@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.

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.

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.

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.},
}

Humans
*Dysbiosis/microbiology
*Systems Biology/methods
*Microbiota
Metagenomics
Metabolomics
Proteomics

@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.

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.

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.

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 (β=-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 (β =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 (β=0.20, SE=0.09 with 95% CI (0.02, 0.39)) and negative in the LGL diet (β =-0.23, SE=0.09 with 95% CI (-0.40, -0.06)).

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.},
}

*High-Throughput Nucleotide Sequencing/methods
Humans
Workflow
*Molecular Diagnostic Techniques/methods
*DNA Primers/genetics
Sensitivity and Specificity
Influenza, Human/diagnosis/virology

@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 & 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.},
}

*Lilium/virology
*Metagenomics/methods
Genome, Viral
*Plant Diseases/virology
Phylogeny
*Caulimoviridae/genetics/isolation & purification/classification
Sequence Analysis, DNA
Genetic Markers

@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.},
}

Humans
*Schizophrenia/microbiology/metabolism/physiopathology
Male
Female
*Gastrointestinal Microbiome
Adult
Middle Aged
Feces/microbiology
Case-Control Studies
Metabolic Networks and Pathways
Fungi

@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.

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.

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.

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 & 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 & 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.

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 ​​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.

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.},
}

*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

@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.

METHODS: In this study, stool samples from 67 patients were collected preoperatively and 1 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.

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 < 0.05). Patients exhibiting increased blood ammonia after TIPS showed significant enrichment of P.vulgatus (LDA > 2.5), accompanied by a reduction in the urea cycle (P < 0.05) and associated enzymes (P < 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.

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.},
}

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

@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.},
}

*Wastewater/microbiology
*Transcriptome
Ecosystem
Fresh Water/microbiology
*Eukaryota/genetics

@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.},
}

*Solanum tuberosum/microbiology/genetics
*Plant Diseases/microbiology/genetics
*Disease Resistance/genetics
*Ralstonia solanacearum/pathogenicity
Soil Microbiology
Pseudomonas/genetics
*Plant Proteins/genetics/metabolism

@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.},
}

*Wastewater/microbiology
*Metagenomics/methods
*Bacteria/genetics/classification
*Microbiota/genetics
Sewage/microbiology
*Metagenome

@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 & 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.

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.

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.

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.},
}

Bayes Theorem
*Microbiota
*Neural Networks, Computer
*Metagenomics/methods
Humans
*Computational Biology/methods
Algorithms
Multiomics

@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.

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.

RESULTS: During chemotherapy, the gut microbiota α-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).

CONCLUSION: During induction chemotherapy in AML patients, gut microbiota α-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.},
}

Humans
*Gastrointestinal Microbiome
*Leukemia, Myeloid, Acute/drug therapy/microbiology
*Induction Chemotherapy
Feces/microbiology
Male
Female
Middle Aged

@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 & 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.

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).

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.

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.},
}

Humans
*Nontuberculous Mycobacteria/genetics/isolation & 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

@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.

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.

SETTING: The study was conducted in quintile 1 and 2 primary schools in Vryheid, KwaZulu-Natal.

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.

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.

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.

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.

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.

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 α-diversity and markedly altered β-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.

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.

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.

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 (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 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.

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 & Melinda Gates Foundation)/ ; UL1TR002544//U.S. Department of Health & 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.},
}

*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

@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 & 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.

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.

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.},
}

Humans
Male
*Extracorporeal Membrane Oxygenation/methods
Middle Aged
*Acinetobacter baumannii/isolation & 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

@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 & 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.},
}

Animals
*Aedes/virology
Phylogeny
Brazil
*Phlebovirus/isolation & purification/genetics/classification
Female
*Mosquito Vectors/virology
Parks, Recreational
High-Throughput Nucleotide Sequencing
RNA, Viral/genetics

@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
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 & 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.},
}

Humans
*Lung Neoplasms/complications/microbiology
*Pneumonia, Pneumocystis/diagnosis/microbiology/complications
*Pneumocystis carinii/genetics/isolation & 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

@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.

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.

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.

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.

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.

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.

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.

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.

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.

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∶1 optimal nearest neighbor, caliper = 0.25) was implemented to address covariate imbalance, followed by univariate logistic regression analyses in the matched cohort.

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).

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 {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 & purification/enzymology ; Phylogeny ; *Halogenation ; *Archaea/genetics/classification/metabolism/isolation & 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.

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 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.

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.},
}

*Geologic Sediments/microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification/enzymology
Phylogeny
*Halogenation
*Archaea/genetics/classification/metabolism/isolation & purification/enzymology
*Seawater/microbiology
Metagenomics/methods
Bacterial Proteins/genetics/metabolism
Metagenome
Oxidation-Reduction

@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.

METHODS: P. johnsonii (10–42) and Lactococcus formosensis (22–2) 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.

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.

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.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-06675-0.},
}

@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 & 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.

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.

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.},
}

Animals
*Chickens
*Poultry Diseases/diagnosis/microbiology/virology
*Escherichia coli Infections/veterinary/diagnosis/microbiology/complications
*Coinfection/veterinary/diagnosis/microbiology
Metagenomics
Escherichia coli/isolation & purification/genetics
Republic of Korea
*Hepatitis, Animal/diagnosis/microbiology/virology
*Purpura/veterinary/diagnosis/microbiology
Liver/pathology/microbiology

@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 & development/microbiology ; Rhizosphere ; Metagenomics ; Soil Microbiology ; *Probiotics ; Plant Roots/microbiology/growth & 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.

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.

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.},
}

*Bacillus cereus/genetics/physiology
*Juglans/growth & development/microbiology
Rhizosphere
Metagenomics
Soil Microbiology
*Probiotics
Plant Roots/microbiology/growth & development

@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)/ ; },
abstract = {BACKGROUND: Antibiotic resistance has become a serious challenge to global public health. The spread of antibiotic resistance genes (ARGs) among humans, animals, and the environment has become a critical issue within the “One Health” framework. Chinese wet market with live poultry trade provides an interface for close interaction between humans and chickens, and is considered as potential source for disease dissemination. However, the understanding of ARGs in this kind of market, including their shared profiles, influencing factors, and potential horizontal transfer subtypes and directions, remains limited.

RESULTS: In this study, we explored the microbiome, resistome, and mobility of ARGs, and identified putative horizontal gene transfer (HGT) events in the Chinese wet market system by utilizing metagenomic assembly and binning. Consequently, a total of 1080 ARG subtypes were identified from 36 metagenomes, and 221 subtypes were shared among human feces, chicken feces, chicken carcasses, and the environment. The composition of ARGs was influenced by mobile genetic elements (MGEs) and bacterial communities. As for the host of ARGs, 89 ARG-carrying genomes (ACGs) were identified, with 18 of them carrying multiple ARGs and MGEs, indicating the potential mobility of ARGs. Notably, six ACGs were identified as opportunistic pathogens carrying multiple ARGs and MGEs, which were annotated as Escherichia coli, Acinetobacter johnsonii, Klebsiella variicola, Klebsiella pneumoniae, and Citrobacter freundii. In addition, 164 potential HGT events were identified based on ACGs, and ParS, vanB, ugd, and macB were annotated as potentially transferred ARG subtypes in humans and the wet market.

CONCLUSIONS: This study offers new insights into the potential for HGT of ARGs within a Chinese wet market setting, highlighting putative transmission patterns among humans, poultry, and the environment. To our knowledge, few studies have explored ARG transfer potential in this context using metagenome-assembled genomes, making this a valuable contribution to One Health surveillance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04115-z.},
}

@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 & 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 Rönströms Stiftelse, Stiftelsen för Gamla Tjänarinnor, Hjärnfonden, Sweden/ ; #860197//European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-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.

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.

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.

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.

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) ε4 status+ vs APOE ε4 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.},
}

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

@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 & Human Services | National Institutes of Health (NIH)/ ; T32CA009001//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35CA253185//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R24DK110499//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's & 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 & 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.},
}

Animals
*Chickens/growth & 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

@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.},
}

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

@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 & 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.},
}

*Acinetobacter/metabolism/genetics/isolation & purification/classification
*Biodegradation, Environmental
Animals
*Water Pollutants, Chemical/metabolism
Zebrafish
Phylogeny
Metagenomics

@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 & 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.},
}

*RNA, Ribosomal, 16S/genetics
*Hot Springs/microbiology
Ethiopia
*Bacteria/genetics/classification/isolation & purification
Phylogeny
*Nanopore Sequencing/methods
Biodiversity

@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.},
}

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

@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 & 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.},
}

*Geologic Sediments/microbiology/chemistry
*Salinity
*Bacteria/classification/genetics/isolation & purification/metabolism
Estuaries
China
Biodiversity
Microbiota
Ecosystem
Metagenome
Phylogeny

@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 = {284},
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},
pmid = {40601719},
issn = {1932-6203},
mesh = {Animals ; *Aedes/virology ; Kenya ; *Dengue Virus/genetics/isolation & 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.},
}

Animals
*Aedes/virology
Kenya
*Dengue Virus/genetics/isolation & purification/classification
*Virome/genetics
*Mosquito Vectors/virology
*Infectious Disease Transmission, Vertical
Metagenomics
High-Throughput Nucleotide Sequencing
Phylogeny
Dengue/transmission/virology
Metagenome
Female

@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.

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.

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.

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.},
}

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

@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.

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.

METHODS: Prospective enrollment of participants <21 years with first AP. Stool samples were obtained at baseline (n = 41), 3 months (n = 19), and 12 months (n = 12) and in healthy controls (HC; n = 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.

RESULTS: Microbial alpha diversity was lower for AP versus HC at all three time points (p < 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 = 0.023) and in follow-up samples with multiple GI symptoms, p < 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 < 0.05). Several pathways involved in protein biosynthesis were depleted in the AP cohort at all time points.

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.

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.

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.

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 {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 {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},
pmid = {40170447},
issn = {1755-0998},
support = {2020.03608.CEECIND//Fundação para a Ciência e a Tecnologia/ ; COVID/BD/152600/2022//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/133159/2017//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência 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.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
Animals
*DNA, Environmental/genetics
*Metagenomics/methods
Mediterranean Region
*Vertebrates/classification/genetics
*Environmental Monitoring/methods

@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},
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.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Metagenomics/methods
Microbiota
Animals
*DNA Barcoding, Taxonomic/methods
Biodiversity
Computational Biology/methods
Sequence Analysis, DNA/methods

@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//Fundação para a Ciência e a Tecnologia/ ; CEECIND/02547/2020//Fundação para a Ciência e a Tecnologia/ ; DL57/2016/CP1440/CP1646/CT0018//Fundação para a Ciência 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 & 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.},
}

*Chiroptera/physiology
Animals
*DNA Barcoding, Taxonomic/methods
*DNA, Plant/genetics/isolation & purification
Feces/chemistry
*Plants/genetics/classification
*Diet
*Metagenomics/methods
Arthropods

@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.

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 β-lactam antibiotics.

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 & 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.

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.

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.

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.

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.

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.},
}

Humans
*Dental Caries/diagnosis/microbiology
Child
*Biomarkers/analysis
*Metagenomics/methods
Saliva/microbiology
Female
Male
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
Metagenome

@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 & 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.},
}

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