistance likelihood by promoting resistant bacterial growth or facilitating gene transfer. Additionally, tetA and tetB exhibited a significant positive correlation with parathion concentration. The results showed that OPs and HMs increase antibiotic resistance by causing gene mutations, altering gene expression, and promoting horizontal gene transfer, resulting in multidrug-resistant strains. This highlights the need for monitoring these pollutants as they affect microbial diversity and accelerate antibiotic resistance. Targeted measures, such as bioremediation and pollution control, are essential to mitigate risks to the environment and public health.}, }
@article {pmid40056517, year = {2025}, author = {Choonut, A and Wongfaed, N and Wongthong, L and Poolpol, A and Chaikitkaew, S and Sittijunda, S and Reungsang, A}, title = {Microbial degradation of polypropylene microplastics and concomitant polyhydroxybutyrate production: An integrated bioremediation approach with metagenomic insights.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137806}, doi = {10.1016/j.jhazmat.2025.137806}, pmid = {40056517}, issn = {1873-3336}, abstract = {The persistence of plastics, particularly polypropylene (PP), and their conversion into microplastics (MPs), specifically PP-MPs, have emerged as serious ecological threats to soil and aquatic environments. In the present study, we aimed to isolate a microbial consortium capable of degrading PP-MPs. The results revealed that three microbial consortia (CPP-KKU1, CPP-KKU2, and CPP-KKU3) exhibited the ability to degrade PP-MPs, achieving weight losses ranging from 11.6 ± 0.2 % to 17.8 ± 0.5 % after 30 days. Fourier transform infrared (FTIR) spectroscopy analysis confirmed the degradation through oxidation, as evidenced by the presence of new functional groups (-OH and -C=O). In particular, CPP-KKU3 showed the highest degradation efficiency, with scanning electron microscopy (SEM) analysis revealing surface cracking after treatment. Additionally, gas chromatography-mass spectrometry (GC-MS) analysis identified various intermediate compounds, including heterocyclic aromatic compounds, phenyl groups, methylthio derivatives, and ethoxycarbonyl derivatives, indicating complex biochemical processes that were likely mediated by microbial enzymes. Furthermore, polyhydroxybutyrate (PHB) production by these consortia was also investigated. The result showed that both CPP-KKU2 and CPP-KKU3 successfully produced PHB, with CPP-KKU3 demonstrating superior performance in terms of PP-MP degradation and PHB production. Metagenomic analysis of CPP-KKU3 revealed abundant carbohydrate-active enzymes (CAZymes), particularly glycosyl transferases and glycoside hydrolases, which are associated with MP digestion. This study presents a promising bioremediation approach that addresses plastic waste degradation and sustainable bioplastic production, offering a potential solution for environmental plastic pollution.}, }
@article {pmid40056474, year = {2025}, author = {Wang, H and Zhong, Y and Yang, Q and Li, J and Li, D and Wu, J and Yang, S and Liu, J and Deng, Y and Song, J and Peng, P}, title = {Coupling of sulfate reduction and dissolved organic carbon degradation accelerated by microplastics in blue carbon ecosystems.}, journal = {Water research}, volume = {279}, number = {}, pages = {123414}, doi = {10.1016/j.watres.2025.123414}, pmid = {40056474}, issn = {1879-2448}, abstract = {Microplastics have increasingly accumulated in sulfate- and organic matter-rich mangrove ecosystems, yet their effects on microbially mediated carbon and sulfur cycling in sediments remains poorly understood. In this study, we performed a 70-day anaerobic microcosm experiment to examine the effects of polylactic acid (PLA) microplastics with different sizes on sulfate reduction and dissolved organic carbon (DOC) degradation in mangrove sediments. Our results demonstrated that millimeter-scale PLA (mm-PLA) more effectively enhanced sulfate reduction, sulfur isotope fractionation, reduced sulfide production, and carbon dioxide (CO2) emission compared to micrometer-scale PLA (m-PLA). These results suggested that mm-PLA had a more pronounced impact on the carbon and sulfur cycles. Integrated 16S rRNA gene amplicon sequencing and metagenomic analyses revealed that mm-PLA preferentially enriched key functional microorganisms, including acetate-producing bacteria (e.g., Acetobacteroides), completely oxidizing sulfate-reducing bacteria (e.g., Desulfobacter), and incompletely oxidizing sulfate-reducing bacteria (e.g., Desulfobulbus). These microorganisms exhibited higher abundances and greater genetic potential for carbon metabolism and sulfate reduction under mm-PLA treatment. Their relative abundances showed positive correlations with sulfate reduction rates, sulfur isotope fractionation, and CO2 emission, identifying them as crucial drivers of coupled carbon-sulfur cycling. Furthermore, the synergistic interactions among Acetobacteroides, Desulfobacter, and Desulfobulbus facilitated the oxidation of sediment-derived DOC, highlighting significant implications for carbon sequestration in blue carbon ecosystems.}, }
@article {pmid40056186, year = {2025}, author = {Chen, XX and Ju, Q and Qiu, D and Zhou, Y and Wang, Y and Zhang, XX and Li, JG and Wang, M and Chang, N and Xu, XR and Zhang, YB and Zhao, T and Wang, K and Zhang, Y and Zhang, J}, title = {Microbial dysbiosis with tryptophan metabolites alteration in lower respiratory tract is associated with clinical responses to anti-PD-1 immunotherapy in advanced non-small cell lung cancer.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {4}, pages = {140}, pmid = {40056186}, issn = {1432-0851}, support = {82103446//National Natural Science Foundation of China/ ; 82273226//National Natural Science Foundation of China/ ; 82473215//National Natural Science Foundation of China/ ; 2020QNRC001//China Association for Science and Technology/ ; 2021LC2115//Fourth Military Medical University/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/immunology/drug therapy/metabolism/therapy ; *Tryptophan/metabolism ; *Lung Neoplasms/immunology/drug therapy/therapy/metabolism ; *Dysbiosis/immunology ; Female ; Male ; Middle Aged ; Aged ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; Microbiota/drug effects/immunology ; Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors/metabolism ; Respiratory System/immunology/metabolism/microbiology ; Adult ; }, abstract = {Lower respiratory tract microbiome constitutes a unique immune microenvironment for advanced non-small cell lung cancer as one of dominant localized microbial components. However, there exists little knowledge on the associations between this regional microbiome and clinical responses to anti-PD-1 immunotherapy from clinical perspectives. Here, we equivalently collected bronchoalveolar lavage fluids from 56 advanced NSCLC participants treated with none (untreated, n = 28) or anti-PD-1 immunotherapy (treated, n = 28), which was further divided into responder (n = 17) and non-responder (n = 11) subgroups according to clinical responses, aiming to compare their microbial discrepancy by performing metagenomic sequencing and targeted metabolic alterations by tryptophan sequencing. Correspondingly, microbial diversities transformed significantly after receiving immunotherapeutic agents, where Gammaproteobacteria and Campylobacter enriched, but Escherichia, Streptococcus, Chlamydia, and Staphylococcus reduced at the genus level, differences of which failed to be achieved among subgroups with various clinical responses (responder or non-responder; LDA > 2, P < 0.05[*]). And the relative abundance of Staphylococcus and Streptomyces was escalated in response subgroup to anti-PD-1 immunotherapy by microbial compositional analysis (as relative abundance ≥ 3%, P < 0.05[*]), no significance of which was achieved among treated and untreated groups. In addition, relative abundances of bacterial tryptophan metabolites and its derivatives were also higher in the responder subgroup, distinctively being associated with divergent genera (VIP > 1, P < 0.05[*]). Our study revealed predictive performance of lower respiratory tract microbiome to antitumoral immunotherapy and further suggested that anti-PD-1 immunotherapy may alter lower respiratory tract microbiome composition and interact with its tryptophan metabolites to regulate therapeutic efficacy in advanced NSCLC, performing as potential biomarkers to prognosis and interventional strategies.}, }
@article {pmid40055840, year = {2025}, author = {Rannon, E and Shaashua, S and Burstein, D}, title = {DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {67}, pmid = {40055840}, issn = {2049-2618}, mesh = {*Machine Learning ; *Metagenomics/methods ; Humans ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; Computational Biology/methods ; Metagenome ; }, abstract = {BACKGROUND: Antibiotics are essential for medical procedures, food security, and public health. However, ill-advised usage leads to increased pathogen resistance to antimicrobial substances, posing a threat of fatal infections and limiting the benefits of antibiotics. Therefore, early detection of antimicrobial resistance genes (ARGs), especially in pathogens, is crucial for human health. Most computational methods for ARG detection rely on homology to a predefined gene database and therefore are limited in their ability to discover novel genes.<br><br>RESULTS: We introduce DRAMMA, a machine learning method for predicting new ARGs with no sequence similarity to known ARGs or any annotated gene. DRAMMA utilizes various features, including protein properties, genomic context, and evolutionary patterns. The model demonstrated robust predictive performance both in cross-validation and an external validation set annotated by an empirical ARG database. Analyses of the high-ranking model-generated candidates revealed a significant enrichment of candidates within the Bacteroidetes/Chlorobi and Betaproteobacteria taxonomic groups.<br><br>CONCLUSIONS: DRAMMA enables rapid ARG identification for global-scale genomic and metagenomic samples, thus holding promise for the discovery of novel ARGs that lack sequence similarity to any known resistance genes. Further, our model has the potential to facilitate early detection of specific ARGs, potentially influencing the selection of antibiotics administered to patients. Video Abstract.}, }
@article {pmid40055835, year = {2025}, author = {Yin, CF and Pan, P and Li, T and Song, X and Xu, Y and Zhou, NY}, title = {The universal accumulation of p-aminophenol during the microbial degradation of analgesic and antipyretic acetaminophen in WWTPs: a novel metagenomic perspective.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {68}, pmid = {40055835}, issn = {2049-2618}, support = {32400079//the National Natural Science Foundation of China/ ; 2024YFA0919000//the National Key R&amp;D Program of China/ ; 2024YFA0919000//the National Key R&amp;D Program of China/ ; }, mesh = {*Acetaminophen/metabolism ; *Metagenomics ; *Biodegradation, Environmental ; *Aminophenols/metabolism ; *Antipyretics ; Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; China ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Humans ; Microbiota ; Analgesics ; Metagenome ; }, abstract = {BACKGROUND: Acetaminophen, a widely used analgesic and antipyretic drug, has become a significant aquatic micro-pollutant due to its extensive global production and increased consumption, particularly during the COVID-19 pandemic. Its high-water solubility leads to its pervasive presence in wastewater treatment plants (WWTPs), posing substantial risks to the environment and human health. Biological treatment is one of the promising approaches to remove such pollutants. Although previous studies have isolated acetaminophen-degrading pure cultures and proposed catabolic pathways, the interactions between microbiotas and acetaminophen, the distribution feature of acetaminophen degradation genes, and the gene-driven fate of acetaminophen in the real-world environment remain largely unexplored.<br><br>RESULTS: Among the water samples from 20 WWTPs across China, acetaminophen was detected from 19 samples at concentrations ranging from 0.06 to 29.20&#xa0;nM. However, p-aminophenol, a more toxic metabolite, was detected in all samples at significantly higher concentrations (23.93 to 108.68&#xa0;nM), indicating the presence of a catabolic bottleneck in WWTPs. Metagenomic analysis from both the above 20 samples and global datasets revealed a consistently higher abundance of initial acetaminophen amidases compared to downstream enzymes, potentially having explained the reason for the bottleneck. Meanwhile, a close correlation between initial amidases and Actinomycetota revealed by genome-based taxonomy suggests a species-dependent degradation pattern. Additionally, a distinct amidase ApaA was characterized by newly isolated Rhodococcus sp. NyZ502 (Actinomycetota), represents a predominant category of amidase in WWTPs. Significant phylogenetic and structural diversity observed among putative amidases suggest versatile acetaminophen hydrolysis potential in WWTPs.<br><br>CONCLUSIONS: This study enhances our understanding of acetaminophen's environmental fate and highlights the possible occurrence of ecological risks driven by imbalanced genes in the process of acetaminophen degradation in global WWTPs. Video Abstract.}, }
@article {pmid40055808, year = {2025}, author = {Avershina, E and Qureshi, AI and Winther-Larsen, HC and Rounge, TB}, title = {Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {66}, pmid = {40055808}, issn = {2049-2618}, support = {2022067//Helse S&#xf8;r-&#xd8;st RHF/ ; }, mesh = {*Software ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation &amp; purification ; *Metagenomics/methods ; Computational Biology/methods ; Ascomycota/genetics/classification/isolation &amp; purification ; Basidiomycota/genetics/isolation &amp; purification/classification ; Databases, Genetic ; }, abstract = {BACKGROUND: The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The characterization of mycobiome taxa from metagenomic data is heavily reliant on the quality of the software and databases. In this study, we evaluated the feasibility of mycobiome profiling using existing bioinformatics tools on simulated fungal metagenomic data.<br><br>RESULTS: We identified seven tools claiming to perform taxonomic assignment of fungal shotgun metagenomic sequences. One of these was outdated and required substantial modifications of the code to be functional and was thus excluded. To evaluate the accuracy of identification and relative abundance of the remaining tools (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, and HumanMycobiomeScan), we constructed 18 mock communities of varying species richness and abundance levels. The mock communities comprised up to 165 fungal species belonging to the phyla Ascomycota and Basidiomycota, commonly found in gut microbiomes. Of the tools, FunOMIC and HumanMycobiomeScan needed source code modifications to run. Notably, only one species, Candida orthopsilosis, was consistently identified by all tools across all communities where it was included. Increasing community richness improved precision of Kraken2 and the relative abundance accuracy of all tools on species, genus, and family levels. MetaPhlAn4 accurately identified all genera present in the communities and FunOMIC identified most species. The top three tools for overall accuracy in both identification and relative abundance estimation were EukDetect, MiCoP, and FunOMIC, respectively. Adding 90% and 99% bacterial background did not significantly impact these tools' performance. Among the whole genome reference tools (Kraken2, HMS, and MiCoP), MiCoP exhibited the highest accuracy when the same reference database was used.<br><br>CONCLUSION: Our survey of mycobiome-specific software revealed a very limited selection of such tools and their poor robustness due to error-prone software, along with a significant lack of comprehensive databases enabling characterization of the mycobiome. None of the implemented tools fully agreed on the mock community profiles. FunOMIC recognized most of the species, but EukDetect and MiCoP provided predictions that were closest to the correct compositions. The bacterial background did not impact these tools' performance. Video Abstract.}, }
@article {pmid40054447, year = {2025}, author = {Xiao, X and Zhao, W and Song, Z and Qi, Q and Wang, B and Zhu, J and Lin, J and Wang, J and Hu, A and Huang, S and Wang, Y and Chen, J and Fang, C and Ji, Q and Zhang, N and Meng, L and Wei, X and Chen, C and Cai, S and Chen, S and Ding, K and Li, D and Liu, S and Song, T and Tian, L and Zhang, H and Zhang, Y and Xu, S and Chen, J and Chen, H and Cen, Q and Jiang, F and Hu, G and Tang, C and Guo, W and Wang, X and Zhan, L and Fan, J and Wang, J and Zhou, C and Li, L and Lv, Z and Hu, Y and Lin, X and Mai, G and Luo, L and Yang, T and Wang, W and Kristiansen, K and Chen, L and Yang, H and Ni, M and Gu, Y and Mu, F and Yang, Y and Zhou, J and Wang, J and Zhang, WJ and Han, M and Xu, X and Liu, S}, title = {Microbial ecosystems and ecological driving forces in the deepest ocean sediments.}, journal = {Cell}, volume = {188}, number = {5}, pages = {1363-1377.e9}, doi = {10.1016/j.cell.2024.12.036}, pmid = {40054447}, issn = {1097-4172}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Oceans and Seas ; *RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Bacteria/genetics/classification/metabolism ; Microbiota/genetics ; Metagenome ; Metagenomics ; }, abstract = {Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in the Mariana Trench, Yap Trench, and Philippine Basin for the Mariana Trench Environment and Ecology Research (MEER) project. Metagenomic and 16S rRNA gene amplicon sequencing generated the 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike in reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) and dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions for hadal adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) and antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism with larger genomes. These findings indicated that environmental factors drive the high taxonomic novelty in the hadal zone, advancing our understanding of the ecological mechanisms governing microbial ecosystems in such an extreme oceanic environment.}, }
@article {pmid40054445, year = {2025}, author = {Turjeman, S and Rozera, T and Elinav, E and Ianiro, G and Koren, O}, title = {From big data and experimental models to clinical trials: Iterative strategies in microbiome research.}, journal = {Cell}, volume = {188}, number = {5}, pages = {1178-1197}, doi = {10.1016/j.cell.2025.01.038}, pmid = {40054445}, issn = {1097-4172}, mesh = {*Microbiota ; Humans ; *Big Data ; Animals ; Clinical Trials as Topic ; Metagenomics/methods ; Metabolomics/methods ; }, abstract = {Microbiome research has expanded significantly in the last two decades, yet translating findings into clinical applications remains challenging. This perspective discusses the persistent issue of correlational studies in microbiome research and proposes an iterative method leveraging in silico, in vitro, ex vivo, and in vivo studies toward successful preclinical and clinical trials. The evolution of research methodologies, including the shift from small cohort studies to large-scale, multi-cohort, and even "meta-cohort" analyses, has been facilitated by advancements in sequencing technologies, providing researchers with tools to examine multiple health phenotypes within a single study. The integration of multi-omics approaches-such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics-provides a comprehensive understanding of host-microbe interactions and serves as a robust hypothesis generator for downstream in vitro and in vivo research. These hypotheses must then be rigorously tested, first with proof-of-concept experiments to clarify the causative effects of the microbiota, and then with the goal of deep mechanistic understanding. Only following these two phases can preclinical studies be conducted with the goal of translation into the clinic. We highlight the importance of combining traditional microbiological techniques with big-data approaches, underscoring the necessity of iterative experiments in diverse model systems to enhance the translational potential of microbiome research.}, }
@article {pmid40054329, year = {2025}, author = {Saticioglu, IB and Ajmi, N and Coskuner-Weber, O and Alpsoy, S and Ay, H and Aydin, F and Abay, S and Karakaya, E and Kayman, T and Dalyan, C and Koca, FD and Tasci, G and Yarim, D and Morick, D and Yibar, A and Erdogan, S and Altun, S and Duman, M}, title = {Three new Microbacterium species isolated from the Marmara Sea mucilage event: Microbacterium istanbulense sp. nov., Microbacterium bandirmense sp. nov., Microbacterium marmarense sp. nov.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {3}, pages = {126600}, doi = {10.1016/j.syapm.2025.126600}, pmid = {40054329}, issn = {1618-0984}, abstract = {Three bacterial strains, Mu-43[T], Mu-80[T], and Mu-86[T], were isolated from the 2021 and 2022 mucilage event in the Marmara Sea and were taxonomically characterized. 16S rRNA gene sequence analysis confirmed that these strains belong to the genus Microbacterium. A polyphasic approach involving genomic and phenotypic analysis was employed to determine their taxonomic positions. A polyphasic approach integrating genomic and phenotypic analyses established their taxonomic positions. M. istanbulense Mu-43[T] showed 99.0 % 16S rRNA similarity to M. bandirmense Mu-80[T], with digital DNA-DNA hybridization (dDDH) and average nucleotide identity using BLAST (ANIb) values of 22.3 % and 78.3 %, respectively. M. bandirmense Mu-80[T] exhibited 99.2 % similarity to M. esteraromaticum DSM 8609[T], with dDDH and ANIb values of 23.6 % and 80 %. M. marmarense Mu-86[T] showed 97.4 % similarity to M. arthrosphaerae JCM 30492[T], with dDDH and ANIb values of 20.1 % and 74.2 %. Metagenomic analysis highlighted their ecological relevance, with relative abundances of 1.43 %, 1.15 %, and 0.95 %, respectively. Further genomic analysis identified biosynthetic gene clusters associated with secondary metabolite production, including non-ribosomal peptide synthetases and terpenoid biosynthesis pathways, suggesting potential antimicrobial activity. Additionally, antibiotic resistance genes, such as ABC efflux pumps and Erm23S_rRNA methyltransferase, indicate adaptation to environmental stress. These findings indicate that these species contribute to nutrient cycling and organic matter decomposition in mucilage-affected environments. Based on genomic and phenotypic data, these strains are proposed as novel species: M. istanbulense sp. nov. Mu-43[T] (LMG 33297[T] = DSM 117065[T]), M. bandirmense sp. nov. Mu-80[T] (LMG 33295[T] = DSM 117210[T]), and M. marmarense sp. nov. Mu-86[T] (LMG 33293[T] = DSM 117066[T]).}, }
@article {pmid40054170, year = {2025}, author = {Aalam, J and Ahmad Shah, SN and Parveen, R}, title = {An extensive review on infectious disease diagnosis using machine learning techniques and next generation sequencing: State-of-the-art and perspectives.}, journal = {Computers in biology and medicine}, volume = {189}, number = {}, pages = {109962}, doi = {10.1016/j.compbiomed.2025.109962}, pmid = {40054170}, issn = {1879-0534}, abstract = {UNLABELLED: Infectious diseases, including tuberculosis (TB), HIV/AIDS, and emerging pathogens like COVID-19 pose severe global health challenges due to their rapid spread and significant morbidity and mortality rates. Next-generation sequencing (NGS) and machine learning (ML) have emerged as transformative technologies for enhancing disease diagnosis and management.<br><br>OBJECTIVE: This review aims to explore integrating ML techniques with NGS for diagnosing infectious diseases, highlighting their effectiveness and identifying existing challenges.<br><br>METHODS: A comprehensive literature review spanning the past decade was conducted using reputable databases, including IEEE Xplore, PubMed, Scopus, SpringerLink, and Science Direct. Research papers, articles, and conference proceedings meeting stringent quality criteria were analysed to assess the performance of ML algorithms applied to NGS and metagenomic NGS (mNGS) data.<br><br>RESULTS: The findings reveal that ML algorithms, such as deep neural networks (DNNs), support vector machines (SVM), and K-nearest neighbours (KNN), achieve high accuracy rates, often exceeding 95&#xa0;%, in diagnosing infectious diseases. Deep learning methods excel in genomic and metagenomic data analysis, while traditional algorithms like Gaussian mixture models (GMM) also demonstrate robust classification capabilities. Challenges include reliance on single data types and difficulty distinguishing closely related pathogens.<br><br>CONCLUSION: The integration of ML and NGS significantly advances infectious disease diagnosis, offering rapid and precise detection capabilities. Addressing current limitations can further enhance the effectiveness of these technologies, ultimately improving global public health outcomes.}, }
@article {pmid40056781, year = {2025}, author = {Chen, H and Li, J and Wu, Y and Li, Y and Zheng, S and Wu, Y and Xuan, R and Wu, L and Miao, J and Wang, Y and Tan, H and Zhou, J and Huang, J and Yan, X}, title = {Structural characteristics of intestinal microbiota of domestic ducks with different body sizes.}, journal = {Poultry science}, volume = {104}, number = {4}, pages = {104930}, doi = {10.1016/j.psj.2025.104930}, pmid = {40056781}, issn = {1525-3171}, abstract = {Domestic ducks are economically important agricultural animals, and their body size is a crucial economic trait. The intestinal flora plays a pivotal role in influencing body metabolism, growth, and development. Currently, no literature is available on the potential effect of the intestinal flora of domestic ducks on body size. This study used 16S rRNA sequencing technology to investigate the fecal microbiota of 229 individuals reared under identical feeding conditions. The findings revealed that partridge ducks with large body sizes (LBS) exhibited a higher level of intestinal microbial diversity than ducks with small body sizes (SBS). Notably, the gut microbiota composition of SBS displayed significantly elevated proportions of Streptococcus, Rothia, and Psychrobacter compared to their counterparts with LBS. Conversely, Lactobacillus was significantly more abundant in LBS. Jeotgalibaca and Psychrobacter were identified as key biomarkers of SBS, whereas Lactobacillus and Bacteroides were predominant biomarkers of LBS. Functional predictions based on intestinal microbiota indicated discernible differences among different body types, particularly evident in non- partridge ducks. The present study investigated the correlation between the intestinal microbiota and body size of domestic ducks, aiming to provide practical insights for the production management of domestic duck farming.}, }
@article {pmid40056745, year = {2025}, author = {Zhu, S and Mao, H and Yang, X and Zhao, W and Sheng, L and Sun, S and Du, X}, title = {Resilience mechanisms of rhizosphere microorganisms in lead-zinc tailings: Metagenomic insights into heavy metal resistance.}, journal = {Ecotoxicology and environmental safety}, volume = {292}, number = {}, pages = {117956}, doi = {10.1016/j.ecoenv.2025.117956}, pmid = {40056745}, issn = {1090-2414}, abstract = {This study investigates the impact of heavy metal contamination in lead-zinc tailings on plant and soil microbial communities, focusing on the resilience mechanisms of rhizosphere microorganisms in these extreme environments. Utilizing metagenomic techniques, we identified a significant association between Coriaria nepalensis Wall. rhizosphere microbial communities and metal(loid) resistance genes. Our results reveal a notable diversity and abundance of bacteria within the rhizosphere of tailings, primarily consisting of Proteobacteria, Actinobacteria, and Chloroflexi. The presence of metal-resistant bacterial taxa, including Afipia, Bradyrhizobium, Sphingomonas, and Miltoncostaea, indicates specific evolutionary adaptations to metal-rich, nutrient-deficient environments. Elevated expression of resistance genes such as znuD, zntA, pbrB, and pbrT underscores the microorganisms' ability to endure these harsh conditions. These resistance genes are crucial for maintaining biodiversity, ecosystem stability, and adaptability. Our findings enhance the understanding of interactions between heavy metal contamination, microbial community structure, and resistance gene dynamics in lead-zinc tailings. Additionally, this research provides a theoretical and practical foundation for employing plant-microbial synergies in the in-situ remediation of contaminated sites.}, }
@article {pmid40056594, year = {2025}, author = {Zhang, H and Zhang, Y and Li, L and Huang, S and Ma, W and Xu, B and Ng, HY and Kim, DH and Kang, S and Shi, X}, title = {An innovative high-rate biofilm-based process: Biopolymer production and recovery from wastewater organic pollutants.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124800}, doi = {10.1016/j.jenvman.2025.124800}, pmid = {40056594}, issn = {1095-8630}, abstract = {In this study, a novel high-rate moving bed biofilm reactor (MBBR) was constructed to enhance wastewater COD bio-conversion and biopolymer recovery with a hydraulic retention time (HRT) of 1.0 h and an organic loading rate (OLR) of 4.8 kg COD·m[-3]·d[-1]. A superior specific COD reduction rate of 4.1 kg COD·m[-3]·d[-1] was obtained. The settleability analyses showed that within a settling time of 30 min, a low effluent suspended solids (SS) concentration (40.6 mg/L) with a high biomass recovery rate (83.3%) was achieved. From the recovered biomass, a remarkably higher alginate-like exopolymer (ALE) yield (274.2-385.1 mg/g VSS) was extracted as compared with seeding sludge (148.3 mg/g VSS). In addition, high protein/polysaccharide ratios of 8.5-12.4 were revealed owing to the short HRT condition. Moreover, key functional genes involving classic ALE synthesis were fully detected in such mixed-cultured bioprocess through metagenomic sequencing. Overall, this study offers a proof of concept that bio-refinery of organics into value-added biopolymers could provide a promising direction for the transformation of wastewater treatment plants from energy/resource-consuming factories to resource-recovery factories.}, }
@article {pmid40056581, year = {2025}, author = {Wu, Y and Xu, L and He, F and Song, X and Ding, J and Ma, J}, title = {Effects of micro-magnetite on anaerobic co-digestion of waste activated sludge and slaughterhouse waste: Microbial community and metabolism analyses.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124896}, doi = {10.1016/j.jenvman.2025.124896}, pmid = {40056581}, issn = {1095-8630}, abstract = {Micro-magnetite has been widely applied to improve anaerobic digestion (AD) performance, while comprehensive investigation of microbial community succession, metabolic pathway and magnetite fate remains unclear. In the current study, the effects of micro-magnetite (Fe3O4) on anaerobic co-digestion (AcD) of waste activated sludge and slaughterhouse waste were investigated. Experimental results indicated that the cumulative methane production was significantly increased from 484.6 mL/g VS to 524.4 mL/g VS with 0.8 g/L Fe3O4 addition. Recycled magnetite remained the initial physicochemical properties, including morphology, particle size and crystal structure, as evidenced by various characterization methods. Microbial community analysis indicated that magnetite addition enriched syntrophic bacteria (Armatimonadota, Syntrophomonas and Petrimonas) and methanogens (Methanosarcina). Metagenomic sequencing analysis demonstrated that hydrolysis and acidogenesis metabolic pathways were reinforced by magnetite addition. Meanwhile, the magnetite stimulated the direct interspecies electron transfer via enriching syntrophic microbes (Syntrophomonas and Methanosarcina) and conductive pili functional genes (pilA, mshA and mshC), finally achieving higher cumulative methane yield. This study provided in-depth investigation of the methane production facilitated by micro-magnetite addition and the magnetite fate during the AcD process.}, }
@article {pmid40056523, year = {2025}, author = {Zhang, Q and Fan, Y and Qian, X and Zhang, Y}, title = {Unraveling the role of microplastics in antibiotic resistance: Insights from long-read metagenomics on ARG mobility and host dynamics.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137804}, doi = {10.1016/j.jhazmat.2025.137804}, pmid = {40056523}, issn = {1873-3336}, abstract = {As two emerging pollutants, microplastics (MPs) potentially serve as vectors for antibiotic resistance genes (ARGs) in aquatic environments, but the mechanisms driving ARG enrichment remain unclear. This study used long-read metagenomics to investigate ARG mobility and hosts dynamics within the biofilms of MPs and rocks in different water environments. We identified distinct enrichment patterns for microbial communities and ARGs, highlighting the significant role of horizontal gene transfer in ARG enrichment. Specifically, plasmid-encoded ARGs varied significantly among MP biofilms, rock biofilms, and water samples, while chromosome-encoded ARGs remained consistent across these environments, emphasizing the impact of plasmids on ARG enrichment. Despite this, 55.1 % of ARGs were on chromosomes, indicating that host organisms also play a crucial role. The related mechanisms driving ARG enrichment included enhanced cell adhesion, increased transmembrane transporter activity, and responses to environmental stressors, which led to an increased presence of plasmid-encoded ARGs on MP biofilms, facilitating more frequent horizontal gene transfer. Additionally, the diversity of hosts on MPs was notably lower compared to the water column, with specific bacteria, including Herbaspirillu, Limnohabitans, Polaromonas, Variovorax, Rubrivivax, and Thauera significantly driving ARG enrichment. This study highlights key mechanisms and bacterial taxa involved in ARG dynamics on MPs.}, }
@article {pmid40056518, year = {2025}, author = {Zhu, Y and Li, R and Yan, S and Li, Y and Xie, S}, title = {Copper contamination determined the impact of phages on microbially-driven nitrogen cycling in coastal wetland sediments.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137870}, doi = {10.1016/j.jhazmat.2025.137870}, pmid = {40056518}, issn = {1873-3336}, abstract = {Phages have garnered increasing attention due to their potential roles in biogeochemical cycling. However, their impacts on nitrogen cycling have primarily been inferred from the presence of putative auxiliary metabolic genes (AMGs) and the virus-host linkage, despite of very limited direct experimental evidence. In this study, a series of microcosms were established with the inoculation of either native or non-native phages to simulate coastal wetlands with different phage sources and different levels of copper (Cu) contamination. Metagenomics and metatranscriptomics were combined to reveal phages' regulation on microbially-driven nitrogen cycling and to explore how the effects were mediated by Cu stress. Phages significantly impacted denitrification-related genes, with their effects depending on Cu level. Phages inhibited nirK-type denitrification under Cu stress but led to up-regulation of nirS gene in the treatments without Cu addition. Non-native phages also promoted the transcription of genes related to nitrogen assimilation and organic nitrogen transformation. Detection of viral AMGs involved in glutamate synthesis suggested that horizontal gene transfer may be a crucial pathway for phages to facilitate microbial nitrogen uptake. Overall, these findings enhance the understanding of phages' impact on biogeochemical metabolism in coastal wetland, offering novel insights into the links of phages' regulation on microbial nitrogen cycling with Cu stress.}, }
@article {pmid40054748, year = {2025}, author = {Wine, E}, title = {Metagenome-informed metaproteomics: a new frontier in gut host-microbe-diet analysis.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.02.024}, pmid = {40054748}, issn = {1528-0012}, }
@article {pmid40054424, year = {2025}, author = {Ding, C and Sun, J}, title = {The potential contribution of microbial communities to carbon fixation and nitrogen cycle in the Eastern Indian Ocean.}, journal = {Marine environmental research}, volume = {207}, number = {}, pages = {107056}, doi = {10.1016/j.marenvres.2025.107056}, pmid = {40054424}, issn = {1879-0291}, abstract = {This study investigated the diversity and metabolic potential of microbial communities in the Eastern Indian Ocean (EIO) through 16S rDNA gene sequencing and metagenomics analyses. Water samples were collected from the surface waters (5 m depth) and 150 m depth layer in the EIO between March 20th and June 6th, 2019. This study reveals microbial-driven biogeochemical dynamics in the oligotrophic Eastern Indian Ocean, where vertically stratified communities (Cyanobacteria/Proteobacteria-dominated surface vs. diversified Proteobacteria at 150 m) and latitudinal diversity gradients reflect nutrient limitations. Metagenomics identified four carbon fixation strategies: the Calvin cycle dominated epipelagic CO2 assimilation, while the 3-hydroxypropionate bicycle showed elevated surface activity, alongside reductive citrate and Wood-Ljungdahl pathways involving novel Actinobacteria. Nitrogen cycling exhibited spatial heterogeneity: nifH-dominated nitrogen fixation in the surface waters, prevalent narGHI nitrate reduction, and divergent nirS/nirK/nosZ distributions tied to nutrient gradients. Proteobacteria and Actinobacteria were key nitrogen fixers, with novel Actinobacteriota diazotrophs expanding known diversity. Elevated nosZ abundance in the Bay of Bengal underscored regional nitrous oxide consumption hotspots. These findings underscore microbial mediation of carbon-nitrogen fluxes in oligotrophic systems, providing genomic insights into ecosystem responses to climate-driven ocean changes.}, }
@article {pmid40054356, year = {2025}, author = {Yu, Y and Wu, J and Tang, Z and Wan, S and Hu, J and Li, B and Wang, J and Li, F}, title = {Unveiling the nitrogen metabolism mechanism for nitrogen retention in compost via in-situ ammonia recycling strategy.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124863}, doi = {10.1016/j.jenvman.2025.124863}, pmid = {40054356}, issn = {1095-8630}, abstract = {A large amount of ammonia volatilization in compost causes environmental pollution and reduces the quality of compost. Ammonia recycling composting strategy (ARCS) is new strategy for reducing ammonia volatilization by absorbing with backfilling ammonia into the compost. This study revealed the mechanism of ARCS on ammonia volatilization and nitrogen retention during chicken manure composting. The results showed that the adsorption layer containing wood vinegar had an obvious inhibition effect on ammonia volatilization. Compared to CK, ARCS treatment could reduce ammonia emissions and nitrogen loss by 20.65% and 39.6% with T3 (12d), respectively. Different adsorption time would affect the occurrence of various nitrogen components in the adsorption layer, especially the change of inorganic nitrogen content. Metagenomic analysis showed that ARCS treatment resulted in significant changes in bacterial communities, and different backfilling times had significant effects on nitrogen metabolism pathways in compost. Glutamate dehydrogenase and glutamate synthase were the key nitrogen metabolism processes during composting, which played an important role in ammonia volatilization and nitrogen retention. The suitable backfilling time (12d) promoted the acceleration of ammonia nitrogen metabolism in the early stage of composting and enhanced the ammonia assimilation and dissimilatory nitrate reduction function in the maturation stage to achieve nitrogen retention. This study provided valuable insights into the effects of in-situ ammonia absorption and backfilling on nitrogen metabolism pathways during composting.}, }
@article {pmid40054196, year = {2025}, author = {Wang, S and Li, T and Yuan, X and Yu, J and Luan, Z and Guo, Z and Yu, Y and Liu, C and Duan, C}, title = {Biotic and abiotic drivers of soil carbon, nitrogen and phosphorus and metal dynamic changes during spontaneous restoration of Pb-Zn mining wastelands.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137818}, doi = {10.1016/j.jhazmat.2025.137818}, pmid = {40054196}, issn = {1873-3336}, abstract = {The biotic and abiotic mechanisms that drive important biogeochemical processes (carbon, nitrogen, phosphorus and metals dynamics) in metal mine revegetation remains elusive. Metagenomic sequencing was used to explored vegetation, soil properties, microbial communities, functional genes and their impacts on soil processes during vegetation restoration in a typical Pb-Zn mine. The results showed a clear niche differentiation between bacteria, fungi and archaea. Compared to bacteria and fungi, the archaea richness were more tightly coupled with natural restoration changes. The relative abundances of CAZyme-related, denitrification-related and metal resistance genes reduced, while nitrification, urease, inorganic phosphorus solubilisation, phosphorus transport, and phosphorus regulation -related genes increased. Redundancy analysis, hierarchical partitioning analysis, relative-importance analysis and partial least squares path modelling, indicated that archaea diversity, primarily influenced by available lead, directly impacts carbon dynamics. Functional genes, significantly affected by available cadmium, directly alter nitrogen dynamics. Additionally, pH affects phosphorus dynamics through changes in bacterial diversity, while metal dynamics are directly influenced by vegetation. These insights elucidate natural restoration mechanisms in mine and highlight the importance of archaea in soil processes.}, }
@article {pmid40053579, year = {2025}, author = {Wöhlbrand, L and Dörries, M and Siani, R and Medrano-Soto, A and Schnaars, V and Schumacher, J and Hilbers, C and Thies, D and Kube, M and Reinhardt, R and Schloter, M and Saier, MH and Winklhofer, M and Rabus, R}, title = {Key role of Desulfobacteraceae in C/S cycles of marine sediments is based on congeneric catabolic-regulatory networks.}, journal = {Science advances}, volume = {11}, number = {10}, pages = {eads5631}, pmid = {40053579}, issn = {2375-2548}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {*Geologic Sediments/microbiology ; *Deltaproteobacteria/metabolism/genetics ; *Carbon Cycle ; Sulfur/metabolism ; Gene Regulatory Networks ; Phylogeny ; Metagenome ; Carbon/metabolism ; Proteome/metabolism ; Oxidation-Reduction ; Metabolic Networks and Pathways ; }, abstract = {Marine sediments are highly bioactive habitats, where sulfate-reducing bacteria contribute substantially to seabed carbon cycling by oxidizing ~77 Tmol Corg year[-1]. This remarkable activity is largely attributable to the deltaproteobacterial family Desulfobacteraceae of complete oxidizers (to CO2), which our biogeography focused meta-analysis verified as cosmopolitan. However, the catabolic/regulatory networks underlying this ecophysiological feat at the thermodynamic limit are essentially unknown. Integrating cultivation-based (80 conditions) proteogenomics of six representative Desulfobacteraceae spp., we identify molecular commonalities explaining the family's environmental relevance and success. Desulfobacteraceae genomes are specifically enriched in substrate uptake, degradation capacities, and regulatory functions including fine-tuned sulfate uptake. Conserved gene arrangements and shared regulatory patterns translate into strikingly similar (sub-)proteome profiles. From 319 proteins, we constructed a meta-network for catabolizing 35 substrates. Therefrom, we defined a Desulfobacteraceae characteristic gene subset, which we found prevalent in metagenomes of organic-rich, marine sediments. These genes are promising targets to advance our mechanistic understanding of Desulfobacteraceae-driven biogeochemical processes in marine sediments and beyond.}, }
@article {pmid40053318, year = {2025}, author = {Nihalani, R and Zola, J and Aluru, S}, title = {Disambiguating a Soft Metagenomic Clustering.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/cmb.2024.0825}, pmid = {40053318}, issn = {1557-8666}, abstract = {Clustering is a popular technique used for analyzing amplicon sequencing data in metagenomics. Specifically, it is used to assign sequences (reads) to clusters, each cluster representing a species or a higher level taxonomic unit. Reads from multiple species often sharing subsequences, combined with lack of a perfect similarity measure, make it difficult to correctly assign reads to clusters. Thus, metagenomic clustering methods must either resort to ambiguity, or make the best available choice at each read assignment stage, which could lead to incorrect clusters and potentially cascading errors. In this article, we argue for first generating an ambiguous clustering and then resolving the ambiguities collectively by analyzing the ambiguous clusters. We propose a rigorous formulation of this problem and show that it is NP-Hard. We then propose an efficient heuristic to solve it in practice. We validate our approach on several synthetically generated datasets and two datasets consisting of 16S rDNA sequences from the microbiome of rat guts.}, }
@article {pmid40053297, year = {2025}, author = {Scholand, KK and Schaefer, L and Govindarajan, G and Yu, Z and Galletti, JG and de Paiva, CS}, title = {Aged regulatory T cells fail to control autoimmune lacrimal gland pathogenic CD4[+] T cells.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {40053297}, issn = {2509-2723}, support = {R01EY030447/EY/NEI NIH HHS/United States ; EY-002520/EY/NEI NIH HHS/United States ; EY021725/EY/NEI NIH HHS/United States ; EY007001/EY/NEI NIH HHS/United States ; R01EY035333/EY/NEI NIH HHS/United States ; P30CA125123/CA/NCI NIH HHS/United States ; CPRIT-RP180672//CPRIT/ ; CA125123//National Institutes of Health (US)/ ; RR024574//National Institutes of Health (US)/ ; 221859/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; PICT 2020-00138//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT 2021-00109//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, abstract = {CD25KO mice are a model of Sjögren disease. CD25KO mice have severe inflammation and infiltrating lymphocytes to the lacrimal glands (LG). Whether the pathogenicity of CD25KO CD4[+] T cells can be controlled in vivo by Tregs is unknown. Eight-week-old B6 and CD25KO mice LGs were submitted for RNA bulk sequencing. A total of 3481 genes were differentially expressed in CD25KO LG compared to B6. Tear washing analysis identified CD25KO mice had elevated protein levels of TNF, IFN-γ, and CCL5 and decreased protein levels of IL-12p40 and VEGF-A. Co-adoptive transfer of CD25KO CD4[+] T cells with either young or aged B6 Tregs was performed in RAG1KO mice. Recipients of CD25KO CD4[+] T cells alone had higher LG inflammation than naive mice. However, in recipients of young B6 Tregs plus CD25KO CD4[+] T cells, LGs had significantly reduced inflammation. Recipients of CD25KO CD4[+] T cells with aged B6 Tregs had more inflamed LGs than young Tregs, suggesting aged Tregs have less suppressive capacity in vivo. Altogether, CD25KO mice have phenotypic and genetic changes resulting in increased inflammation and severe lymphocytic infiltration in the LGs. However, this autoimmunity can be controlled by the addition of young, but not aged, Tregs, suggesting that aging Tregs have dysfunctional suppression.}, }
@article {pmid40052570, year = {2025}, author = {Shen, M and Gao, S and Zhu, R and Wang, W and Gao, W and Tao, L and Chen, W and Zhu, X and Yang, Y and Xu, T and Zhao, T and Jiao, N and Zhi, M and Zhu, L}, title = {Multimodal Metagenomic Analysis Reveals Microbial InDels as Superior Biomarkers for Pediatric Crohn's Disease.}, journal = {Journal of Crohn's &amp; colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjaf039}, pmid = {40052570}, issn = {1876-4479}, abstract = {BACKGROUND AND AIMS: The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.<br><br>METHODS: A total of 1,175 fecal metagenomic sequencing samples, predominantly from three cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.<br><br>RESULTS: We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1,357 KO genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1,256 insertions/deletions (InDels), and 3,567 single nucleotide variants, with a considerable portion of these variants occurred in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an AUC of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC=0.996) and five other microbiome-associated pediatric cohorts.<br><br>CONCLUSIONS: Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of the non-invasive diagnostic tools and targeted therapies.}, }
@article {pmid40052474, year = {2025}, author = {Bamigbade, GB and Abdin, M and Subhash, A and Arachchi, MP and Ullah, N and Gan, RY and Ali, A and Kamal-Eldin, A and Ayyash, M}, title = {Plant polysaccharide-capped nanoparticles: A sustainable approach to modulate gut microbiota and advance functional food applications.}, journal = {Comprehensive reviews in food science and food safety}, volume = {24}, number = {2}, pages = {e70156}, doi = {10.1111/1541-4337.70156}, pmid = {40052474}, issn = {1541-4337}, support = {//United Arab Emirates University/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; *Nanoparticles/chemistry ; *Polysaccharides/chemistry ; *Functional Food ; Humans ; Plants/chemistry ; }, abstract = {Plant-derived polysaccharides have emerged as sustainable biopolymers for fabricating nanoparticles (polysaccharide-based nanomaterials [PS-NPs]), presenting unique opportunities to enhance food functionality and human health. PS-NPs exhibit exceptional biocompatibility, biodegradability, and structural versatility, enabling their integration into functional foods to positively influence gut microbiota. This review explores the mechanisms of PS-NPs interaction with gut microbiota, highlighting their ability to promote beneficial microbial populations, such as Lactobacilli and Bifidobacteria, and stimulate the production of short-chain fatty acids. Key synthesis and stabilization methods of PS-NPs are discussed, focusing on their role in improving bioavailability, stability, and gastrointestinal delivery of bioactive compounds in food systems. The potential of PS-NPs to address challenges in food science, including enhancing nutrient absorption, mitigating intestinal dysbiosis, and supporting sustainable food production through innovative nanotechnology, is critically evaluated. Barriers such as enzymatic degradation and physicochemical stability are analyzed, alongside strategies to optimize their functionality within complex food matrices. The integration of PS-NPs in food systems offers a novel approach to modulate gut microbiota, improve intestinal health, and drive the development of next-generation functional foods. Future research should focus on bridging knowledge gaps in metagenomic and metabolomic profiling of PS-NPs, optimizing their design for diverse applications, and advancing their role in sustainable and health-promoting food innovations.}, }
@article {pmid40052450, year = {2025}, author = {Qian, Z and Chen, S and Liao, X and Xie, J and Xu, Y and Zhong, H and Ou, L and Zuo, X and Xu, X and Peng, J and Wu, J and Cai, S}, title = {Decreased intestinal abundance of Akkermansia muciniphila is associated with metabolic disorders among people living with HIV.}, journal = {Annals of medicine}, volume = {57}, number = {1}, pages = {2474730}, doi = {10.1080/07853890.2025.2474730}, pmid = {40052450}, issn = {1365-2060}, mesh = {Humans ; Male ; *HIV Infections/complications/microbiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Akkermansia ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Prospective Studies ; Feces/microbiology ; Metagenomics/methods ; Hyperlipidemias/microbiology ; Metabolic Diseases/microbiology/epidemiology ; Verrucomicrobia/isolation &amp; purification ; Overweight/microbiology/complications ; }, abstract = {BACKGROUND: Previous studies have shown changes in gut microbiota after human immunodeficiency virus (HIV) infection, but there is limited research linking the gut microbiota of people living with HIV (PLWHIV) to metabolic diseases.<br><br>METHODS: A total of 103 PLWHIV were followed for 48&#x2009;weeks of anti-retroviral therapy (ART), with demographic and clinical data collected. Gut microbiome analysis was conducted using metagenomic sequencing of fecal samples from 12 individuals. Nonalcoholic fatty liver disease (NAFLD) was diagnosed based on controlled attenuation parameter (CAP) values of 238&#x2009;dB/m from liver fibro-scans. Participants were divided based on the presence of metabolic disorders, including NAFLD, overweight, and hyperlipidemia. Akkermansia abundance in stool samples was measured using RT-qPCR, and Pearson correlation and logistic regression were applied for analysis.<br><br>RESULTS: Metagenomic sequencing revealed a significant decline in gut Akkermansia abundance in PLWHIV with NAFLD. STAMP analysis of public datasets confirmed this decline after HIV infection, while KEGG pathway analysis identified enrichment of metabolism-related genes. A prospective cohort study with 103 PLWHIV followed for 48&#x2009;weeks validated these findings. Akkermansia abundance was significantly lower in participants with NAFLD, overweight, and hyperlipidemia at baseline, and it emerged as an independent predictor of NAFLD and overweight. Negative correlations were observed between Akkermansia abundance and both CAP values and body mass index (BMI) at baseline and at week 48. At the 48-week follow-up, Akkermansia remained a predictive marker for NAFLD.<br><br>CONCLUSIONS: Akkermansia abundance was reduced in PLWHIV with metabolic disorders and served as a predictive biomarker for NAFLD progression over 48&#x2009;weeks of ART.}, }
@article {pmid40052378, year = {2025}, author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H}, title = {Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf055}, pmid = {40052378}, issn = {1365-2672}, abstract = {AIMS: Microbial communities in paddy soils act as potential sinks of nitrous oxide (N2O), a notorious greenhouse gas, but their potential to reduce external N2O is unclear. The direct observation of N2O reduction in submerged field soils is technically difficult. Here, we aimed to identify soil microbial clades that underpin the strong N2O mitigation capacity.<br><br>METHODS AND RESULTS: We constructed paddy soil microcosms with external N2O amendment that enabled the simultaneous evaluation of N2O reductase gene (nosZ) transcripts and N2O consumption. Although the amount of N2O amended was large, it was mostly consumed after 6-8 days of microcosm incubation. Metatranscriptomic sequencing revealed that betaproteobacterial nosZ, especially those classified as clade II nosZ belonging to the orders Rhodocyclales or Nitrosomonadales, occupied&#xa0;>&#xa0;50% of the nosZ transcripts in three of the five paddy soils used. On the other hand, publicly available shotgun metagenomic sequences of 46 paddy soils were not dominated by betaproteobacterial clade II nosZ sequences, although they were ubiquitous. The same applied to the 16S rRNA sequences of Rhodocyclales or Nitrosomonadales.<br><br>CONCLUSIONS: The results indicated that betaproteobacterial N2O reducers potentially serve as powerful N2O sinks. Betaproteobacteria holding clade II nosZ can be targets of biostimulation, although further studies are required to understand their ecophysiology.}, }
@article {pmid40052334, year = {2025}, author = {Lu, Y and Dong, Y and Zhang, M and Mao, L}, title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14095}, doi = {10.1111/1755-0998.14095}, pmid = {40052334}, issn = {1755-0998}, support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; }, abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.}, }
@article {pmid40052063, year = {2025}, author = {Zheng, H and Peng, P and Wang, S and Zhang, B and Yang, L and Wang, Y and Li, L and Pang, G}, title = {Microbiological Diagnostic Performance and Clinical Effect of Metagenomic Next-Generation Sequencing for the Detection of Immunocompromised Patients With Community-Acquired Pneumonia.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1223-1236}, pmid = {40052063}, issn = {1178-6973}, abstract = {OBJECTIVE: Community-acquired pneumonia (CAP) presents a significant public health concern, necessitating timely and precise diagnosis. Metagenomic next-generation sequencing (mNGS) has shown promise as a powerful tool for pathogen identification in infectious diseases. This study aimed to evaluate the diagnostic efficacy and clinical applicability of mNGS for immunocompromised patients with CAP compared to the culture method.<br><br>METHODS: This study included 168 patients. We used both mNGS and conventional culture methods to identify the pathogen spectrum and evaluate diagnostic performance. Treatment regimens and clinical outcomes were meticulously documented.<br><br>RESULTS: The sensitivity of mNGS was greater than that of the culture method across all samples (79.05% vs 16.03%; p < 0.001). mNGS identified pathogens missed by culture in 59.52% of patients and detected polymicrobial infections that were not detected by culture in 47.62% of patients. Streptococcus pneumoniae, Candida albicans, and Human herpesvirus 4 at classification level emerged as the predominant pathogens identified in CAP patients through mNGS. When examining the mNGS results between groups, the proportions of immunocompromised patients with bacterial (p < 0.001), fungal (p < 0.001), viral (p < 0.05), and mixed infections (p < 0.001) were all significantly higher than those in immunocompetent patients. Treatment adjustments guided by mNGS were observed in 73.21% of patients. Specifically, a beneficial clinical effect was observed in 50.60% (85/168) of patients, treatment confirmation in 22.62% (38/168) of patients, and no clinical benefit in 26.80% (45/168) of patients based on mNGS-guided antibiotic treatment adjustments.<br><br>CONCLUSION: These findings highlight the diagnostic performance of mNGS for identifying pathogens, particularly in immunocompromised patients vulnerable to infections, offering valuable insights for clinical decision-making.}, }
@article {pmid40051621, year = {2025}, author = {Chen, Y and Liang, S and Lu, Y and Zhou, X and Zheng, R and Chen, Y}, title = {Case Report: First report of Legionella micdadei pneumonia and organizing pneumonia in a patient with myelodysplastic and Sweet syndromes.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1510948}, pmid = {40051621}, issn = {1664-3224}, mesh = {Humans ; *Myelodysplastic Syndromes/complications ; *Sweet Syndrome/diagnosis/drug therapy ; Male ; Legionella ; Pneumonia, Bacterial/diagnosis/drug therapy/microbiology/immunology ; Immunocompromised Host ; Legionellosis/diagnosis/drug therapy/microbiology ; Aged ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; Glucocorticoids/therapeutic use ; Female ; Legionnaires' Disease/diagnosis/drug therapy/complications/immunology ; Organizing Pneumonia ; }, abstract = {The immunocompromised population is susceptible to Legionella pneumonia. The diagnosis and treatment of Legionella pneumonia in immunocompromised individuals are challenging clinical endeavors. Previous studies have identified Legionella pneumonia as a potential cause of organizing pneumonia (OP), however, the association between Legionella pneumonia and OP has not received enough clinical attention. We retrospectively evaluated a case involving Legionella micdadei infection and OP in a patient with myelodysplastic syndrome and concurrent Sweet syndrome. The diagnosis of Legionella micdadei pneumonia was confirmed through various methods: metagenomic next generation sequencing (mNGS), Giemsa-staining and fluorescence in situ hybridization of lung tissue, as well as serum immunofluorescence antibody testing. Histopathological analysis of lung tissue revealed OP. The patient was successfully treated with a combination of antibiotics and low-dose glucocorticoids. In immunocompromised individuals, mNGS was capable of detection non-Legionella pneumophila serogroup 1. The pathological examination is important for identifying secondary OP and provides the evidence for treatment with glucocorticoids.}, }
@article {pmid40051412, year = {2025}, author = {Houttu, V and Boulund, U and Troelstra, M and Csader, S and Stols-Gonçalves, D and Mak, AL and Dijk, AV and Bouts, J and Winkelmeijer, M and Verdoes, X and van den Berg-Faay, S and Lek, D and Ronteltap, T and de Haan, F and Jorstad, H and Männistö, V and Savonen, K and Pentikäinen, H and Hanhineva, K and Babu, AF and Panagiotou, G and van Delden, O and Verheij, J and Doukas, M and Nederveen, A and Schwab, U and Grefhorst, A and Nieuwdorp, M and Holleboom, AG}, title = {Deep phenotyping of patients with MASLD upon high-intensity interval training.}, journal = {JHEP reports : innovation in hepatology}, volume = {7}, number = {3}, pages = {101289}, pmid = {40051412}, issn = {2589-5559}, abstract = {BACKGROUND &amp; AIMS: Exercise is a key component of lifestyle management in patients with metabolic dysfunction-associated steatotic liver disease (MASLD), but neither its therapeutic effect on the active stage of the disease, that is metabolic dysfunction-associated steatohepatitis (MASH) nor the mediating mechanisms have been characterized. Therefore, we performed multi-omic phenotyping of patients with MASLD-MASH on an exercise program.<br><br>METHODS: Fifteen patients with MASLD conducted high-intensity interval training (HIIT) combined with home-based training for 12 weeks. MASLD was evaluated using histology, transient elastography, and multiparametric magnetic resonance imaging (MRI) before and after the intervention. Change in maximal oxygen consumption (VO2max) and MRI-determined liver fat were compared with a control group of patients with MASLD (n&#xa0;= 22). RNA sequencing was performed on liver, muscle, and fat biopsies of patients in the exercise group. Stool was analyzed by shotgun metagenomics and untargeted metabolomics was performed on plasma, urine, adipose, and stool.<br><br>RESULTS: HIIT increased VO2max by 10.1% and improved mitochondrial metabolism in skeletal muscle, indicating improved cardiorespiratory fitness and adherence. VO2max increased significantly in the exercise group compared with controls. Histologically, no reduction in steatosis, MASH, or liver fibrosis was observed; however, transient elastography tended to improve. MRI-determined liver fat did not change in the exercise group compared with controls. HIIT induced changes in mRNA expression of genes related to beiging of adipose tissue and fibrogenesis in liver. In addition, specific gut microbial taxa and metabolites changed.<br><br>CONCLUSIONS: HIIT increased cardiorespiratory fitness and induced beneficial gene expression changes in muscle, adipose tissue, and liver, but without translation into histological improvement of MASLD. Longer exercise intervention trials are warranted to validate or refute current recommendations for exercise as a cornerstone treatment for MASLD-MASH.<br><br>IMPACT AND IMPLICATIONS: Despite exercise being considered as a key component of lifestyle management for steatotic liver disease, neither the clinical effects nor the mechanisms involved are completely understood. We show that a high-intensity interval training (HIIT) program in 15 patients with metabolic dysfunction-associated steatotic liver disease (MASLD) improved cardiorespiratory fitness, compared with 22 control patients with MASLD who did not participate in an exercise program, however, it did not improve MASLD. HIIT induced a positive effect on fat tissue and muscle metabolism which was accompanied with changes in certain gut bacteria and metabolites in blood and urine. These findings improve our understanding of the effects of exercise on the whole-body metabolism in relation to steatotic liver disease. As such, this study provides a basis for future exercise interventions in patients with MASLD, required to thoroughly test current guideline advice for exercise as a cornerstone treatment for MASLD of all stages.<br><br>CLINICAL TRIAL REGISTRY: Dutch Trial Register (registration number NL7932).}, }
@article {pmid40050994, year = {2025}, author = {Talat, A and Bashir, Y and Khalil, N and Brown, CL and Gupta, D and Khan, AU}, title = {Antimicrobial resistance transmission in the environmental settings through traditional and UV-enabled advanced wastewater treatment plants: a metagenomic insight.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {27}, pmid = {40050994}, issn = {2524-6372}, support = {BT/PR40148/BTIS/137/20/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {BACKGROUND: Municipal wastewater treatment plants (WWTPs) are pivotal reservoirs for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Selective pressures from antibiotic residues, co-selection by heavy metals, and conducive environments sustain ARGs, fostering the emergence of ARB. While advancements in WWTP technology have enhanced the removal of inorganic and organic pollutants, assessing ARG and ARB content in treated water remains a gap. This metagenomic study meticulously examines the filtration efficiency of two distinct WWTPs-conventional (WWTPC) and advanced (WWTPA), operating on the same influent characteristics and located at Aligarh, India.<br><br>RESULTS: The dominance of Proteobacteria or Pseudomonadota, characterized the samples from both WWTPs and carried most ARGs. Acinetobacter johnsonii, a prevailing species, exhibited a diminishing trend with wastewater treatment, yet its persistence and association with antibiotic resistance underscore its adaptive resilience. The total ARG count was reduced in effluents, from 58 ARGs, representing 14 distinct classes of antibiotics in the influent to 46 and 21 in the effluents of WWTPC and WWTPA respectively. However, an overall surge in abundance, particularly influenced by genes such as qacL, blaOXA-900, and rsmA was observed. Numerous clinically significant ARGs, including those against aminoglycosides (AAC(6')-Ib9, APH(3'')-Ib, APH(6)-Id), macrolides (EreD, mphE, mphF, mphG, mphN, msrE), lincosamide (lnuG), sulfonamides (sul1, sul2), and beta-lactamases (blaNDM-1), persisted across both conventional and advanced treatment processes. The prevalence of mobile genetic elements and virulence factors in the effluents possess a high risk for ARG dissemination.<br><br>CONCLUSIONS: Advanced technologies are essential for effective ARG and ARB removal. A multidisciplinary approach focused on investigating the intricate association between ARGs, microbiome dynamics, MGEs, and VFs is required to identify robust indicators for filtration efficacy, contributing to optimized WWTP operations and combating ARG proliferation across sectors.}, }
@article {pmid40050500, year = {2025}, author = {Dave, M and Tattar, R}, title = {Antimicrobial resistance genes in the oral microbiome.}, journal = {Evidence-based dentistry}, volume = {}, number = {}, pages = {}, pmid = {40050500}, issn = {1476-5446}, abstract = {A COMMENTARY ON: Sukumar S, Rahmanyar Z, El Jurf H Q et al. Mapping the oral resistome: a systematic review. J Med Microbiol 2024; https://doi.org/10.1099/jmm.0.001866 .<br><br>DESIGN: This systematic review, without meta-analysis, aimed to map the oral resistome by analysing clinical studies that detected bacterial antimicrobial resistance genes (ARGs) in the oral cavity using molecular techniques.<br><br>DATA SOURCES: The researchers used Medline, Embase, Web of Science, CINAHL and Scopus databases from January 2015 to August 2023.<br><br>STUDY SELECTION: This systematic review included cross-sectional or longitudinal clinical studies that detected ARGs using molecular techniques; specifically polymerase chain reaction (PCR) or next-generation sequencing (NGS) metagenomics&#xa0;for samples from the oral cavity (saliva, gingival biofilm, pulp, or oral mucosa). Studies were excluded if they were in vitro or animal studies, literature reviews and not focused on ARG detection.<br><br>DATA EXTRACTION AND SYNTHESIS: Five reviewers independently screened titles and abstracts based on inclusion criteria. Full-text reports were then independently assessed for eligibility by three reviewers. Extracted data encompassed publication details, sample size, country, molecular methods used, number of ARGs detected, participants' health status, antibiotic exposure, and sample location within the oral cavity.<br><br>RESULTS: Out of 580 initially identified studies, 15 met the inclusion criteria. These studies, published between 2015 and 2023 from 12 different countries, employed either PCR (n&#x2009;=&#x2009;10) or NGS metagenomics (n&#x2009;=&#x2009;5) to detect ARGs from a pool of 1486 participants (1 study did not report on the number of participants). PCR-based studies identified an average of 7 ARGs (range 1-20), while NGS studies identified an average of 34 ARGs (range 7-70). In total, 159 unique ARGs conferring resistance to 22 antibiotic classes were identified across six regions of the oral cavity. The supragingival biofilm and saliva exhibited the highest richness of ARGs, defined by the number of unique ARGs detected. Genes conferring resistance to 19 antibiotic classes were present in the supragingival biofilm. Notably, 49 ARGs, including tetracycline and macrolide resistance genes, were found across all sampled locations, indicating a widespread distribution within the oral cavity. Thirteen studies reported on bacterial species associated with ARGs. NGS studies identified a mean of 65 ARG-carrying bacterial species, compared to a mean of 4 species in PCR studies. Specifically, 25 ARG-carrying species were identified in PCR studies, while NGS studies identified 177 species. Four studies reported ARGs associated with streptococcal species implicated in distant-site infections such as infective endocarditis. ESKAPE pathogens (group of highly virulent multidrug-resistant bacteria) were detected with ARGs in various oral sites using both PCR and NGS methods. Comparisons between healthy and diseased states revealed that a healthy oral microbiome harbours a more diverse resistome at the antibiotic class level. The supragingival resistome demonstrated the richest composition in both health and disease, with tetracycline ARGs predominating in the supragingival and saliva resistomes in cases of dental caries.<br><br>CONCLUSIONS: The analysis of the oral resistome from these 15 studies identified three ARGs present in all sites of the oral cavity, suggesting the presence of a core resistome. NGS studies provided greater insights compared to PCR studies; however, the overall research base is limited. Further comprehensive studies are necessary to fully map the oral resistome.}, }
@article {pmid39726137, year = {2025}, author = {Schwesig, K and Zizka, V and Scherber, C and Hölzel, N}, title = {Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14060}, doi = {10.1111/1755-0998.14060}, pmid = {39726137}, issn = {1755-0998}, support = {01UT2101C//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 01UT2101B//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, mesh = {*Biodiversity ; Animals ; *Amphibians/genetics/classification ; *Ponds ; Germany ; *DNA Barcoding, Taxonomic/methods ; *Lakes ; Odonata/genetics/classification ; Metagenomics/methods ; DNA, Environmental/genetics ; Aquatic Organisms/genetics/classification ; }, abstract = {Biodiversity monitoring increasingly relies on molecular methods such as eDNA metabarcoding. However, sound applications have so far been only established for a limited number of taxonomic groups. More information on the strengths and weaknesses of eDNA methods, especially for poorly covered groups, is essential for practical applications to achieve the highest possible reliability. We compared amphibian and Odonata data from eDNA metabarcoding and traditional transect walks on N = 56 plots in 38 water bodies distributed over six extraction sites for building materials in Northwest Germany. The traditional amphibian assessment included visual encounters, dip netting and acoustic detection, while Odonata were assessed through exuviae. In total, both methods detected 8 out of 11 amphibian species, while the remaining three species were detected by eDNA only. We did not find differences in amphibian species numbers per plot, but mean detection probabilities were higher with metabarcoding. In contrast, both methods detected 10 out of 29 Odonata species, while the remaining 19 species were detected by exuviae only. Species numbers per plot were higher for exuviae and only 30% of species were detected with metabarcoding. The species identified by eDNA were those with high abundance, and their detection probabilities were similar to transect walks. The results for amphibians show equal suitability and high complementarity of the compared methods. Metabarcoding detected species more efficiently and therefore offers a suitable protocol for biodiversity monitoring. For Odonata, eDNA metabarcoding showed considerable gaps, implying the need for protocol evaluation and improvement in assessment of ecological communities based on eDNA.}, }
@article {pmid40050382, year = {2025}, author = {Liu, C and Wang, H and Wang, Z and Liang, L and Li, Y and Liu, D and Lu, Q}, title = {Distinct assembly processes of intestinal and non-intestinal microbes of bark beetles from clues of metagenomic insights.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7910}, pmid = {40050382}, issn = {2045-2322}, support = {32230071//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Coleoptera/microbiology/genetics ; Metagenome ; Bacteria/genetics/classification/metabolism ; Microbiota ; Symbiosis ; Weevils/microbiology/genetics ; Phylogeny ; }, abstract = {Ips (Curculionidae: Scolytinae) bark beetles (BBs) are ecologically and economically devastating coniferous pests in the Northern Hemisphere. Although the microbial diversity associated with these beetles has been well studied, mechanisms of community assembly and the functional roles of key microbes remain poorly understood. This study investigates the microbial community structures and functions in both intestinal and non-intestinal environments of five Ips BBs using a metagenomic approach. The findings reveal similar microbial community compositions, though the α-diversity of dominant taxa differs between intestinal and non-intestinal environments due to the variability in bark beetle species, host trees, and habitats. Intestinal microbial communities are predominantly shaped homogenizing dispersal (HD) and undominated processes (UP), whereas non-intestinal microbial communities are primarily driven by heterogeneous selection (HS). Functional analysis shows that genes and enzymes associated with steroid biosynthesis and oxidative phosphorylation are primarily found in non-intestinal fungal symbionts Ogataea, Wickerhamomyce, Ophiostoma, and Ceratocystis of Ips species. Genes and enzymes involved in degrading terpenoids, phenolic compounds, and polysaccharides are predominately found in the intestinal Acinetobacter, Erwinia, and Serratia. This study provides valuable and in-depth insights into the symbiotic relationships between Ips BBs and their microbial partners, enhancing our understanding of insect-microbe coevolution and suggesting new strategies for pest management.}, }
@article {pmid40050078, year = {2025}, author = {Zheng, YJ and Hou, JY and Zhong, J and Ye, XW}, title = {[A case of COVID-19-associated pulmonary aspergillosis combined with COVID-19-associated pulmonary mucormycosis].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {48}, number = {3}, pages = {267-271}, doi = {10.3760/cma.j.cn112147-20240809-00476}, pmid = {40050078}, issn = {1001-0939}, support = {82460015//National Natural Science Foundation of China/ ; 2019PT320003//Special Fund for Basic Scientific Research Operations of the Chinese Academy of Medical Sciences/ ; }, mesh = {Humans ; *Mucormycosis/diagnosis/complications ; *COVID-19/complications ; *Pulmonary Aspergillosis/complications/diagnosis ; Male ; Tomography, X-Ray Computed ; SARS-CoV-2/isolation &amp; purification ; Lung Diseases, Fungal/diagnosis/complications ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Lung/pathology/diagnostic imaging/microbiology ; Antifungal Agents/therapeutic use ; }, abstract = {COVID-19-associated invasive fungal infections are fungal infections that develop during COVID-19, including pulmonary aspergillosis (CAPA) and pulmonary mucormycosis (CAPM). This report presents a case of a patient with recurrent COVID-19 infections who showed pulmonary cavities and pleural effusion on chest CT. A mixed diagnosis of CAPA and CAPM was confirmed by histopathological analysis of bronchoalveolar lavage fluid and metagenomic next-generation sequencing. This study highlights the importance of suspecting CAPA and CAPM in diabetic COVID-19 patients with unexplained radiological findings that cannot be attributed to common infections or pulmonary tumors. Prompt and thorough diagnostic investigations, including histopathology, microbiology, and molecular techniques, are essential for accurate diagnosis. Early and effective antifungal treatment can significantly improve patient outcomes.}, }
@article {pmid40049907, year = {2025}, author = {Jia, Z and Li, C and Zhang, S and Tang, Y and Ma, S and Liu, X and Zhang, J}, title = {Microbial inoculants modify the functions of soil microbes to optimize plant growth at abandoned mine sites.}, journal = {Journal of environmental sciences (China)}, volume = {154}, number = {}, pages = {678-690}, doi = {10.1016/j.jes.2024.10.002}, pmid = {40049907}, issn = {1001-0742}, mesh = {*Soil Microbiology ; *Mining ; *Plant Development ; *Soil/chemistry ; Phosphorus/metabolism ; Carbon/metabolism ; Biodegradation, Environmental ; Nitrogen/metabolism ; Microbiota ; Bacillus thuringiensis ; }, abstract = {Mining activities have caused significant land degradation globally, emphasizing the need for effective restoration. Microbial inoculants offer a promising solution for sustainable remediation by enhancing soil nutrients, enzyme activities, and microbial communities to support plant growth. However, the mechanisms by which inoculants influence soil microbes and their relationship with plant growth require further investigation. Metagenomic sequencing was employed for this study, based on a one-year greenhouse experiment, to elucidate the effects of Bacillus thuringiensis NL-11 on the microbial functions of abandoned mine soils. Our findings revealed that the application of microbial inoculants significantly enhanced the soil total carbon (TC), total sulfur (TS), organic carbon (SOC), available phosphorus (AP), ammonium (NH4[+]), urease, arylsulfatase, phosphatase, β-1,4-glucosidase (BG), β-1,4-N-acetylglucosaminidase (NAG). Moreover, this led to substantial improvements in plant height, as well as aboveground and belowground biomass. Microbial inoculants impacted functional gene structures without altering diversity. The normalized abundance of genes related to the degradation of carbon and nitrogen, methane metabolism, and nitrogen fixation were observed to increase, as well as the functional genes related to phosphorus cycling. Significant correlations were found between nutrient cycling gene abundance and plant biomass. Partial Least Squares Path Model analysis showed that microbial inoculants not only directly influenced plant biomass but also indirectly affected the plant biomass through C cycle modifications. This study highlights the role of microbial inoculants in promoting plant growth and soil restoration by improving soil properties and enhancing normalized abundance of nutrient cycling gene, making them essential for the recovery of abandoned mine sites.}, }
@article {pmid40049896, year = {2025}, author = {Yu, Q and Hu, X and Qian, Y and Wang, Y and Shi, C and Qi, R and Heděnec, P and Nan, Z and Li, H}, title = {Virus communities rather than bacterial communities contribute more on nutrient pool in polluted aquatic environment.}, journal = {Journal of environmental sciences (China)}, volume = {154}, number = {}, pages = {550-562}, doi = {10.1016/j.jes.2024.08.026}, pmid = {40049896}, issn = {1001-0742}, mesh = {*Bacteria/metabolism/classification/genetics ; *Viruses ; Phosphorus/analysis ; RNA, Ribosomal, 16S/genetics ; Nitrogen/analysis ; Carbon/metabolism ; Water Microbiology ; Water Pollutants, Chemical/analysis ; Nutrients/analysis ; }, abstract = {The degradation of animal carcasses can lead to rapid waste release (e.g., pathogenic bacteria, viruses, prions, or parasites) and also result in nutrient accumulation in the surrounding environment. However, how viral profile responds and influences nutrient pool (carbon (C), nitrogen (N), phosphorus (P) and sulfur (S)) in polluted water caused by animal carcass decomposition had not been explored. Here, we combined metagenomic analysis, 16S rRNA gene sequencing and water physicochemical assessment to explore the response of viral communities under different temperatures (23 °C, 26 °C, 29 °C, 32 °C, and 35 °C) in water polluted by cadaver, as well as compare the contribution of viral/bacterial communities on water nutrient pool. We found that a total of 15,240 viral species were classified and mainly consisted of Siphoviridae. Both temperature and carrion reduced the viral diversity and abundance. Only a small portion of the viruses (∼8.8 %) had significant negative correlations with temperature, while most were not sensitive. Our results revealed that the viruses had lager contribution on nutrient pool than bacteria. Besides, viral-related functional genes involved in C, N, P and S cycling. These functional genes declined during carcass decomposition and covered part of the central nutrient cycle metabolism (including carbon sugar transformation, denitrification, P mineralization and extracelluar sulfate transfer, etc.). Our result implies that human regulation of virus communities may be more important than bacterial communities in regulating and managing polluted water quality and nutrition.}, }
@article {pmid40049874, year = {2025}, author = {Yao, W and Chang, R and Chen, K and Yang, C and Lu, Y and Wang, S and Dong, K and Huang, B and Jin, R}, title = {Performance and mechanism of enhanced phosphorus release and volatile fatty acid production from Fe-P sludge via co-fermenting with agricultural wastes.}, journal = {Journal of environmental sciences (China)}, volume = {154}, number = {}, pages = {290-299}, doi = {10.1016/j.jes.2024.07.019}, pmid = {40049874}, issn = {1001-0742}, mesh = {*Phosphorus/metabolism ; *Fatty Acids, Volatile/metabolism ; *Sewage ; *Fermentation ; *Agriculture/methods ; *Waste Disposal, Fluid/methods ; Iron/metabolism ; }, abstract = {Anaerobic fermentation is an efficient method to extract phosphorus from excess sludge, thereby facilitating its recovery and mitigating the phosphorus resource shortage. However, the prevalent metal-bound phosphorus species within sludge was difficult to release into the fermentation liquor. To address this, this study evaluated the enhanced phosphorus release performance from sludge containing iron-phosphorus compounds (Fe-P) via co-fermenting it with agriculture wastes. Specifically, protein-rich feather (Feather Group) and polysaccharide-rich tea residue (Tea Group) was respectively dosed into batch-scale fermentation jar. Results showed that the Feather Group exhibited significantly higher levels of released soluble phosphorus (2.1 folds) and volatile fatty acids (41.4 folds) compared to the Control Group, with concentrations reaching up to 280 mg/L and 9366 mg chemical oxygen demand /L, respectively. The activities of α-glucosidase, neutral protease and acetate kinase in the Feather group were increased by 11.1 %, 92.3 % and 37.6 %, respectively, compared with the Control group. Methanogen abundance decreased while hydrolytic acid-producing bacteria and iron-reducing bacteria increased significantly after supplying agricultural wastes. Metagenomic analysis demonstrated a significant increase in genes related to acetic acid synthesis. Mechanism elucidation suggested that increased iron-reducing bacteria abundance promoted Fe[3+] reduction into Fe[2+], thus enhancing phosphorus release from Fe-P compounds. This work may provide valuable information for developing effective strategy to extract phosphorus resource from complex environmental wastes.}, }
@article {pmid40049354, year = {2025}, author = {Sun, RZ and Pan, Y and Wang, J and Gao, T and Yu, HQ and Wang, J}, title = {Metabolic and Ecological Responses of Denitrifying Consortia to Different Carbon Source Strategies Under Fluctuating C/N Conditions.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121292}, doi = {10.1016/j.envres.2025.121292}, pmid = {40049354}, issn = {1096-0953}, abstract = {Frequent fluctuations in the carbon-to-nitrogen (C/N) ratio of urban wastewater influent can undermine denitrification performance, posing challenges for stable nitrogen removal. Although supplying additional carbon sources is a recognized strategy to mitigate these issues, the underlying microbial interactions and metabolic reconfigurations triggered by changing C/N ratios remain incompletely understood. Here, we employed methanol, glycerol, sodium acetate, and glucose in long-term denitrification reactors and integrated denitrification kinetics, 16S rRNA gene amplicon sequencing, metagenomic binning, and metabolic modeling to elucidate how these systems respond to a declining C/N ratio. Our results show that lower C/N ratios diminished denitrification efficiency in all treatments, with each carbon source eliciting distinct shifts in microbial assemblages. Fluctuations in the C/N ratio determine the extent of directional selection of microbial communities based on carbon source metabolism and induce significant changes in non-dominant microorganisms. Throughout the process, the synthesis potential of PHA is closely linked to the system's ability to withstand fluctuations. Notably, metabolic modeling indicated that heightened tricarboxylic acid (TCA) cycle activity in the methanol- and glucose-fed communities was associated with suboptimal nitrogen removal. These findings offer novel insights into the metabolic and ecological mechanisms governing carbon source-driven denitrification under fluctuating C/N conditions, providing a valuable framework for optimizing nitrogen removal in urban wastewater treatment systems.}, }
@article {pmid40049094, year = {2025}, author = {Yu, C and He, Q and Nie, WB and Zhang, T and Wu, H and Yang, Y and Fu, S and Tan, X and Chen, Y}, title = {Effluent organic matter facilitates anaerobic methane oxidation coupled with nitrous oxide reduction in river sediments.}, journal = {Water research}, volume = {278}, number = {}, pages = {123415}, doi = {10.1016/j.watres.2025.123415}, pmid = {40049094}, issn = {1879-2448}, abstract = {Effluent organic matter (EfOM) from wastewater treatment plants (WWTPs) contains humic-like substances that function as electron shuttles, thereby facilitating microbially-mediated redox reactions. However, the mechanisms governing the coupled processes of anaerobic oxidation of methane (CH4) (AOM) and nitrous oxide (N2O) reduction in river sediments, which receive WWTPs effluents, remain poorly understood. In this study, an incubation experiment with anoxic river sediments was conducted to assess the impacts of EfOM on AOM and nitrous oxide reduction using different effluent dilution ratios. The results showed that EfOM significantly enhanced both processes. Specifically, the AOM rate increased from 8.1 to 14.3 μg gdw[-1] d[-1], while the N2O reduction rate increased from 29.2 to 56.5 μg gdw[-1] d[-1]. The results of batch tests demonstrated that AOM process enhanced N2O reduction in the presence of EfOM, highlighting the critical role of EfOM in linking these processes. Nitrate-dependent anaerobic methane oxidation (n-DAMO) archaea and denitrifying bacteria dominated the sediment incubated with EfOM. Metagenomic and metatranscriptomic analyses revealed that the denitrifying bacteria exclusively reduce N2O, confirming the role of EfOM in facilitating electron transfer between n-DAMO archaea and N2O reducers. This indicates that effluent discharge could be a potential factor driving the concurrent sinks of methane and nitrous oxide, offering a perspective for investigating the impacts of WWTPs effluent on greenhouse gas sinks in freshwater ecosystems.}, }
@article {pmid40048953, year = {2025}, author = {Tamai, S and Okuno, M and Ogura, Y and Suzuki, Y}, title = {Genetic diversity of dissolved free extracellular DNA compared to intracellular DNA in wastewater treatment plants.}, journal = {The Science of the total environment}, volume = {970}, number = {}, pages = {178989}, doi = {10.1016/j.scitotenv.2025.178989}, pmid = {40048953}, issn = {1879-1026}, abstract = {Dissolved free extracellular DNA (free-exDNA) coexists with intracellular DNA (inDNA) in aquatic environments. Free-exDNA can be taken up by bacteria through transformation, and wastewater treatment plants (WWTPs) are positioned as potential hot spots for genetic contamination. However, studies comparing the composition of free-exDNA and inDNA is limited. This study employed colloidal adsorption and foam concentration method to recover free-exDNA from different WWTP stages and compared its diversity with inDNA via metagenomic analysis. Free-exDNA concentrations were observed to increase after chlorination. Genetic analysis revealed a higher abundance of specific genes following chlorination, suggesting that free-exDNA in effluent originated from bacterial death in secondary treated water. This result indicates that free-exDNA, which increases due to chlorination, is subsequently released into the catchment. Additionally, several high-risk antibiotic-resistance genes (ARGs) were detected that colocalized with mobile genetic elements. These ARGs were expected to have a high potential for gene transfer via transformation, and the risk was highlighted. Overall, these findings deepen our understanding of horizontal gene transfer risks in WWTPs.}, }
@article {pmid40048849, year = {2025}, author = {Bargheet, A and Noordzij, HT and Ponsero, AJ and Jian, C and Korpela, K and Valles-Colomer, M and Debelius, J and Kurilshikov, A and Pettersen, VK}, title = {Dynamics of gut resistome and mobilome in early life: a meta-analysis.}, journal = {EBioMedicine}, volume = {114}, number = {}, pages = {105630}, doi = {10.1016/j.ebiom.2025.105630}, pmid = {40048849}, issn = {2352-3964}, abstract = {BACKGROUND: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut.<br><br>METHODS: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers.<br><br>FINDINGS: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E.&#xa0;coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults.<br><br>INTERPRETATION: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow.<br><br>FUNDING: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Troms&#xf8; Research Foundation, Norway.}, }
@article {pmid40048707, year = {2025}, author = {Hernández-Verdin, I and Kirasic, E and Mokhtari, K and Barillot, N and Rincón de la Rosa, L and Sourdeau, E and Abada, Y and Le Tarff-Tavernier, M and Nichelli, L and Rozenblum, L and Kas, A and Mathon, B and Choquet, S and Houillier, C and Hoang-Xuan, K and Alentorn, A}, title = {Gut microbiome modulates the outcome in primary central nervous system lymphoma patients undergoing chemotherapy: an ancillary study from the BLOCAGE trial.}, journal = {Neuro-oncology}, volume = {}, number = {}, pages = {}, doi = {10.1093/neuonc/noaf059}, pmid = {40048707}, issn = {1523-5866}, abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) treatment relies on a high-dose methotrexate based chemotherapy (HD-MTX-based CT) regimen; however, whether there is a specific microbiota composition association with treatment response and clinical outcomes remains incompletely understood.<br><br>METHODS: We conducted a prospective study of PCNSL patients, included in the clinical trial NCT02313389 and the ancillary study NCT04253496 from 2020 to 2023, where patients were treated with first line HD-MTX-based polychemotherapy without a consolidation treatment. Stool (n=52), cerebrospinal fluid (CSF, n=52), and plasma samples (n=35) were collected before and/or after therapy initiation to perform metagenomic, flow cytometry, and metabolomic analyses. Plasma metabolomic data of 90 patients also included in the BLOCAGE clinical trial was subsequently used as a validation cohort.<br><br>RESULTS: Unsupervised clustering of microbial data identified two distinct gut microbial communities, differing in Parabacteroides distasonis abundance, which correlated with progression-free survival and overall survival in both uni- and multivariate analyses. Higher P. distasonis levels were linked to increased plasma betaine/valine metabolites and enhanced CD8 T cell infiltration in the CSF, suggesting a connection between gut microbiota and immune regulation. Stratifying the validation cohort by betaine/valine content confirmed these clinical associations.<br><br>CONCLUSIONS: Our findings suggest that gut microbiome communities modulate clinical outcomes in PCNSL patients undergoing standard treatment. Moreover, after future validation in external cohorts, the quantification of Parabacteroides distasonis could potentially provide a basis for patient stratification and guide personalized therapeutic strategies in the near future.}, }
@article {pmid40047424, year = {2025}, author = {Li, N and Li, M and Zhang, H and Bai, Z and Fei, Z and Dong, Y and Zhang, X and Xiao, P and Sun, X and Zhou, D}, title = {Effects of post-adulthood environmental hygiene improvement on gut microbiota and immune tolerance in mice.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0247724}, doi = {10.1128/aem.02477-24}, pmid = {40047424}, issn = {1098-5336}, abstract = {UNLABELLED: Changes in diet, cleanliness, stress, and exercise patterns may contribute to the disappearance of various gut microbes in humans who relocate to developed countries from developing countries. To explore the impact of environmental cleanliness on the gut microbiota, adult mice housed in a general animal room were divided into three groups. The control group was subjected to an unchanged living environment, SPF mice were moved to a specific pathogen-free (SPF) animal room with higher environmental cleanliness, and SPFL (specific pathogen-free specific with a fecal leakage grid) mice were moved to the SPF animal room and reared in cages with the function of preventing mice from eating feces as much as possible. Metagenome sequencing results showed that the gut microbial diversity decreased after the environmental change, accompanied by a substantial loss in gut microbiota, including genera known to have protective effects against allergies and those involved in short-chain fatty acid production. Additionally, the abundance of functional genes involved in short-chain fatty acid metabolism, amino acid synthesis, vitamin metabolism, flagellar assembly, and bacterial chemotaxis decreased. The environmental hygiene improvement also resulted in significant increases in total serum IgE, IL-4, IL-5, and IL-13 levels in mice with artificially induced chronic inflammatory dermatosis. Compared with SPF mice, preventing mice from eating feces as much as possible decreased the gut microbial diversity but did not markedly change functional gene expression or total serum cytokine levels.<br><br>IMPORTANCE: Research has indicated that the human gut microbial diversity gradually decreases, while the prevalence of allergic diseases increases after movement from developing countries to developed countries. A healthy gut microbiota is necessary for proper human immune function. Movement from undeveloped to developed regions is often accompanied by an increase in environmental cleanliness. However, whether changes in environmental cleanliness are an important factor contributing to the decreased gut microbial diversity and increased prevalence of allergic diseases has not been reported. This study demonstrates the impact of increased environmental cleanliness on gut microbiota and susceptibility to allergic diseases and contributes to a better understanding of the increased incidence rate of various chronic diseases.}, }
@article {pmid40047330, year = {2025}, author = {Gong, S and Li, M and Gao, J and Huang, S and Song, W and Sun, L}, title = {Cucumaria frondosa intestines and ovum hydrolysates intervention ameliorates the symptoms of dextran sulfate sodium-induced colitis by modulating gut microbiota and its metabolites.}, journal = {Journal of food science}, volume = {90}, number = {3}, pages = {e70106}, doi = {10.1111/1750-3841.70106}, pmid = {40047330}, issn = {1750-3841}, support = {42106111//National Natural Science Foundation of China/ ; ZR2021QD030//Natural Science Foundation of Shandong Province/ ; NYJG202303//Fund of Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, China/ ; 2023KJ241//Program for Scientific Research Innovation Team of Young Scholar in Colleges and Universities of Shandong Province/ ; R20076//Doctoral Startup Project of Guangdong Ocean University funded by W.S/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colitis/chemically induced ; *Dextran Sulfate ; Mice ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Colon/metabolism/microbiology/drug effects ; Cytokines/metabolism ; Intestines/microbiology/drug effects ; }, abstract = {Colitis, a troublesome inflammatory disease that significantly impacts daily life, has garnered considerable attention in recent times. Protolysates play a crucial role in the treatment of colitis, and the intestines and ovum of Cucumaria frondosa represent a readily available source of these hydrolysates. However, the effects of C. frondosa intestines and ovum hydrolysates (CFHs) on colitis have not been thoroughly investigated. We initially examined the molecular weight distribution of CFHs and found that the fraction of molecules with a weight less than 1000 Da accounted for 86.98%, indicating that the hydrolysis primarily produced oligopeptides. Subsequently, we employed a dextran sulfate sodium-induced experimental colitis model to assess the therapeutic potential of CFHs. The findings indicated that preventive administration of CFHs dramatically attenuated the pathological manifestations associated with colitis in mice, including weight loss, colon shortening, and tissue damage. Furthermore, CFHs suppressed the secretion of pro-inflammatory cytokines IL-6, TNF-α, and IL-1β, as well as MPO in colon tissue. Metagenomic sequencing demonstrated that CFHs could restore balance to the dysregulated gut microbiota by reinforcing Bacteroidota and suppressing Verrucomicrobia populations, impacting various microbial functions. Metabolomic analyses further revealed that CFHs exhibited a more efficacious modulatory effect on DSS-induced metabolic abnormalities, including amino acid biosynthesis, linoleic acid metabolism, and dopaminergic synapses. In conclusion, CFHs showed promise in alleviating colitis, laying the groundwork for the development and application of CFHs as functional food for colitis relief.}, }
@article {pmid40047235, year = {2025}, author = {Garg, RK}, title = {Tuberculosis of the central nervous system: current concepts in diagnosis and treatment.}, journal = {Current opinion in neurology}, volume = {}, number = {}, pages = {}, pmid = {40047235}, issn = {1473-6551}, abstract = {PURPOSE OF REVIEW: The outcome of central nervous system (CNS) tuberculosis has shown little improvement over several decades, with diagnosis remaining unconfirmed in nearly half of the cases. This review highlights current insights and advancements in the diagnosis and treatment of CNS tuberculosis.<br><br>RECENT FINDINGS: Miliary pulmonary tuberculosis is often linked to CNS tuberculosis and is associated with a worse prognosis. Complications, such as, optochiasmatic arachnoiditis, strokes, and transverse myelitis severely affect prognosis and quality of life. Nearly half of tuberculous meningitis patients exhibited impaired cognition. Diagnosing CNS tuberculosis is challenging because of the low accuracy of standard tests. Advanced techniques like metagenomic and nanopore sequencing enhance detection but are hindered by high costs and limited access. Treatment outcomes remain suboptimal but approaches such as higher drug doses, novel medications, and host-directed therapies are being explored. Drug-resistant tuberculous meningitis is increasingly recognized, posing significant challenges to both diagnosis and treatment. Artificial intelligence (AI) enhances care by enabling early diagnosis, disease monitoring, and personalized treatments, improving outcomes.<br><br>SUMMARY: CNS tuberculosis diagnosis faces challenges due to limited sensitivity and delayed results of available tests. Treatments remain suboptimal, with multidrug-resistant cases posing high mortality risks. AI aids in early diagnosis and personalized care.}, }
@article {pmid40046986, year = {2025}, author = {Zhang, D and Deng, M and Li, F and Shen, R}, title = {A Report of Primary Pyogenic Ventriculitis Caused by Streptococcus Constellatus Diagnosed by Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1209-1214}, pmid = {40046986}, issn = {1178-6973}, abstract = {BACKGROUND: Primary ventriculitis is a rare but serious brain infection characterized by inflammation of the ependyma and purulence within the ventricular system. Due to the challenges in early diagnosis and the potential for suboptimal treatment, this condition carries a significant risk of complications such as recurrence, hydrocephalus, and death. Metagenomic next-generation sequencing (mNGS) enables the rapid and broad-spectrum identification of pathogens, facilitating timely and precise diagnosis.<br><br>CASE REPORT: This study presents the first reported case of primary ventriculitis caused by Streptococcus constellatus. An 81-year-old female patient with hydrocephalus and clinical signs of central nervous system infection was diagnosed with primary ventriculitis based on brain magnetic resonance imaging (MRI) and cerebrospinal fluid (CSF) analysis using mNGS. The patient underwent external ventricular drainage (EVD) and received a five-week course of ceftriaxone and linezolid. Following timely and targeted therapy, she demonstrated significant clinical improvement and was discharged without residual symptoms.<br><br>CONCLUSION: Key insights from this case include: 1) mNGS is an invaluable tool for the early and accurate diagnosis of primary ventriculitis; 2) MRI is indispensable for identifying characteristic radiological features of the condition; 3) prompt initiation and completion of appropriate antibiotic regimens significantly improve clinical outcomes.}, }
@article {pmid40046887, year = {2025}, author = {Kim, M and Damronglerd, P and Molina Garcia, S and Yetmar, ZA and Razi, S and Ranganath, N and Mahmood, M and Abu Saleh, OM}, title = {Illuminating the Challenges and Diagnostic Utility of Plasma Microbial Cell-Free DNA Sequencing in Suspected Infective Endocarditis: A Retrospective Observational Cohort Study.}, journal = {Open forum infectious diseases}, volume = {12}, number = {3}, pages = {ofaf099}, pmid = {40046887}, issn = {2328-8957}, abstract = {BACKGROUND: Infective endocarditis (IE) is a life-threatening infection often challenging to diagnose, particularly in culture-negative cases. Plasma microbial cell-free DNA (mcfDNA) sequencing has shown potential for detecting pathogens in IE. However, its clinical utility, diagnostic impact, and limitations remain debated. This study evaluates its use in diagnosing and managing IE in a tertiary care setting.<br><br>METHODS: This single-center retrospective cohort study included adult patients (&#x2265;18 years) who underwent mcfDNA sequencing via the Karius test for suspected IE at Mayo Clinic Rochester between December 2019 and February 2024. Diagnostic classification followed the 2023 Duke-International Society of Cardiovascular Infectious Diseases criteria. Data on demographics, clinical features, routine microbiologic workup, and mcfDNA sequencing results were collected. Statistical analysis was conducted to evaluate diagnostic utility and treatment impact.<br><br>RESULTS: Among 141 patients, 66 had a diagnosis of IE, with mcfDNA sequencing identifying pathogens in 60.6% of them, compared with 39.4% with routine workup. mcfDNA sequencing was the sole microbiologic test with positive results in 33.3% of patients, leading to antimicrobial adjustments in 50.0% of that group. Clinically insignificant mcfDNA sequence detection occurred in 28.6% of patients without a diagnosis of IE.<br><br>CONCLUSIONS: mcfDNA sequencing is a valuable adjunctive tool for diagnosing culture-negative IE and guiding antimicrobial therapy when clinical suspicion is high. However, its utility depends on appropriate clinical context, highlighting the need for careful test interpretation and further prospective studies to assess patient-centered outcomes and cost-effectiveness.}, }
@article {pmid40046856, year = {2025}, author = {Tan, L and He, Z and Liang, Y and Wang, K and Chen, X}, title = {Correlation analysis between the severity of respiratory syncytial virus pneumonia and the expression levels of inflammatory cytokines in bronchoalveolar lavage fluid among infants and young children.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1482029}, pmid = {40046856}, issn = {2296-2360}, abstract = {PURPOSE: RSV is the primary cause of lower respiratory tract infections in infants and young children. Current study aims to investigate the correlation between the severity of respiratory syncytial virus pneumonia (RSVP) in infants and young children and the number of RSV infection sequences as well as the levels of cytokines in bronchoalveolar lavage fluid (BALF).<br><br>METHODS: Metagenomics next-generation sequencing (mNGS) and enzyme-linked immunosorbent assay (ELISA) were used to detect the number of RSV infection sequences and the levels of related inflammatory cytokines in BALF samples. Comparisons between groups and Logistic regression analysis were performed to examine the differences in RSV infection sequences and inflammatory cytokine levels between the sRSVP and nsRSVP groups. Spearman's correlation coefficient was used to analyze the correlations among PCIS, RSV infection sequences, and inflammatory cytokines. Finally, ROC curve analysis was conducted to assess the diagnostic performance of inflammatory cytokines as biomarkers in determining the severity of RSVP.<br><br>RESULTS: A total of 49 infants and young children diagnosed with RSV infection were enrolled and divided into severe RSVP (sRSVP) and non-severe RSVP (nsRSVP) groups based on the pediatric critical illness score (PCIS) scale. The levels of Interleukin (IL)-6, IL-8, IL-10, tumor necrosis factor &#x3b1; (TNF-&#x3b1;), IL-17A, and monocyte chemotactic protein 1 (MCP-1) as well as the number of RSV sequences in BALF were significantly higher in the sRSVP group than in the nsRSVP group. Additionally, elevated levels of IL-6, IL-10, TNF-&#x3b1;, IL-17A, and the number of RSV sequences were identified as risk factors for the severity of RSVP. Spearman's correlation analysis revealed significant negative correlations between the levels of IL-6, IL-10, TNF-&#x3b1;, IL-17A, and MCP-1 in BALF with PCIS, and significant positive correlations with the number of RSV sequences. Furthermore, a significant negative correlation was observed between RSV sequence count and PCIS. ROC curve analysis showed that the levels of IL-6, IL-10, TNF-&#x3b1;, IL-17A, and MCP-1, as well as their combined diagnostic approach, exhibited high diagnostic performance in determining the severity of RSVP.<br><br>CONCLUSION: The levels of inflammatory cytokines and RSV sequences in BALF are significantly correlated with the severity of RSVP in infants and young children. The levels of IL-6, IL-10, TNF-&#x3b1;, IL-17A, and MCP-1 can serve as potential biomarkers for diagnosing the severity of RSVP.}, }
@article {pmid40046438, year = {2025}, author = {Lin, K and Lin, W and Guo, Z and Chen, C and Chen, L and Cai, X}, title = {Plasma exosomal miRNA expression and gut microbiota dysbiosis are associated with cognitive impairment in Alzheimer's disease.}, journal = {Frontiers in neuroscience}, volume = {19}, number = {}, pages = {1545690}, pmid = {40046438}, issn = {1662-4548}, abstract = {INTRODUCTION: The gut microbiota composition and the expression profiles of microRNAs (miRNAs) in the brain tissue, cerebrospinal fluid, and blood of patients with Alzheimer's disease (AD) differ significantly from those with normal cognition function. The study aimed to initially explore the relationship between plasma exosomal microRNAs, gut microbiota, and cognitive impairment, providing insights into the pathogenesis and treatment of AD.<br><br>METHODS: The study enrolled 8 participants with AD and 8 participants with normal cognition. The Mini-Mental State Examination (MMSE) was utilized to evaluate cognitive function. High-throughput sequencing was used to identify differentially expressed miRNAs in plasma exosomes, while metagenomic sequencing was employed to detect differences in the abundance of gut microbiota. Furthermore, the associations among them were analyzed.<br><br>RESULTS: Four exosomal miRNAs and 14 microbiota taxa, which exhibited differential expression and abundance, respectively, in comparison between AD group and normal cognition group, were identified to be significantly associated with MMSE scores. Notably, the abundance of potential probiotics, including Faecalibacterium prausnitzii, Roseburia intestinalis and Roseburia inulinivorans, which was decreased in AD patients, exhibited positive correlations with specific exosomal miRNAs: Roseburia intestinalis correlated with miR-3120-3p and miR-6529-5p; Roseburia inulinivorans correlated with miR-3120-3p, miR-6529-5p and miR-124-3p; Faecalibacterium prausnitzii correlated with miR-3120-3p.<br><br>DISCUSSION: The study revealed a close association among gut microbiota, plasma exosomal miRNAs, and cognitive impairment in AD, and suggested that specific components of gut microbiota and exosomal miRNAs may serve as potential biomarkers and therapeutic targets for AD on the microbiota-gut-brain axis.}, }
@article {pmid40046298, year = {2025}, author = {Sun, W and Li, M and Zhu, X}, title = {Bordetella pertussis bacteremia in infants co-infected with cytomegalovirus and respiratory syncytial virus.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1544935}, pmid = {40046298}, issn = {1664-302X}, abstract = {INTRODUCTION: Hematogenous infections caused by Bordetella pertussis are rare. This study aimed to increase clinicians' knowledge of B. pertussis bacteremia.<br><br>METHODS: We described a case of an infant with B. pertussis bacteremia, searched and reviewed for B. pertussis bacteremia-related literatures published in the PubMed database between 1946 to 2022.<br><br>RESULTS: A 3-month-old male infant was admitted to the hospital with a respiratory tract infection. Respiratory pathogen testing indicated the presence of B. pertussis, cytomegalovirus, and respiratory syncytial viruses. Blood metagenomic next-generation sequencing (mNGS) confirmed B. pertussis bacteremia. After 32&#x202f;days of anti-infective treatment and supportive therapy, the patient's condition improved, and he was discharged. The literature review found that B. pertussis bacteremia is rare, often with fever as the first symptom, and is most common in individuals with underlying diseases or prolonged immunosuppressive therapy.<br><br>DISCUSSION: In infants lacking specific protective antibodies against B. pertussis, B. pertussis bacteremia should be considered when bacteremia-associated clinical manifestations are present and the causative organism remains undetected. Timely refinement of mNGS can help clarify the diagnosis.}, }
@article {pmid40046038, year = {2025}, author = {Bird, E and Pickens, V and Molik, D and Silver, K and Nayduch, D}, title = {BALROG-MON: a high-throughput pipeline for Bacterial AntimicrobiaL Resistance annOtation of Genomes-Metagenomic Oxford Nanopore.}, journal = {microPublication biology}, volume = {2025}, number = {}, pages = {}, pmid = {40046038}, issn = {2578-9430}, abstract = {BALROG-MON is a Nextflow pipeline for automated analysis of metagenomic long-read data to detect pathogens, annotate antimicrobial resistance genes (ARGs), link ARGs to specific pathogens, predict ARG origin (e.g., plasmid, chromosomal) and optionally perform steps like community analysis. With both assembly-based and assembly-free workflows, BALROG-MON is applicable to a wide range of sample types with low or high coverage, varying complexities and origins. Optional genome binning provides a comprehensive overview of ARGs within the dataset. BALROG-MON additionally presents results in summarized reports, overall serving as a flexible analysis tool for exploring diverse metagenomic samples for pathogens and antibiotic resistance.}, }
@article {pmid40045326, year = {2025}, author = {Zhang, R and Yu, J and Shang, X and Wang, Z and Li, H and Cao, B}, title = {Heterogeneity in clinical patterns of adult lung abscess patients: an 8-year retrospective study in a tertiary hospital.}, journal = {BMC pulmonary medicine}, volume = {25}, number = {1}, pages = {101}, pmid = {40045326}, issn = {1471-2466}, support = {NO. 82030002/H0102//National Natural Science Foundation of China/ ; NO.20220484049//Beijing Nova Program of Science and Technology under grant/ ; No. ZRJY2021-QM09//National High Level Hospital Clinical Research Funding, the Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; }, mesh = {Humans ; *Lung Abscess/microbiology ; Male ; Retrospective Studies ; Female ; Middle Aged ; China/epidemiology ; *Tertiary Care Centers ; Aged ; *Tomography, X-Ray Computed ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Hospital Mortality ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: The widespread use of broad-spectrum antibiotics has led to changes in both the microbiological and clinical characteristics of lung abscesses. It is necessary to re-evaluate the bacterial spectrum associated with these infections. As a novel method for pathogen detection, metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical practice. There is limited research evaluating the use of mNGS in patients with lung abscesses.<br><br>METHODS: A retrospective analysis was conducted on patients with lung abscess who were hospitalized between July 2015 and July 2023 at a teaching hospital in China. Patients who underwent both computerized tomography (CT) imaging and conventional pathogen testing were included in the study. The efficacy of pathogen detection using conventional methods was compared with that of mNGS. Additionally, the clinical and radiological features were analyzed to provide a comprehensive understanding of the disease patterns.<br><br>RESULTS: A total of 782 patients with lung abscess were included in the study and hematogenous abscess accounting for 7.16% (56/782) of cases. The overall hospital mortality rate was 1.53%. The mean age of the patients with lung abscess was 60 years, with a male predominance (80.2%). A significant proportion of patients had comorbid conditions, including diabetes (29.7%) and cardiovascular disease (18.2%). Lung abscesses were predominantly located in the right lung, and pleural effusion was more commonly observed in the deceased group. The detection rate of pathogen via conventional test was lower at 41.8% (327/782). Among patients with positive mNGS results, only 51.9% had pathogens identified through conventional testing methods. Klebsiella pneumoniae was the most frequently detected pathogen by conventional culture, while mNGS identified was Parvimonas micra. Infections caused solely by anaerobic bacteria or facultative anaerobes were associated with shorter hospital stays. Patient infected with Gram-negative bacilli (GNB) had a higher proportion of liver abscesses (11.8%).<br><br>CONCLUSION: Compared to conventional testing methods, mNGS demonstrates superior performance in detecting anaerobic and facultative anaerobic bacteria. The low detection rate of conventional tests may result in an underestimation of the clinical significance of anaerobic bacteria infections. In patients with lung abscess caused by GNB, hematogenous dissemination, liver abscess and diabetes were more commonly observed and these patients tended to have longer hospital stays.}, }
@article {pmid40045185, year = {2025}, author = {Freund, L and Hung, C and Topacio, TM and Diamond, C and Fresquez, A and Lyons, TW and Aronson, EL}, title = {Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {120}, pmid = {40045185}, issn = {1471-2180}, support = {NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; }, mesh = {California ; *Sulfur/metabolism ; *Microbiota ; *Lakes/microbiology ; *Seawater/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Seasons ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Biodiversity ; }, abstract = {BACKGROUND: Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.<br><br>RESULTS: We observed that the water column microbiome significantly varied by season (R[2]&#x2009;=&#x2009;0.59, P&#x2009;=&#x2009;0.003). Temperature (R[2]&#x2009;=&#x2009;0.27, P&#x2009;=&#x2009;0.004), dissolved organic matter (R[2]&#x2009;=&#x2009;0.13, P&#x2009;=&#x2009;0.004), and dissolved oxygen (R[2]&#x2009;=&#x2009;0.089, P&#x2009;=&#x2009;0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.<br><br>CONCLUSIONS: Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.}, }
@article {pmid40045177, year = {2025}, author = {Torshizi Esfahani, A and Zafarjafarzadeh, N and Vakili, F and Bizhanpour, A and Mashaollahi, A and Karimi Kordestani, B and Baratinamin, M and Mohammadpour, S}, title = {Gut Microbiome in Colorectal Cancer: Metagenomics from Bench to Bedside.}, journal = {JNCI cancer spectrum}, volume = {}, number = {}, pages = {}, doi = {10.1093/jncics/pkaf026}, pmid = {40045177}, issn = {2515-5091}, abstract = {Colorectal cancer (CRC) is a major global health challenge. Emerging research highlights the pivotal role of the gut microbiota in influencing CRC risk, progression, and treatment response. Metagenomic approaches, especially high-throughput shotgun sequencing, have provided unprecedented insights into the intricate connections between the gut microbiome and CRC. By enabling comprehensive taxonomic and functional profiling, metagenomics has revealed microbial signatures, activities, and biomarkers associated with colorectal tumorigenesis. Furthermore, metagenomics has shown a potential to guide patient stratification, predict treatment outcomes, and inform microbiome-targeted interventions. Despite remaining challenges in multi-omics data integration, taxonomic gaps, and validation across diverse cohorts, metagenomics has propelled our comprehension of the intricate gut microbiome-CRC interplay. This review underscores the clinical relevance of microbial signatures as potential diagnostic and prognostic tools in CRC. Furthermore, it discusses personalized treatment strategies guided by this omics' approaches.}, }
@article {pmid40044917, year = {2025}, author = {Štůsková, K and Vavřiník, A and Hakalová, E and Čechová, J and Gramaje, D and Eichmeier, A}, title = {Arbuscular mycorrhizal fungi strongly influence the endorhizosphere of grapevine rootstock with soil type as a key factor.}, journal = {Mycorrhiza}, volume = {35}, number = {2}, pages = {17}, pmid = {40044917}, issn = {1432-1890}, support = {CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; }, mesh = {*Mycorrhizae/physiology ; *Vitis/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Czech Republic ; Plant Roots/microbiology ; Mycobiome ; Basidiomycota/genetics/physiology ; Rhizosphere ; Phosphorus/metabolism/analysis ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the health and productivity of host plants, including grapevine. By forming symbiotic relationships with plant roots, AMF significantly improve water uptake and nutrient absorption, particularly phosphorus (P) and nitrogen (N). This study evaluated the microbiome composition and AMF colonization in the grapevine endorhizosphere across five wine-growing sub-regions in the Czech Republic. In all five sub-regions, in terms of composition of the fungal microbiome, the phyla Ascomycetes and Basidiomycetes were most numerous. Additionally, the study confirmed that LSU primers are more sensitive than ITS primers for AMF sequencing. While the representation of the phylum Glomeromycetes ranged from 0.07% to 5.65% in the ITS library, it was significantly higher, ranging from 83.74% to 98.71%, in the LSU library. The most significant difference compared to other sub-regions was observed in the Slovácko sub-region, where the soil had a low pH, a different texture (sandy loam), reduced micronutrient concentration, and low organic matter. The application of chemical plant protection products to grapevines also could have played a significant role, with 49 applications recorded in the Slovácko sub-region during the three years preceding sample collection. In other sub-regions, chemical treatments were conducted only 19-26 times. These factors resulted in only trace amounts of AMF being detected in Slovácko. Furthermore, it was demonstrated that AMF positively influenced the phosphorus concentration in the soil and reduced the presence of certain fungal pathogens.}, }
@article {pmid40044690, year = {2025}, author = {Zheng, K and Sun, J and Liang, Y and Kong, L and Paez-Espino, D and Mcminn, A and Wang, M}, title = {VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2226}, pmid = {40044690}, issn = {2041-1723}, support = {41976117//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42176111//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*RNA, Viral/genetics ; *RNA Viruses/genetics/classification/isolation &amp; purification ; *DNA Viruses/genetics/classification ; *DNA, Viral/genetics ; Software ; Phylogeny ; Genome, Viral/genetics ; Metagenomics/methods ; Virome/genetics ; Computational Biology/methods ; }, abstract = {The rapid growth in the number of newly identified DNA and RNA viral sequences underscores the need for an accurate and comprehensive classification system for all viral realms at different taxonomic levels. Here, we establish the Viral Taxonomic Assignment Pipeline (VITAP), which addresses classification challenges by integrating alignment-based techniques with graphs, offering high precision in classifying both DNA and RNA viral sequences and providing confidence level for each taxonomic unit. This tool automatically updates its database in sync with the latest references from the International Committee on Taxonomy of Viruses (ICTV), efficiently classifying viral sequences as short as 1,000 base pairs to genus level. VITAP possesses good generalization capabilities, maintaining accuracy comparable to other pipelines while achieving higher annotation rates across most DNA and RNA viral phyla. Its application in deep-sea viromes has led to significant taxonomic updates, providing comprehensive diversity information of viruses from deep-sea. VITAP is available at https://github.com/DrKaiyangZheng/VITAP .}, }
@article {pmid40044673, year = {2025}, author = {Wood, JR and Zhou, C and Cole, TL and Coleman, M and Anderson, DP and Lyver, PO and Tan, S and Xiang, X and Long, X and Luo, S and Lou, M and Southon, JR and Li, Q and Zhang, G}, title = {Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1798}, pmid = {40044673}, issn = {2041-1723}, mesh = {Animals ; Antarctic Regions ; *Spheniscidae/genetics ; *DNA, Mitochondrial/genetics ; *Geologic Sediments ; Phylogeny ; Seals, Earless ; Metagenome ; Ecosystem ; Diet ; }, abstract = {We report 156 sediment metagenomes from Adélie penguin (Pygoscelis adeliae) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine and terrestrial eukaryotes, including locally occurring bird and seal species. The data reveal spatiotemporal patterns of Adélie penguin diet, including spatial patterns in consumption of cnidarians, a historically overlooked component of Adélie penguin diets. Relative proportions of Adélie penguin mitochondrial lineages detected at each colony are comparable to those previously reported from bones. Elevated levels of Adélie penguin mitochondrial nucleotide diversity in upper stratigraphic samples of several active colonies are consistent with recent population growth. Moreover, the highest levels of Adélie penguin mitochondrial nucleotide diversity recovered from surface sediment layers are from the two largest colonies, indicating that sedaDNA could provide estimates for the former size of abandoned colonies. SedaDNA also reveals prior occupation of the Cape Hallett Adélie penguin colony site by southern elephant seal (Mirounga leonina), demonstrating how terrestrial sedaDNA can detect faunal turnover events in Antarctica driven by past climate or sea ice conditions. Low rates of cytosine deamination indicate exceptional sedaDNA preservation within the region, suggesting there is high potential for recovering much older sedaDNA records from local Pleistocene terrestrial sediments.}, }
@article {pmid40043990, year = {2025}, author = {Lou, D and Xiao, S and Cui, J and Duan, J and Duan, H and Cao, Y and Wang, D and Zhou, B and Tan, J}, title = {Discovery and characterization of the first hyperthermophilic 3-quinuclidinone reductase from hot-spring metagenomes.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {141706}, doi = {10.1016/j.ijbiomac.2025.141706}, pmid = {40043990}, issn = {1879-0003}, abstract = {Extremozymes play an essential part in the biosynthesis of pharmaceuticals (intermediates). In this study, a mixed assembly was performed for five metagenomes from hot springs. Via a series of procedures, including homology analysis, heterologous expression, and catalytic property characterization, the first hyperthermophilic 3-quinuclidinone reductase (SbQR) was successfully identified. The SbQR exhibits an optimal temperature of ≥95 °C and demonstrates remarkable thermal stability, with over 80 % of its activity retained following a 48-hour incubation at 50 °C. At particular concentrations, Mg[2+], Na[+], and Mn[2+] can substantially enhance the enzymatic activity. However, no significant influence of K[+] on the activity of SbQR was detected within the concentration range of 0-400 mM. Employing AlphaFold2, the three-dimensional structure of SbQR was predicted, which presents the typical traits of the Rossmann fold and is classified as a member of the short-chain dehydrogenases/reductases (SDR) superfamily. Molecular dynamics simulations were carried out and the results showed that when the temperature was increased to 390 K, the flexibility of residues 90-104 and the C-terminal increased significantly. This increase might lead to the destruction of the three-dimensional structure of the enzyme. In conclusion, this study identified the first hyperthermophilic 3-quinuclidinone reductase, providing a potential biocatalyst for the biopreparation of (R)-3-quinuclidinol.}, }
@article {pmid40043973, year = {2025}, author = {Liu, N and Dai, S and Fan, X and Li, B and Chen, M and Gong, P and Chen, X}, title = {In vitro fermentation of Auricularia auricula polysaccharides and their regulation of human gut microbiota and metabolism.}, journal = {International journal of biological macromolecules}, volume = {306}, number = {Pt 4}, pages = {141714}, doi = {10.1016/j.ijbiomac.2025.141714}, pmid = {40043973}, issn = {1879-0003}, abstract = {Auricularia auricula is abundant in polysaccharides that received increasing attention due to their variety biological activities and prebiotic potential. In order to explore the role of A. auricula polysaccharides (AAP) in regulating human gut microbiota and metabolic health, this study employed metagenomic and metabolomic analyses to examine the impact of AAP on the gut microbiota via in vitro fecal fermentation experiments. After in vitro fermentation, the data indicated that gut microbiota utilized AAP to produce rich short-chain fatty acids (SCFAs) including acetic acid, propionic acid, butyric acid and modulate gut microbiota structure, such as increasing the proportion of Bacteroidetes to Firmicutes, elevating the abundance of beneficial bacteria, including Bacteroides, especially the Parabacteroides, and inhibiting the abundance of harmful bacteria such as Bilophila, Morganella, and Escherichia-Shigella. Furthermore, the metabolomic analysis indicated that AAP utilization by gut microbes substantially alters the metabolic profile, in which 26 potential biological biomarkers were found and affects tryptophan, bile acids, purines, and butyric acid pathways to promote host health. In conclusion, this research indicated that AAP has a prebiotic potential, which can regulate the gut microbiota and promote host health. Moreover, this study provided scientific evidence for using AAP as a functional food with prebiotic effect.}, }
@article {pmid40043931, year = {2025}, author = {Li, HQ and Wang, WL and Shen, YJ and Su, JQ}, title = {Mangrove Plastisphere as a Hotspot for High-Risk Antibiotic Resistance Genes and Pathogens.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121282}, doi = {10.1016/j.envres.2025.121282}, pmid = {40043931}, issn = {1096-0953}, abstract = {Microplastics (MPs) are critical vectors for the dissemination of antibiotic resistance genes (ARGs); however, the prevalence and ecological risks of high-risk ARGs in mangrove ecosystems-globally vital yet understudied coastal habitats-remain poorly understood. To address this gap, this study investigated polyethylene, polystyrene, and polyvinyl chloride incubated in mangrove sediments for one month, focusing on high-risk ARGs, virulence gene (VGs), and pathogenic antibiotic-resistant bacteria within the mangrove plastisphere. High-throughput PCR and metagenomic analyses revealed that high-risk ARGs, VGs, and mobile genetic elements (MGEs) were significantly enriched on MPs compared to surrounding sediments. Pathogenic bacteria and MGEs were also more abundant in the plastisphere, highlighting its role as a hotspot for ARG dispersal. Metagenome-assembled genome analysis identified Pseudomonas and Bacillus as key hosts for ARGs, MGEs, and VGs, particularly multidrug resistance genes, integrase genes, and adherence factors. Notably, polystyrene harbored the highest abundance of pathogenic bacteria carrying ARGs, MGEs, and VGs, and mangrove root exudates were found to amplify horizontal gene transfer on MPs, uncovering a previously overlooked mechanism driving antibiotic resistance in coastal ecosystems. These findings not only elucidate how MPs accelerate the spread of ARGs, but also underscore the urgent need for targeted mitigation strategies to address the adverse impacts microplastic pollution on human, animal, and environmental health.}, }
@article {pmid40043916, year = {2025}, author = {Yang, H and Zhu, X and Zhan, Z and Wu, X and Mou, S and Zhou, P and Peng, Q and Wang, W and Teng, H and Tang, H}, title = {Metagenomic Analysis of Pathogenic Microorganisms in Bloodstream Infections Following Venomous Snakebites.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {}, number = {}, pages = {108304}, doi = {10.1016/j.toxicon.2025.108304}, pmid = {40043916}, issn = {1879-3150}, abstract = {PURPOSE: This study aimed to investigate the biometric characterization of pathogenic microorganisms associated with bloodstream infections in patients bitten by venomous snakes, and to determine whether the composition of these microorganisms influences the effects of snake venom.<br><br>METHODS: The composition and relative abundance of microorganisms were statistically analyzed using metagenomic next-generation sequencing (mNGS) on blood samples from patients with varying degrees of snakebite injuries. These patients were admitted to the our study.<br><br>RESULTS: In the light injury group (group L), the dominant phylum and genus were Pseudomonadota (73.31%) and Pseudomonas (35.32%). In the moderate injury group (group M), the predominant phylum was Bacillota (56.74%) and Aerococcus (45.45%). There was no statistically significant difference in the microbial composition between group L and group M based on &#x3b1;- and &#x3b2;- diversity analyses. LEfSe differential analysis revealed that the absolute abundances of Actinomycetota and Actinomycetes were higher in group L, while Pseudomonas aeruginosa emerged as a significantly differential species in Group M.<br><br>CONCLUSION: The study found that differences in bacterial bloodstream infections due to venomous snakebite may enhance the effects of snake venom, leading to more severe injuries. The mNGS technique can rapidly detect pathogens related to venomous snakebites and has the potential for broader clinical use.}, }
@article {pmid40043765, year = {2025}, author = {Yang, Y and Wu, X and Xu, Y and Shuang, Q and Xia, YN}, title = {Influence of Feeding Systems on the Microbial Community and Flavor Characteristics of Raw Milk: A Comparative Analysis.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-25959}, pmid = {40043765}, issn = {1525-3198}, abstract = {This study analyzed the composition of the microbial community in raw milk and its effects on flavor compounds by comparing samples from cows raised on pasture (PXN) and in housing (HXN). In August 2023, 9 raw milk samples from Holstein cows were collected from a pasture in the Xilin Gol League, Inner Mongolia, China, and labeled as the PXN group. Simultaneously, 9 raw milk samples were collected from Holstein cows raised by individual farmers in the region and labeled as the HXN group. Metagenomic sequencing technology was used to detect and analyze the dynamics of microbial community in milk samples. At the same time, headspace solid phase microextraction, electronic nose and electronic tongue technology were used to monitor the flavor characteristics of raw milk under the 2 feeding conditions and to analyze the correlations between them. The results showed that raw milk protein (PXN 3.43%; HXN 3.36%) and fat (PXN 4.01%; HXN 3.79%) content in pasture group were higher than that in the housed group, while lactose content (PXN 4.98%; HXN 5.12%) and total solid content (PXN 4.98%; HXN 5.12%) were lower than that under the housed system. However, there was no significant difference between non-milk fat solid contents of the 2 groups. W1C, W5C, W5S, W2S sensors of electronic nose played an important role in distinguishing the 2 groups of samples. The sour taste of raw milk in pasture group was different from that in house feeding group. There were significant differences in the microbial communities of the 2 groups, with Macrococcus caseolyticus (39.85%) in PXN group and Lactococcus lactis (49.59%) in HXN group being the dominant bacteria. The volatile compounds of raw milk in PXN and HXN groups were detected by headspace solid phase microextraction method. A total of 62 and 53 flavor compounds were detected in PXN and HXN groups, respectively. Terpenoids, esters and aldehydes were dominant in PXN group, while acids were dominant in HXN group. The saturated fatty acid (SFA) content in HXN group (76.13%) was higher than that in PXN group (72.47%). The gamma-linolenic acid (GLA) content in PXN group (3.56 g/100g) was higher than that in HXN group (1.32 g/100g). The dominant strains, i.e., Macrococcus caseolyticus, Lactococcus lactis and Lactococcus cremoris, in both PXN and HXN groups exhibited positive effects on the formation of alcohols, esters, phenols and unsaturated fatty acids. In addition, Macrococcus caseolyticus in PXN group showed significant positive correlation with calcium lactate (CAL). This study comprehensively elaborates the microbial community structure and flavor quality of raw milk under different feeding methods, which may serve as a reference to control the quality of raw milk.}, }
@article {pmid40043731, year = {2025}, author = {Wang, M and Liu, YB and Tong, WM and Leung, WK and He, LL and Xu, X and Xu, D and Zhou, Q}, title = {Periodontitis History Shapes the Early Peri-Implant Microbiome Formation: A Metagenomic Analysis.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.14147}, pmid = {40043731}, issn = {1600-051X}, support = {32270188//National Natural Science Foundation of China/ ; 32070134//National Natural Science Foundation of China/ ; 2023-YBSF-162//Key Research and Development Program of Shaanxi Province, China/ ; //National Training Program of Innovation and Entrepreneurship for Undergraduates/ ; }, abstract = {AIM: This study aims to investigate the early alterations in microbiome construction and succession around dental implants in both periodontally healthy individuals and patients with a history of periodontitis during the first month after implant-crown placement.<br><br>MATERIALS AND METHODS: Ninety-five subgingival plaque samples were collected from 10 periodontally compromised patients (PCP) and nine periodontally healthy patients (PHP) at four time points with a 1-week interval and analysed using dynamic metagenomic analysis. The study compared the formation and temporal change in the peri-implant microbiome in the PCP and PHP groups during the first month after the implant crown placement. A two-year follow-up examination was conducted to assess the clinical outcomes of early peri-implant dysbiosis.<br><br>RESULTS: The results showed that PCP groups exhibited distinctively dysbiotic features in their peri-implant microbiome upon initial establishment, with an earlier and elevated emergence of periodontopathogens. This dysbiosis in the PCP group was associated with significantly higher modified sulcus bleeding index (mBI) scores compared with the PHP group. Neisseria was identified as a key driver of early peri-implant dysbiosis in patients with a periodontitis history.<br><br>CONCLUSIONS: This study established the first microbial link between periodontitis history and early peri-implant dysbiosis, highlighting the importance of early prevention strategies against peri-implant diseases in patients with a periodontitis history.}, }
@article {pmid40043574, year = {2025}, author = {Wang, B and Chen, X and Wen, G and Duan, Z and Xue, P and Gao, H}, title = {Treating nitrobenzene (NB) wastewater via an enhanced iron‒manganese oxides electron transfer strategy: Methods and mechanisms.}, journal = {Water research}, volume = {278}, number = {}, pages = {123407}, doi = {10.1016/j.watres.2025.123407}, pmid = {40043574}, issn = {1879-2448}, abstract = {Nitrobenzene (NB) is widely used in the fine chemical, pharmaceutical, and textile industries, but its toxicity and resistance to degradation present challenges, and traditional treatment methods are limited due to costs and a lack of efficiency. In this study, using a three-dimensional biofilm electrode reactor (3D-BER) enhanced with iron-manganese oxide catalysts was explored for the treatment of NB wastewater. Modifying polyurethane (PU) sponge fillers with Fe3O4 and Mn3O4 improved the conductivity and microbial electron transfer of the 3D-BER, significantly enhancing organic compound degradation, nitrogen and phosphorus removal. At the optimal voltage of 6 V and hydraulic retention time (HRT) of 24 h, the reactor achieved CODCr and ammonia nitrogen removal rates of 93.04 % and 86.25 %, respectively, which were more than 20 % higher than those in the control group. The iron and manganese present facilitated increased microbial activity and electron transfer efficiency, and metagenomic sequencing revealed shifts in the microbial communities and the enrichment of specific functional genes related to NB degradation. This integrated bioelectrochemical approach offers an effective and low-cost solution for treating NB wastewater, with broader implications for organic chemical wastewater management.}, }
@article {pmid40043404, year = {2025}, author = {Pang, L and Chen, J and Li, W and Chatzisymeon, E and Xu, K and Yang, P}, title = {Particle size of zero-valent iron affects the risks from antibiotic resistance genes in waste activated sludge during anaerobic digestion.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137785}, doi = {10.1016/j.jhazmat.2025.137785}, pmid = {40043404}, issn = {1873-3336}, abstract = {Zero-valent iron (ZVI) is the promising enhancer for sludge anaerobic digestion (AD) performance and for mitigating the proliferation of antibiotic resistance genes (ARGs). However, concerns about its size effects in shifting the behavior and risk of ARGs in sludge, during the AD process. Here, the metagenomics-based profile of ARGs, along with their potential (pathogenic) hosts in sludge were investigated, during mesophilic AD enhanced by ZVI with three different sizes. Results showed that the size of ZVI affected the profiles of ARGs, with nano-ZVI (nZVI, 50 nm) demonstrating the most significant reduction in abundance (by 45.0 %) and diversity (by 8.6 %) of total ARGs, followed by micron-ZVI (150 μm) and iron scrap (1 mm). Similar trends were also observed for high-risk ARGs, pathogens, and potential pathogenic hosts for ARGs. Notably, nZVI achieved the greatest reductions in the abundance of risk ARGs and potential pathogenic hosts (superbugs) by 58.8 % and 53.9 %, respectively. Correlation and redundancy analyses revealed that, the size of ZVI induced concentration differences in ammonium nitrogen, pH, carbonaceous matters, iron, and potential microbial hosts were the main reasons for the variation in the risk of ARGs. Moreover, the down-regulation of genes involved in oxidative stress contributed to the lower risk of ARGs in the three ZVI groups, especially in nZVI. This study provides insights into AD processes of solid wastes using ZVI enhancers.}, }
@article {pmid40043390, year = {2025}, author = {Li, F and Zeng, Z and Wu, Y and Wang, Y and Shen, L and Huang, X and Wang, X and Sun, Y}, title = {Characteristics of microplastics in typical poultry farms and the association of environment microplastics colonized-microbiota, waterfowl gut microbiota, and antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137808}, doi = {10.1016/j.jhazmat.2025.137808}, pmid = {40043390}, issn = {1873-3336}, abstract = {Microplastics (MPs) pollution is a growing global environmental concern. MPs serve as ecological niches for microbial communities, which may accelerate the spread of antibiotic resistance genes (ARGs), posing risks to the breeding industry. While studies on MPs in aquatic organisms are common, research on farmed poultry is limited. This study investigates MPs in poultry farm environments and waterfowl intestines for the first time. MPs were isolated via density separation and analyzed for characterization in soil, pond water, and waterfowl intestines. Metagenomics was used to investigate the association between environment MPs colonized-microbiota and waterfowl gut microbiota. Our findings reveal that MPs are abundant in soil (6.75 ± 2.78 items/g d.w.), pond water (0.94 ± 0.28 items/g w.w.), and poultry intestines (45.35 ± 19.52 items/g w.w.), primarily appearing as fragmented particles sized 20-50 μm. MPs abundance in intestines correlates with environmental levels. Colonized-microbiota on MPs are linked to poultry intestinal microbiota, with greater diversity and microbial functions. Network analysis reveals that Corynebacterium plays a key role in MPs and poultry intestinal. Polymyxin resistance exhibits high clustering. Procrustes analysis reveals correlations between MPs, bacteria, and ARGs in the farming environment. Overall, MPs in poultry farms may facilitate pathogen and ARGs transmission, posing risks to animal gut health.}, }
@article {pmid40043057, year = {2025}, author = {Mercado-Juárez, RA and Valdespino-Castillo, PM and Merino Ibarra, M and Batista, S and Mac Cormack, W and Ruberto, L and Carpenter, EJ and Capone, DG and Falcón, LI}, title = {What defines a photosynthetic microbial mat in western Antarctica?.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0315919}, pmid = {40043057}, issn = {1932-6203}, mesh = {Antarctic Regions ; *Bacteria/genetics/classification/isolation &amp; purification ; Photosynthesis ; Archaea/genetics/classification/isolation &amp; purification ; Biodiversity ; Phylogeny ; Microbiota ; }, abstract = {Antarctic microbial mats, with their significant biodiversity and key role in biogeochemical cycling, were the focus of our study. We employed a metagenomic approach to analyze 14 microbial mats from meltwater streams of western Antarctica, covering the Maritime, Peninsula, and Dry Valleys regions. Our findings revealed that the taxonomic compositional level of the microbial mat communities is characterized by similar bacterial groups, with diatoms being the main distinguishing factor between the rapidly warming Maritime Antarctica and the other mats. Bacteria were found to be the predominant component of all microbial mats (>90%), followed by Eukarya (>3%), Archaea (<1%), and Viruses (<0.1%). The average abundance of the main phyla composing Antarctic microbial mats included Bacteroidota (35%), Pseudomonadota (29%), Cyanobacteriota (19%), Verrucomicrobiota (3%), Bacillariophyta (2%), Planctomycetota (2%), Acidobacteriota (2%), Actinomycetota (2%), Bacillota (1%), and Chloroflexota (1%). We also identified some microeukaryotes that could play essential roles in the functioning of Antarctic microbial mats. Notably, all mats were found in sites with varied environmental characteristics, showed N-limitation, and shared functional patterns.}, }
@article {pmid40042766, year = {2025}, author = {Kumar, A and Saini, S and Anvikar, A and Mishra, N and Misra, G}, title = {Evolving Landscape of Emerging Virus Diagnosis: Challenges and Innovations.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40042766}, issn = {1559-0305}, abstract = {Emerging and re-emerging viruses (like Spanish flu, SARS-CoV-2, etc.) have substantially impacted global public health since the early twentieth century. These outbreaks are unpredictable and novel viruses are difficult to understand due to emerging variations. Advanced virology and diagnostic technologies have revolutionized viral diagnostics, enabling accurate early identification and successful treatment and containment. Next-generation sequencing (NGS) technologies, such as metagenomics and whole-genome sequencing, have played a crucial role in the detection and monitoring of emerging viruses, such as SARS-CoV-2 and its variants. Advanced diagnostic methods, such as digital PCR, CRISPR-based tools, and serological techniques like ELISA, enhance viral detection's sensitivity, specificity, and speed. Research has shown that innovations such as lateral flow immunoassays, biosensors, and aptamers have the potential to significantly enhance diagnostic accuracy in various fields. The integration of AI in diagnostics aids researchers in understanding viral evolution and outbreak management, offering new avenues for rapid response. This review aims to examine the latest advancements in virus diagnosis technologies, identify unresolved accuracy and detection issues, and discuss emerging ideas that are transforming the future of viral diagnostics. It is important to improve early identification, rendering the system more cost-effective and adaptable to new viral threats.}, }
@article {pmid39902625, year = {2025}, author = {Pelosi, JA and Sorojsrisom, ES and Barbazuk, WB and Sessa, EB}, title = {Population genomics of the gametophyte-only fern Vittaria appalachiana provides insights into clonal plant evolution.}, journal = {The New phytologist}, volume = {246}, number = {1}, pages = {349-364}, doi = {10.1111/nph.20433}, pmid = {39902625}, issn = {1469-8137}, support = {2024-67012-43394//National Institute of Food and Agriculture/ ; 1701708//Division of Environmental Biology/ ; 1754911/2310485//Division of Integrative Organismal Systems/ ; //Department of Biology, University of Florida/ ; //Southern Appalachian Botanical Society/ ; }, mesh = {*Germ Cells, Plant/physiology ; *Ferns/genetics/physiology ; *Genetic Variation ; *Biological Evolution ; Reproduction, Asexual/genetics ; Genome, Plant ; Metagenomics ; Genetics, Population ; Mutation/genetics ; Clone Cells ; }, abstract = {How asexually reproducing organisms maintain genetic diversity and adaptive potential is a long-standing question in evolutionary biology. Asexual lineages have historically been thought of as evolutionary dead ends, yet some exhibit remarkable persistence through time. The gametophyte-only fern Vittaria appalachiana is a clonal eukaryote, the focus of extensive study due to its peculiar habit and life history, and is an excellent system to explore the consequences of asexuality. Using reduced representation sequencing and life cycle simulations, we assess theoretical expectations for genomic consequences of long-term asexual reproduction and test hypotheses about its origin and demographic history. We show that V. appalachiana colonies are not patches of single genotypes but are mosaics of genetic diversity, and the accumulation of mutations in the absence of recombination plays an important role in driving this diversity. We identify increased genomic variation, excess heterozygosity, decreased population differentiation, and increased effective population size, all of which are consistent with the expectations for prolonged clonality. Our analyses support the hypothesis that the loss of sexual reproduction in V. appalachiana occurred during the Last Glacial Maximum. Our results from empirical and simulation-based analyses illuminate how an asexual eukaryote generates, retains, and partitions genomic diversity.}, }
@article {pmid40042720, year = {2025}, author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y}, title = {Unraveling the multiple interactions between phages, microbes and flavor in the fermentation of strong-flavor Baijiu.}, journal = {Bioresources and bioprocessing}, volume = {12}, number = {1}, pages = {14}, pmid = {40042720}, issn = {2197-4365}, abstract = {The fermentation process of strong-flavor Baijiu represents a complex and unique ecosystem, characterized by the involvement of various microorganisms that drive intricate biochemical reactions, ultimately contributing to the distinct flavor profile of the Baijiu. Viruses may affect the succession of microorganisms and thus affect the style and quality of the product. However, the interaction between viruses and microorganisms during the fermentation of Baijiu is still unclear. Here we combined viral metagenomics and amplicon sequencing, physicochemical analysis, and GC-MS detection with temporal sampling to study the dynamics of viral and microbial communities, physicochemical properties, and flavor compounds during strong-flavor Baijiu fermentation. Viral metagenomic analysis revealed 513 viral operational taxonomic units (vOTUs), encompassing 34 viral families. Principal coordinates analysis (PCoA) demonstrated significant differences in vOTUs at different fermentation stages. Notably, the microbial community exhibited distinct succession patterns at various fermentation stages; it changed rapidly during the initial five days, with similarities observed between days 10 and 20. Volatile profile analysis identified 38 flavor components in fermented grains, comprising 16 ester compounds, 11 alcohols, and 8 acids, with the majority formed between days 10 and 30. The Spearman's rank correlation analysis revealed that Peduoviridae exhibited a negative correlation with Gluconobacter. Genomoviridae showed a negative correlation with Issatchenkia, Penicillium, and Monascus. These findings highlight the potential for complex interactions between viruses and microbial communities during Baijiu fermentation, underscoring the importance of considering viral communities in studies of the microbial ecology of fermented foods.}, }
@article {pmid40042334, year = {2025}, author = {Venturini, AM and Gontijo, JB and Berrios, L and Rodrigues, JLM and Peay, KG and Tsai, SM}, title = {Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0156124}, doi = {10.1128/spectrum.01561-24}, pmid = {40042334}, issn = {2165-0497}, abstract = {Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.}, }
@article {pmid40042126, year = {2025}, author = {Hayden, HS and Nelson, MT and Ross, SE and Verster, AJ and Bouzek, DC and Eng, A and Waalkes, A and Penewit, K and Kopp, BT and Siracusa, C and Rock, MJ and Salipante, SJ and Hoffman, LR and Sanders, DB}, title = {Effects of Therapeutic Antibiotic Exposure on the Oropharyngeal and Fecal Microbiota in Infants With Cystic Fibrosis.}, journal = {Pediatric pulmonology}, volume = {60}, number = {3}, pages = {e71024}, doi = {10.1002/ppul.71024}, pmid = {40042126}, issn = {1099-0496}, support = {//This work was supported by the Cystic Fibrosis Foundation (CFF; SANDER16Y5, SANDER18A0-I) and the National Institutes of Health (NIH; NIH NHLBI K24HL141669)./ ; }, mesh = {Humans ; *Cystic Fibrosis/microbiology/drug therapy ; *Feces/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Infant ; *Oropharynx/microbiology ; Male ; Female ; *Microbiota/drug effects ; beta-Lactams/pharmacology/therapeutic use ; Bacterial Load/drug effects ; Longitudinal Studies ; }, abstract = {BACKGROUND: Systemic antibiotics can impact all microbes inhabiting patients, regardless of the intended target organism(s). We studied the simultaneous effects on respiratory and fecal microbiomes of β-lactam antibiotics administered for respiratory symptoms in infants with cystic fibrosis (IWCF).<br><br>OBJECTIVE: To compare the magnitude and duration of intended (respiratory) and unintended (fecal) antimicrobial action by analyzing oropharyngeal (OP) and fecal microbiota in IWCF.<br><br>DESIGN: Shotgun metagenomic sequencing and qPCR were performed on OP and fecal samples collected longitudinally from 14 IWCF (ages 1-17 months) during ("On Antibiotics") and after ("Off Antibiotics") &#x3b2;-lactam therapy, and from 5 IWCF (3-16 months) never treated with antibiotics.<br><br>RESULTS: Total bacterial loads (TBL) for On Antibiotics samples were lower than for both Never (OP and fecal) and Off Antibiotics samples (fecal only). &#x3b1;-diversities (within-sample) for OP On Antibiotics samples were lower than for Never and Off Antibiotics samples but did not differ between fecal sample groups. &#x3b2;-diversity (between-sample) differed between all OP sample groups and between fecal On and Never Antibiotics and Off and Never antibiotics samples; however, fecal On and Off Antibiotics sample &#x3b2;-diversities did not differ. Patterns of change in antibiotic resistance gene abundances reflected shifts in microbial community composition.<br><br>CONCLUSIONS: &#x3b2;-lactam antibiotic exposure was followed by marked alterations in both OP and fecal microbiota. While microbiota appeared to rebound after treatment in both sample types, our results suggest that fecal microbiota recovered less than OP. The clinical consequences of these findings should be studied in IWCF and other populations frequently treated with antibiotics.}, }
@article {pmid40041876, year = {2025}, author = {Zhang, Y and Peng, J and Wang, Z and Zhou, F and Yu, J and Chi, R and Xiao, C}, title = {Metagenomic analysis revealed the bioremediation mechanism of lead and cadmium contamination by modified biochar synergized with Bacillus cereus PSB-2 in phosphate mining wasteland.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1529784}, pmid = {40041876}, issn = {1664-302X}, abstract = {INTRODUCTION: Phosphate mining wasteland is contaminated with heavy metals, such as lead (Pb) and cadmium (Cd), which pose significant environmental risks. Ecological restoration of these lands is crucial, but limited research has focused on the remediation of heavy metal-contaminated soils using modified biochar and functional microorganisms.<br><br>METHODS: In this study, we investigated the bioremediation of phosphate mining wasteland soil using modified biochar in combination with the phosphate-solubilizing bacterium Bacillus cereus. The effects of this synergistic approach on soil nutrient content, heavy metal immobilization, and microbial community structure were assessed.<br><br>RESULTS AND DISCUSSION: The results indicated that the available phosphate content in the soil increased by 59.32%. The content of extractable state Pb[2 +] and Cd[2 +] decreased by 65.06 and 71.26%, respectively. And the soil nutrient conditions were significantly improved. Synergistic remediation can significantly increase the diversity and abundance of soil microbial communities (p < 0.05). Janibacter, Lysobacter, Ornithinimicrobium, Bacillus, and Salinimicrobium were the main functional flora during soil remediation, with significant correlations for the promotion of Pb[2 +] and Cd[2 +] immobilization and the increase of available phosphate and organic matter. ZitB, czcD, zntA, and cmtR are the major heavy metal resistance genes and regulate metabolic pathways to make microbial community function more stable after soil remediation in phosphate mining wasteland.}, }
@article {pmid40041864, year = {2025}, author = {Brick, S and Niggemann, J and Reckhardt, A and Könneke, M and Engelen, B}, title = {Interstitial microbial communities of coastal sediments are dominated by Nanoarchaeota.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1532193}, pmid = {40041864}, issn = {1664-302X}, abstract = {Microbial communities in subsurface coastal sediments are highly diverse and play an important role in nutrient cycling. While the major fraction of microorganisms in sandy sediments lives as epipsammon (attached to sand grains), only a small fraction thrives in the interstitial porewaters. So far, little is known about the composition of these free-living microbial communities. In the subsurface of the sandy beach, investigated in this study, we compared the archaeal and bacterial community structures within sediments and corresponding porewaters applying 16S rRNA gene sequencing. We found that the free-living prokaryotes only had a proportion of about 0.2-2.3% of the bulk communities, depending on the pore space. The interstitial microbial communities showed a small overlap with the attached fraction of 4-7% ASVs, and comprised a unique composition of 75-81% ASVs found exclusively in the porewaters. They were more diverse than the respective sediment-attached fraction and showed a much higher archaea-to-bacteria ratio. The archaea were mainly affiliated to Nanoarchaeota of the DPANN superphylum, with a relative abundance up to 50% of the interstitial communities. The bacterial fraction included several species related to the Candidate Phyla Radiation (CPR). Both prokaryotic lineages are known to have small cell sizes, comprising not-yet cultured species with unidentified metabolic functions. Our findings were supported by the investigation of an adjacent tidal flat, showing a similar trend. Thus, our results indicate the presence of distinct interstitial microbial communities in the subsurface of coastal sediments. This natural enrichment of not-yet cultured Nanoarchaeota and members of the CPR provides the opportunity for targeted metagenomic analyses or even isolating members of these groups for further metabolic characterization.}, }
@article {pmid40041703, year = {2025}, author = {Sato, Y}, title = {Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf021}, pmid = {40041703}, issn = {2730-6151}, abstract = {Rumen deoxyribonucleic acid viruses that infect and replicate within bacteria and archaea are key modulators of the prokaryotic community. These viruses influence prokaryotic community abundance, composition, and function impacting host productivity and methane production. In this study, viral genomes were assembled from the rumen of 37 Japanese Black cattle using virus-like particle metagenome sequencing, providing insights into viral diversity, functional potential, and virus-host interactions. The relationship between the rumen deoxyribonucleic acid virome and carcass traits, particularly carcass weight and marbling, was also investigated. A total of 22 942 viral operational taxonomic units of medium-quality or higher (≥5 kb length and ≥ 50% completeness), referred to as Japanese Black Rumen Viral genomes, were reconstructed. Among these, 5973 putative novel genera were identified, significantly expanding the catalog of rumen viral genomes. Hosts were predicted for 2364 viral operational taxonomic units, including carbohydrate-degrading bacteria and methanogens. Additionally, 27 auxiliary metabolic genes were categorized as glycosyl hydrolases which are responsible for the degradation of cellulose, hemicellulose, and oligosaccharides, suggesting that rumen viruses may enhance the breakdown of complex carbohydrates during infection. Furthermore, the rumen virome differed considerably between high vs low carcass weight cattle and high vs low marbling cattle. Viruses associated with Methanobrevibacter were linked to higher carcass weight. This database and the insights from this study provide primary information for the development and improvement of beef production.}, }
@article {pmid40041700, year = {2025}, author = {Wang, X and Cao, D and Zhang, H and Chen, W and Sun, J and Hu, H}, title = {Utilizing metagenomic profiling and machine learning model to identify bacterial biomarkers for major depressive disorder.}, journal = {Frontiers in psychiatry}, volume = {16}, number = {}, pages = {1539596}, pmid = {40041700}, issn = {1664-0640}, abstract = {BACKGROUND: Major depressive disorder (MDD) is highly heterogeneous, which provides a significant challenge in the management of this disorder. However, the pathogenesis of major depressive disorder is not fully understood. Studies have shown that depression is highly correlated with gut flora. The objective of this study was to explore the potential of microbial biomarkers in the diagnosis of major depressive disorder.<br><br>METHODS: In this study, we used a metagenomic approach to analyze the composition and differences of gut bacterial communities in 36 patients with major depressive disorder and 36 healthy individuals. We then applied a Support Vector Machine Recursive Feature Elimination (SVM-RFE) machine learning model to find potential microbial markers.<br><br>RESULTS: Our results showed that the alpha diversity of the intestinal flora did not differ significantly in major depressive disorder compared to healthy populations. However, the beta diversity was significantly altered. Machine learning identified 8 MDD-specific bacterial biomarkers, with Alistipes, Dysosmobacter, Actinomyces, Ruthenibacterium, and Thomasclavelia being significantly enriched, while Faecalibacterium, Pseudobutyrivibrio, and Roseburia were significantly reduced, demonstrating superior diagnostic accuracy (area under the curve, AUC = 0.919). In addition, the gut bacteria performed satisfactorily in the validation cohort with an AUC of 0.800 (95% CI: 0.6334-0.9143).<br><br>CONCLUSION: This study reveals the complex relationship between gut microbiota and major depressive disorder and provides a scientific basis for the development of a microbiota-based diagnostic tool for depression.}, }
@article {pmid40041441, year = {2025}, author = {Xu, C and Shen, Y and Chen, S and Liu, T and Chen, X and Yu, Y and Liu, L and Ma, R and Zhang, L and Liu, X and Zhou, L and Zhu, G and Feng, S}, title = {Effect of Interpretation of Positive Metagenomic Next-Generation Sequencing Reports on the Infection Diagnosis in Patients With Hematological Disorders.}, journal = {Open forum infectious diseases}, volume = {12}, number = {2}, pages = {ofaf076}, pmid = {40041441}, issn = {2328-8957}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has become a crucial diagnostic tool for infectious diseases in patients with hematological disorders. However, despite the abundant microbial information provided by positive mNGS reports, interpreting these results remains challenging due to the lack of standardized criteria.<br><br>METHODS: We surveyed 92 clinicians to identify common challenges in understanding mNGS reports. Microbiologists then provided additional "report interpretation cards" (RICs) for positive mNGS results alongside original reports. The aim of using RICs was to determine whether each detected microorganism was likely cause of infection. After a 3-month period, a panel of clinical experts retrospectively reviewed 281 cases, involving 728 detected microorganisms, to assess RIC accuracy.<br><br>RESULTS: In total, 82.6% of clinicians (76 of 92) experienced difficulties in interpreting mNGS reports. After receiving RICs, 97.8% of clinicians (90 of 92) reported satisfaction. The overall concordance rates between interpretation and adjudication in the 281 cases was 79.0% (222 of 281). In 203 cases in which multiple microorganisms were detected, 37.9% (77 of 203) and 37.4% (76 of 203) were interpreted and adjudicated as mixed infections. Among the 728 microorganisms, interpretation and adjudication revealed concordance rates of 93.9% (154 of 164), 95.7% (88 of 92), and 72.3% (339 of 469) for bacterial, fungal, and viral infections, respectively. In 68.7% of the cases (193 of 281), mNGS positively influenced pathogen diagnosis.<br><br>CONCLUSIONS: Not all microorganisms detected by mNGS are responsible for infection, and appropriate interpretation is essential. The provision of interpretations by microbiologists aids clinicians in accurately using mNGS for infection diagnosis.}, }
@article {pmid40040800, year = {2025}, author = {He, J and Ye, L and Xu, H and Yang, H and Shen, J and Li, M and Weng, S and Jiao, D and Chu, C and Liao, Q and Zou, H and Zhu, J and Wang, C and Xu, X}, title = {Multi-omics analysis reveals a novel NFE2L3 variant impairing choroidal vasculature development in high myopia and myopic maculopathy.}, journal = {National science review}, volume = {12}, number = {2}, pages = {nwae291}, pmid = {40040800}, issn = {2053-714X}, }
@article {pmid40040609, year = {2025}, author = {Liu, FQ and An, ZY and Cui, LJ and Xiao, MY and Wu, YJ and Li, W and Zhang, BS and Yu, L and Feng, J and Liu, ZG and Feng, R and Jiang, ZX and Huang, RB and Jing, HM and Ren, JH and Zhu, XY and Cheng, YF and Li, YH and Zhou, HB and Gao, D and Liu, Y and Yu, F and Wang, X and Qiao, JL and Hu, DH and Wang, LL and Zang, MT and Chen, Q and Qu, QY and Zhou, JY and Li, ML and Chen, YX and Huang, QS and Fu, HX and Li, YY and Wang, QF and Huang, XJ and Zhang, XH and , }, title = {Correlation Between Fecal Microbiota and Corticosteroid Responsiveness in Primary Immune Thrombocytopenia: an Exploratory Study.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2410417}, doi = {10.1002/advs.202410417}, pmid = {40040609}, issn = {2198-3844}, support = {2023YFC2507803//Key Technologies Research and Development Program/ ; 82300149//National Natural Science Foundation of China/ ; 82130008//National Natural Science Foundation of China/ ; 82230004//National Natural Science Foundation of China/ ; 82350004//National Natural Science Foundation of China/ ; 82430006//National Natural Science Foundation of China/ ; 2024M761208//China Postdoctoral Science Foundation/ ; 2023ZB182//Department of Human Resources and Social Security of Jiangsu Province/ ; 2022-1-4082//Capital Health Research and Development of Special Fund/ ; 7242154//Natural Science Foundation of Beijing Municipality/ ; 7232188//Natural Science Foundation of Beijing Municipality/ ; 71003Y3035//Peking University Medicine/ ; }, abstract = {Corticosteroids (CSs) are the initial therapy for immune thrombocytopenia (ITP); however, their efficacy is not adequately predicted. As a novel biomarker, the composition of the gut microbiota is non-invasively tested and altered in patients with ITP. This study aims to develop a predictive model that leverages gut microbiome data to predict the CS response in patients with ITP within the initial four weeks of treatment. Metagenomic sequencing is performed on fecal samples from 212 patients with ITP, 152 of whom underwent CS treatment and follow-up. Predictive models are trained using six machine-learning algorithms, integrating clinical indices and gut microbiome data. The support vector machine (SVM) algorithm-based model has the highest accuracy (AUC = 0.80). This model utilized a comprehensive feature set that combined clinical data (including sex, age, duration, platelet count, and bleeding scales) with selected microbial species (including Bacteroides ovatus, Bacteroides xylanisolvens, and Parabacteroides gordonii), alpha diversities, KEGG pathways, and microbial modules. This study will provide new ideas for the prediction of clinical CS efficacy, enabling informed decision-making regarding the initiation of CS or personalized treatment in patients with ITP.}, }
@article {pmid40040342, year = {2025}, author = {Ren, M and Hu, A and Zhao, Z and Yao, X and Kimirei, IA and Zhang, L and Wang, J}, title = {Trait-environmental relationships reveal microbial strategies of environmental adaptation.}, journal = {Ecology}, volume = {106}, number = {3}, pages = {e70047}, doi = {10.1002/ecy.70047}, pmid = {40040342}, issn = {1939-9170}, support = {BK20240111//Basic Research Program of Jiangsu/ ; 067GJHZ2023034MI//the International Collaboration Program of Chinese Academy of Sciences/ ; 151542KYSB20210007//the International Collaboration Program of Chinese Academy of Sciences/ ; SAJC202403//the International Collaboration Program of Chinese Academy of Sciences/ ; 42002304//National Natural Science Foundation of China/ ; 42107445//National Natural Science Foundation of China/ ; 42225708//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; 92251304//National Natural Science Foundation of China/ ; 92351303//National Natural Science Foundation of China/ ; }, mesh = {*Lakes/microbiology ; *Adaptation, Physiological ; *Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Microbiota ; Hydrogen-Ion Concentration ; }, abstract = {Microbial trait variation along environmental gradients is crucial to understanding their ecological adaptation mechanisms. With the increasing availability of microbial genomes, making full use of the genome-based traits to decipher their adaptation strategies becomes promising and urgent. Here, we examined microbial communities in water and sediments of 20 East African lakes with pH values ranging from 7.2 to 10.1 through taxonomic profiling and genome-centric metagenomics. We identified functional traits important for microbial adaptation to the stresses of alkalinity and salinity based on the significant trait-environment relationships (TERs), including those involved in cytoplasmic pH homeostasis, compatible solute accumulation, cell envelope modification, and energy requisition. By integrating these significant traits, we further developed an environmental adaptation index to quantify the species-level adaptive capacity for environmental stresses, such as high pH environments. The adaptation index of pH showed consistently significant positive relationships with species pH optima across regional and global genomic datasets from freshwater, marine, and soda lake ecosystems. The generality of the index for quantifying environmental adaptation was demonstrated by showing significant relationships with the species niche optima for the gradients of soil temperature and seawater salinity. These results highlight the importance of TERs in facilitating the inference of microbial genomic-based adaptation mechanisms and expand our understanding of ecological adaptive strategies along environmental gradients.}, }
@article {pmid40038896, year = {2025}, author = {Zhang, H and Ruan, Y and Kuzyakov, Y and Sun, H and Huang, Q and Guo, S and Shen, Q and Ling, N}, title = {Viruses Facilitate Energy Acquisition Potential by Their Bacterial Hosts in Rhizosphere of Grafted Plants.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.15458}, pmid = {40038896}, issn = {1365-3040}, support = {//This study was supported by the National Nature Science Foundation of China (32302670) and Nanjing Agricultural University (XUEKEN2023039)./ ; }, abstract = {Viruses alter the ecological and evolutionary trajectories of bacterial host communities. Plant grafting is a technique that integrates two species or varietiies and have consequences on the rhizosphere functioning. The grafting effects on the taxonomic and functional assembly of viruses and their bacterial host in the plant rhizosphere remain largely elusive. Using shotgun metagenome sequencing, we recover a total of 1441 viral operational taxonomic units from the rhizosphere of grafted and ungrafted plants after 8-year continuous monoculture. In the grafted and ungrafted rhizosphere, the Myoviridae, Zobellviridae and Kyanoviridae emerged as the predominant viral families, collectively representing around 40% of the viral community in each respective environment. Grafting enriched the members in viral family Kyanoviridae, Tectiviridae, Peduoviridae and Suoliviridae, and auxiliary metabolic genes related to pyruvate metabolism and energy acquisition (e.g., gloB, DNMT1 and dcyD). The virus-bacterial interactions increased the rapid growth potential of bacteria, which explains the strong increase in abundance of specific bacterial hosts (i.e., Chitinophagaceae, Cyclobacteriaceae and Spirosomaceae) in the grafted-plant rhizosphere. Overall, these results deepen our understanding of microbial community assembly and ecological services from the perspective of virus-host interactions.}, }
@article {pmid40038838, year = {2025}, author = {Thiruppathy, D and Moyne, O and Marotz, C and Williams, M and Navarro, P and Zaramela, L and Zengler, K}, title = {Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {65}, pmid = {40038838}, issn = {2049-2618}, support = {S10 OD026929/NH/NIH HHS/United States ; S10 OD026929/NH/NIH HHS/United States ; }, mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Bacterial Load ; Healthy Volunteers ; Adult ; Female ; Male ; }, abstract = {BACKGROUND: As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowledge of the skin microbiome. However, current characterizations do not discriminate between DNA from live cells and remnant DNA from dead organisms (relic DNA), resulting in a combined readout of all microorganisms that were and are currently present on the skin rather than the actual living population of the microbiome. Additionally, most methods lack the capability for absolute quantification of the microbial load on the skin, complicating the extrapolation of clinically relevant information.<br><br>RESULTS: Here, we integrated relic-DNA depletion with shotgun metagenomics and bacterial load determination to quantify live bacterial cell abundances across different skin sites. Though we discovered up to 90% of microbial DNA from the skin to be relic DNA, we saw no significant effect of this on the relative abundances of taxa determined by shotgun sequencing. Relic-DNA depletion prior to sequencing strengthened underlying patterns between microbiomes across volunteers and reduced intraindividual similarity. We determined the absolute abundance and the fraction of population alive for several common skin taxa across body sites and found taxa-specific differential abundance of live bacteria across regions to be different from estimates generated by total DNA (live&#x2009;+&#x2009;dead) sequencing.<br><br>CONCLUSIONS: Our results reveal the significant bias relic DNA has on the quantification of low biomass samples like the skin. The reduced intraindividual similarity across samples following relic-DNA depletion highlights the bias introduced by traditional (total DNA) sequencing in diversity comparisons across samples. The divergent levels of cell viability measured across different skin sites, along with the inconsistencies in taxa differential abundance determined by total vs live cell DNA sequencing, suggest an important hypothesis for certain sites being susceptible to pathogen infection. Overall, our study demonstrates a characterization of the skin microbiome that overcomes relic-DNA bias to provide a baseline for live microbiota that will further improve mechanistic studies of infection, disease progression, and the design of therapies for the skin. Video Abstract.}, }
@article {pmid40038823, year = {2025}, author = {Liu, F and Yang, J and Shen, W and Fu, J and Meng, J and Zhang, Y and Li, J and Yuan, Z}, title = {Effects of drainage and long-term tillage on greenhouse gas fluxes in a natural wetland: insights from microbial mechanisms.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {26}, pmid = {40038823}, issn = {2524-6372}, support = {No. ES202308//Open Project of State Key Laboratory of Urban Water Resource and Environment/ ; No. 2024M763244//China Postdoctoral Science Foundation/ ; No. 242300421652//Natural Science Foundation of Henan Province/ ; No. 30501300//Top Talent Foundation of Henan Agricultural University/ ; }, abstract = {BACKGROUND: The conversion of natural wetlands to agricultural land through drainage contributes to 62% of the global wetland loss. Such conversion significantly alters greenhouse gas (GHG) fluxes, yet the underlying mechanisms of GHG fluxes resulting from drainage and long-term tillage practices remain highly uncertain. In this study, we measured GHG fluxes of a natural reed wetland (referred to as "Wetland") and a drained wetland that used as farmland (referred to as "Dryland").<br><br>RESULTS: The results demonstrated that annual cumulative N2O and CO2 fluxes in Dryland were 282.77% and 53.79% higher than those in Wetland, respectively. However, CH4 annual cumulative fluxes decreased from 12,669.45&#x2009;&#xb1;&#x2009;564.69&#xa0;kg&#xb7;ha[-&#x2009;1] to 8,238.40&#x2009;&#xb1;&#x2009;207.72&#xa0;kg&#xb7;ha[-&#x2009;1] in Dryland compared to Wetland. The global warming potential (GWP) showed no significant difference between Dryland and Wetland, with comparable average rates of 427.50&#x2009;&#xb1;&#x2009;48.83 and 422.21&#x2009;&#xb1;&#x2009;73.59&#xa0;mg&#xb7;CO2-eq&#xb7;m[-&#x2009;2]&#xb7;h[-&#x2009;1], respectively. Metagenomic analysis showed a decrease in the abundance of acetoclastic methanogens and their functional genes responsible for CH4 production. Functional genes related to CH4 oxidation (pmoA) and gene related to N2O reduction (nosZ) exhibited a substantial sensitivity to variations in TOC concentration (p&#x2009;<&#x2009;0.05). Candidatus Methylomirabilis, belonging to the NC10 phylum, was identified as the dominant methanotroph and accounted for 49.26% of the methanotrophs. Its relative abundance was significantly higher in Dryland than in Wetland, as the nitrogenous fertilizer applied in Dryland acted as an electron acceptor, with the nearby Wetland produced CH4 serving as an electron donor. This suggests that Dryland may act as a CH4 sink, despite the significant enhancement in CO2 and N2O fluxes.<br><br>CONCLUSIONS: In conclusion, this study provides insights into the influence of drainage and long-term tillage on GHG fluxes in wetlands and their contribution to global warming.}, }
@article {pmid40038809, year = {2025}, author = {Reyes, G and Betancourt, I and Andrade, B and Pozo, Y and Sorroza, L and Trujillo, LE and Bayot, B}, title = {Genomic sequence data of Thiohalocapsa marina: a sulfur-oxidizing bacterium prevalent in treated municipal wastewater and commercial shrimp hatchery effluents.}, journal = {BMC research notes}, volume = {18}, number = {1}, pages = {97}, pmid = {40038809}, issn = {1756-0500}, mesh = {*Wastewater/microbiology ; Animals ; *Genome, Bacterial ; *Sulfur/metabolism ; Oxidation-Reduction ; Biodegradation, Environmental ; Chlorobi/genetics/metabolism ; Aquaculture ; Penaeidae/microbiology ; Phylogeny ; }, abstract = {OBJECTIVES: This study highlighted the gap in the genetic characterization of marine bacteria, specifically within the genus Thiohalocapsa. This genus thrives in contaminated environments with high concentrations of sulfide, such as treated municipal wastewater. Thc. marina is a phototrophic purple bacterium known for its role in sulfur oxidation and bioremediation in marine aquaculture systems. To date, only one Thc. marina genome has been published in the GenBank database. This study enhances the understanding of the ecological adaptation and bioremediation capabilities of Thc. marina in treated municipal wastewater effluents.<br><br>DATA DESCRIPTION: We present a draft genome of Thc. marina LNA26 recovered from treated municipal wastewater effluents using shotgun metagenomic sequencing. The genome of Thc. marina LNA26 harbors 4,356,720 bp and contains 4,032 genes (3,936 CDSs, 50 RNA genes, and 46 pseudogenes), some of them involved in sporulation, siderophores biosynthesis, arsenate bioremediation, sulfide metabolism, capacity for nitrogen fixation, the biosynthesis of PHA, and NHPL bacteriocins. Thc. marina LNA26 exhibits 3 CRISPR Arrays and a high abundance of COGs in signal transduction, energy production, and cell wall biogenesis, indicating advanced environmental responsiveness, energy efficiency, and cellular robustness.}, }
@article {pmid40038603, year = {2025}, author = {Gao, M and Zhong, S and Han, G and Kuang, D and Yun, C and Fu, C}, title = {Atypical rat bite fever associated with knee joint infection in a Chinese patient: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {312}, pmid = {40038603}, issn = {1471-2334}, mesh = {*Rat-Bite Fever/microbiology/diagnosis/drug therapy ; Humans ; *Streptobacillus/isolation &amp; purification/genetics ; *Knee Joint/microbiology/pathology ; Animals ; Male ; *Anti-Bacterial Agents/therapeutic use ; *RNA, Ribosomal, 16S/genetics ; Synovial Fluid/microbiology ; Arthroscopy ; China ; Middle Aged ; Rats ; East Asian People ; }, abstract = {BACKGROUND: Rat bite fever (RBF) is a rare zoonosis transmitted from rodents to humans through bites and scratches. However, diagnosis and treatment of atypical clinical cases can be challenging.<br><br>CASE PRESENTATION: Herein, we report an atypical case of RBF with unilateral knee joint infection caused by Streptobacillus moniliformis. Streptobacillus moniliformis was isolated from the knee synovial fluid of the patient via microbiological culture and metagenomic next-generation sequencing (mNGS). After treatment with antibiotics and arthroscopic surgery, the patient reported symptom alleviation and was subsequently discharged home. This is the first reported detection of intraarticular histopathological changes caused by Streptobacillus moniliformis during knee arthroscopy.<br><br>CONCLUSIONS: In atypical cases, importantly, clinical healthcare professionals should promptly obtain microbiological culture results. When culture is negative, 16S ribosomal RNA gene polymerase chain reaction (16S rRNA PCR) or mNGS can be considered for identification, with inquiring about the patient's disease history, including any contact with rodents. Surgical interventions, such as arthroscopy, may be included in treatment. Streptobacillus moniliformis infection should be considered when considerable fibrous connective tissue and capillary proliferation are observed under arthroscopic guidance.}, }
@article {pmid40038315, year = {2025}, author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C}, title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {378}, pmid = {40038315}, issn = {2052-4463}, support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//&#xc9;cole Nationale d'Ing&#xe9;nieurs de Saint-Etienne (National Engineering School of Saint-&#xc9;tienne)/ ; }, mesh = {China ; *Microbiota ; *Archaea/genetics ; *Bacteria/genetics/classification ; *Bays ; Seawater/microbiology ; Metagenome ; Multiomics ; }, abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.}, }
@article {pmid38892504, year = {2024}, author = {Duysburgh, C and Govaert, M and Guillemet, D and Marzorati, M}, title = {Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties.}, journal = {Nutrients}, volume = {16}, number = {11}, pages = {}, pmid = {38892504}, issn = {2072-6643}, mesh = {*Gastrointestinal Microbiome ; *Prebiotics ; *Gum Arabic/therapeutic use ; *Adansonia ; *Plant Preparations/therapeutic use ; Metabolome ; Metagenome ; Colon/microbiology ; }, abstract = {Arabic gum, a high molecular weight heteropolysaccharide, is a promising prebiotic candidate as its fermentation occurs more distally in the colon, which is the region where most chronic colonic diseases originate. Baobab fiber could be complementary due to its relatively simple structure, facilitating breakdown in the proximal colon. Therefore, the current study aimed to gain insight into how the human gut microbiota was affected in response to long-term baobab fiber and Arabic gum supplementation when tested individually or as a combination of both, allowing the identification of potential complementary and/or synergetic effects. The validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), an in vitro gut model simulating the entire human gastrointestinal tract, was used. The microbial metabolic activity was examined, and quantitative 16S-targeted Illumina sequencing was used to monitor the gut microbial composition. Moreover, the effect on the gut microbial metabolome was quantitatively analyzed. Repeated administration of baobab fiber, Arabic gum, and their combination had a significant effect on the metabolic activity, diversity index, and community composition of the microbiome present in the simulated proximal and distal colon with specific impacts on Bifidobacteriaceae and Faecalibacterium prausnitzii. Despite the lower dosage strategy (2.5 g/day), co-supplementation of both compounds resulted in some specific synergistic prebiotic effects, including a biological activity throughout the entire colon, SCFA synthesis including a synergy on propionate, specifically increasing abundance of Akkermansiaceae and Christensenellaceae in the distal colon region, and enhancing levels of spermidine and other metabolites of interest (such as serotonin and ProBetaine).}, }
@article {pmid40038282, year = {2025}, author = {Li, Z and Riley, WJ and Marschmann, GL and Karaoz, U and Shirley, IA and Wu, Q and Bouskill, NJ and Chang, KY and Crill, PM and Grant, RF and King, E and Saleska, SR and Sullivan, MB and Tang, J and Varner, RK and Woodcroft, BJ and Wrighton, KC and ,  and Brodie, EL}, title = {A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2186}, pmid = {40038282}, issn = {2041-1723}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; SCW1746//DOE | Office of Science (SC)/ ; DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; (#FP00005182//DOE | Office of Science (SC)/ ; 2022070//National Science Foundation (NSF)/ ; }, mesh = {*Ecosystem ; *Methane/metabolism ; *Genomics/methods ; *Microbiota/genetics ; Arctic Regions ; Metagenomics/methods ; Wetlands ; Greenhouse Gases/metabolism ; Climate Change ; Bacteria/genetics/metabolism/classification ; }, abstract = {Microbes drive the biogeochemical cycles of earth systems, yet the long-standing goal of linking emerging genomic information, microbial traits, mechanistic ecosystem models, and projections under climate change has remained elusive despite a wealth of emerging genomic information. Here we developed a general genome-to-ecosystem (G2E) framework for integrating genome-inferred microbial kinetic traits into mechanistic models of terrestrial ecosystems and applied it at a well-studied Arctic wetland by benchmarking predictions against observed greenhouse gas emissions. We found variation in genome-inferred microbial kinetic traits resulted in large differences in simulated annual methane emissions, quantitatively demonstrating that the genomically observable variations in microbial capacity are consequential for ecosystem functioning. Applying microbial community-aggregated traits via genome relative-abundance-weighting gave better methane emissions predictions (i.e., up to 54% decrease in bias) compared to ignoring the observed abundances, highlighting the value of combined trait inferences and abundances. This work provides an example of integrating microbial functional trait-based genomics, mechanistic and pragmatic trait parameterizations of diverse microbial metabolisms, and mechanistic ecosystem modeling. The generalizable G2E framework will enable the use of abundant microbial metagenomics data to improve predictions of microbial interactions in many complex systems, including oceanic microbiomes.}, }
@article {pmid40038255, year = {2025}, author = {Cui, B and Luo, H and He, B and Liu, X and Lv, D and Zhang, X and Su, K and Zheng, S and Lu, J and Wang, C and Yang, Y and Zhao, Z and Liu, X and Wang, X and Zhao, Y and Nie, X and Jiang, Y and Zhang, Z and Liu, C and Chen, X and Cai, A and Lv, Z and Liu, Z and An, F and Zhang, Y and Yan, Q and Kelley, KW and Xu, G and Xu, L and Liu, Q and Peng, F}, title = {Gut dysbiosis conveys psychological stress to activate LRP5/β-catenin pathway promoting cancer stemness.}, journal = {Signal transduction and targeted therapy}, volume = {10}, number = {1}, pages = {79}, pmid = {40038255}, issn = {2059-3635}, support = {82373096//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82473131//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Low Density Lipoprotein Receptor-Related Protein-5/genetics/metabolism ; Animals ; Mice ; *Gastrointestinal Microbiome ; Humans ; *Dysbiosis/genetics/microbiology/metabolism ; Female ; *beta Catenin/genetics/metabolism ; *Stress, Psychological/genetics/microbiology/metabolism ; Neoplastic Stem Cells/metabolism/pathology ; Wnt Signaling Pathway/genetics ; Breast Neoplasms/genetics/metabolism/pathology/microbiology ; }, abstract = {Psychological stress causes gut microbial dysbiosis and cancer progression, yet how gut microbiota determines psychological stress-induced tumor development remains unclear. Here we showed that psychological stress promotes breast tumor growth and cancer stemness, an outcome that depends on gut microbiota in germ-free and antibiotic-treated mice. Metagenomic and metabolomic analyses revealed that psychological stress markedly alters the composition and abundance of gut microbiota, especially Akkermansia muciniphila (A. muciniphila), and decreases short-chain fatty acid butyrate. Supplement of active A. muciniphila, butyrate or a butyrate-producing high fiber diet dramatically reversed the oncogenic property and anxiety-like behavior of psychological stress in a murine spontaneous tumor model or an orthotopic tumor model. Mechanistically, RNA sequencing analysis screened out that butyrate decreases LRP5 expression to block the activation of Wnt/β-catenin signaling pathway, dampening breast cancer stemness. Moreover, butyrate as a HDAC inhibitor elevated histone H3K9 acetylation level to transcriptionally activate ZFP36, which further accelerates LRP5 mRNA decay by binding adenine uridine-rich (AU-rich) elements of LRP5 transcript. Clinically, fecal A. muciniphila and serum butyrate were inversely correlated with tumoral LRP5/β-catenin expression, poor prognosis and negative mood in breast cancer patients. Altogether, our findings uncover a microbiota-dependent mechanism of psychological stress-triggered cancer stemness, and provide both clinical biomarkers and potential therapeutic avenues for cancer patients undergoing psychological stress.}, }
@article {pmid40038232, year = {2025}, author = {Gohar, M and Shaheen, N and Goyal, SM and Mor, SK and Rodriguez-R, LM and Imran, M}, title = {Probiotic Potential of Yeast, Mold, and Intermediate Morphotypes of Geotrichum candidum in Modulating Gut Microbiota and Body Physiology in Mice.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40038232}, issn = {1867-1314}, support = {No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; MPC-2022-02167//OeAD-GmbH, Austria &#x301;s Agency for Education and Internationalization/ ; MPC-2022-02167//OeAD-GmbH, Austria &#x301;s Agency for Education and Internationalization/ ; No. PSF/CRP/C-QU/T-Helix (70)//Pakistan Science Foundation (PSF) Research/ ; }, abstract = {Geotrichum candidum, a polymorphic fungus, exists in yeast, mold, and intermediate morphotypes, each with varying genome sizes and phenotypic traits. While G. candidum has been studied as a probiotic in dairy cattle and aquaculture, the differential probiotic potential of its morphotypes has not been fully investigated; therefore, the current study was designed to investigate their impact on the modulation of physiological and gut microbial diversity in BALB/c male mice. In this study, four strains of G. candidum were used, comprising two yeast morphotypes (QAUGC01 and UCMA3730), one mold morphotype (UCMA103), and one intermediate morphotype (UCMA91). BALB/c male mice were administered G. candidum yeast, intermediate, and mold morphotypes via drinking water for 4 weeks. After 4 weeks of experimentation, the yeast morphotype (QAUGC01) notably facilitated healthy weight gain compared to other groups. This was accompanied by significant increases in red blood cell count (p = 0.01). Importantly, QAUGC01 showed no detrimental effects on kidney function, as evidenced by significantly reduced CPK levels (77.25 ± 4.87 U/L) and low cholesterol levels (64.75 ± 0.83 mg/dL). Metagenomic analysis revealed that Firmicutes, Bacteroidetes, and Proteobacteria were predominant bacterial phyla, while Ascomycota and Basidiomycota dominated the fungal populations. Lactobacillus and Bifidobacterium were prominent in the gastrointestinal tract of QAUGC01-treated mice, while Lactococcus correlated with intermediate and mold morphotypes. Predictive functional annotation (PICRUSt2) has revealed the maximum relative abundance of metabolic pathways in mold and intermediate-supplemented mice gut. In contrast, the yeast morphotype (UCMA3730) exhibited a higher metabolic pathway activity in the large intestine. Conclusively, yeast morphotypes increase beneficial bacterial diversity, including Brevibacillus and Bacillus, particularly lactic acid bacteria throughout the gastrointestinal tract. These findings suggest that different G. candidum morphotypes have distinct probiotic potentials, with implications for enhancing gut health in food and feed applications.}, }
@article {pmid40038088, year = {2025}, author = {Leung, MBW and Chan, DYL and Fok, EKL and Yim, HCH and Jiang, X and Li, TC}, title = {Semen metagenomics and spent culture media in patients undergoing conventional in vitro fertilisation: abridged secondary publication.}, journal = {Hong Kong medical journal = Xianggang yi xue za zhi}, volume = {31 Suppl 1}, number = {1}, pages = {45-47}, pmid = {40038088}, issn = {1024-2708}, }
@article {pmid40037896, year = {2025}, author = {Chen, N and Kishida, K and Stari, L and Moriuchi, R and Ohtsubo, Y and Damborsky, J and Nagata, Y}, title = {Haloalkane dehalogenases other than LinB can contribute to the γ-hexachlorocyclohexane utilization.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/bbb/zbaf022}, pmid = {40037896}, issn = {1347-6947}, abstract = {Haloalkane dehalogenases (HLDs) convert halogenated compounds to corresponding alcohols by a simple hydrolytic mechanism. Although many bacterial strains possess HLDs or HLD homologues, LinB is the only HLD known to be involved in the utilization of γ-hexachlorocyclohexane (γ-HCH), a man-made chlorinated pesticide. In this study, to gain insight into the functional evolution of HLDs toward the γ-HCH utilization, the linB gene in γ-HCH-degrading Sphingobium japonicum strain UT26 was replaced by 7 other HLD or HLD homologous genes, including 3 putative ancestral enzymes. Interestingly, strains carrying genes for DmmA from marine metagenome or Rluc_anc, an ancestor of Renilla-luciferin 2-monooxygenase (Rluc) and LinB, produced 2,5-dichlorophenol and 2,5-dichlorohydroquinone from γ-HCH, which are indicators of LinB activity, and grew in minimal medium supplied with γ-HCH as a sole carbon source. These results indicated that other HLDs in addition to LinB can play roles in the γ-HCH utilization.}, }
@article {pmid40037607, year = {2025}, author = {Antaliya, K and Godhaniya, M and Galawala, J and Vansia, A and Mangrola, A and Ghelani, A and Patel, R}, title = {Microbial community transition in Surti buffalo-based fermented formulations sustainably enhances soil fertility and plant growth.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovaf030}, pmid = {40037607}, issn = {1472-765X}, abstract = {This study investigates the role of microbial dynamics during the fermentation of Buffalo dung and urine-fermented plant growth-promoting formulation, a natural biofertilizer, and its impact on plant growth and soil health. This formulation was prepared using Surti buffalo dung, urine, jaggery, gram flour, and soil and fermented for up to 14 days. Metagenomic analysis revealed microbial succession from a diverse initial community to a Bacillus-dominated population, especially the Lactic Acid Bacteria, after eight days of fermentation. The changes were accompanied by increases in the plant growth-promoting genes related to nutrient acquisition, phytohormone production, and stress resistance. The pot experiment revealed a significant increase in mung bean growth, with the maximum effect obtained from the 8th-day fermented formulation. The experiment showed considerable improvement in the physicochemical properties of soil, including increased organic carbon and nutrient availability. These findings underscore the ecological importance of microbial input preparation in enhancing soil fertility and plant growth sustainably. Future research should delve deeper into the specific mechanisms these microbes facilitate nutrient cycling and resilience in various agroclimatic conditions.}, }
@article {pmid40037564, year = {2025}, author = {Miller, SJ and Zhang, F and Taylor, S and Woodman, R and Shoubridge, AP and Papanicolas, LE and Rogers, GB}, title = {Oropharyngeal Staphylococcus aureus is linked to higher mortality in long-term aged care residents.}, journal = {Age and ageing}, volume = {54}, number = {3}, pages = {}, doi = {10.1093/ageing/afaf042}, pmid = {40037564}, issn = {1468-2834}, support = {//Australian Medical Research Future Fund/ ; GNT1152268//Australian Department of Health/ ; //Australian Department of Health/ ; GNT119378//National Health and Medical Research Council/ ; //Matthew Flinders Professorial Fellowship/ ; GNT2008625//NHMRC Emerging Leadership/ ; }, mesh = {Humans ; Male ; Female ; *Staphylococcal Infections/mortality/microbiology/diagnosis ; Aged, 80 and over ; Aged ; *Staphylococcus aureus/isolation &amp; purification ; *Oropharynx/microbiology ; *Homes for the Aged/statistics &amp; numerical data ; Risk Factors ; South Australia/epidemiology ; Nursing Homes/statistics &amp; numerical data ; Age Factors ; Long-Term Care/statistics &amp; numerical data ; Carrier State/microbiology/diagnosis ; Time Factors ; Metagenomics ; Microbiota ; Comorbidity ; Cause of Death ; Risk Assessment ; Methicillin-Resistant Staphylococcus aureus/isolation &amp; purification ; }, abstract = {BACKGROUND: Biological ageing, healthcare interactions, and pharmaceutical and environmental exposures in later life alter the characteristics of the oropharyngeal (OP) microbiome. These changes, including an increased susceptibility to colonisation by pathobiont species, have been linked with diverse health outcomes.<br><br>OBJECTIVES: To investigate the relationship between OP microbiome characteristics and all-cause mortality in long-term aged care residents.<br><br>METHODS: OP swabs were collected from 190 residents of five aged care facilities in South Australia. Microbiota composition was assessed by shotgun metagenomics and related to health outcomes during a 12-month follow-up period. OP carriage of Staphylococcus aureus and methicillin resistance was confirmed by qPCR.<br><br>RESULTS: OP carriage of S. aureus was identified in 13 (6.8%) residents. Detection of S. aureus was significantly associated with an increased risk of mortality (adjusted HR [95% CI]: 9.7 [3.8-24.9], P&#x2009;<&#x2009;.0001), compared with non-carriers, independent of methicillin resistance. Staphylococcus aureus carriage demonstrated a stronger association with mortality risk than the total number of comorbidities at the univariate level (S. aureus HR [95% CI]: 7.2 [3.4-15.5], P&#x2009;<&#x2009;.0001 vs. comorbidity count HR [95% CI]: 1.1 [1.0-1.3], P&#x2009;=&#x2009;.03), and remained significant after multivariable adjustment. Staphylococcus aureus detection was significantly associated with total number of comorbidities (adjusted OR [95% CI]: 1.4 [1.0-2.0], P&#x2009;=&#x2009;.04).<br><br>CONCLUSION: OP S. aureus carriage predicts all-cause mortality in long-term aged care. We speculate that S. aureus carriage represents a marker of general health, including prior healthcare exposures. OP S. aureus carriage could contribute to estimations of general health in older individuals and thereby inform care strategies.}, }
@article {pmid40037293, year = {2025}, author = {Delherbe, NA and Gomez, O and Plominsky, AM and Oliver, A and Manzanera, M and Kalyuzhnaya, MG}, title = {Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf026}, pmid = {40037293}, issn = {1751-7370}, abstract = {Drylands cover one-third of the Earth's surface and are one of the largest terrestrial sinks for methane. Understanding the structure-function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors-water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 to 12.73 μmol m2 h-1, peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum, two Methylobacter, and uncultivated Methylococcaceae). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum. Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.}, }
@article {pmid40037072, year = {2025}, author = {Meng, JX and Li, MH and Wang, XY and Li, S and Zhang, Y and Ni, HB and Ma, H and Liu, R and Yan, JC and Li, XM and Sun, YZ and Yang, X and Zhang, XX}, title = {Temporal variability in the diversity, function and resistome landscapes in the gut microbiome of broilers.}, journal = {Ecotoxicology and environmental safety}, volume = {292}, number = {}, pages = {117976}, doi = {10.1016/j.ecoenv.2025.117976}, pmid = {40037072}, issn = {1090-2414}, abstract = {Understanding the dynamic and stability of gut microbiota over the course of production cycle of broiler chicken can help identify microbial features that associate with better health and productivity. In the present study, we profile the changes in the composition and stability of gut microbiota of commercially raised broilers at nine distinct time points using shotgun metagenomics and culturomics approaches. We demonstrate, within the first week post-hatching, a rapid decline in relative abundance of 122 pioneer microbial species including Bacteroides fragilis, Lachnospira eligens and Ruminococcus gnavus, accompanied by a substantial decrease in both microbial richness and diversity. This was followed by a gradual increase and stabilization in the microbial diversity and population structure that persisted until the broilers reached the marketing age. Throughout the production cycle, key bacterial families such as Lachnospiraceae, Bacteroidaceae, and Ruminococcaceae were identified. However, significant shifts at the lower taxonomic levels occurred at different production stages, influencing the functional capacities and resistance profiles of the microbiota. During the rapid growth phase, enzymes crucial to vitamin and amino acid metabolism dominated, whereas enzymes associated with carbohydrate and energy metabolism were notably more abundant during the fattening stage. Many predicted antibiotic resistance genes were detected in association with typical commensal bacterial species in the gut microbiota, indicating a sustained resistance of the gut microbiota to antibiotic classes such as aminoglycosides and tetracyclines, which persist even in the absence of antibiotic selection pressure. Our research carries important implications for the management and health surveillance of broiler production.}, }
@article {pmid40036691, year = {2025}, author = {Gao, Y and Luo, H and Lyu, H and Yang, H and Yousuf, S and Huang, S and Liu, YX}, title = {Benchmarking short-read metagenomics tools for removing host contamination.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf004}, pmid = {40036691}, issn = {2047-217X}, support = {2024M753580//China Postdoctoral Science Foundation/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; }, mesh = {*Metagenomics/methods ; *Benchmarking ; Microbiota/genetics ; Humans ; DNA Contamination ; Metagenome ; Software ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; }, abstract = {BACKGROUND: The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences.<br><br>RESULTS: In this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools.<br><br>CONCLUSIONS: Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.}, }
@article {pmid40036505, year = {2025}, author = {Langenfeld, K and Hegarty, B and Vidaurri, S and Crossette, E and Duhaime, MB and Wigginton, KR}, title = {Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.}, journal = {Nucleic acids research}, volume = {53}, number = {5}, pages = {}, doi = {10.1093/nar/gkaf118}, pmid = {40036505}, issn = {1362-4962}, support = {1&#xa0;545&#xa0;756//NSF/ ; //University of Michigan Integrated Training in Microbial Systems (ITiMS)/ ; //University of Michigan/ ; //NSF/ ; //ITiMS/ ; //Burroughs Wellcome Fund/ ; }, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Humans ; Wastewater/virology/microbiology ; DNA Viruses/genetics ; DNA, Viral/genetics ; Bacteriophages/genetics ; Genome, Viral/genetics ; Viruses/genetics ; }, abstract = {Quantitative metagenomic methods are maturing but continue to lack clearly-defined analytical limits. Here, we developed a computational tool, QuantMeta, to determine the absolute abundance of targets in metagenomes spiked with synthetic DNA standards. The tool establishes (i) entropy-based detection thresholds to confidently determine the presence of targets, and (ii) an approach to identify and correct read mapping or assembly errors and thus improve the quantification accuracy. Together this allows for an approach to confidently quantify absolute abundance of targets, be they microbial populations, genes, contigs, or metagenome-assembled genomes. We applied the approach to quantify single- and double-stranded DNA viruses in wastewater viral metagenomes, including pathogens and bacteriophages. Concentrations of total DNA viruses in wastewater influent and effluent were >108 copies/ml using QuantMeta. Human-associated DNA viruses were detected and quantifiable with QuantMeta thresholds, including polyomavirus, papillomavirus, and crAss-like phages, at concentrations similar to previous reports that utilized quantitative polymerase chain reaction (PCR)-based assays. Our results highlight the higher detection thresholds of quantitative metagenomics (approximately 500 copies/μl) as compared to PCR-based quantification (approximately 10 copies/μl) despite a sequencing depth of 200 million reads per sample. The QuantMeta approach, applicable to both viral and cellular metagenomes, advances quantitative metagenomics by improving the accuracy of measured target absolute abundances.}, }
@article {pmid40036345, year = {2025}, author = {Hemeda, AA and Zahran, SA and Tammam, MA and Ewida, MA and Kashef, MT and Yassin, AS and Mitra, A and Youssef, NH and Elshahed, MS}, title = {Metagenomic mining unveils a novel GH130 enzyme with exclusive xylanase activity over a wide temperature and pH ranges.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jimb/kuaf006}, pmid = {40036345}, issn = {1476-5535}, abstract = {The equine gut harbours a diverse microbial community and represents a rich source of carbohydrate-active enzymes (CAZymes). To identify and characterize potentially novel CAZymes from a horse's hindgut metagenome, shotgun metagenomic sequencing was performed on DNA extracted from a stool sample of a male horse followed by CAZyme annotation. Here, we report on the characterization of a novel enzyme (AH2) that was identified, synthesized, cloned and characterized from the obtained CAZyme dataset. AH2 was identified as a GH130 family member and displayed an exclusive xylanase activity, a trait hitherto unreported in prior characterization of GH130 CAZymes. AH2 displayed an optimal activity at a pH of 5.6 and a temperature of 50°C. AH2 maintained significant activity across a pH range of 4 to 10 (62 -72%) and temperatures of 30 to 70°C (77-86%). The enzyme had remarkable stability, with minimal reductions in activity across a temperature range of 4 to 70°C and pH levels of 3, 7, and 9. Docking studies identified AH2's amino acids (Glu90 and Glu149) to be involved in substrate binding. Molecular dynamics simulation confirmed the structural stability of AH2 at pH 5.6 and 50°C, further supporting its resilience under these conditions. Our results expand on the known activities associated with the GH130 CAZyme family and demonstrate that the horse gut metagenome represents an unexplored source of novel CAZymes.}, }
@article {pmid40035787, year = {2025}, author = {Tappauf, N and Lamers, Y and Sham, HP and Piper, HG}, title = {Multiomics profiling and parenteral nutrition weaning in pediatric patients with intestinal failure: A longitudinal cohort study.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpen.2742}, pmid = {40035787}, issn = {1941-2444}, support = {//This study was funded through a 2021-2022 Healthy Starts Catalyst Grant, awarded by the BC Children's Hospital Research Institute in Vancouver, Canada./ ; }, abstract = {BACKGROUND: Intestinal failure (IF) is a life-limiting condition that includes a variety of intestinal pathologies. Currently, there are few clinical biomarkers that reflect intestinal function or a patient's potential to wean off parenteral nutrition (PN), making it difficult to predict the clinical trajectory. By associating gut microbiome taxonomic and functional features and blood analytes with the proportion of daily energy delivered via PN-a proxy for intestinal function-our study aimed to discover potential predictors of intestinal function and PN weaning potential.<br><br>METHODS: In this longitudinal multiomics cohort study, we followed 18 pediatric patients with IF and PN support for &#x2264;1.5 years. Fecal and stoma samples were analyzed using metagenomic shotgun sequencing to assess bacterial taxonomy and function and internal transcribed spacer 2 ribosomal RNA sequencing to characterize the fungal community. Targeted metabolomics was used to quantify 257 blood analytes. Linear mixed models were used to analyze the associations of PN dependence with microbiome features and blood analytes.<br><br>RESULTS: The bacterial and fungal taxonomic composition exhibited substantial interpatient and intrapatient variability, with no link to PN dependence. In contrast, bacterial functional analysis revealed 63 MetaCyc pathways significantly associated with PN dependence. Additionally, 32 blood analytes were associated with PN dependence.<br><br>CONCLUSION: In this exploratory study, we found that functional microbiome features and blood metabolomic profiles-particularly urea cycle metabolites, creatinine, asparagine, and tryptophan-derived metabolites-show promise for predicting intestinal function. Furthermore, they may have therapeutic implications for promoting intestinal adaptation. Confirmatory trials with larger sample sizes are needed to validate these findings.}, }
@article {pmid40034816, year = {2024}, author = {Liu, Z and Jiang, A and Ma, D and Liu, D and Han, X and Zhao, M and Zhou, C and Tan, Z}, title = {The impact of rumen microbial composition on apparent digestibility, rumen fermentation and metabolism in Sanhe cows and Holstein cows of different parities under identical dietary conditions.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1463209}, pmid = {40034816}, issn = {2297-1769}, abstract = {Previous studies have discussed the association between serum metabolism and lactation performance among Sanhe and Holstein cows of different parities and found that the metabolic profiles of these two breeds vary differently with parity. Since the rumen is the central organ for nutrient absorption and production transformation in dairy cows, it remains unknown whether the differences observed under the same dietary conditions are related to the structure of the rumen microbiome. This study measured the apparent digestibility and rumen fermentation parameters of Sanhe cows (S1/S2/S3/S4) and Holstein cows (H1/H2/H3/H4) across four parities and generated a comprehensive rumen microbiome dataset using high-throughput sequencing technology. Significant differences in dry matter digestibility (p = 0.001) and ammonia nitrogen (p = 0.024) were observed among the S groups, with higher trends of various VFA contents in S1 (0.05 < p < 0.1). The H group showed significant differences in crude protein digestibility (p = 0.001), higher isovaleric acid content in H1 (p = 0.002), and the lowest acetate to propionate ratio (p = 0.002) in H3. Metagenomic sequencing results indicated consistency between rumen microbiome patterns and metabolic changes, with S1 distinctly different from S2/S3/S4, and H1 and H2 different from H3 and H4. The species composition of the rumen microbiome was similar between Sanhe and Holstein cows, but differences in abundance were noted. Rhizophagus <glomeromycetes>, Neocallimastix, and Piromyces were more abundant in S1, H1, and H2, and pathways such as autophagy-animal, plant-pathogen interaction, and endocytosis were significantly enriched in these parities. Multiparous Sanhe cows had higher abundances of ATP