@article {pmid40333210,
year = {2025},
author = {Trujillo, HA and Komeili, A},
title = {Revealing the diversity of bacterial and archaeal organelles via comparative genomics.},
journal = {Molecular biology of the cell},
volume = {36},
number = {5},
pages = {pe4},
doi = {10.1091/mbc.E20-08-0564},
pmid = {40333210},
issn = {1939-4586},
mesh = {*Archaea/genetics/metabolism ; Genomics/methods ; *Bacteria/genetics/metabolism ; *Organelles/genetics/metabolism ; Metagenomics/methods ; Magnetosomes/genetics/metabolism ; Genome, Archaeal ; },
abstract = {Like eukaryotes, bacteria and archaea rely on intracellular organelles to manage biological activities. Despite their prevalence, the understanding of the diversity of these organelles and the molecular mechanisms governing their function remain limited. In this review, we examine the potential of genomics and metagenomics to augment classical approaches for the study and discovery of microbial organelles. First, we highlight how the intimate interplay between model system studies and metagenomics have been critical in illuminating the function, diversity, and ancient evolutionary origins of the lipid-bounded magnetosome organelles of magnetotactic bacteria. We next discuss the central role of open genome databases and mechanistic studies in identification and characterization of protein-bounded encapsulin organelles with novel roles in sulfur metabolism and other cellular processes. Finally, we focus on the mostly uncultured Asgard archaea superphylum, whose metagenomes are challenging our views on organelle evolution and eukaryogenesis.},
}

*Archaea/genetics/metabolism
Genomics/methods
*Bacteria/genetics/metabolism
*Organelles/genetics/metabolism
Metagenomics/methods
Magnetosomes/genetics/metabolism
Genome, Archaeal

@article {pmid40333159,
year = {2025},
author = {Gao, Y and Lou, Y and Hui, Y and Chen, H and Sang, H and Liu, F},
title = {Characterization of the Gut Microbiota in Patients with Psoriasis: A Systematic Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040358},
pmid = {40333159},
issn = {2076-0817},
support = {22LCYY-QH10//Jinling Hospital/ ; },
mesh = {Humans ; *Psoriasis/microbiology/therapy ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; *Dysbiosis/microbiology/therapy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background: Psoriasis is a prevalent and persistent inflammatory disorder with systemic manifestations. Emerging evidence implicates the gut microbiota in regulating inflammatory responses, metabolic pathways, and immune homeostasis. This review synthesizes current evidence on gut microbiota dysbiosis in psoriasis and evaluates the therapeutic potential of probiotics and fecal microbiota transplantation (FMT) in disease management. Method: Following PRISMA guidelines, we systematically reviewed studies investigating gut microbiome profiles in psoriasis through the MEDLINE, EMBASE, and Web of Science databases (January 2015-December 2024). Included studies utilized 16S rRNA gene sequencing or metagenomic analyses for microbial characterization. Results: Comparative analyses revealed distinct gut microbiota patterns in psoriasis patients compared with healthy controls, although specific microbial signatures exhibited inconsistencies across studies. Notably, interventions modulating gut microbiota composition-particularly probiotic supplementation-demonstrated measurable improvements in psoriasis severity scores and inflammatory markers. Conclusions: Gut microbiome modulation represents a promising therapeutic strategy for psoriasis; however, current evidence highlights the need for standardized microbial analysis methodologies and larger longitudinal studies to establish causality. Future research should prioritize the functional characterization of microbiota-host interactions to optimize therapeutic applications.},
}

Humans
*Psoriasis/microbiology/therapy
*Gastrointestinal Microbiome
Fecal Microbiota Transplantation
Probiotics/therapeutic use
*Dysbiosis/microbiology/therapy
RNA, Ribosomal, 16S/genetics

@article {pmid40333137,
year = {2025},
author = {McHugh, JW and Challener, DW and Tabaja, H},
title = {Change of Heart: Can Artificial Intelligence Transform Infective Endocarditis Management?.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040371},
pmid = {40333137},
issn = {2076-0817},
mesh = {Humans ; *Artificial Intelligence ; *Endocarditis/diagnosis/therapy/diagnostic imaging ; Echocardiography ; Machine Learning ; Disease Management ; },
abstract = {Artificial intelligence (AI) has emerged as a promising adjunct in the diagnosis and management of infective endocarditis (IE), a disease characterized by diagnostic complexity and significant morbidity. Machine learning (ML) models such as SABIER and SYSUPMIE have demonstrated strong predictive accuracy for early IE diagnosis, embolic risk stratification, and postoperative mortality, surpassing traditional clinical scoring systems. In imaging, AI-enhanced echocardiography and advanced modalities like FDG-PET/CT offer improved sensitivity, specificity, and reduced inter-observer variability, potentially transforming clinical decision making. Additionally, AI-powered microbiological techniques, including MALDI-TOF mass spectrometry combined with ML and neural network-based metagenomic classifiers, show promise in rapidly identifying pathogens and predicting antimicrobial resistance. Despite encouraging early results, widespread adoption faces barriers, including data limitations, interpretability issues, ethical concerns, and the need for robust validation. Future directions include leveraging generative AI as clinical consultative tools, provided their capabilities and limitations are carefully managed. Ultimately, collaborative efforts addressing these challenges could transform IE care, enhancing diagnostic accuracy, clinical outcomes, and patient safety.},
}

Humans
*Artificial Intelligence
*Endocarditis/diagnosis/therapy/diagnostic imaging
Echocardiography
Machine Learning
Disease Management

@article {pmid40333054,
year = {2025},
author = {Matos, JSS and Demoliner, M and Gularte, JS and Filippi, M and de Abreu Góes Pereira, VM and da Silva, MS and Weber, MN and de Barros, MP and Spilki, FR},
title = {Virome of Terrestrial Mammals and Bats from Southern Brazil: Circulation of New Putative Members of the Togaviridae Family and Other Findings.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040310},
pmid = {40333054},
issn = {2076-0817},
support = {405786/2022-0//CNPQ/ ; },
mesh = {Animals ; Brazil/epidemiology ; *Chiroptera/virology ; *Virome ; *Mammals/virology ; Phylogeny ; Metagenomics ; Humans ; },
abstract = {The surveillance of wildlife viromes is essential for identifying zoonotic threats within the One Health framework. This study analyzed rectal and oral swabs from 88 individuals representing 13 species as felids, wild rodents, marsupials and non-human primates in Southern Brazil using metagenomic sequencing. Akodon montensis (n = 15 individuals) and Coendou spinosus (n = 4) harbored Chikungunya virus (ChikV, Togaviridae), marking its first detection in these hosts. Molossus molossus (n = 17) presented Coronaviridae and Orthoherpesviridae, while Eptesicus furinalis (n = 1) also carried Coronaviridae. A broad virome diversity, including Togaviridae and Adenoviridae members, was identified in Didelphis albiventris (n = 43), with significant relevance to human health. Additional species, such as Callithrix jacchus (n = 1), Leopardus guttulus (n = 1), Myocastor coypus (n = 1), Monodelphis iheringi (n = 1), Thaptomys nigrita (n = 1), Sooretamys angouya (n = 1), Brucepattersonius iheringi (n = 1), and Lasiurus blossevillii (n = 1), contributed to insights into viral reservoirs. These results underscore the importance of virome studies in regions harboring high biodiversity, emphasizing genomic surveillance as a vital tool for monitoring zoonotic viruses and safeguarding global health.},
}

Animals
Brazil/epidemiology
*Chiroptera/virology
*Virome
*Mammals/virology
Phylogeny
Metagenomics
Humans

@article {pmid40332920,
year = {2025},
author = {Liu, H and Chen, W and Fang, X and Li, D and Xiong, Y and Xie, W and Chen, Q and You, Y and Lin, C and Wang, Z and Wang, J and Chen, D and Li, Y and Cai, P and Nie, C and Hong, Y},
title = {Impact of Ectropis grisescens Warren (Lepidoptera: Geometridae) Infestation on the Tea Plant Rhizosphere Microbiome and Its Potential for Enhanced Biocontrol and Plant Health Management.},
journal = {Insects},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/insects16040412},
pmid = {40332920},
issn = {2075-4450},
support = {2023XQ019//Key Technological Innovation and Industrialization Project/ ; 2022J011198//Project of Fujian Provincial Department of Science and Technology/ ; 2024J01917//Project of Fujian Provincial Department of Science and Technology/ ; 2024J01916//Project of Fujian Provincial Natural Science Fund/ ; N2023Z007//Nanping Academy of Resource Industrialization Chemistry Project/ ; N2023J004//Key Project of the Nanping Natural Fund/ ; 202410397010//National College Student Innovation and Entrepreneurship Project/ ; },
abstract = {The root-associated microbiome significantly influences plant health and pest resistance, yet the temporal dynamics of its compositional and functional change in response to Ectropis grisescens Warren (Lepidoptera: Geometridae) infestation remain largely unexplored. The study took samples of leaves, roots, and rhizosphere soil at different times after the plants were attacked by E. grisescens. These samples were analyzed using transcriptomic and high-throughput sequencing of 16S rRNA techniques. The goal was to understand how the plant's defense mechanisms and the microbial community around the roots changed after the attack. Additionally, bacterial feedback assays were conducted to evaluate the effects of selected microbial strains on plant growth and pest defense responses. By conducting 16S rRNA sequencing on the collected soil samples, we found significant shifts in bacterial communities by the seventh day, suggesting a lag in community adaptation. Transcriptomic analysis revealed that E. grisescens attack induced reprogramming of the tea root transcriptome, upregulating genes related to defensive pathways such as phenylpropanoid and flavonoid biosynthesis. Metagenomic data indicated functional changes in the rhizosphere microbiome, with enrichment in genes linked to metabolic pathways and nitrogen cycling. Network analysis showed a reorganization of core microbial members, favoring nitrogen-fixing bacteria like Burkholderia species. Bacterial feedback assays confirmed that selected strains, notably Burkholderia cepacia strain ABC4 (T1) and a nine-strain consortium (T5), enhanced plant growth and defense responses, including elevated levels of flavonoids, polyphenols, caffeine, jasmonic acid, and increased peroxidase (POD) and superoxide dismutase (SOD) activities. This study emphasizes the potential of utilizing root-associated microbial communities for sustainable pest management in tea cultivation, thereby enhancing resilience in tea crops while maintaining ecosystem balance.},
}

@article {pmid40332799,
year = {2025},
author = {Bai, C and Duan, Y and Zhao, C and Yan, L and Suthisut, D and Lü, J and Bai, Y and Zeng, F and Zhang, M},
title = {Abundance of the Dominant Endosymbiont Rickettsia and Fitness of the Stored-Product Pest Liposcelis bostrychophila (Psocoptera: Liposcelididae).},
journal = {Insects},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/insects16040349},
pmid = {40332799},
issn = {2075-4450},
support = {32172260//National Natural Science Foundation of China/ ; },
abstract = {Endosymbiotic bacteria are key factors that regulate the biological traits of Liposcelis bostrychophila. This study employed metagenomic methods to analyze the dominant species of symbiotic microorganisms associated with L. bostrychophila. By controlling the environmental temperature, we were able to manipulate the abundance of endosymbionts and establish populations with high, medium, and low levels of these bacteria. This allowed us to examine the fitness parameters of L. bostrychophila under different levels of endosymbiont abundance. The experimental results revealed that L. bostrychophila hosts 51 genera of symbiotic microorganisms, with Rickettsia being the dominant genus, accounting for 84.11% to 98.16% of the total share. Environmental temperature significantly affected the abundance of Rickettsia, with notable differences observed during the adult stage of L. bostrychophila. A temperature gradient of 28 °C, 35 °C, and 37 °C was established, allowing for the classification of populations based on Rickettsia abundance into three categories: high-abundance populations (LBhp), medium-abundance populations (LBmp), and low-abundance populations (LBlp). The abundance of Rickettsia had a significant impact on the fitness of L. bostrychophila. Specifically, a high abundance of Rickettsia contributed positively to population fitness by increasing egg production, prolonging egg hatching time, enhancing lifespan, and improving both survival and reproductive rates. Therefore, the endosymbiont Rickettsia plays a crucial role in the growth and development of L. bostrychophila. In the future, our research will help further uncover the interactions between Rickettsia and its host, providing new perspectives for pest control and offering a better understanding of insect biology and ecology.},
}

@article {pmid40331433,
year = {2025},
author = {Meyer, F and Robertson, G and Deng, ZL and Koslicki, D and Gurevich, A and McHardy, AC},
title = {CAMI Benchmarking Portal: online evaluation and ranking of metagenomic software.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf369},
pmid = {40331433},
issn = {1362-4962},
support = {//NFDI4Microbiota consortium/ ; 460129525//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Finding appropriate software and parameter settings to process shotgun metagenome data is essential for meaningful metagenomic analyses. To enable objective and comprehensive benchmarking of metagenomic software, the community-led initiative for the Critical Assessment of Metagenome Interpretation (CAMI) promotes standards and best practices. Since 2015, CAMI has provided comprehensive datasets, benchmarking guidelines, and challenges. However, benchmarking had to be conducted offline, requiring substantial time and technical expertise and leading to gaps in results between challenges. We introduce the CAMI Benchmarking Portal-a central repository of CAMI resources and web server for the evaluation and ranking of metagenome assembly, binning, and taxonomic profiling software. The portal simplifies evaluation, enabling users to easily compare their results with previous and other users' submissions through a variety of metrics and visualizations. As a demonstration, we benchmark software performance on the marine dataset of the CAMI II challenge. The portal currently hosts 28 675 results and is freely available at https://cami-challenge.org/.},
}

@article {pmid40331220,
year = {2025},
author = {Wang, Y and Wei, C and Chen, Z and Zhou, M and Huang, L and Chen, C},
title = {Characterization of the diversity, genomic features, host bacteria, and distribution of crAss-like phages in the pig gut microbiome.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1582122},
pmid = {40331220},
issn = {2297-1769},
abstract = {Phages play an important role in shaping the gut microbiome. CrAss-like phages, which are key members of the gut virome, show high abundance in the human gut and have attracted increasing interest. However, few studies have been found in pigs, and the distribution of crAss-like phages across broader pig populations remains unknown. Here, we obtained 1,251 pig crAss-like phage genomes from 403 metagenomes publicly available and a pig gut virome dataset constructed by ourselves. These crAss-like phage genomes were further clustered into 533 virus operational taxonomic units (vOTUs). Phylogenetic analysis revealed that crAss-like phages in pig guts were distributed across four well-known family-level clusters (Alpha, Beta, Zeta, and Delta) but were absent in the Gamma and Epsilon clusters. Genomic structure analysis identified 149 pig crAss-like phage vOTUs that utilize alternative genetic codes. Gene blocks encoding replication and assembly proteins varied across crAss-like phage clusters. Approximately 64.73% of crAss-like phage genes lacked functional annotations, highlighting a gap in understanding their functional potential. Numerous anti-CRISPR protein genes were identified in crAss-like phage genomes, and CAZymes encoded by these phages were primarily lysozymes. Host prediction indicated that bacterial hosts of pig crAss-like phages primarily belonged to Prevotella, Parabacteroides, and UBA4372. We observed that interactions between crAss-like phages and Prevotella copri might have a possible effect on fat deposition in pigs. Finally, all detected vOTUs exhibited low prevalence across pig populations, suggesting heterogeneity in crAss-like phage compositions. This study provides key resources and novel insights for investigating crAss-like phage-bacteria interactions and benefits research on the effects of crAss-like phages on pig health and production traits.},
}

@article {pmid40330784,
year = {2025},
author = {Krivonos, D and Pavlenko, A and Lukina-Gronskaya, A and Korneenko, E and Speranskaya, A and Ilina, E},
title = {Case Report: Fatal case of dual infection Metapneumovirus complicated by Streptococcus pyogenes.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1576583},
pmid = {40330784},
issn = {2296-858X},
abstract = {Human Metapneumovirus (hMPV) is a common cause of acute respiratory viral infection in humans, typically occurring in children and causing no serious complications. However, the severity of the disease can be exacerbated by certain bacterial pathogens that lead to severe illness and even death. This report details a fulminant case of dual infection with hMPV and group A Streptococcus (Streptococcus pyogenes) in a three-year-old child. The whole genome sequencing of isolated clinical S. pyogenes strains was conducted, followed by an analysis of the genomic characteristics of the pathogen. Also, potential viral and bacterial pathogens were identified by qPCR and 16S rRNA metagenomic sequencing in any autopsy materials obtained from the patient. Children who had contact with the patient and began to exhibit symptoms of a cold were also tested and confirmed to have uncomplicated hMPV infection. The S. pyogenes strain has been found to contain five genes for various streptococcal exotoxins (speA, speB, speJ, speG and smeZ). In addition, the speA gene is situated in close proximity to the prophage, which may suggest that it is encoded and transferred specifically by the bacteriophage. We hypothesize that it was the cumulative effects of different streptococcal exotoxins that led to the patient's death.},
}

@article {pmid40330742,
year = {2025},
author = {Liu, C and Cai, Y and Yuan, K and Lu, M and Deng, Y and Chen, X and Ye, L and Cui, S and Lyu, J and Ling, Y},
title = {Confirmation of Tuberculous Meningitis Using Metagenomic Next-Generation Sequencing: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2209-2214},
pmid = {40330742},
issn = {1178-6973},
abstract = {BACKGROUND: Tuberculous meningitis (TBM) remains a significant clinical challenge due to limitations in traditional diagnostic methods, such as cerebrospinal fluid (CSF) analysis and tuberculosis culture, which often have long turnaround times and low sensitivity and specificity. This case report highlights the pivotal role of metagenomic next-generation sequencing (mNGS) in enhancing clinical knowledge for the diagnosis and management of TBM, supplementing insights into its clinical presentation and treatment.

CASE PRESENTATION: A 56-year-old male patient was admitted to the hospital with a chief complaint of "unconsciousness for 4 days". Following five days of antimicrobial therapy, the patient showed significant improvement with no fever or headache, but exhibited a suspicious left-sided Babinski sign (+). MRI revealed evidence of cerebral infarction, while spiral CT imaging showed hydrocephalus accompanied by interstitial cerebral edema. A lumbar puncture revealed elevated intracranial pressure, increased protein levels in CSF, reduced glucose and chloride concentrations, and negative results for CSF smear, CSF culture, and blood culture. T-SPOT testing was positive, and mNGS of CSF detected Mycobacterium tuberculosis (M. tuberculosis) Based on clinical and etiological findings, a diagnosis of tuberculous meningitis was confirmed. The patient was treated with quadruple anti-tuberculosis therapy combined with linezolid, resulting in clinical improvement. He was subsequently transferred to a specialized chest hospital for further management.

CONCLUSION: The patient's condition improved after 5 days of treatment. TBM is notoriously challenging to diagnose and treat. Traditional diagnostic methods, such as smear microscopy and tuberculosis culture, often yield low positive rates, delaying timely diagnosis and intervention. Early detection, accurate diagnosis, and prompt treatment are crucial for improving patient outcomes. mNGS of CSF has proven to be a powerful tool in TBM diagnosis, enabling early and precise identification of the pathogen, thereby facilitating timely treatment and reducing TBM-related mortality.},
}

@article {pmid40330288,
year = {2025},
author = {Bhowmik, S and Hajra, A and Bandyopadhyay, D},
title = {Genetic insights in infectious diseases: Insights from a case report and implications for personalized medicine.},
journal = {World journal of clinical cases},
volume = {13},
number = {13},
pages = {101438},
pmid = {40330288},
issn = {2307-8960},
abstract = {The relationship between genetics and infectious diseases is important in shaping our understanding of disease susceptibility, progression, and treatment. Recent research shows the impact of genetic variations, such as heme-oxygenase promoter length, on diseases like malaria and sepsis, revealing both protective and inconclusive effects. Studies on vaccine responses highlight genetic markers like human leukocyte antigens, emphasizing the potential for personalized immunization strategies. The ongoing battle against drug-resistant tuberculosis (TB) illustrates the complexity of genomic variants in predicting resistance, highlighting the need for integrated diagnostic tools. Additionally, genome-wide association studies reveal antibiotic resistance mechanisms in bacterial genomes, while host genetic polymorphisms, such as those in solute carrier family 11 member 1 and vitamin D receptor, demonstrate their role in TB susceptibility. Advanced techniques like metagenomic next-generation sequencing promise detailed pathogen detection but face challenges in cost and accessibility. A case report involving a highly virulent Mycobacterium TB strain with the pks1 gene further highlights the need for genetic insights in understanding disease severity and developing targeted interventions. This evolving landscape emphasizes the role of genetics in infectious diseases, while also addressing the need for standardized studies and accessible technologies.},
}

@article {pmid40330019,
year = {2025},
author = {Fang, P and Wen, Y and Deng, W and Liang, R and He, P and Wang, C and Fan, N and Huo, K and Zhao, K and Li, C and Bai, Y and Ma, Y and Hu, L and Guan, Y and Yang, S},
title = {Investigation of dynamic microbial migration patterns in the respiratory tract.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1542562},
pmid = {40330019},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/microbiology ; Prospective Studies ; Male ; Female ; Middle Aged ; *Microbiota ; Sputum/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Respiratory System/microbiology ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Oropharynx/microbiology ; Bayes Theorem ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The role of the respiratory microbiome in lung diseases is increasingly recognized, with the potential migration of respiratory pathogens being a significant clinical consideration. Despite its importance, evidence elucidating this phenomenon remains scarce.

METHODS: This prospective study collected clinical samples from patients with suspected lower respiratory tract infections (LRTI), including oropharyngeal swabs (OPS), sputum, and bronchoalveolar lavage fluid (BALF). Metagenomic next-generation sequencing (mNGS) was employed to analyze respiratory microbial diversity, complemented by Bayesian source tracking and sequence alignment analyses to explore pathogen migration patterns.

RESULTS: A cohort of 68 patients was enrolled, with 56 diagnosed with LRTI and 12 with non-infectious respiratory conditions. A statistically significant disparity in respiratory microbiome diversity was observed between infected and non-infected groups (p < 0.05). Intriguingly, no significant variations in microbial community structure, including alpha and beta diversity, were detected across different respiratory tract sites within individuals. The Bayesian source tracking analysis revealed a pronounced migration pattern among pathogens compared to the overall microbial community, with migration ratios of 51.54% and 1.92%, respectively (p < 0.05). Sequence similarity analysis further corroborated these findings, highlighting a notable homology among specific migrating pathogens.

CONCLUSION: This study represents a pioneering effort in deducing pathogen migration patterns through microbial source tracking analysis. The findings provide novel insights that could significantly advance clinical diagnostics and therapeutic strategies for respiratory infections.},
}

Humans
*Respiratory Tract Infections/microbiology
Prospective Studies
Male
Female
Middle Aged
*Microbiota
Sputum/microbiology
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Respiratory System/microbiology
Adult
High-Throughput Nucleotide Sequencing
Metagenomics
Oropharynx/microbiology
Bayes Theorem
*Bacteria/classification/genetics/isolation & purification

@article {pmid40330015,
year = {2025},
author = {Manimaran, A and Desingu, PA and Kumaresan, A and Singh, P and Subramanya, K and Dodamani, P and Dineshbhai, PA},
title = {The metagenomic and whole-genome metagenomic detection of multidrug-resistant bacteria from subclinical mastitis-affected cow's milk in India.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1549523},
pmid = {40330015},
issn = {2235-2988},
mesh = {Animals ; India ; *Milk/microbiology ; Cattle ; *Drug Resistance, Multiple, Bacterial/genetics ; Female ; *Mastitis, Bovine/microbiology ; *Metagenomics/methods ; *Genome, Bacterial ; *Bacteria/genetics/isolation & purification/drug effects/classification ; Whole Genome Sequencing ; Virulence Factors/genetics ; Humans ; },
abstract = {Multidrug-resistant (MDR) bacteria in farm animal products threaten human health by causing zoonotic infections. The complete genome sequences of MDR bacteria from subclinical mastitis-affected cow's milk have not yet been comprehensively documented in India. In this study, using a bacterial metagenomic sequencing approach, we detected the nearly complete genome sequences of Pseudomonas veronii and Staphylococcus xylosus from subclinical mastitis-affected cow's milk. Furthermore, we sequenced the nearly complete genome sequences of Escherichia coli, Klebsiella pneumoniae, Staphylococcus hominis, and S. xylosus from subclinical mastitis-affected cow's milk using a whole-genome metagenomic sequencing method. Our analysis subsequently revealed that the complete genome sequences of the identified bacteria contained MDR genes and genes for multiple virulence factors. These MDR bacteria may pose a public health risk through exposure to milkers, milk handlers, and farm workers or through the handling and consumption of unpasteurized milk.},
}

Animals
India
*Milk/microbiology
Cattle
*Drug Resistance, Multiple, Bacterial/genetics
Female
*Mastitis, Bovine/microbiology
*Metagenomics/methods
*Genome, Bacterial
*Bacteria/genetics/isolation & purification/drug effects/classification
Whole Genome Sequencing
Virulence Factors/genetics
Humans

@article {pmid40329854,
year = {2025},
author = {Buddle, S and Torres, O and Morfopoulou, S and Breuer, J and Brown, JR},
title = {The use of metagenomics to enhance diagnosis of Encephalitis.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2025.2500655},
pmid = {40329854},
issn = {1744-8352},
abstract = {INTRODUCTION: Encephalitis has a broad etiology, including infectious and auto-immune causes. In infectious encephalitis the breadth of causative organisms results in incomplete testing and low diagnostic yields.Metagenomics sequences all DNA and RNA allows untargeted detection of all organisms in a single specimen; this is of particular use in diagnosis of encephalitis with a broad etiology.

AREAS COVERED: We review the literature and discuss metagenomics workflows, host depletion and pathogen enrichment methods, bioinformatics analysis and potential analysis of the host transcriptome to aid diagnosis. We discuss the clinical use of metagenomics for diagnosis of neurological infection including time to result, cost, quality assurance, patient cohorts in whom metagenomics adds the most value, recommended specimen types, limitations and review published cases in which metagenomics has been used to diagnose encephalitis.

EXPERT OPINION: There is good evidence for the utility of metagenomics to diagnose infection in encephalitis. Due to infections with rare, unexpected or novel pathogens, metagenomics adds most value to diagnosis in immunocompromised patients and the greatest diagnostic yield is in brain biopsies. Technical advances are needed to reduce the complexity, cost and time to result which will enable wider adoption in clinical laboratories and use as a first line test.},
}

@article {pmid40329496,
year = {2025},
author = {Rose, S and Johnson, H and Cartozzo, C and Swall, J and Simmons, T and Singh, B},
title = {Testing the efficacy of surface swab sampling to determine postmortem submersion interval (PMSI), using the microbiome colonization of skeletal remains.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.70039},
pmid = {40329496},
issn = {1556-4029},
abstract = {Postmortem interval (PMI) estimation contributes valuable information in the medicolegal investigation of decomposed human remains, and estimating the postmortem submersion interval (PMSI) can specifically aid investigations involving victims discovered in aquatic environments. Microbial succession-driven models in long-term decomposition studies have utilized the abundant colonizing bacterial community of skeletal remains to estimate the PMSI using bone powder. This study investigates the use of bone surface swabbing as an effective alternative method that minimizes time and resources required for bone sampling and also provides a highly replicable method for decomposition studies. Skeletal porcine (Sus scrofa) remains were caged and submerged in both lentic and lotic environments (Henley Lake in White Hall and James River at the Rice Rivers Center in Charles City, respectively) in Central Virginia from November 2017 to November 2018. Bone surface swabs and water samples were analyzed at 500 accumulated degree days (ADD) intervals, from baseline (0 ADD) to 4500 ADD. Variable region 4 (V4) of 16S rDNA was amplified and sequenced using the Illumina MiSeq Sequencing platform and analyzed using Mothur (v.1.39.5) and R (v.4.04). Analysis of Molecular Variance (AMOVA) indicated a significant difference in bacterial community structure among and between the swab, bone, and water samples (p < 0.001, F = 7.92331), and among and between lake and river samples (p < 0.001, F = 9.38829). PMSI models were constructed using random forest models for lake swabs (R[2] = 0.83, RMSE = 623.24) and river swabs (R[2] = 0.83, RMSE = 580.2). Swab samples from both aquatic environments predicted PMSI, albeit slightly less accurately than those previously reported from bone powder (lake: R[2] = 0.96, 334.1; river: R[2] = 0.94, 498.47).},
}

@article {pmid40329426,
year = {2025},
author = {Ren, L and Yang, J and Xiao, Y and Guo, L and Rao, J and Wu, C and Wang, X and Wang, Y and Zhang, L and Zhang, L and Jiang, X and Zhong, J and Zhong, J and Yang, W and Wang, C and Wang, J and Li, M},
title = {Transmission of the human respiratory microbiome and antibiotic resistance genes in healthy populations.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {115},
pmid = {40329426},
issn = {2049-2618},
support = {2020-I2M-2-013//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2019PT310029//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2022YFA1304300//National Key R&D Program of China/ ; 2022YFA1304300//National Key R&D Program of China/ ; NSFC82221004//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota/genetics ; Female ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Male ; Adult ; Metagenomics/methods ; *Oropharynx/microbiology ; Middle Aged ; *Drug Resistance, Microbial/genetics ; Family Characteristics ; Young Adult ; Metagenome ; },
abstract = {BACKGROUND: The human microbiome is transmissible between individuals, including pathogens and commensals with metabolic and immune-modulating effects, which could influence susceptibility, severity, and outcomes of both infection and non-infection diseases. However, limited studies of respiratory microbiome transmission within populations have been conducted. Herein, we performed species- and strain-level metagenomic analyses on oropharyngeal (OP) swabs from 1046 healthy urban dwellers across 13 districts, including 111 households with at least two cohabitants, to elucidate the transmission dynamics of the respiratory microbiome within households and communities.

RESULTS: We found that geographic districts accounted for the greatest variation in the OP microbiome, with unrelated individuals from the same district showing greater microbiome similarity and higher strain-sharing rates than those from different districts. Cohabitants, especially spouses and siblings, exhibited similar microbial abundances and shared more strains, with 16.7% (IQR 0.0-33.3%) of strains shared among cohabitants, compared to 0.0% (IQR 0.0-11.1%) in non-cohabiting pairs (p < 0.05). Both respiratory commensals and opportunistic pathogens were shared among cohabitants. In contrast, no evidence of vertical transmission was detected between mother-offspring pairs. Additionally, the OP microbiome contained diverse antibiotic resistance genes (ARGs), with 15.0% linked to mobile genetic elements (MGEs) or plasmids; the flanking sequences of these ARGs were more conserved across species than those of non-MGE-associated ARGs, suggesting horizontal transfer of ARGs among respiratory microorganisms.

CONCLUSIONS: In summary, we characterized the transmissible nature of the OP microbiome and the risk of ARG dissemination among respiratory microorganisms. These findings underscore the role of respiratory microbes and ARGs exchange in shaping the microbiome of healthy populations and emphasize their relevance to public health strategies for respiratory health management. Video Abstract.},
}

Humans
*Microbiota/genetics
Female
*Bacteria/genetics/classification/isolation & purification/drug effects
Male
Adult
Metagenomics/methods
*Oropharynx/microbiology
Middle Aged
*Drug Resistance, Microbial/genetics
Family Characteristics
Young Adult
Metagenome

@article {pmid40329425,
year = {2025},
author = {Vigneron, A and Cloarec, LA and Brochier-Armanet, C and Flandrois, JP and Troussellier, M and Bernard, C and Agogué, H and Oger, PM and Hugoni, M},
title = {Genomic characterisation of novel extremophile lineages from the thalassohaline lake Dziani Dzaha expands the metabolic repertoire of the PVC superphylum.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {48},
pmid = {40329425},
issn = {2524-6372},
support = {project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; project MARWEL, ANR-21-CE20-0049//Agence Nationale de la Recherche/ ; project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Extreme environments are useful systems to investigate limits of life, microbial biogeography and ecology, and the adaptation and evolution of microbial lineages. Many novel microbial lineages have been discovered in extreme environments, especially from the Planctomycetota-Verrucomicrobiota-Chlamydiota (PVC) superphyla. However, their evolutionary history and roles in ecosystem functioning and microbiome assemblage are poorly understood.

RESULTS: Applying a genome-centric approach on an 8-year metagenomic timeseries produced from the hypersaline and hyperalkaline waters of Lake Dziani Dzaha (Mayotte), we recovered 5 novel PVC extremophilic candidate lineages from the biosphere of the lake. Sibling to Elusimicrobia and Omnitrophota, these lineages represented novel halophilic clades, with global distributions bounded to soda lakes and hypersaline hydrosystems. Genome mining of these newly defined clades revealed contrasted, but ecologically relevant, catabolic capabilities involved in the carbon, hydrogen and iron/electron cycles of the Dziani Dzaha ecosystem. This also includes extracellular electron transfer for two of them, suggesting metal reduction or potential electron exchanges with other members of the lake community. By contrast, a putative extracellular giant protein with multiple carbohydrate binding domains and toxin-like structures, as observed in virulence factors, was identified in the genome of another of these clades, suggesting predatory capabilities.

CONCLUSIONS: Our results provided genomic evidences for original metabolism in novel extremophile lineages of the PVC superphyla, revealing unforeseen implications for members of this widespread and diverse bacterial radiation in aquatic saline ecosystems. Finally, monitoring the in-situ distribution of these lineages through the timeseries reveals the drastic effects of environmental perturbations on extreme ecosystem biodiversity.},
}

@article {pmid40329403,
year = {2025},
author = {Huang, Y and Cheng, S and Shi, J and He, P and Ma, Y and Yang, R and Zhang, X and Cao, Y and Lei, Z},
title = {Enhancing Holstein steers growth performance: oregano essential oil's impact on rumen development, functionality and microorganism.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {44},
pmid = {40329403},
issn = {2524-4671},
support = {GSA-XMLZ-2021-01//Beef Cattle Quality Fattening Project of Gansu Province/ ; GSSLCSX-2020-1//Major Science and Technology Special Project of Gansu Province/ ; 2024CYZC-36//Industry Support Project of Gansu Province/ ; },
abstract = {BACKGROUND: Dietary supplementation with oregano essential oil (OEO), a natural plant extracts, is an effective and acceptable method to improve growth, beef quantity and quality, but the undergoing mechanism in rumen has not yet been reported in Holstein steers. This study investigated the effects of oregano essential oil (OEO) on growth performance, fermentation parameters, digestive enzymes activity, rumen development and microbiota in Holstein steers. Eighteen steers were randomly divided into two groups (n = 9) and fed either a basal diet (CCK) or the same diet supplemented with 20 g/(d·head) OEO (CEO) for 270 days.

RESULTS: OEO increased the rumen contents of volatile fatty acids (VFA, acetate (P = 0.011), propionate (P = 0.008), butyrate (P = 0.018)) and digestive enzymes activity (cellulase (P = 0.018), protease and β-glucosidase (P < 0.001)), and improved rumen development (papillae width (P = 0.008) and micropapillary density (P = 0.001)), which reasons contribute to increase body weight (BW, P = 0.022), average daily gain (ADG, P = 0.021), carcass weight (P = 0.001), dressing percentage (P < 0.001), and net meat production (P = 0.001) of steers. Meanwhile, metagenomic and metabolomic analysis revealed OEO significantly reduced abundance of rumen microorganisms, especially methanogenic archaea and viruses while beneficial bacteria (Bifidobacterium) and virulence factors were not affected. KEGG analysis revealed that OEO significantly reduces the host risk of disease, improves the digestive system, and reduces the energy basic metabolism level. A correlation analysis indicated fourteen kinds key microbiome and six downregulated metabolites interfere with each other and together influence the growth performance of steers.

CONCLUSION: These results suggest that feed with 20 g/(d·head) OEO in steers diets could improve growth performance, and reduces virus abundance and disease risk. And the findings provide fundamental insights into OEO, as an alternative source of natural bioactive compounds, how effect on rumen development, composition and function of microorganisms.},
}

@article {pmid40329386,
year = {2025},
author = {Hou, L and Zhao, Z and Steger-Mähnert, B and Jiao, N and Herndl, GJ and Zhang, Y},
title = {Microbial metabolism in laboratory reared marine snow as revealed by a multi-omics approach.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {114},
pmid = {40329386},
issn = {2049-2618},
support = {42206098//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; 42125603//National Natural Science Foundation of China-China Academy of General Technology Joint Fund for Basic Research/ ; MELRS2327//State Key Laboratory of Marine Environmental Science/ ; I4978-B//Austrian Science Fund/ ; },
mesh = {*Snow/microbiology ; Gammaproteobacteria/metabolism/genetics/classification ; Metagenomics/methods ; Metagenome ; *Seawater/microbiology ; *Microbiota ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Phytoplankton/microbiology/metabolism ; Multiomics ; },
abstract = {BACKGROUND: Marine snow represents an organic matter-rich habitat and provides substrates for diverse microbial populations in the marine ecosystem. However, the functional diversity and metabolic interactions within the microbial community inhabiting marine snow remain largely underexplored, particularly for specific metabolic pathways involved in marine snow degradation. Here, we used a multi-omics approach to explore the microbial response to laboratory-reared phytoplankton-derived marine snow.

RESULTS: Our results demonstrated a dramatic shift in both taxonomic and functional profiles of the microbial community after the formation of phytoplankton-derived marine snow using a rolling tank system. The changes in microbial metabolic processes were more pronounced in the metaproteome than in the metagenome in response to marine snow. Fast-growing taxa within the Gammaproteobacteria were the most dominant group at both the metagenomic and metaproteomic level. These Gammaproteobacteria possessed a variety of carbohydrate-active enzymes (CAZymes) and transporters facilitating substrate cleavage and uptake, respectively. Analysis of metagenome-assembled genomes (MAGs) revealed that the response to marine snow amendment was primarily mediated by Alteromonas, Vibrio, and Thalassotalea. Among these, Alteromonas exclusively expressing auxiliary activities 2 (AA2) of the CAZyme subfamily were abundant in both the free-living (FL) and marine snow-attached (MA) microbial communities. Thus, Alteromonas likely played a pivotal role in the degradation of marine snow. The enzymes of AA2 produced by these Alteromonas MAGs are capable of detoxifying peroxide intermediates generated during the breakdown of marine snow into smaller poly- and oligomers, providing available substrates for other microorganisms within the system. In addition, Vibrio and Thalassotalea MAGs exhibited distinct responses to these hydrolysis products of marine snow in different size fractions, suggesting a distinct niche separation. Although chemotaxis proteins were found to be enriched in the proteome of all three MAGs, differences in transporter proteins were identified as the primary factor contributing to the niche separation between these two groups. Vibrio in the FL fraction predominantly utilized ATP-binding cassette transporters (ABCTs), while Thalassotalea MAGs in the MA fraction primarily employed TonB-dependent outer membrane transporters (TBDTs).

CONCLUSIONS: Our findings shed light on the essential metabolic interactions within marine snow-degrading microbial consortia, which employ complementary physiological mechanisms and survival strategies to effectively scavenge marine snow. This work advances our understanding of the fate of marine snow and the role of microbes in carbon sequestration in the ocean. Video Abstract.},
}

*Snow/microbiology
Gammaproteobacteria/metabolism/genetics/classification
Metagenomics/methods
Metagenome
*Seawater/microbiology
*Microbiota
*Bacteria/classification/metabolism/genetics/isolation & purification
Phytoplankton/microbiology/metabolism
Multiomics

@article {pmid40329334,
year = {2025},
author = {Lu, D and Kalantar, KL and Glascock, AL and Chu, VT and Guerrero, ES and Bernick, N and Butcher, X and Ewing, K and Fahsbender, E and Holmes, O and Hoops, E and Jones, AE and Lim, R and McCanny, S and Reynoso, L and Rosario, K and Tang, J and Valenzuela, O and Mourani, PM and Pickering, AJ and Raphenya, AR and Alcock, BP and McArthur, AG and Langelier, CR},
title = {Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID platform.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {46},
pmid = {40329334},
issn = {1756-994X},
support = {5R01HL155418//NIH/NHLBI/ ; 5R01HL155418//NIH/NHLBI/ ; 5R01HL155418//NIH/NHLBI/ ; PJT-156214/CAPMC/CIHR/Canada ; PJT-156214/CAPMC/CIHR/Canada ; PJT-156214/CAPMC/CIHR/Canada ; David Braley Chair in Computational Biology//McMaster University/ ; },
mesh = {Humans ; *Cloud Computing ; *Drug Resistance, Bacterial/genetics ; Software ; Whole Genome Sequencing ; *Bacteria/genetics/drug effects ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; },
abstract = {BACKGROUND: Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next-generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences.

RESULTS: To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and single-isolate whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes from Illumina data. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and single-isolate WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections.

CONCLUSIONS: In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and single-isolate WGS data. Its development represents an important step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.},
}

Humans
*Cloud Computing
*Drug Resistance, Bacterial/genetics
Software
Whole Genome Sequencing
*Bacteria/genetics/drug effects
High-Throughput Nucleotide Sequencing
Metagenomics/methods
Computational Biology/methods
Anti-Bacterial Agents/pharmacology

@article {pmid40329323,
year = {2025},
author = {Duarte, B and Feijão, E and Cruz-Silva, A and Pascoal, P and Nunes, M and Pereira, M and Figueiredo, A and Dias, RP and Tanner, SE and Fonseca, VF},
title = {Reveal your microbes, and i'll reveal your origins: geographical traceability via Scomber colias intestinal tract metagenomics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {43},
pmid = {40329323},
issn = {2524-4671},
support = {http://doi.org/10.54499/UIDB/04292/2020//Fundação para a Ciência e a Tecnologia/ ; 2022.11260.BD//Fundação para a Ciência e a Tecnologia/ ; UI/BD/153050/2022//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {The commercial demand for small pelagic fish, such as Atlantic chub mackerel (Scomber colias), renders them susceptible to provenance fraud. Scomber colias specimens intestinal tract bacteriome from five distinct fishing areas along the Portuguese Atlantic coastline were analyzed by 4th-generation sequencing. Bacteria diversity indices and differential abundance revealed dissimilarities in operational taxonomic unit (OTU) abundance among specimens from distinct fishing sites. Random forest-based model yielded an 85% accuracy rate in attributing sample provenance based on intestinal tract bacteriome OTU relative abundance. Further refinement of microbial features using Indicator Species Analysis, Linear Discriminant Analysis Effect Size (LEfSe) and OTU Gini scores enabled the identification of 3-5 bacterial OTU location biomarkers per fishing site. The intestinal tract bacteriome revealed sequences linked to pathogenic bacteria, particularly in specimens from Center-North and Center-South fishing areas. While this doesn't imply active pathogens, it highlights potential public health concerns and complements efforts to improve seafood microbiological quality and traceability.},
}

@article {pmid40328980,
year = {2025},
author = {Liébana-García, R and López-Almela, I and Olivares, M and Romaní-Pérez, M and Manghi, P and Torres-Mayo, A and Tolosa-Enguís, V and Flor-Duro, A and Bullich-Vilarrubias, C and Rubio, T and Rossini, V and Segata, N and Sanz, Y},
title = {Gut commensal Phascolarctobacterium faecium retunes innate immunity to mitigate obesity and metabolic disease in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40328980},
issn = {2058-5276},
abstract = {The gut microbiota may protect against obesity and chronic metabolic conditions by regulating the immune response to dietary triggers. Yet the specific bacteria that control the overactivation of the immune system in obesity and their mode of action remain largely unknown. Here we surveyed 7,569 human metagenomes and observed an association between the gut symbiont Phascolarctobacterium faecium and non-obese adults regardless of nationality, sex or age. In a mouse model of diet-induced obesity, we confirmed the specificity of P. faecium DSM 32890 anti-obesogenic properties compared with other species of the same genus. P. faecium reversed the inflammatory phenotype associated with obesity. Specifically, P. faecium promoted polarization of alternatively activated macrophages (M2), which reversed the obesity-induced increase in gut-resident type 1 innate lymphoid cells. This resulted in mitigation of glucose intolerance, adiposity and body weight gain irrespective of treatment with live or pasteurized bacteria. The metabolic benefits were independent of the adaptive immune system, but they were abolished by an inhibitor of M2 polarization in mice. P. faecium directly promoted M2-macrophage polarization through TLR2 signalling and these effects seemed to be independent of gut microbiota changes. Overall, we identify a previously undescribed gut commensal bacterium that could help mitigate obesity and metabolic comorbidities by retuning the innate immune response to hypercaloric diets.},
}

@article {pmid40328944,
year = {2025},
author = {Kim, Y and Worby, CJ and Acharya, S and van Dijk, LR and Alfonsetti, D and Gromko, Z and Azimzadeh, PN and Dodson, KW and Gerber, GK and Hultgren, SJ and Earl, AM and Berger, B and Gibson, TE},
title = {Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.},
journal = {Nature microbiology},
volume = {10},
number = {5},
pages = {1184-1197},
pmid = {40328944},
issn = {2058-5276},
support = {R35GM143056//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21AI154075//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM149270//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK121822//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U19AI110818//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM141861//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Feces/microbiology ; Female ; *Metagenomics/methods ; Bayes Theorem ; Longitudinal Studies ; Escherichia coli/genetics/isolation & purification/classification ; Infant ; Algorithms ; Enterococcus faecalis/genetics/isolation & purification/classification ; Adult ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {The ability to detect and quantify microbiota over time from shotgun metagenomic data has a plethora of clinical, basic science and public health applications. Given these applications, and the observation that pathogens and other taxa of interest can reside at low relative abundance, there is a critical need for algorithms that accurately profile low-abundance microbial taxa with strain-level resolution. Here we present ChronoStrain: a sequence quality- and time-aware Bayesian model for profiling strains in longitudinal samples. ChronoStrain explicitly models the presence or absence of each strain and produces a probability distribution over abundance trajectories for each strain. Using synthetic and semi-synthetic data, we demonstrate how ChronoStrain outperforms existing methods in abundance estimation and presence/absence prediction. Applying ChronoStrain to two human microbiome datasets demonstrated its improved interpretability for profiling Escherichia coli strain blooms in longitudinal faecal samples from adult women with recurring urinary tract infections, and its improved accuracy for detecting Enterococcus faecalis strains in infant faecal samples. Compared with state-of-the-art methods, ChronoStrain's ability to detect low-abundance taxa is particularly stark.},
}

Humans
*Microbiota/genetics
Feces/microbiology
Female
*Metagenomics/methods
Bayes Theorem
Longitudinal Studies
Escherichia coli/genetics/isolation & purification/classification
Infant
Algorithms
Enterococcus faecalis/genetics/isolation & purification/classification
Adult
*Bacteria/genetics/classification/isolation & purification

@article {pmid40328731,
year = {2025},
author = {Wei, C and Xu, X and Zhang, J and Wang, X and Han, T and Zhang, Y and Pan, S and Ming, Z and Li, R and Lou, F and Cheng, Y and Xu, H and Sun, X and Geng, G and Pan, Y and Liu, Q and Qi, H and Yan, X and Dang, K and Zhou, J and Sun, C and Li, Y},
title = {Timing of unsaturated fat intake improves insulin sensitivity via the gut microbiota-bile acid axis: a randomized controlled trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4211},
pmid = {40328731},
issn = {2041-1723},
support = {Key Program 82030100//National Natural Science Foundation of China (National Science Foundation of China)/ ; Joint Fund Project U24A20768//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The timing of dietary total fat intake influences glucose homeostasis, however, the impact of unsaturated fat (USFA) intake has yet to be explored. This 12-week, double-blind, randomized, controlled, 2 × 2 factorial-designed feeding trial investigated the effects of timing (lunch or dinner) and types of dietary USFA (high monounsaturated fat or polyunsaturated fat diet) intake on glucose metabolism in seventy prediabetes participants (mean age, 57 years). Sixty participants with completed fecal samples were included in the final analysis (n = 15 for each group). Postprandial serum glucose was first primary outcome, postprandial insulin levels and insulin sensitivity indices were co-primary outcomes Secondary outcomes were continuous glucose levels, serum fatty acid profile, gut microbiome (metagenomic sequencing) and fecal metabolites. Results showed no significant differences in postprandial glucose between groups. However, USFA intake at lunch (vs. dinner) improved insulin sensitivity and reduced postprandial insulin and serum free saturated fatty acid (Ptiming < 0.05, Ptype > 0.05, Pinteraction > 0.05), which was associated with alterations in gut microbiome and bile acid metabolism, regardless of USFA type. In summary, these results suggest that advancing timing of USFA intake improves insulin sensitivity through the gut microbiome and bile acid metabolism. Trial registration: ChiCTR2100045645.},
}

@article {pmid40328237,
year = {2025},
author = {Teitelbaum, J and Madan, S and Patel, S and Coyle, C and Chiu, CY and Thwe, PM and Uehara, M and Jermyn, R and Hemmige, V},
title = {Chagas Meningoencephalitis Diagnosed in Heart Transplant Patient Using Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.24-0553},
pmid = {40328237},
issn = {1476-1645},
abstract = {Chagas meningoencephalitis can present in immunocompromised patients after organ transplantation. We present the first reported instance in which metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid diagnosed Chagas meningoencephalitis in a patient. The diagnosis of Chagas in this case underscores the role of mNGS in identifying rare or unexpected pathogens.},
}

@article {pmid40328153,
year = {2025},
author = {Chu, Y and Dong, X and Fang, S and Gan, L and Lee, X and Zhou, L},
title = {Viruses in human-impacted estuarine ecotones: Distribution, metabolic potential, and environmental risks.},
journal = {Water research},
volume = {282},
number = {},
pages = {123750},
doi = {10.1016/j.watres.2025.123750},
pmid = {40328153},
issn = {1879-2448},
abstract = {Estuaries, as dynamic ecological interfaces between marine and terrestrial systems, are characterized by high productivity and intricate microbial communities. Viruses exert critical regulatory effects on microbial processes, influencing ecological functions and contributing to environmental dynamics in estuarine ecosystems. Despite their significance, the diversity and ecological roles of estuarine viruses remain insufficiently understood. This study explored the viral biogeographic patterns, metabolic potential, and influencing factors in 30 subtropical estuaries in China. Few estuarine viruses (< 22 %) exhibited homology with known viruses, and the low overlap of virus clusters with other environments highlights their novelty and habitat specificity. Mantel tests and random forest analysis identified salinity, temperature, nutrients, and pollutants as key factors influencing viral composition and functional profiles. In addition, correlation analysis between virus and host confirmed significant virus-host interactions, while functional analyses highlighted the role of environmental conditions and horizontal gene transfer in shaping auxiliary metabolic genes linked to elemental biogeochemical cycles, particularly phosphorus, sulfur, and nitrogen. The detection of antibiotic resistance genes (ARGs) and virulence factors (VFs) within viral genomes underscores the role of viruses as reservoirs of ARGs and VFs in these ecosystems. These results demonstrate the profound influence of abiotic and host factors on viral community structures in subtropical estuarine ecotones and underscore the ecological significance of metabolic genes in biogeochemical cycling. By clarifying these interactions, this study advances the understanding of viral contributions to ecosystem functioning and biogeochemical dynamics in estuarine environments.},
}

@article {pmid40328090,
year = {2025},
author = {Xia, Y and Lan, Y and Xu, Y and Liu, F and Chen, X and Luo, J and Xu, H and Liu, Y},
title = {Effects of microplastics and tetracycline induced intestinal damage, intestinal microbiota dysbiosis, and antibiotic resistome: metagenomic analysis in young mice.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109512},
doi = {10.1016/j.envint.2025.109512},
pmid = {40328090},
issn = {1873-6750},
abstract = {Microplastics (MPs) and antibiotic tetracycline (TC) are widespread in the environment and constitute emerging combined contaminants. Young individuals are particularly vulnerable to agents that disrupt intestinal health and development. However, the combined effects of MPs and TC remain poorly understood. In this study, we developed a young mouse model exposed to polystyrene MPs, either alone or in combination with TC for 8 weeks to simulate real-life dietary exposure during early life. Our findings revealed that concurrent exposure to MPs and TC caused the most severe intestinal barrier dysfunction driven by inflammatory activation and oxidative imbalance. Moreover, exposure to MPs and TC reduced the abundance of potential probiotics while promoting the growth of opportunistic pathogens. Metagenomic analysis further indicated that co-exposure to MPs and TC enhanced the abundance of bacteria carrying either antibiotic resistance genes (ARGs) or virulence factor genes (VFGs), contributing to the widespread dissemination of potentially harmful genes. Finally, a strong positive correlation was observed between microbiota dysbiosis, ARGs, and VFGs. In general, this study highlighted the hazards of MPs and antibiotics to intestinal health in young mice, which provided a new perspective into the dynamics of pathogens, ARGs, and VFGs in early-life intestinal environments.},
}

@article {pmid40328065,
year = {2025},
author = {Ye, Y and Yan, X and Jiang, Y and Wang, S and Liu, D and Ren, Y and Li, D and Ngo, HH and Guo, W and Cheng, D and Jiang, W},
title = {Optimized feeding schemes of heterotrophic anodic denitrification coupled with cathodic phosphate recovery from wastewater using a microbial fuel cell.},
journal = {The Science of the total environment},
volume = {981},
number = {},
pages = {179590},
doi = {10.1016/j.scitotenv.2025.179590},
pmid = {40328065},
issn = {1879-1026},
abstract = {Enhanced water quality standards and increasing resource scarcity have prompted extensive research into low-cost nitrogen removal and phosphate recovery from wastewater. Microbial fuel cells (MFCs) offer a viable solution by simultaneously removing nitrogen, recovering phosphorus, and generating electrical energy. This study employed MFCs to achieve simultaneous nitrogen removal and phosphorus recovery, investigating the impact of different feeding schemes. The experimental results indicated that replacing the entire anode chamber solution and recycling the anode effluent to the cathode chamber effectively prevented the accumulation of nitrifying bacteria while achieving the highest pollutant removal performance. Under closed circuit conditions, the system consistently maintained low nitrite concentrations, achieving an average nitrate removal efficiency of 68.09 ± 1.86 % and phosphate recovery efficiency of 83.46 ± 5.30 %. Furthermore, this feeding scheme facilitated microbial growth and reproduction while also improving operational convenience. The study utilized metagenomics and other technologies to comprehensively analyze the system's operation mechanism and reasons for its excellent performance.},
}

@article {pmid40327993,
year = {2025},
author = {Grafakou, ME and Pferschy-Wenzig, EM and Aziz-Kalbhenn, H and Kelber, O and Moissl-Eichinger, C and Bauer, R},
title = {Bidirectional interactions between St. John´s wort and gut microbiome: Potential implications on gut-brain-axis.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {187},
number = {},
pages = {118111},
doi = {10.1016/j.biopha.2025.118111},
pmid = {40327993},
issn = {1950-6007},
abstract = {Emerging evidence highlights the role of gut microbiome in mental health disorders, including depression, raising the question whether the action of antidepressants could be mediated, at least in part, via the microbiome-gut-brain axis. To explore this, we subjected a St. John's wort extract (STW 3-VI), clinically proven to be effective in mild to moderate depression, to a model of the upper and lower intestinal tract, including static in vitro predigestion followed by ex vivo incubation with human microbiota samples. To cover the interindividual diversity of gut microbiome composition, fecal samples from ten healthy volunteers were used. Although unchanged levels of most annotated compounds were observed during simulated upper intestinal tract digestion, incubation with fecal microbiota led to a significant change of the chemical profile of the extract. While hyperforins remained stable, flavonoids and hypericins were rapidly biotransformed, suggesting that they may act as prodrugs. Several metabolites were formed, many of which are known to be involved in gut-brain communication. Differential abundance analysis revealed significant changes in microbiome composition, particularly for taxa known to be potentially associated with depression. Among others, the Firmicutes/Bacteroidetes ratio, known to be lowered in depressive patients, was increased. Functional profiling revealed modulation of pathways involved in gut-brain communication, such as tyrosine and tryptophan metabolism. These bidirectional interactions suggest for the first time the gut microbiome as a potential mediator of the pharmacological effects of St. John's wort extracts via the microbiome-gut-brain axis.},
}

@article {pmid40327934,
year = {2025},
author = {Yu, Y and Huang, W and Tang, S and Xiang, Y and Yuan, L and Yin, H and Dang, Z},
title = {Degradation mechanisms of isodecyl diphenyl phosphate (IDDP) and bis-(2-ethylhexyl)-phenyl phosphate (BEHPP) using a novel microbially-enriched culture.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138453},
doi = {10.1016/j.jhazmat.2025.138453},
pmid = {40327934},
issn = {1873-3336},
abstract = {Organophosphate esters (OPEs) pose significant environmental concerns due to their widespread presence, potential toxicity, and persistence. This study investigated the degradation of the isodecyl diphenyl phosphate (IDDP) and bis-(2-ethylhexyl)-phenyl phosphate (BEHPP) using a novel enrichment culture, which could degrade 85.4 % and 78.2 % of 1 mg/L IDDP and BEHPP after 192 h and 172 h, respectively, under extremely low bacterial dosage (the initial OD600 nm= 0.0075, biomass was approximately 1 mg/L). The identification of intermediate products suggested that the degradation reactions likely included hydrolysis, hydroxylation, methylation, carboxylation, and glycosylation. Metagenomic analysis highlighted the crucial role of enzymes in degrading IDDP and BEHPP, including phosphatase, phosphodiesterase, cytochrome P450, and hydroxylase. Pure strains Burkholderia cepacia ZY1, Sphingopyxis terrae ZY2, and Amycolatopsis ZY3 were isolated, and their efficient individual degradation abilities were confirmed. These efficiencies were lower compared to the enrichment culture, emphasizing the importance of microbial interactions for effective degradation. The pathways identified for these strains illustrated their involvement in different degradation steps, reinforcing the synergy between different degraders. Molecular dynamics simulations provided insights into the interactions between alkaline phosphatase (ALP), cytochrome P450 (CYP450), and hydroxylase with OPEs. These enzymes demonstrated a strong binding capacity with both BEHPP and IDDP, exhibiting distinct binding site preferences that may contribute to varied metabolic pathways. These findings comprehensively reveal the transformation mechanisms of OPEs.},
}

@article {pmid40327666,
year = {2025},
author = {Yang, X and Zhang, Y and Xu, Y and Xu, Y and Zhang, M and Guan, Q and Hu, W and Tun, HM and Xia, Y},
title = {Microbial Disturbances Caused by Pesticide Exposure and Their Predictive Implications for Gestational Diabetes Mellitus.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01076},
pmid = {40327666},
issn = {1520-5851},
abstract = {Previous studies have suggested that pesticide exposure and gut microbiome alterations are associated with gestational diabetes mellitus (GDM) risk. Understanding the complex interactive effect of these factors on GDM is essential. In a cohort of 852 pregnant women, we assessed pesticide levels in serum and analyzed the gut microbiota using 16S rRNA and shotgun metagenomic sequencing. We explored the interactions between pesticides and gut microbiota, assessed their roles in GDM development, and proposed a predictive model based on identified biomarkers. We identified an environmental risk score (ERS), denoting the pesticide mixture level significantly associated with GDM, with the gut microbiota, particularly involving the Dorea branch, playing a crucial mediating role. In addition, we found an interactive effect of pesticide exposure and gut microbiota on GDM risk. Notably, low Prevotella enrichment combined with high ERS arisen from pesticide levels led to a 10.36-fold increased GDM risk. The identified pesticide and gut microbial biomarkers achieved high predictive accuracy for GDM (AUC: 0.833, 95% CI: 0.748-0.918). Collectively, maternal pesticide exposure may induce disrupted microbiome-dependent glycemic alteration, necessitating future assessment of clinical implications. Potential GDM markers can serve as targets for therapeutic intervention caused by pesticides, leading to prevention.},
}

@article {pmid40327160,
year = {2025},
author = {Li, N and Gao, G and Zhang, T and Zhao, C and Zhao, Y and Zhang, Y and Sun, Z},
title = {Co-variation of Host Gene Expression and Gut Microbiome in Intestine-Specific Spp1 Conditional Knockout Mice.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {282},
pmid = {40327160},
issn = {1432-0991},
support = {32325040//National Natural Science Foundation of China/ ; 2022BINCMCF007//Nutrition and Care of Maternal & Child Research Fund Project" of Biostime Institute of Nutrition & Care/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Osteopontin/genetics/metabolism ; Mice, Knockout ; Lipid Metabolism/genetics ; *Intestines/microbiology ; Mice, Inbred C57BL ; Transcriptome ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Osteopontin, which is a highly phosphorylated and glycosylated acidic secreted protein encoded by the secreted phosphoprotein 1 (Spp1) gene, plays a crucial role in immune regulation, inflammatory responses, and cell adhesion. However, its impact on intestinal gene expression and gut microbiota remains underexplored. In this study, we developed an Spp1 conditional knockout mouse model to investigate alterations in the intestinal transcriptome and microbiome, with particular emphasis on changes in gene expression and predicted metabolic pathways. Our findings demonstrated that Spp1 gene conditional knockout significantly modified the expression of genes involved in immune regulation and lipid metabolism. Moreover, metagenomic analysis revealed marked shifts in gut microbial diversity and predicted the metabolic pathways associated with digestion, absorption, and lipid metabolism. These results suggest that Spp1 is instrumental in maintaining gut microbial equilibrium and in regulating host lipid metabolism and immune responses. This study offers new insights into the role of Spp1 in host-microbiota interactions and the potential foundations for developing related therapeutic strategies.},
}

Animals
*Gastrointestinal Microbiome/genetics
Mice
*Osteopontin/genetics/metabolism
Mice, Knockout
Lipid Metabolism/genetics
*Intestines/microbiology
Mice, Inbred C57BL
Transcriptome
Bacteria/classification/genetics/isolation & purification

@article {pmid40327041,
year = {2025},
author = {Hao, Q and Wang, O and Gong, X and Liu, F and Zhang, Y and Xie, Z and Tang, J and Sang, Y and Li, F and Liu, F},
title = {Cadmium-Induced Responses and Tolerance Mechanisms of Aerobic Methanotrophs in Rice Paddy Soils.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00031},
pmid = {40327041},
issn = {1520-5851},
abstract = {Paddy fields are major sources of atmospheric methane and are at risk of cadmium (Cd) contamination. Aerobic methanotrophs, which serve as biological methane sinks, play a key role in methane cycling, but their responses to Cd stress remain poorly understood. Here, we examined the relationship between Cd pollution levels and aerobic methane oxidation potential in paddy soils. We evaluated methanotrophic enrichments under Cd exposure, applied metagenomic sequencing to identify functional microbes, and investigated Cd tolerance mechanisms in pure culture. Aerobic methane oxidation rates were positively correlated with Cd levels in paddy soils from South China, with Methylocystis and Methylomonas emerging as dominant genera possessing diverse Cd tolerance genes. Notably, interspecific differences in Cd tolerance were observed among methanotrophic strains. The faster-growing Methylomonas sp., endowed with more robust antioxidant defenses and extracellular polymeric substances synthesis genes, exhibited Cd resistance through markedly enhanced loosely bound extracellular polymeric substances production, in contrast to the Cd-sensitive Methylobacter sp. Gene knockout experiments confirmed the essential roles of glutathione synthase, glutathione peroxidase, and exosortase in exopolysaccharide extrusion for Cd detoxification. These findings advance our understanding of the methane cycle in Cd-contaminated rice paddies and suggest potential strategies to mitigate methane emissions while addressing Cd detoxification.},
}

@article {pmid40326928,
year = {2025},
author = {Wang, R and Deng, P and Hu, X and Shen, C and Dong, X and Hu, K and Li, R},
title = {Optimizing Watershed Land Use to Achieve the Benefits of Lake Carbon Sinks while Maintaining Water Quality.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00190},
pmid = {40326928},
issn = {1520-5851},
abstract = {Greenhouse gas emissions and water quality decline are two major issues currently affecting lakes worldwide. Determining how to control both greenhouse gas emissions and water quality decline is a long-term challenge. We compiled data on the annual average carbon dioxide (CO2) flux and water quality parameters for 422 global lakes, revealing that 82.42% of the lakes act as carbon sources and that 66.56% have experienced water quality deterioration. Carbon sources and eutrophication trends were observed for lakes from the 1990s to 2020s, with further deterioration expected over the next 80 years. Unmanaged land use change in lake watersheds could exacerbate the CO2 flux into lakes and water quality degradation. In this study, a watershed land use planning (WLUP) framework was established, and a 24.83% reduction in the CO2 flux into lake water, a 5.07% reduction in chlorophyll a (Chl-a), a 4.70% reduction in total phosphorus, and a 12.92% increase in Secchi depth were achieved. The WLUP framework identifies Asia and Europe as the regions experiencing the greatest demands for land use transformation, where optimization leads to the most significant improvements. Metagenomic analysis revealed that forests enhance carbon fixation and that grasslands reduce carbon degradation and phosphorus metabolism in lake watersheds, explaining and supporting the possibility of WLUP. This work provides a win-win solution for improving CO2 fluxes and water quality in global lakes to mitigate the effects of climate change and promote lake protection.},
}

@article {pmid40326765,
year = {2025},
author = {Lindner, BG and Graham, KE and Phaneuf, JR and Hatt, JK and Konstantinidis, KT},
title = {SourceApp: A Novel Metagenomic Source Tracking Tool that can Distinguish between Fecal Microbiomes Using Genome-To-Source Associations Benchmarked Against Mixed Input Spike-In Mesocosms.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03603},
pmid = {40326765},
issn = {1520-5851},
abstract = {Methodologies utilizing metagenomics are attractive to fecal source tracking (FST) aims for assessing the presence and proportions of various fecal inputs simultaneously. Yet, compared to established culture- or PCR-based techniques, metagenomic approaches for these purposes are rarely benchmarked or contextualized for practice. We performed shotgun sequencing experiments (n = 35) of mesocosms constructed from the water of a well-studied recreational and drinking water reservoir spiked with various fecal (n = 6 animal sources, 3 wastewater sources, and 1 septage source) and synthetic microbiome spike-ins (n = 1) introduced at predetermined cell concentrations to simulate fecal pollution events of known composition. We built source-associated genome databases using publicly available reference genomes and metagenome assembled genomes (MAGs) recovered from short- and long-read sequencing of the fecal spike-ins, and then created an associated bioinformatic tool, called SourceApp, for inferring source attribution and apportionment by mapping the metagenomic data to these genome databases. SourceApp's performance varied substantially by source, with cows being underestimated due to under sampling of cow fecal microbiomes. Parameter tuning revealed sensitivity and specificity near 0.90 overall, which exceeded all alternative tools. SourceApp can assist researchers with analyzing and interpreting shotgun sequencing data and developing standard operating procedures on the frontiers of metagenomic FST.},
}

@article {pmid40326511,
year = {2025},
author = {Zhu, Y and Liu, Q and Alffenaar, JW and Wang, S and Cao, J and Dong, S and Zhou, X and Li, X and Li, X and Xiong, H and Zhu, L and Hu, Y and Wang, W},
title = {Gut Microbiota in Patients with Tuberculosis Associated with Different Drug Exposures of Antituberculosis Drugs.},
journal = {Clinical pharmacology and therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1002/cpt.3687},
pmid = {40326511},
issn = {1532-6535},
support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-03//Shanghai New Three-year Action Plan for Public Health/ ; 82073612//National Natural Science Foundation of China/ ; },
abstract = {Interindividual variability in drug exposure can significantly influence treatment outcomes and may lead to drug concentration-related side effects during tuberculosis (TB) treatment. Although the gut microbiota is known to affect drug metabolism, its impact on anti-TB drugs has not been thoroughly explored. This study sought to elucidate the relationship between pre-treatment gut microbiota and drug exposure levels among patients with pulmonary TB. Two cohorts were analyzed: a discovery cohort (N = 99) and a validation cohort (N = 32), both comprising patients undergoing anti-TB therapy with rifampicin, isoniazid, pyrazinamide, and ethambutol. The gut microbiota patterns of participants from the discovery cohort and the validation cohort were profiled by 16S rRNA gene sequencing and metagenomics, respectively. Analyses of both cohorts robustly established a positive association between pre-treatment microbial diversity and drug exposure, as well as significant differences in gut microbiota composition across various drug exposure groups. At the species level, Faecalibacterium prausnitzii was positively associated with drug exposure to rifampicin. Moreover, functional analysis revealed that starch and sucrose metabolism and secondary bile acid biosynthesis were more abundant in the high drug exposure group. To identify biomarkers capable of stratifying patients based on their drug exposure levels, 11 taxa, represented by Faecalibacterium, were selected in the discovery cohort (AUC = 0.992) and were confirmed in the validation cohort with high predictive accuracy (AUC = 0.894). This study demonstrated a correlation between microbial dysbiosis and reduced exposure to anti-TB medications. Optimizing treatment by regulating gut microbiota to improve drug exposure levels requires further validation through larger scale multicenter clinical trials.},
}

@article {pmid40326136,
year = {2025},
author = {Wu, B and Wang, J and Zhang, LN and Tang, W and Chen, KL},
title = {[Value of Pathogenic Detection by Next-Generation Sequencing in Bronchoalveolar Lavage Fluid on Children with Hematological Malignancies].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {33},
number = {2},
pages = {569-574},
doi = {10.19746/j.cnki.issn.1009-2137.2025.02.039},
pmid = {40326136},
issn = {1009-2137},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Hematologic Neoplasms/microbiology/complications ; Child ; Child, Preschool ; Infant ; Retrospective Studies ; Male ; Female ; Adolescent ; *High-Throughput Nucleotide Sequencing ; *Pneumonia/diagnosis/microbiology ; },
abstract = {OBJECTIVE: To investigate the application value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in etiological diagnosis of children with hematological malignancies complicated with pneumonia.

METHODS: We retrospectively analyzed the clinical data of children with hematological malignancies who underwent BALF mNGS pathogenic detection due to pneumonia. All patients underwent mNGS detection of bronchoalveolar lavage fluid as well as traditional methods(including sputum culture, bronchoalveolar lavage fluid culture, blood culture, serological detection of pathogens, etc.). By analyzing the results of mNGS and traditional methods, we compared key indicators such as the positive rate, etiological distribution.

RESULTS: A total of 26 children with hematological malignancies enrolled in the study, including 12 males and 14 females, with a median age of 4.9 (1.8-14.9) years, underwent bronchoalveolar lavage (BAL) 35 times. A total of 17 pathogenic microorganisms were detected in BALF mNGS, including 9 cases of bacterial infection, 10 cases of viral infection, 3 cases of fungal infection, 2 cases of mycoplasma infection and 8 cases of mixed infection, and the most commonly detected bacteria, viruses and fungi were streptococcus pneumoniae, cytomegalovirus and pneumocystis jirovecii, respectively. The positive rate of mNGS detection (91.43%) was significantly higher than that of traditional methods detection (20%, P <0.001). A total of 25 cases were adjusted according to BALF mNGS results.

CONCLUSION: The application of BALF mNGS technology can improve the detection rate of the pathogens in children with hematological malignancies complicated with pneumonia, initially revealed the pathogen spectrum of pulmonary infection in this group, and effectively guide clinical medication, improve treatment outcomes.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology
*Hematologic Neoplasms/microbiology/complications
Child
Child, Preschool
Infant
Retrospective Studies
Male
Female
Adolescent
*High-Throughput Nucleotide Sequencing
*Pneumonia/diagnosis/microbiology

@article {pmid40325896,
year = {2025},
author = {Ikegwuoha, NPP and Hanekom, T and Booysen, E and Jason, C and Parker-Nance, S and Davies-Coleman, MT and van Zyl, LJ and Trindade, M},
title = {Fimsbactin Siderophores From a South African Marine Sponge Symbiont, Marinomonas sp. PE14-40.},
journal = {Microbial biotechnology},
volume = {18},
number = {5},
pages = {e70155},
doi = {10.1111/1751-7915.70155},
pmid = {40325896},
issn = {1751-7915},
support = {//South African Medical Research Council (Self-Initiated grant)/ ; 87326//DSI/NRF SARChI research chair in Microbial Genomics/ ; 312184//European Union PharmaSea Consortium/ ; 129660//National Research Foundation/ ; },
mesh = {*Siderophores/chemistry/metabolism/genetics/isolation & purification ; Multigene Family ; Animals ; Biosynthetic Pathways/genetics ; *Porifera/microbiology ; Symbiosis ; Hydroxamic Acids/metabolism/chemistry ; },
abstract = {Low iron levels in marine habitats necessitate the production of structurally diverse siderophores by many marine bacterial species for iron acquisition. Siderophores exhibit bioactivities ranging from chelation for iron reduction in hemochromatosis sufferers to antimicrobial activity either in their own right or when coupled to known antibiotics for targeted delivery or for molecular imaging. Thus, marine environments are a sought-after resource for novel siderophores that could have pharmaceutical or industrial application. The fimsbactins A-F (1-6) are mixed catechol-hydroxamate siderophores that have only been reported to be produced by Acinetobacter species with the fimsbactin biosynthetic gene clusters (BGCs) widespread among species within this genus. Here, we identified a putative fimsbactin BGC from an uncharacterized marine isolate, Marinomonas sp. PE14-40. Not only was the gene synteny not conserved when comparing the pathway from Marinomonas sp. PE14-40 to the fimsbactin BGC from Acinetobacter sp., but five of the core biosynthetic genes found in the canonical fimsbactin BGC are located elsewhere on the genome and do not form part of the core cluster in Marinomonas sp. PE14-40, with four of these, fbsBCDL, colocalized. Through ESI-MS/MS analysis of extracts from Marinomonas sp. PE14-40, the known fimsbactin analogues 1 and 6 were identified, as well as two new fimsbactin analogues, 7 and 8, containing a previously unreported L-lysine-derived hydroxamate moiety, N1-acetyl-N1-hydroxycadaverine. Feeding experiments using stable isotope-label L-lysine provided further evidence of the N1-acetyl-N1-hydroxycadaverine moiety in 7 and 8. The study demonstrates functional conservation in seemingly disparate biosynthetic pathways and enzyme promiscuity's role in producing structurally diverse compounds.},
}

*Siderophores/chemistry/metabolism/genetics/isolation & purification
Multigene Family
Animals
Biosynthetic Pathways/genetics
*Porifera/microbiology
Symbiosis
Hydroxamic Acids/metabolism/chemistry

@article {pmid40325616,
year = {2025},
author = {Xu, HY and Jiang, MT and Yang, YF and Huang, Y and Yang, WD and Li, HY and Wang, X},
title = {Microalgae-Based Fucoxanthin Attenuates Rheumatoid Arthritis by Targeting the JAK-STAT Signaling Pathway and Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c12474},
pmid = {40325616},
issn = {1520-5118},
abstract = {Fucoxanthin, an abundant carotenoid in marine algae, has garnered attention for its diverse health benefits, including anti-inflammatory and anticancer properties. Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by joint inflammation and damage. This study investigated the therapeutic potential of fucoxanthin extracted from Phaeodactylum tricornutum in collagen-induced RA. Our results demonstrated that fucoxanthin significantly alleviated RA symptoms, including weight loss, joint swelling, and decreased appetite. Histological analysis revealed that fucoxanthin mitigated synovial inflammation, cartilage damage, and bone erosion. Mechanistically, transcriptomic analysis and cell experiments indicated that fucoxanthin suppressed the JAK-STAT signaling pathway by downregulating the expression of inflammatory cytokines, such as IL-6 and IL-1β. Furthermore, metagenomic analysis suggested that fucoxanthin restored the altered gut microbiota composition associated with RA. These findings highlight the therapeutic potential of fucoxanthin from P. tricornutum in the management of RA by targeting multiple pathways, including inflammation and gut microbiota.},
}

@article {pmid40325428,
year = {2025},
author = {Liu, H and Zhu, Y and Huang, Y and Jiang, H},
title = {The application of metagenomic next generation sequencing in diagnosing tuberculous otitis media: a case report and review of the literature.},
journal = {Journal of medical case reports},
volume = {19},
number = {1},
pages = {207},
pmid = {40325428},
issn = {1752-1947},
support = {LQ24H130002//Natural Science Foundation of Zhejiang Province/ ; 2024C03238//Key Research and Development Program of Zhejiang Province/ ; },
mesh = {Humans ; Female ; Middle Aged ; *Otitis Media/diagnosis/microbiology/drug therapy ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Tuberculosis/diagnosis/drug therapy/microbiology ; Antitubercular Agents/therapeutic use ; Tomography, X-Ray Computed ; Mastoidectomy ; },
abstract = {BACKGROUND: Tuberculous otitis media is a chronic Mycobacterium tuberculosis infection of the middle ear tissues. Diseases with varied and insidious clinical features can make diagnosis difficult and delay treatment.

CASE PRESENTATION: Here, we document a case of tuberculous otitis media in a 46-year-old ethnic Han woman that manifested as nonspecific chronic otitis media. A mastoidectomy and tympanoplasty were performed for the initial diagnosis of cholesteatoma. The histopathology of the tissue specimen revealed granuloma formation with necrosis. Staining for acid-fast bacilli and the polymerase chain reaction method for Mycobacterium tuberculosis yielded negative results. However, the chest computed tomography scan demonstrated a pulmonary miliary nodule. Next, metagenomic next-generation sequencing was applied and the Mycobacterium tuberculosis was identified. The patient recovered after receiving antituberculous treatment.

CONCLUSION: This report highlights the application of novel diagnostic tools such as metagenomic next-generation sequencing as a supplementary method for the diagnosis of tuberculous otitis media in highly suspected patients.},
}

Humans
Female
Middle Aged
*Otitis Media/diagnosis/microbiology/drug therapy
*Mycobacterium tuberculosis/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing
*Metagenomics/methods
*Tuberculosis/diagnosis/drug therapy/microbiology
Antitubercular Agents/therapeutic use
Tomography, X-Ray Computed
Mastoidectomy

@article {pmid40325409,
year = {2025},
author = {Herbert, J and Thompson, S and Beckett, AH and Robson, SC},
title = {Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {47},
pmid = {40325409},
issn = {2524-6372},
support = {Expanding Excellence in England (E3)//Research England/ ; Expanding Excellence in England (E3)//Research England/ ; Expanding Excellence in England (E3)//Research England/ ; },
abstract = {INTRODUCTION: Metagenomics, the genomic analysis of all species present within a mixed population, is an important tool used for the exploration of microbiomes in clinical and environmental microbiology. Whilst the development of next-generation sequencing, and more recently third generation long-read approaches such as nanopore sequencing, have greatly advanced the study of metagenomics, recovery of unbiased material from microbial populations remains challenging. One promising advancement in genomic sequencing from Oxford Nanopore Technologies (ONT) is adaptive sampling, which enables real-time enrichment or depletion of target sequences. As sequencing technologies continue to develop, and advances such as adaptive sampling become common techniques within the microbiological toolkit, it is essential to evaluate the benefits of such advancements to metagenomic studies, and the impact of methodological choices on research outcomes.

AIM AND METHODS: Given the rapid development of sequencing tools and chemistry, this study aimed to demonstrate the impacts of choice of DNA extraction kit and sequencing chemistry on downstream metagenomic analyses. We first explored the quality and accuracy of 16S rRNA amplicon sequencing for DNA extracted from the ZymoBIOMICS Microbial Community Standard, using a range of commercially available DNA extraction kits to understand the effects of different kit biases on assessment of microbiome composition. We next compared the quality and accuracy of metagenomic analyses for two nanopore-based ligation chemistry kits with differing levels of base-calling error; the older and more error-prone (~ 97% accuracy) LSK109 chemistry, and newer more accurate (~ 99% accuracy) LSK112 Q20 + chemistry. Finally, we assessed the impact of the nanopore sequencing chemistry version on the output of the novel adaptive sampling approach for real-time enrichment of the genome for the yeast Saccharomyces cerevisiae from the microbial community.

RESULTS: Firstly, DNA extraction kit methodology impacted the composition of the yield, with mechanical bead-beating methodologies providing the least biased picture due to efficient lysis of Gram-positive microbes present in the community standard, with differences in bead-beating methodologies also producing variation in composition. Secondly, whilst use of the Q20 + nanopore sequencing kit chemistry improved the base-calling data quality, the resulting metagenomic assemblies were not significantly improved based on common metrics and assembly statistics. Most importantly, we demonstrated the effective application of adaptive sampling for enriching a low-abundance genome within a metagenomic sample. This resulted in a 5-7-fold increase in target enrichment compared to non-adaptive sequencing, despite a reduction in overall sequencing throughput due to strand-rejection processes. Interestingly, no significant differences in adaptive sampling enrichment efficiency were observed between the older and newer ONT sequencing chemistries, suggesting that adaptive sampling performs consistently across different library preparation kits.

CONCLUSION: Our findings underscore the importance of selecting a DNA extraction methodology that minimises bias to ensure an accurate representation of microbial diversity in metagenomic studies. Additionally, despite the improved base-calling accuracy provided by newer Q20 + sequencing chemistry, we demonstrate that even older ONT sequencing chemistries can achieve reliable metagenomic sequencing results, enabling researchers to confidently use these approaches depending on their specific experimental needs. Critically, we highlight the significant potential of ONT's adaptive sampling technology for targeted enrichment of specific genomes within metagenomic samples. This approach offers broad applicability for enriching target organisms or genetic elements (e.g., pathogens or plasmids) or depleting unwanted DNA (e.g., host DNA) in diverse sample types from environmental and clinical studies. However, researchers should carefully weigh the benefits of adaptive sampling against the potential trade-offs in sequencing throughput, particularly for low-abundance targets, where strand rejection can lead to pore blocking. These results provide valuable guidance for optimising adaptive sampling in metagenomic workflows to achieve specific research objectives.},
}

@article {pmid40325330,
year = {2025},
author = {Panicucci, C and Casalini, S and Fiorito, G and Rinaldi, AB and Biagioli, V and Cangelosi, D and Brolatti, N and Principi, E and Baratto, S and Pedemonte, M and Morando, S and Riva, A and Venturino, C and Striano, P and Uva, P and Bruno, C},
title = {Exploratory Analysis of Gut Microbiota Profile in Duchenne Muscular Dystrophy (DMD) Patients with Intellectual Disability.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {40325330},
issn = {1559-1182},
abstract = {This study investigates the differences in gut microbiota composition between DMD patients with (DMD +) and without (DMD -) intellectual disability (ID) and its potential role in cognitive outcomes. In this study, we assessed the gut microbiota in 50 genetically confirmed DMD patients (median age 13.1 years) using 16S rRNA gene sequencing. Cognitive assessment was performed using the Wechsler Intelligence Scales, with ID defined as an IQ < 70. Stool samples were analyzed, and statistical methods were used to assess alpha- and beta-diversity. Thirty-four percent of patients had ID. No significant differences were found in alpha-diversity or in the Firmicutes/Bacteroidetes ratio. However, beta-diversity analysis revealed significant differences between DMD + and DMD - groups, including, in DMD + , an increased abundance of Propionibacterium and Bifidobacterium, and a reduction in Bulleidia. These bacteria are involved in metabolic pathways that can influence neurological health through the gut-brain axis, particularly via the production of short-chain fatty acids. While these preliminary findings suggest a possible association between gut microbiota profile and cognitive impairment in DMD, further research is needed to explore a causal relationship and consider microbiota-targeted therapeutic strategies.},
}

@article {pmid40325116,
year = {2025},
author = {Yiminniyaze, R and Zhang, Y and Zhu, N and Zhang, X and Wang, J and Li, C and Wumaier, G and Zhou, D and Xia, J and Li, S and Dong, L and Zhang, Y and Zhang, Y and Li, S},
title = {Characterizations of lung cancer microbiome and exploration of potential microbial risk factors for lung cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15683},
pmid = {40325116},
issn = {2045-2322},
support = {82241028//National Clinical Key Specialty Project Foundation/ ; 82270058//National Natural Science Foundation of China/ ; 22Y11900600//Shanghai Year 2022 Science and Technology Innovation Action Plan Medical Innovation Research Special Project/ ; },
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; Risk Factors ; *Microbiota/genetics ; Middle Aged ; Aged ; Lung/microbiology/pathology ; High-Throughput Nucleotide Sequencing ; Adult ; Shewanella/isolation & purification/genetics ; },
abstract = {Recent studies have indicated that the lung microbiome may contribute to the development and progression of lung cancer, although the precise mechanisms remain to be fully elucidated. This study sought to delineate the microbial composition within lung cancer tissues and identify potential microbial risk factors. Tissue samples were collected from patients newly diagnosed with pulmonary opacities, and metagenomic next-generation sequencing was employed to analyze these samples. Tissue samples were collected from 130 patients with pulmonary opacities, categorized into lung cancer (50 cases), pulmonary infection (53 cases), and non-infectious pulmonary diseases (27 cases). The non-infectious group served as the primary control. The diversity of the lung microbiome in lung cancer tissues was found to be comparable to that observed in non-infectious benign pulmonary conditions. Specific phyla and genera exhibited increased abundance in lung cancer tissues. Additionally, correlations were established between certain microorganisms and clinical characteristics associated with lung cancer. Multivariate binary logistic regression analysis revealed that age and Shewanella were independent risk factors for lung cancer development. This study suggests that the composition of the lung microbiome differs significantly between individuals with lung cancer and those with benign pulmonary conditions, with certain microbes such as Shewanella potentially serving as risk factors for lung cancer progression.},
}

Humans
*Lung Neoplasms/microbiology/pathology
Male
Female
Risk Factors
*Microbiota/genetics
Middle Aged
Aged
Lung/microbiology/pathology
High-Throughput Nucleotide Sequencing
Adult
Shewanella/isolation & purification/genetics

@article {pmid40324989,
year = {2025},
author = {Gibbs, AJ and Fuentes, S and Adams, I and Hajizadeh, M and Ben Mansour, K and Guy, PL and Fribourg, C and Ziebell, H and Kreuze, J and Fox, A and Jones, RAC},
title = {A phylogeny of the tymoviruses, sensu stricto, and its global interpretation in space and time.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-01-25-0061-RE},
pmid = {40324989},
issn = {0191-2917},
abstract = {Maximum likelihood (ML) phylogenies of 109 tymoviruses, including three obtained directly from metagenomes, were calculated from all three open reading frames separately, but the concatenated sequences of their replicase and coat protein genes gave the most representative trees. ML phylogenies were also calculated from all recorded tymomvirus coat protein genes, and from datasets of the turnip yellow mosaic virus cluster, and separately of tomato yellow blotch, Andean potato latent and Andean potato mild mosaic viruses. These phylogenies showed that the basal divergence of tymoviruses occurred in a population infecting Eurasian brassicas (rosids), and more recently, one of the basal lineages diversified and adapted to infect some solanaceous (asterid) plants and crops of Central and South America. Heterochronous dating of the phylogenies failed, but heuristic comparisons based on patristic distances, branching patterns and external events suggested that the 'most recent common ancestor' of all known tymoviruses existed before the last Ice Age. Some lineages reached the Americas about 15,000 years ago. However, most spread of the few tymoviruses now found on more than one continent occurred during the past two centuries. The only recombinants were two sequences of Chiltepin yellow mosaic virus both with Nemesia ring necrosis virus as minor parent. Population genetic analysis found significant evidence of population contraction in the tymovirus populations infecting asterid hosts in the Americas. It also found the replicase and coat protein genes were significantly negatively selected. By contrast, the overlapping movement protein genes were positively selected which may help them adapt to new host species, including infecting economically significant crops. This knowledge about tymoviruses is important to plant biosecurity authorities.},
}

@article {pmid40324646,
year = {2025},
author = {Shen, H and Wang, D and Huang, Y and Yang, Y and Ji, S and Zhu, W and Liu, Q},
title = {2,3,7,8-tetrachlorodibenzofuran modulates intestinal microbiota and tryptophan metabolism in mice.},
journal = {Life sciences},
volume = {373},
number = {},
pages = {123679},
doi = {10.1016/j.lfs.2025.123679},
pmid = {40324646},
issn = {1879-0631},
abstract = {Persistent organic pollutants (POPs) are known to disrupt gut microbiota composition and host metabolism, primarily through dietary exposure. In this study, we investigate the impact of 2,3,7,8-tetrachlorodibenzofuran (TCDF) on gut microbiota and host metabolic processes. RNA-seq analysis revealed that TCDF exposure significantly affected tryptophan metabolism, lipid metabolic pathways, and immune system function. Metagenomic and metabolomic analyses further showed that TCDF reduced the abundance of Mucispirillum schaedleri and levels of two key tryptophan metabolites, indole-3-carboxaldehyde (3-IAld) and Indole acrylic acid (IA). Supplementation with 3-IAld and IA alleviated TCDF-induced liver toxicity in mouse, as evidenced by reduced Cyp1a1 expression, and mitigated intestinal inflammation, reflected by lower pro-inflammatory cytokines (Ifn-γ and Il-1β) in the colon. Additionally, 3-IAld and IA supplementation enhanced intestinal barrier function, as demonstrated by increased Mucin 2 (MUC2) expression in the gut mucosa of mouse. These findings suggest that TCDF exposure disrupts the gut microbiome and host metabolic balance, and highlight the potential therapeutic role of tryptophan-derived metabolites in mitigating environmental pollutant-induced damage.},
}

@article {pmid40324616,
year = {2025},
author = {Zhao, X and Chen, Y and Hu, J and Wang, H and Ye, Z and Zhang, J and Meng, J and Li, J and Dahlgren, RA and Zhang, S and Gao, H and Chen, Z},
title = {Efficacy of nitrate and biochar@birnessite composite microspheres for simultaneous suppression of As(III) mobilization and greenhouse gas emissions in flooded paddy soils.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121757},
doi = {10.1016/j.envres.2025.121757},
pmid = {40324616},
issn = {1096-0953},
abstract = {Elevated As(III) pollution and greenhouse gas (GHG) emissions are two primary environmental concerns associated with flooded paddy soils. Herein, a novel biochar@birnessite composite microsphere was engineered using a biochar, birnessite and sodium alginate formulation. The microspheres were applied along with nitrate to examine their efficacy in suppressing As(III) mobilization and GHG emissions in an As-contaminated flooded paddy soil. After a 10-day incubation period, the combined nitrate+microsphere treatment achieved desirable remediation effects versus a nitrate-alone treatment, with mobile As(III) (initially 0.1 mM in flooded layer) completely immobilized and N2O, CH4 and CO2 emissions declining by 89%, 73% and 31%, respectively. As(III) immobilization was ascribed to oxidation/adsorption/coprecipitation by FeOx/MnOx regenerated from successive cycles of Feammox/Mnammox and nitrate-reduction coupled with Fe(II) oxidation (NRFO)/nitrate-reduction coupled with Mn(II) oxidation (NRMO). Moreover, NRFO/NRMO-derived full denitrification displayed high thermodynamic feasibility, leading to full denitrification with the generation of N2 rather than N2O. The co-occurrence of anaerobic oxidation of methane (AOM) driven by biochar-shuttling and coupled reduction of nitrate/FeOx/MnOx fostered anaerobic oxidation of CH4 to CO2. A portion of the resulting CO2 was incorporated into poorly-soluble carbonate minerals leading to lower CO2 emission and soil carbon sequestration. Metagenomic sequencing revealed that the nitrate+microsphere treatment enriched the abundances of key microorganisms linked to As/Fe/Mn oxidation and GHG mitigation (e.g., Geobacter, Streptomyces, Cupriavidus and Chloroflexus). Our findings document the efficacy of nitrate+biochar@birnessite microsphere treatment as an effective remediation strategy to simultaneously mitigate As(III) pollution and GHG emissions in flooded paddy soils.},
}

@article {pmid40323477,
year = {2025},
author = {Kiran, NS and Chatterjee, A and Yashaswini, C and Deshmukh, R and Alsaidan, OA and Bhattacharya, S and Prajapati, BG},
title = {The gastrointestinal mycobiome in inflammation and cancer: unraveling fungal dysbiosis, pathogenesis, and therapeutic potential.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {6},
pages = {195},
pmid = {40323477},
issn = {1559-131X},
mesh = {Humans ; *Dysbiosis/microbiology ; *Mycobiome ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Inflammation/microbiology ; *Gastrointestinal Neoplasms/microbiology ; Fungi/pathogenicity ; Animals ; },
abstract = {The gastrointestinal mycobiome, comprising diverse fungal species, plays a significant role in gastrointestinal carcinogenesis and inflammatory bowel disease (IBD) pathogenesis. Recent studies have demonstrated that dysbiosis of the gut mycobiome, characterized by an overrepresentation of pathogenic fungi such as Candida albicans and Aspergillus, correlates with increased inflammation and cancer risk. For instance, C. albicans has been shown to induce colonic inflammation through the activation of pattern recognition receptors and the release of pro-inflammatory cytokines, exacerbating IBD symptoms and potentially facilitating tumorigenesis. Additionally, metagenomic analyses have revealed distinct fungal signatures in colorectal cancer tissues compared to adjacent healthy tissues, highlighting the potential of fungi as biomarkers for disease progression. Mechanistically, gut fungi contribute to disease through biofilm formation, mycotoxin secretion (e.g., aflatoxins, candidalysin), pro-inflammatory cytokine induction (e.g., IL-1β, IL-17), and disruption of epithelial barriers-creating a tumor-promoting and inflammation-prone environment. Furthermore, the interplay between fungi and the bacterial microbiome can amplify inflammatory responses, contributing to chronic inflammation and cancer development. Fungal interactions with bacterial communities also play a synergistic role in shaping mucosal immune responses and enhancing disease severity in both cancer and IBD contexts. As research continues to elucidate these complex fungal-host and fungal-bacterial interactions, targeting the gut mycobiome may offer novel therapeutic avenues for managing IBD and gastrointestinal cancers, emphasizing the need for integrated, mechanistically informed approaches to microbiome research.},
}

Humans
*Dysbiosis/microbiology
*Mycobiome
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
*Inflammation/microbiology
*Gastrointestinal Neoplasms/microbiology
Fungi/pathogenicity
Animals

@article {pmid40323435,
year = {2025},
author = {Reynolds, J and Yoon, JY},
title = {Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis.},
journal = {Mikrochimica acta},
volume = {192},
number = {6},
pages = {334},
pmid = {40323435},
issn = {1436-5073},
mesh = {*Machine Learning ; *Microbiota ; Humans ; Spectrometry, Fluorescence/methods ; *Bacteria/isolation & purification/genetics ; },
abstract = {Most microbiota determination (skin, gut, soil, etc.) are currently conducted in a laboratory using expensive equipment and lengthy procedures, including culture-dependent methods, nucleic acid amplifications (including quantitative PCR), DNA microarray, immunoassays, 16S rRNA sequencing, shotgun metagenomics, and sophisticated mass spectrometric methods. In situ and rapid analysis methods are desirable for fast turnaround time and low assay cost. Fluorescence identification of bacteria and their mixtures is emerging to meet this demand, thanks to the recent development in various machine learning methods. High-dimensional spectroscopic or microscopic imaging data can be obtained to identify the bacterial makeup and its implications for human health and the environment. For example, we can classify healthy versus non-healthy skin microbiome, inflammatory versus non-inflammatory gut microbiome, degraded versus non-degraded soil microbiome, etc. This tutorial summarizes the various machine-learning algorithms used in bacteria identification and microbiota determinations. It also summarizes the various fluorescence spectroscopic methods used to identify bacteria and their mixtures, including fluorescence lifetime spectroscopy, fluorescence resonance energy transfer (FRET), and synchronous fluorescence (SF) spectroscopy. Finally, various fluorescence microscopic imaging methods were summarized that have been used to identify bacteria and their mixtures, including epi-fluorescence microscopy, confocal microscopy, two-photon/multi-photon microscopy, and super-resolution imaging methods (STED, SIM, PALM, and STORM). Finally, it discusses how these methods can be applied to microbiota determinations, what can be demonstrated in the future, opportunities and challenges, and future directions.},
}

*Machine Learning
*Microbiota
Humans
Spectrometry, Fluorescence/methods
*Bacteria/isolation & purification/genetics

@article {pmid40323169,
year = {2025},
author = {Zhu, D and Galley, J and Pizzini, J and Musteata, E and Douglas, MV and Chazin, WJ and Skaar, EP and Tabor, JJ and Britton, RA},
title = {Microbial Biosensor for Sensing and Treatment of Intestinal Inflammation.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2504364},
doi = {10.1002/advs.202504364},
pmid = {40323169},
issn = {2198-3844},
support = {//Baylor College of Medicine Seed Funding/ ; //Crohn's and Colitis Foundation Litwin Pioneer Award (RAB)/ ; R01AI123278//National Institutes of Health grants/ ; U19AI157981//National Institutes of Health grants/ ; R01AI155586//National Institutes of Health grants/ ; R01AI164587//National Institutes of Health grants/ ; U19AI174999//National Institutes of Health grants/ ; },
abstract = {Synthetic biology has enabled the development of biosensors to detect intestinal inflammation, yet few target the clinically validated biomarker of intestinal inflammation calprotectin with both diagnostic and therapeutic capabilities. Here, an optimized calprotectin biosensor is presented that leverages a zinc uptake regulator (Zur) controlled promoter coupled with a memory circuit to detect and record intestinal inflammation in vivo. The level of biosensor activation strongly correlates with calprotectin levels in the colon of two independent mouse models of colitis. Coupling of the biosensor with the production of the anti-inflammatory cytokine IL10 allowed for the resolution of chemically induced colitis, demonstrating the ability of the biosensor to sense and respond to disease. This work highlights the utility of developing synthetic organisms for the diagnosis and treatment of intestinal disease using clinically validated biomarkers.},
}

@article {pmid40322835,
year = {2025},
author = {Luo, Z and Lu, X and Zhang, T and Shi, S and Zhao, R and He, Y and Yao, H and Zhu, W and Zhang, C},
title = {Moxibustion Enhances Ovarian Function by Inhibiting the Th17/IL-17 Pathway and Regulating Gut Microbiota in POI Rats.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {93},
number = {5},
pages = {e70082},
doi = {10.1111/aji.70082},
pmid = {40322835},
issn = {1600-0897},
support = {BE2020624//Natural Science Foundation of Jiangsu Province/ ; },
mesh = {Animals ; Female ; *Moxibustion/methods ; *Gastrointestinal Microbiome/immunology ; Rats ; *Th17 Cells/immunology ; *Interleukin-17/metabolism ; *Primary Ovarian Insufficiency/therapy/immunology/chemically induced ; Rats, Sprague-Dawley ; *Ovary/physiology ; Signal Transduction ; Disease Models, Animal ; },
abstract = {PROBLEM: Premature ovarian insufficiency (POI) is a significant cause of female infertility, severely impacting physical and mental health. Current treatments, primarily hormone replacement therapy, fail to restore ovarian function and may cause adverse effects. Moxibustion, a traditional Chinese medicine therapy, has shown potential in treating POI, but its mechanisms remain unclear. This study investigated the therapeutic effects of moxibustion on POI rats and explored its underlying mechanisms.

METHOD OF STUDY: A POI rat model was established using cyclophosphamide, and moxibustion was applied daily to the CV4 and SP6 acupoints for 4 weeks. We analyzed hormone levels, estrous cycles, follicle count, and gut microbiota. Transcriptomic and metagenomic sequencing were performed to identify potential pathways. Network pharmacology was used to predict active components and targets.

RESULTS: Moxibustion restored estrous cycles, improved hormonal imbalances, and increased ovarian reserve function. Network pharmacology identified five active components in moxa, and based on the results of network pharmacology and transcriptome sequencing, we believe that the regulation of the IL-17 pathway is the key mechanism. Further experiments showed moxibustion downregulated the Th17/IL-17 pathway, reduced key proteins such as IL-17R, NF-κB, MMP3, IκBα, IL-1β, MMP9, TRAF6, and Cox2. Flow cytometry confirmed a decrease in Th17 cell proportion. Gut microbiota analysis revealed that moxibustion enhanced microbial diversity and modulated specific bacterial species, which correlated with improved hormone levels.

CONCLUSION: Moxibustion has a therapeutic effect on POI rats by regulating the Th17/IL17 pathway and gut microbiota, which provides evidence for the clinical application of moxibustion.},
}

Animals
Female
*Moxibustion/methods
*Gastrointestinal Microbiome/immunology
Rats
*Th17 Cells/immunology
*Interleukin-17/metabolism
*Primary Ovarian Insufficiency/therapy/immunology/chemically induced
Rats, Sprague-Dawley
*Ovary/physiology
Signal Transduction
Disease Models, Animal

@article {pmid40322711,
year = {2025},
author = {Kulsum, U and Patankar, C and Biswas, D},
title = {MOSMAP: Mosquito metagenome analysis pipeline.},
journal = {Bioinformation},
volume = {21},
number = {2},
pages = {110-112},
pmid = {40322711},
issn = {0973-2063},
abstract = {MosMAP is a bioinformatics pipeline designed for mosquito metagenome analysis. MosMAP automates essential processes like quality control, taxonomic classification, species abundance estimation and visualization by integrating tools such as Trimgalore, Kraken 2, Bracken and Krona into a user-friendly workflow. Each of these tools is integrated to ensure a smooth and efficient workflow from raw data to interpretable results. The pipeline simplifies complex bioinformatics tasks, making them accessible to researchers with limited computational expertise. MosMAP demonstrated high concordance with standard bioinformatics workflows such as Kraken and Bracken in terms of read retention, taxonomic accuracy and abundance estimation when applied to metagenomes of mosquito collected in Bhopal, India. This accessible pipeline promotes the simplification of meta-genomics, supporting research in microbiology, ecology and vector-borne diseases.},
}

@article {pmid40322468,
year = {2025},
author = {Shan, H and Wang, J and Zhang, Q and Ming, Z and Zhang, Y and He, P and Fang, P and Zhang, M and Li, W and Shi, H and Guan, Y and Yang, S},
title = {Pathogen surveillance and risk factors for pulmonary infection in patients with lung cancer: A retrospective single-center study.},
journal = {Open medicine (Warsaw, Poland)},
volume = {20},
number = {1},
pages = {20251180},
pmid = {40322468},
issn = {2391-5463},
abstract = {BACKGROUND: Early and accurate diagnosis of pulmonary infection (PI) is crucial for the timely implementation of appropriate treatment strategies in lung cancer patients.

METHODS: Metagenomic next-generation sequencing and conventional testing were performed in lung cancer patients with and without PI. The pathogen profiles were analyzed, and risk factors for PI were explored using univariate and multivariate logistic regression models.

RESULTS: A total of 55 lung cancer patients with PI and 59 non-infected lung cancer patients were included. There were 41 underlying pathogens identified by both methods in lung cancer patients with PI. The coexistence of different pathogen types was common, particularly between fungi and viruses, which was observed in 28.57% of cases. The incidence of Streptococcus pneumoniae and Pneumocystis jirovecii is significantly higher in small-cell lung carcinoma patients compared to that in non-small-cell lung carcinoma patients. Besides, cytomegalovirus, P. jirovecii, and Aspergillus were more likely to be found in advanced-stage patients. Risk factor analysis revealed that Karnofsky Performance Status <90 and chemotherapy were strongly associated with PI in lung cancer patients.

CONCLUSIONS: This study highlights the complexity of PI in lung cancer patients, emphasizing the need for tailored diagnostic and therapeutic strategies based on cancer type and stage.},
}

@article {pmid40321823,
year = {2025},
author = {Yupanqui García, GJ and Badotti, F and Ferreira-Silva, A and da Cruz Ferraz Dutra, J and Martins-Cunha, K and Gomes, RF and Costa-Rezende, D and Mendes-Pereira, T and Delgado Barrera, C and Drechsler-Santos, ER and Góes-Neto, A},
title = {Microbial diversity of the remote Trindade Island, Brazil: a systematic review.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19305},
pmid = {40321823},
issn = {2167-8359},
mesh = {Brazil ; *Soil Microbiology ; *Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; Islands ; *Fungi/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Ecosystem ; *Microbiota ; },
abstract = {Trindade Island is a unique volcanic environment in the South Atlantic, characterized by acidic soils, rich organic matter and a high diversity of micro- and macroorganisms. Such diversity can represent a range of ecological niches and functions, potentially offering valuable ecosystem services. This systematic review aimed to synthesize the current knowledge of the island's microbial communities, focusing on their ecological roles and biotechnological potential. Following the PRISMA guidelines, a comprehensive search of the scientific literature was conducted to identify studies that performed DNA sequencing of samples collected on Trindade Island, Brazil. The selected studies used approaches, such as shotgun metagenomics and marker gene sequencing, including samples from microcosm experiments and culture-dependent samples. A total of eight studies were selected, but only six provided detailed taxonomic information, from which more than 850 genera of Bacteria, Archaea, and Fungi were catalogued. Soil communities were dominated by Actinobacteriota, Acidobacteriota, and Ascomycota (Fungi) while marine and coral environments showed high diversity of Pseudomonadota and Cyanobacteria. Microcosm experiments revealed adaptive responses to hydrocarbon contamination, mainly for Alcanivorax and Mortierella (Fungi). Compared to other ecosystems, such as the oligotrophic Galapagos Islands and the sea-restricted Cuatro Cienegas Basin, Cyanobacteria were shown to be more adaptive.},
}

Brazil
*Soil Microbiology
*Biodiversity
*Bacteria/genetics/classification/isolation & purification
Islands
*Fungi/genetics/classification/isolation & purification
*Archaea/genetics/classification/isolation & purification
Ecosystem
*Microbiota

@article {pmid40321713,
year = {2025},
author = {De Coninck, L and Hadermann, A and Ingletto, L and Colebunders, R and Gamnsi Njamnshi, K and Njamnshi, AK and Mokili, JL and Siewe Fodjo, JN and Matthijnssens, J},
title = {Cameroonian blackflies (Diptera: Simuliidae) harbour a plethora of RNA viruses.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf024},
pmid = {40321713},
issn = {2057-1577},
abstract = {Strong epidemiological evidence suggests that onchocerciasis may be associated with epilepsy-hence the name onchocerciasis-associated epilepsy (OAE). However, the pathogenesis of OAE still needs to be elucidated, as recent studies have failed to detect Onchocerca volvulus in the central nervous system of persons with OAE. Therefore, it was suggested that a potentially neurotropic virus transmitted by blackflies could play a role in triggering OAE. To investigate this hypothesis, adult blackflies were collected in an onchocerciasis-endemic area with a high OAE prevalence in the Ntui Health District, Cameroon. A viral particle-based shotgun sequencing approach was used to detect viral sequences in 55 pools of 10 blackflies. A very high abundance of viral reads was detected across multiple (novel) viral families, including viral families associated with human disease. Although no genomes closely related to known neurotropic viruses were found in the blackfly virome, the plethora of novel viruses representing novel species, genera and even families warrant further exploration for their potential to infect vertebrates. These results could serve as a first step for studying the viruses associated with the haematophagous blackfly, which also could be present in their nematode host O. volvulus. Exploring the diversity of viruses in blackflies should be included in the active surveillance of zoonotic diseases.},
}

@article {pmid40321599,
year = {2025},
author = {Zhou, Z and Song, Y and Yan, Y and Zheng, Y},
title = {Metagenomic Next-Generation Sequencing Improves the Diagnosis Efficiency of Mixed Periprosthetic Joint Infections.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2165-2174},
pmid = {40321599},
issn = {1178-6973},
abstract = {PURPOSE: To explore the clinical significance of metagenomic next-generation sequencing (mNGS) in the diagnosis of mixed periprosthetic joint infections (PJI).

METHODS: The data pertaining to patients suspected of PJI who underwent arthroplasty at our hospital between January 2020 and June 2024 were analyzed. Patients included in the study were subjected to microbial culture and mNGS analyses to evaluate the efficacy of mNGS in diagnosing mixed PJIs.

RESULTS: Among the 44 PJI patients included, 20 (45.45%) were culture-positive, and 35 (79.55%) were mNGS-positive. Compared to microbial culture, mNGS demonstrated significantly higher sensitivity, negative predictive value, and accuracy (79.55% vs 45.45%, 55.00% vs 35.14%, and 80.70% vs 57.89%, respectively; all P<0.05). However, the specificity of mNGS was significantly lower than culture (84.62% vs 100.00%, P<0.05). For mixed PJIs, the sensitivity of mNGS was notably higher, albeit with lower specificity and positive predictive value compared to microbial culture (72.23% vs 27.27%, 85.19% vs 100.00%, 66.67% vs 100.00%, respectively; all P<0.05). mNGS enables more sensitive detection of co-pathogens in mixed PJI, accelerating targeted therapy and reducing inappropriate broad-spectrum therapy. While its lower specificity requires clinical integration, it clarifies complex diagnoses and streamlines stewardship for improved outcomes.

CONCLUSION: mNGS is a promising technique for rapidly and accurately detecting co-pathogens in mixed PJI.},
}

@article {pmid40321269,
year = {2025},
author = {Tronel, A and Roger-Margueritat, M and Plazy, C and Biennier, S and Craspay, A and Mohanty, I and Cools Portier, S and Laiola, M and Roeselers, G and Mathieu, N and Hupe, M and Dorrestein, PC and Alcaraz, JP and Martin, D and Cinquin, P and Silvent, AS and Giai, J and Proust, M and Soranzo, T and Buelow, E and Le Gouellec, A},
title = {Profiling the human luminal small intestinal microbiome using a novel ingestible medical device.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.18.25326056},
pmid = {40321269},
abstract = {The invasive nature of sample collection for studying the small intestinal (SI) microbiome often results in its poor characterization. This study evaluated a novel ingestible medical device (MD) for SI luminal sample collection. A monocentric interventional trial (NCT05477069) was conducted on 15 healthy subjects. Metagenomics, metabolomics and culturomics assessed the MD's effectiveness in characterizing the healthy SI microbiome and identifying potential biomarkers. The SI microbiota differed significantly from the fecal microbiota, displaying high inter-individual variability, lower species richness, and reduced alpha diversity. A combined untargeted and semi-targeted LC-MS/MS metabolomics approach identified a distinct SI metabolic footprint, with bile acids and amino acids being the most abundant classes of metabolites. Host and host/microbe-derived bile acids were particularly abundant in SI samples. The application of a fast culturomics approach to two SI samples enabled species-level characterization, resulting in the identification of 90 bacterial species, including five potential novel species. The present study demonstrates the efficacy of our novel sampling MD in enabling comprehensive SI microbiome analysis through an integrative multi-omics approach, allowing the identification of distinct microbiome signatures between SI and fecal samples.},
}

@article {pmid40320901,
year = {2025},
author = {Gervasoni, KN and Iacia, MVMS and Silva, KO and Franco, LG and Mendes, MEF and Neves, TJDC and Sanches, WS and Oliveira, LB and Saito, EA and Vieira, KCO and Pereira, VC and Nai, GA and Winkelstroter, LK},
title = {Protective Effect of Piperine on Indomethacin-Induced Intestinal Damage.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70097},
doi = {10.1002/mnfr.70097},
pmid = {40320901},
issn = {1613-4133},
abstract = {Nonsteroidal antiinflammatory drugs (NSAIDs) are widely prescribed for the treatment of inflammation and chronic pain. Chronic use of NSAIDs is associated with adverse events and organ damage, especially to the gastric mucosa and small intestine. This study evaluates the protective effect of piperine on indomethacin-induced intestinal damage. Eighteen male Mus musculus mice, aged 6-8 weeks, were used. Intestinal damage was induced with indomethacin (10 mg/mL) and cotreatment with piperine (20 mg/mL), both administered orally. After 14 days, the animals were euthanized. Biochemical serological analysis was performed. Intestinal inflammation was assessed based on macroscopic, histopathological, and metagenomic analyses. Histopathological analysis showed a reduction in small intestine inflammation (p < 0.05) and the disappearance of necrosis in the intestinal wall of the large intestine. Crypt and villus measurements showed increased values in the piperine-treated group (p < 0.05). An approximately six-fold increase in aspartate aminotransferase (AST) was observed in the Indomethacin group (p < 0.05). Regarding the intestinal microbiota, an increase in genus diversity was observed in the piperine-treated group (p < 0.05). There was a 50% reduction in micronucleus formation with the administration of piperine 20 mg/kg (p < 0.05). It was concluded that cotreatment with piperine has great potential in mitigating the side effects caused by NSAIDs.},
}

@article {pmid40320531,
year = {2025},
author = {Vidaur, L and Guridi, A and Leizaola, O and Marin, J and Rello, J and Sarasqueta, C and Sorarrain, A and Marimón, JM},
title = {Respiratory dysbiosis as prognostic biomarker of disease severity for adults with community-acquired pneumonia requiring mechanical ventilation.},
journal = {Pneumonia (Nathan Qld.)},
volume = {17},
number = {1},
pages = {10},
pmid = {40320531},
issn = {2200-6133},
support = {FIS17/01463//Instituto de Salud Carlos III/ ; FIS17/01463//Instituto de Salud Carlos III/ ; },
abstract = {OBJETIVES: To ascertain the role of the lung microbiome in the development of severe pneumonia and its potential as a biomarker for disease progression.

METHODS: BAL samples from 34 adults with severe community-acquired pneumonia (CAP) (17 viral, 8 viral coinfected with bacteria and 9 bacterial) admitted to the ICU for acute respiratory failure between 2019 and 2021 were collected within the first 48 h of admission to the ICU. The microbiome was characterized via the Ion 16S Metagenomics Kit and the Ion Torrent sequencing platform. Clinical factors, including survival, mechanical ventilation duration, blood biomarkers and organ failure in terms of acute respiratory distress syndrome (ARDS), shock or acute renal failure, were correlated with microbiome characteristics.

RESULTS: The microbiome diversity in patients with viral pneumonia was significantly greater than that in patients with bacterial or coinfected pneumonia: the Shannon diversity index was 3.75 (Q1-Q3: 2.5-4.1) versus 0.4 (Q1-Q3: 0.2-1.3) and 0.48 (Q1-Q3: 0.3-1.1), respectively (p < 0.05). The microbiome diversity index was associated with severity-of-illness (APACHE II), independent of the etiology of pneumonia (B coefficient -1.845; p < 0.01). Patients with severe viral CAP who developed ARDS had a lower presence of Proteobacteria, and those who were complicated with ventilator-associated pneumonia had a higher prevalence of Acinetobacter at admission. The mortality of patients with bacterial or coinfected pneumonia was 35%. In coinfected patients, the diversity index was associated with the development of shock.

CONCLUSION: Patients with severe CAP have low respiratory microbiome diversity, indicating that respiratory microbiome diversity is a potential biomarker of disease severity.},
}

@article {pmid40320520,
year = {2025},
author = {Liu, S and Wu, J and Cheng, Z and Wang, H and Jin, Z and Zhang, X and Zhang, D and Xie, J},
title = {Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {111},
pmid = {40320520},
issn = {2049-2618},
support = {2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; },
mesh = {*Microbiota/physiology ; *Stress, Physiological ; *Plants/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Soil Microbiology ; Droughts ; },
abstract = {BACKGROUND: Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.

RESULTS: This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.

CONCLUSIONS: Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.},
}

*Microbiota/physiology
*Stress, Physiological
*Plants/microbiology
*Bacteria/classification/genetics/isolation & purification
Soil Microbiology
Droughts

@article {pmid40320100,
year = {2025},
author = {Kogoj, R and Bosilj, M and Šturm, AC and Korva, M and Smrdel, KS and Kvas, E and Pirš, M and Lepen, L and Triglav, T},
title = {Bioinformatic challenges in metagenomic next generation sequencing data analysis while unravelling a case of uncommon campylobacteriosis.},
journal = {Journal of biomedical informatics},
volume = {},
number = {},
pages = {104841},
doi = {10.1016/j.jbi.2025.104841},
pmid = {40320100},
issn = {1532-0480},
abstract = {OBJECTIVE: This study aimed to employ advanced bioinformatics and modern sequencing approaches to solve a diagnostic problem of persistent Campylobacter spp. molecular detection yet negative culture results from four consecutive stool samples of a previously healthy patient with newly diagnosed selective IgA deficiency with prolonged diarrhoea METHODS: Metagenomic next-generation sequencing (mNGS) based on short-paired end reads with basic bioinformatic read classification analysis was used at first. Due to confusing results, advanced bioinformatics involving contigs construction and classification, reference genome mappings and reads filtering with BBSplit, additionally coupled with metagenomic long-reads sequencing and Full-length 16S rRNA metabarcoding were employed to further elucidate the results. Virulence factors were analysed using the Prokka Genome Annotation tool. Modified classical bacteriology methods were finally used for further clarification.

RESULTS: Short-pair end reads analysis identified several Campylobacter species in all four samples. After advanced bioinformatic approaches were applied, candidatus C. infans was suspected as the putative pathogen. This result was further supported by metagenomic long-reads sequencing and Full-length 16S rRNA metabarcoding. Nevertheless, after modifying the culture conditions based on mNGS results, a mixed culture of candidatus C. infans and C.ureolyticus was obtained. Sequencing of the mixed culture resulted in an 87.48 % and 73.47 % genome coverage of candidatus C. infans and C. ureolyticus, respectively. In the candidatus C. infans genome more virulence factors hits were found than in the C. ureolyticus genome thus supporting the first as the most probable cause of symptoms.

CONCLUSION: This study shows the pivotal role and strengths of mNGS in unravelling an unusual case of diarrhoea and demonstrates how mNGS can guide established microbiological methods to improve on current limitations. However, it also emphasises the need for careful interpretation of sequencing data, particularly for closely related bacterial species from clinical samples that are known to support complex microbial communities.},
}

@article {pmid40320026,
year = {2025},
author = {Zheng, Y and Yue, Y and Liu, C and Pang, L and Wang, Y and Yang, Z},
title = {The role of riverbed substrates in N2O and CH4 emission: Insights from metagenomic analysis of epilithic biofilms.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121772},
doi = {10.1016/j.envres.2025.121772},
pmid = {40320026},
issn = {1096-0953},
abstract = {Riverbed substrates are critical in N2O and CH4 emission with functional microbes adhering to them. However, the role of substrates remains to be fully understood. This study monitors N2O and CH4 emission and collects epilithic biofilms on riverbed substrates with various diameters and size heterogeneity from 10 sections along a mountain river. Compared with the global range, moderate water-air exchange rates of N2O (-2.34-29.2 μg/m[2]/h) and rapid CH4 emission (-2.58-35.2 mg/m[2]/h) are observed. Based on metagenomic analysis, the abundances of nirS and fmdA genes, which encode catalysts in the denitrification and the hydrogenotrophic methanogenesis process, are found to be significantly higher in the medium diameter group (2-100 mm), implying higher N2O and CH4 emission. Meanwhile, the abundance of nirS and nirK genes, which are key to N2O production, is significantly higher in the low size heterogeneity group, promoting N2O release. In contrast, the abundance of ftr, pta,ackA and ACS genes critical in the methanogenesis processes are significantly lower in the low size heterogeneity group, inhibiting CH4 emission. For N2O production, the nitrification process is found to be dominated by species of Nocardioides and Planctomycetales, denitrification process by species of Tabrizicola and Rhodobacteraceae, and dissimilatory nitrate reduction to ammonium process by Leptospiraceae species. In contrast, CH4 is mainly generated by species of Pirellula and Proteobacteria through hydrogenotrophic, acetoclastic and methylotrophic methanogenesis respectively. A structural equation model indicated that substrate physical properties are equally or even more important as/than the aquatic nutrients concentration for N2O or CH4 emission in mountain rivers.},
}

@article {pmid40319779,
year = {2025},
author = {Zhu, J and Li, X and Wang, Y and Gu, X and Wang, H and Ma, J and Huang, Y},
title = {Organic sulfur-driven denitrification pretreatment for enhancing autotrophic nitrogen removals from thiourea-containing wastewater: performance and microbial mechanisms.},
journal = {Water research},
volume = {282},
number = {},
pages = {123753},
doi = {10.1016/j.watres.2025.123753},
pmid = {40319779},
issn = {1879-2448},
abstract = {Thiourea (CH4N2S) is a widely used industrial reagent and is frequently detected in both sewage and industrial wastewater. However, treating thiourea-containing wastewater remains challenging due to its toxicity, high ammonium concentration, and low C/N ratio. In this study, a novel integrated autotrophic-heterotrophic denitrification (IAHD)- completely autotrophic nitrogen removal over nitrite (CANON) process was developed. The degradation pathway of toxic compounds, nitrogen, and sulfur release and transformation, as well as variations in functional genes were comprehensively examined. The results show that by incorporating an IAHD unit, prior to CANON, toxic thiourea was effectively degraded by the recycled nitrate from CANON. The released sulfur and organic carbon served as electron donors facilitating efficient NO3[-]-N reduction. The optimal thiourea/NO3[-]-N ratio for IAHD operation was determined to be 4:1 (m:m), achieving NO3[-] and thiourea removal efficiencies of 90 % and 99 %, respectively. Additionally, NH4[+]-N and SO4[2-]-S concentrations increased by 199.9 mg/L and 201.9 mg/L, respectively. Approximately 53.3 % of thiourea was converted into high-molecular-weight biological metabolites in the IAHD unit, which were subsequently and completely degraded in the CANON unit, where a robust nitrite-shunt and anammox process occurred. 16S rRNA amplicon sequencing revealed that Thiobacillus (with a relative abundance of 39.9 %) was the dominant genera in the IAHD unit, followed by Arenimonas (10.8 %) and norank_o_1013-28-CG33 (12.4 %), indicating that sulfur autotrophic denitrification was the primary pathway for thiourea degradation. Metagenomic analysis further confirmed that thiourea, acting as an electron donor, stimulated the expression of key functional genes involved in denitrification, sulfur oxidation, dissimilatory nitrate reduction, hydrolytic oxidation, and amino acid synthesis and transport pathways. These processes contributed to the active biological transformation of carbon, nitrogen and sulfur in the IAHD unit. This study demonstrates that implementing a prior autotrophic-heterotrophic denitrification unit effectively degrades toxic thiourea, thereby ensuring the subsequent nitrogen removal performance of CANON. This approach offers a new paradigm for the treatment of thiourea-containing wastewater, promoting a more efficient and low-carbon process.},
}

@article {pmid40319631,
year = {2025},
author = {Zhao, Z and Gao, B and Henawy, AR and Rehman, KU and Ren, Z and Jiménez, N and Zheng, L and Huang, F and Yu, Z and Yu, C and Zhang, J and Cai, M},
title = {Mitigating the transfer risk of antibiotic resistance genes from fertilized soil to cherry radish during the application of insect fertilizer.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109510},
doi = {10.1016/j.envint.2025.109510},
pmid = {40319631},
issn = {1873-6750},
abstract = {The transfer of antibiotic resistance genes (ARGs) from fertilized soil to vegetables, particularly those consumed raw, causes significant public health risks through the food chain. Black soldier fly larvae can efficiently convert animal manure into organic fertilizer with reduced antibiotic resistance. This study utilized metagenomic sequencing to investigate fields treated with control organic fertilizer (COF), black soldier fly organic fertilizer (BOF), and no fertilizer, with the aim of assessing the transfer risks of ARGs from soil to cherry radish. The results indicated that BOF significantly reduced the richness and abundance of ARGs in both soil and cherry radish compared to COF, reducing 13 ARG subtypes and a 27.6% decrease in ARG abundance in cherry radish. Moreover, a significant positive correlation was observed between mobile genetic elements (MGEs) and virulence factors (VFs) with ARGs, with BOF treatment resulting in a relative abundance reduction of 32.8% and 29.1%, respectively. The complexity of networks involving ARGs with MGEs, VFs, and microbial communities in the BOF treatment was 54.2%, 32.3%, and 32.8% lower, respectively, than the COF treatment. Further analysis of metagenomic-assembled genomes (MAGs) revealed the co-occurrence of ARGs, MGEs, and VFs in cherry radish, indicating the presence of potential pathogenic antibiotic-resistant bacteria (PARB). Notably, the abundance of these PARB in BOF radishes decreased by 45.6% compared to COF. These findings underscore the efficacy of insect fertilizer in mitigating the transfer risks of ARGs to radish, highlighting the significance of sustainable agricultural practices in managing the environmental and health risks associated with ARGs.},
}

@article {pmid40319164,
year = {2025},
author = {Fan, Y and Chen, J and Xu, S and Zhou, H and Shang, Y and Tian, X and Wang, B and Zhao, Y and Shan, G and Zhao, Y and Zhang, P and Chen, X},
title = {Bacillus cereus is a key microbial determinant of intractable otitis media with effusion.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {150},
pmid = {40319164},
issn = {2730-664X},
abstract = {BACKGROUND: Currently, the mechanisms by which otitis media with effusion (OME) progresses to intractable OME is unclear. Since crosstalk between microbiome and host contributes to many diseases, we hypothesized that similar interactions could occur in the middle ear effusion (MEE) samples from patients with OME and influence intractable OME pathogenesis. This study aimed to evaluate the microbial profile of MEE samples and to determine whether there were microbial differences between the MEE microbiota of patients with intractable OME and those with rapidly cured OME.

METHODS: MEE samples were collected from 46 OME patients, including 20 from the long course group and 26 from the short course group. Metagenomic sequencing was performed on 30 of these samples, allowing the identification of microbial differences associated with varying disease durations. The difference was verified by further experimental validation, including fluorescence in situ hybridization (FISH) and quantitative polymerase chain reaction (qPCR).

RESULTS: The alpha diversity indices and overall MEE microbial structure show no significant difference between the long course and short course groups, but species such as Bacillus cereus, Nocardiopsis dassonvillei, and Rothia aeria are significantly more prevalent in the MEE of long course OME patients. qPCR analyses and FISH also confirm the difference in the abundance of Bacillus cereus between the two groups.

CONCLUSIONS: Bacillus cereus plays a role in the persistence of OME infection and serves as a potential biomarker to predict OME prognosis. Further studies are warranted to explore the value of Bacillus cereus detection in informing early intervention.},
}

@article {pmid40297421,
year = {2025},
author = {Mejia, ME and Bowman, S and Lee, J and El-Halwagi, A and Ferguson, K and Maliekel, M and Zhou, Y and Serchejian, C and Robertson, CM and Ballard, MB and Lu, LB and Khan, S and Oladunjoye, OO and Huang, S and Agarwal, SK and Patras, KA},
title = {A cross-sectional analysis of the vaginal microenvironment in rheumatoid arthritis.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40297421},
support = {F31 AI167538/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; },
abstract = {OBJECTIVE: The human microbiota is implicated in the development and progression of rheumatoid arthritis (RA). Given the increased RA burden in women, and well-known correlations between the vaginal microbiota and local inflammation, we seek to understand the vaginal microenvironment in the context of RA pathology.

METHODS: Self-collected vaginal swabs and questionnaires on dietary and health practices were obtained from 36 RA and 50 demographically-matched control women, 18-63 years of age. Additionally, medication regimen and disease activity and severity were captured for the RA cohort. Vaginal swabs were subjected to full-length 16S rRNA gene sequencing, multiplex cytokine analyses, and quantification of rheumatoid factor, c-reactive protein, and anti-citrullinated protein antibodies (ACPAs).

RESULTS: Vaginal microbial richness and genera Peptoniphilus and Prevotella, among other rare taxa, were elevated in RA versus control samples. Vaginal IL-18 and EGF levels were increased in the RA group; IL-18 correlated with multiple microbial features whereas EGF levels were not associated with bacterial composition or other host factors. Within the RA cohort, decreased relative abundance of Streptococcus was associated with joint pathologies, and Lactobacillus gasseri was lower in individuals with serum detection of ACPAs and rheumatoid factor. Vaginal ACPAs were higher in the RA group and positively correlated with Streptococcus and multiple vaginal inflammatory cytokines.

CONCLUSIONS: We describe vaginal microbial and immunological differences in women with RA, particularly when accounting for diet and menopausal status, disease activity and severity, and medication use. This work opens a new avenue in the multidisciplinary approach to RA patient care.},
}

@article {pmid40318372,
year = {2025},
author = {Chu, D and Zhang, H and Wang, Z and Ning, K},
title = {Microbial resources and interactions across three-dimensional space for a freshwater ecosystem.},
journal = {The Science of the total environment},
volume = {980},
number = {},
pages = {179522},
doi = {10.1016/j.scitotenv.2025.179522},
pmid = {40318372},
issn = {1879-1026},
abstract = {Freshwater ecosystems are important natural resources but face serious threats. Nevertheless, they host diverse microorganisms crucial for biosynthetic potential and global biochemical cycles. To fully understand the enrichment and interaction of species and functional resources in freshwater ecosystems, it is essential to profile the microbial resources in the whole three-dimensional space. We profiled 131 metagenomic samples to construct the Honghu Microbial Catalog, comprising 2617 metagenome-assembled genomes, 1718 candidate species, over 60 million non-redundant gene clusters, and 7396 biosynthetic gene clusters. We emphasized surface water may be the primary source of microbial species and ARGs for Honghu Lake. We also found the impact of surface water on groundwater had an "influence sphere". Furthermore, we have identified groundwater as a potential refuge for microbial resources, enriched with CPR bacteria and ARGs. These findings are crucial for the understanding, management, and protection of freshwater ecosystems.},
}

@article {pmid40318358,
year = {2025},
author = {Karatas, M and Bloemen, M and Swinnen, J and Roukaerts, I and Gucht, SV and Van Ranst, M and Wollants, E and Matthijnssens, J},
title = {Untapped potential of wastewater for animal and potentially zoonotic virus surveillance: Pilot study to detect non-human animal viruses in urban settings.},
journal = {Environment international},
volume = {199},
number = {},
pages = {109500},
doi = {10.1016/j.envint.2025.109500},
pmid = {40318358},
issn = {1873-6750},
abstract = {INTRODUCTION: Wastewater surveillance has become an essential tool for monitoring viral outbreaks and surveillance of human viruses. While PCR-based methods are most frequently used, more advanced techniques, such as shotgun metagenomics in combination with viral capture methods, have been developed. These capture methods significantly improve the ability to detect nearly all (known) viruses at once in complex samples, including wastewater. In this study, we focus on tracking animal specific and zoonotic viruses in city wastewater using metagenomics combined with hybrid-capture approach.

METHODS: We collected 6 wastewater samples from Leuven and Brussels, situated in the center of Belgium. Automated wastewater samplers collected 50 mL samples every 10 min resulting in a 24 h composite influent wastewater. All samples were processed using the TWIST comprehensive research panel capture, designed to target over 3,000 human and animal viruses species and 15,000 strains. Sequencing was performed on the AVITI sequencing platform, targeting an average of ten million reads per sample. The sequencing data were analyzed using the EsViritu tool.

RESULTS: Over 2294 viral genomes or segments were recovered from wastewater samples. Of these, 168 were associated with non-human vertebrate animals, including cats, dogs, pigeons, and rats, spanning 51 virus species. We identified near-complete genomes of clinically relevant animal viruses, such as pigeon circovirus, chicken anemia virus, feline bocaparvovirus 2, canine minute virus, rat coronavirus, canine parvovirus, and porcine circovirus. Additionally, we noted the presence of viruses with known cross-species transmission potential, including porcine torovirus, rosavirus, hepatitis E virus, rat hepatitis virus, and cardiovirus.

CONCLUSION: The results demonstrate the ability to track a wide range of animal viruses in urban wastewater, potentially forming an early warning system for zoonotic diseases, ultimately being a useful tool for One Health based public health approaches.},
}

@article {pmid40318224,
year = {2025},
author = {Maritan, AJ and Clements, CS and Pratte, ZA and Hay, ME and Stewart, FJ},
title = {Sea cucumber grazing linked to enrichment of anaerobic microbial metabolisms in coral reef sediments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf088},
pmid = {40318224},
issn = {1751-7370},
abstract = {Sea cucumbers have been overharvested world-wide, making assessments of their ecological effects challenging, but recent research demonstrated that sea cucumbers increase coral survival via disease suppression and were therefore important for facilitating reef health. The mechanisms underpinning the sea cucumber-coral interaction therefore are not well understood but are likely mediated through sea cucumber grazing of microbes from reef sediments. We explored how sea cucumber grazing alters the sediment microbiome by leveraging a healthy sea cucumber population on a reef in French Polynesia. We used quantitative PCR, 16S rRNA gene sequencing, and shotgun metagenomics to compare the sediment microbiome in cages placed in situ with or without sea cucumbers. We hypothesized that grazing would lower microbial biomass, change sediment microbiome composition, and deplete sediment metagenomes of anaerobic metabolisms, likely due to aeration of the sediments. Sea cucumber grazing resulted in a 75% reduction in 16S rRNA gene abundances and reshaped microbiome composition, causing a significant decrease of cyanobacteria and other phototrophs relative to ungrazed sediments. Grazing also resulted in a depletion of genes associated with cyanotoxin synthesis, suggesting a potential link to coral health. In contrast to expectations, grazed sediment metagenomes were enriched with marker genes of diverse anaerobic or microaerophilic metabolisms, including those encoding high oxygen affinity cytochrome oxidases. This enrichment differs from patterns linked to other bioturbating invertebrates. We hypothesize that grazing enriches anaerobic processes in sediment microbiomes through removal of oxygen-producing autotrophs, fecal deposition of sea cucumber gut-associated anaerobes, or modification of sediment diffusibility. These results suggest that sea cucumber harvesting influences biogeochemical processes in reef sediments, potentially mediating coral survival by altering the sediment microbiome and its production of coral-influencing metabolites.},
}

@article {pmid40316928,
year = {2025},
author = {Zhang, Y and Sun, D and Fang, Y and Feng, Y and Wu, Y and Shen, W and Wu, W and Gao, X and Sun, Y and Ma, X and Gao, F and Zhu, C and Zhou, J and Gu, C},
title = {Uncommon pulmonary manifestation of hepatitis B virus: a case report of secondary organizing pneumonia.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {645},
pmid = {40316928},
issn = {1471-2334},
support = {Z-2014-06-2301//China International Medical Exchange Foundation Xiansheng Clinical Research Special Fund Research Project/ ; 2023-SSGJ-002//Key Construction Disciplines of Provincial and Municipal Co construction of Zhejiang/ ; 2021-GFXK-04//Peak Discipline of Jiaxing First Hospital/ ; 2021AD30177//Science and Technology Project of Jiaxing/ ; },
mesh = {Humans ; Male ; Middle Aged ; *Hepatitis B virus/genetics/isolation & purification ; *Hepatitis B/complications/virology/diagnosis ; Lung/pathology/virology ; DNA, Viral/genetics ; Viral Load ; Organizing Pneumonia ; },
abstract = {BACKGROUND: Hepatitis B virus (HBV) primarily affects the liver, but increasingly, it is recognized for its potential extrahepatic manifestations. This case highlights the importance of considering viral infections in the differential diagnosis of pulmonary nodules.

CASE PRESENTATION: A 63-year-old man presented with a new mixed ground-glass nodule in the left lower lobe during a routine check-up. He had a history of liver resection for hepatocellular carcinoma, with results negative for hepatitis B virus surface antigen. The HBV viral load in the patient's serum was below the detection limit of quantitative PCR (qPCR). Immunohistological analysis of lung biopsy samples indicated chronic inflammation. However, after a course of intravenous antibiotics, the nodule increased in size, prompting further investigation. Therefore, lung biopsy tissue was subjected to metagenomic next-generation sequencing (mNGS), and HBV DNA was detected. The patient was diagnosed with secondary organizing pneumonia associated with HBV. Then he was treated with prednisone acetate and had remission.

CONCLUSION: This case underscores the potential for HBV to manifest as pulmonary complications, such as secondary organizing pneumonia. Therefore, in the stage of infectious diseases in patients with a history of hepatocellular carcinoma, HBV needs to be the focus of monitoring, so as to clarify the cause of diagnosis and treatment as soon as possible.

CLINICAL TRIAL: Not applicable.},
}

Humans
Male
Middle Aged
*Hepatitis B virus/genetics/isolation & purification
*Hepatitis B/complications/virology/diagnosis
Lung/pathology/virology
DNA, Viral/genetics
Viral Load
Organizing Pneumonia

@article {pmid40316630,
year = {2025},
author = {Aya, V and Pardo-Rodriguez, D and Vega, LC and Cala, MP and Ramírez, JD},
title = {Integrating metagenomics and metabolomics to study the gut microbiome and host relationships in sports across different energy systems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15356},
pmid = {40316630},
issn = {2045-2322},
support = {Small grant//Universidad del Rosario/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Energy Metabolism ; Adult ; Athletes ; Young Adult ; *Sports ; Feces/microbiology ; Female ; Lipidomics ; },
abstract = {The gut microbiome plays a critical role in modulating host metabolism, influencing energy production, nutrient utilization, and overall physiological adaptation. In athletes, these microbial functions may be further specialized to meet the unique metabolic demands of different sports disciplines. This study explored the role of the gut microbiome in modulating host metabolism among Colombian athletes by comparing elite weightlifters (n = 16) and cyclists (n = 13) through integrative omics analysis. Fecal and plasma samples collected one month before an international event underwent metagenomic, metabolomic, and lipidomic profiling. Metagenomic analysis revealed significant microbial pathways, including L-arginine biosynthesis III and fatty acid biosynthesis initiation. Key metabolic pathways, such as phenylalanine, tyrosine, and tryptophan biosynthesis; arginine biosynthesis; and folate biosynthesis, were enriched in both athlete groups. Plasma metabolomics and lipidomics revealed distinct metabolic profiles and a separation between athlete types through multivariate models, with lipid-related pathways such as lipid droplet formation and glycolipid synthesis driving the differences. Notably, elevated carnitine, amino acid, and glycerolipid levels in weightlifters suggest energy system-specific metabolic adaptations. These findings underscore the complex relationship between the gut microbiota composition and metabolic responses tailored to athletic demands, laying the groundwork for personalized strategies to optimize performance. This research highlights the potential for targeted modulation of the gut microbiota as a basis for tailored interventions to support specific energy demands in athletic disciplines.},
}

Humans
*Gastrointestinal Microbiome
*Metabolomics/methods
*Metagenomics/methods
Male
*Energy Metabolism
Adult
Athletes
Young Adult
*Sports
Feces/microbiology
Female
Lipidomics

@article {pmid40316568,
year = {2025},
author = {Joshi, P and Bhattacharjee, R and Sahu, M and Gajjar, D},
title = {Insights into urinary catheter colonisation and polymicrobial biofilms of Candida- bacteria under flow condition.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15375},
pmid = {40316568},
issn = {2045-2322},
mesh = {*Biofilms/growth & development ; Humans ; *Urinary Catheters/microbiology ; *Candida/physiology/isolation & purification/growth & development ; Urinary Tract Infections/microbiology ; *Bacteria/growth & development/isolation & purification/genetics ; Catheter-Related Infections/microbiology ; Coinfection/microbiology ; Metagenomics ; Pseudomonas aeruginosa ; Escherichia coli ; Klebsiella pneumoniae ; },
abstract = {Most hospital-acquired urinary tract infections are the result of implanted urinary catheter, with majority of studies focused on a single species colonisation, but recently polymicrobial colonisations are being reported. In this study, indwelling urinary catheters were collected from ICU patients and the colonising microbiome was isolated and identified by the traditional; culturing method and metagenomics. It was observed that majority of catheters were colonised by polymicrobial biofilms, containing both bacterial and fungal isolates making them diverse and complex. However, the metagenomics results were quite surprising showing the presence of multiple organisms of which only 1or 2 showed growth when cultured. Later, in vitro assays were performed by selecting 6 combinations, with each combination containing one Candida spp. - C. albicans or C. tropicalis with one bacteria K. pneumoniae, P. aeruginosa or E. coli. It was observed that polymicrobial biofilms were stronger than mono-microbial biofilms, suggesting their increased surface adhesion. Furthermore, to simulate the dynamic environment in which cells are exposed to a certain level of fluid movement, a flow system was established to imitate the flow generated in colonized urinary catheter. We have observed changes in biofilm architecture, adhesion and thickness under flow conditions compared with static conditions, with a uniformly adhered biofilm with increased thickness of polymicrobial biofilms as compared to mono-species biofilms. The biofilm formed under flow was more viable than the static biofilm with higher number of live cells in flow condition.},
}

*Biofilms/growth & development
Humans
*Urinary Catheters/microbiology
*Candida/physiology/isolation & purification/growth & development
Urinary Tract Infections/microbiology
*Bacteria/growth & development/isolation & purification/genetics
Catheter-Related Infections/microbiology
Coinfection/microbiology
Metagenomics
Pseudomonas aeruginosa
Escherichia coli
Klebsiella pneumoniae

@article {pmid40315933,
year = {2025},
author = {Cheng, Z and Wang, J and Liu, X and Cao, S},
title = {Accelerated sludge granulation of novel complete ammonium and nitrate removal via denitratation anammox over nitrite process at elevated loading rates.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132610},
doi = {10.1016/j.biortech.2025.132610},
pmid = {40315933},
issn = {1873-2976},
abstract = {The Complete Ammonium and Nitrate Removal via Denitratation Anammox Over Nitrite (CANDAN) process was evaluated for rapid sludge granulation in a lab-scale sequencing batch reactor. Over 119 days under increasing nitrogen loading rates (NLRs), the system finally achieved average 89.2 % total nitrogen removal at 1.93 kg N/m[3]/d NLR, with sludge particle sizes increasing from 215.6 μm to 924.5 μm. Higher NLRs significantly increased extracellular polymeric substances, especially hydrophobic proteins, enhancing sludge hydrophobicity and aggregation. Metagenomic analysis identified Candidatus Brocadia and Thauera as predominant and key microbial genera for nitrogen removal. Furthermore, the upregulation of carbon metabolism under heightened NLRs facilitated the synthesis of hydrophobic amino acids, promoting sludge granulation. These findings demonstrate NLR-driven granulation mechanisms, highlight optimizing NLR as key for accelerating granulation, providing insights to improve start-up and operational efficiency of CANDAN systems.},
}

@article {pmid40315837,
year = {2025},
author = {Baker, JS and Qu, E and Mancuso, CP and Tripp, AD and Conwill, A and Lieberman, TD},
title = {Intraspecies dynamics underlie the apparent stability of two important skin microbiome species.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.04.010},
pmid = {40315837},
issn = {1934-6069},
abstract = {Adult human facial skin microbiomes are remarkably similar at the species level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 356 metagenomes, we reconstruct on-person evolutionary history to reveal on- and between-person strain dynamics. We find that multiple cells are typically involved in transmission, indicating ample opportunity for migration. Despite this accessibility, family members share only some of their strains. S. epidermidis communities are dynamic, with each strain persisting for an average of only 2 years. C. acnes strains are more stable and have a higher colonization rate during the transition to an adult facial skin microbiome, suggesting this window could facilitate engraftment of therapeutic strains. These previously undetectable dynamics may influence the design of microbiome therapeutics and motivate the study of their effects on hosts.},
}

@article {pmid40315739,
year = {2025},
author = {Ma, G and Yang, P and Lu, T and Deng, X and Meng, L and Xie, H and Zhou, J and Xiao, X and Tang, X},
title = {Comparative analysis of oral, placental, and gut microbiota characteristics, functional features and microbial networks in healthy pregnant women.},
journal = {Journal of reproductive immunology},
volume = {169},
number = {},
pages = {104535},
doi = {10.1016/j.jri.2025.104535},
pmid = {40315739},
issn = {1872-7603},
abstract = {AIM: Most studies on pregnant women focus on analyzing individual microbial species at specific body sites. This study aims to explore the characteristics, functions, and microbial networks of the oral, placental, and gut microbiota in healthy pregnant women.

METHODS: A total of 23 healthy pregnant women were enrolled in this study. We analyzed the microbial composition, functional profiles, and microbial networks of the oral, placental, and gut microbiota using 16S rRNA gene sequencing.

RESULTS: Our findings revealed significant differences in microbial composition across these three sites. The placental microbiota contained a relatively high proportion of low-abundance microorganisms, which were more diverse and evenly distributed compared to the gut and oral microbiota. The microbial composition at each site displayed distinct characteristics, likely influenced by environmental, physiological, and biological factors. The placental microbiota exhibited a complex network of tightly interconnected genera, whereas the gut microbiota showed sparser connections, with fewer closely related genera compared to the placental and oral microbiota. Functional differences were also observed among the three microbiota, with each playing a unique role in maintaining host health and metabolic balance. While the oral and gut microbiota shared functional similarities, the placental microbiota exhibited distinct functional characteristics.

CONCLUSIONS: This study provides valuable insights into the microbial communities of healthy pregnant women, offering important data for microbiological research during pregnancy and laying the foundation for future investigations into the roles of these microbial communities in maternal health.},
}

@article {pmid40315479,
year = {2025},
author = {Kharey, G and Palace, V and Whyte, L and Greer, C},
title = {Pangenomic analysis of three putative hydrocarbon degrading genera Limnohabitans, Aquabacterium, and Novosphingobium collected from freshwater sources.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2023-0099},
pmid = {40315479},
issn = {1480-3321},
abstract = {A pangenome analysis offers a unique exploration of the metabolic and genetic diversity, range of ecological niches, and evolution of a particular genus or species. However, such pangenomic analyses are uncommon among environmentally relevant genera. Here, we present freshwater pangenomes of 3 environmentally relevant genera, Limnohabitans, Aquabacterium, and Novosphingobium. These genera had been detected in hydrocarbon degrading cultures in previous research by our group. Using pangenomic tools we attempted to characterize the extent of hydrocarbon degradation potential within each pangenome and determine what ecological niche each genus occupies within hydrocarbon degradation. In total 46 Limnohabitans, 10 Aquabacterium, and 32 Novosphingobium freshwater genomes were collected from various databases and compiled into pangenomes. We found that each pangenome harbours downstream hydrocarbon degrading potential and unexpected genetic diversity within its core and accessory pangenomes possibly stemming from geographic and metagenomic data processing influences. This work was the first to explore pangenomes of these environmentally relevant genera.},
}

@article {pmid40315414,
year = {2025},
author = {Galperina, A and Lugli, GA and Milani, C and De Vos, WM and Ventura, M and Salonen, A and Hurwitz, B and Ponsero, AJ},
title = {The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1012268},
doi = {10.1371/journal.pcbi.1012268},
pmid = {40315414},
issn = {1553-7358},
abstract = {The growing interest in the role of the gut virome in human health and disease, has led to several recent large-scale viral catalogue projects mining human gut metagenomes each using varied computational tools and quality control criteria. Importantly, there has been to date no consistent comparison of these catalogues' quality, diversity, and overlap. In this project, we therefore systematically surveyed nine previously published human gut viral catalogues. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy between the ressources and suggesting the need for an aggregated resource bringing these viral sequences together. We further expanded these viral catalogues by mining 7,867 infant gut metagenomes from 12 large-scale infant studies collected in 9 different countries. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Using computational inference tools, annotations were obtained for each vOTU representative sequence quality, viral taxonomy, predicted viral lifestyle, and putative host. This project aims to facilitate the reuse of previously published viral catalogues by the research community and follows a modular framework to enable future expansions as novel data becomes available.},
}

@article {pmid40315131,
year = {2025},
author = {Donvil, L and Housmans, JAJ and Peeters, E and Vranken, W and Orlando, G},
title = {In-silico identification of archaeal DNA-binding proteins.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf169},
pmid = {40315131},
issn = {1367-4811},
abstract = {MOTIVATION: The rapid advancement of next-generation sequencing technologies has generated an immense volume of genetic data. However, this data is unevenly distributed, with well-studied organisms being disproportionately represented, while other organisms, such as from archaea, remain significantly underexplored. The study of archaea is particularly challenging due to the extreme environments they inhabit and the difficulties associated with culturing them in the laboratory. Despite these challenges, archaea likely represent a crucial evolutionary link between eukaryotic and prokaryotic organisms, and their investigation could shed light on the early stages of life on Earth. Yet, a significant portion of archaeal proteins are annotated with limited or inaccurate information. Among the various classes of archaeal proteins, DNA-binding proteins are of particular importance. While they represent a large portion of every known proteome, their identification in archaea is complicated by the substantial evolutionary divergence between archaeal and the other better studied organisms.

RESULTS: To address the challenges of identifying DNA-binding proteins in archaea, we developed Xenusia, a neural network-based tool capable of screening entire archaeal proteomes to identify DNA-binding proteins. Xenusia has proven effective across diverse datasets, including metagenomics data, successfully identifying novel DNA-binding proteins, with experimental validation of its predictions.

AVAILABILITY: Xenusia is available as a PyPI package, with source code accessible at https://github.com/grogdrinker/xenusia, and as a Google Colab web server application at xenusia.ipynb.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid40314681,
year = {2025},
author = {Li, X and Su, K and He, Y and Shao, S and Lan, L and Zhang, Q},
title = {Knowledge Mapping of International Microbiota Research: Analyzing Thirty-Year Citation Classics and Exploring Future Expectations.},
journal = {The new microbiologica},
volume = {48},
number = {1},
pages = {46-59},
pmid = {40314681},
issn = {1121-7138},
mesh = {Humans ; *Microbiota ; *Biomedical Research ; Bibliometrics ; Gastrointestinal Microbiome ; },
abstract = {Microbiota research has rapidly emerged as a pivotal field, with over 250,000 publications and more than ten million citations recorded in the Web of Science Core Collection database by 2024. There were 1682 original microbiota citation classics (each receiving 400 citations or more) identified over the past three decades, totaling 1,559,594 citations and averaging 927 citations per paper. Collaborative efforts in the production of these citation classics involved 87 out of 89 participating countries and 2107 out of 2142 institutions. The USA, various European countries, and China emerged as the leading contributors to this burgeoning research area. Jeffrey I. Gordon, Rob Knight, and Curtis Huttenhower were the prominent figures in microbiota research. Author keywords were analyzed, which revealed a notable shift in research focus from environmental microorganisms to human gut microbiota. Advances such as high-throughput 16S rRNA sequencing and metagenomics expanded the scope of investigations into host-microbiota interactions. Current research interests encompass exploring mechanisms underlying gut-X-axis conditions, including inflammatory bowel disease, obesity, diabetes, colorectal cancer, liver diseases, and neurological disorders. Moreover, environmental exposures have been evidenced to alter gut microbiota and metabolites, contributing a novel research direction. Future research direction is also anticipated to delve further into biosynthetic gene engineering technologies aimed at microbial interventions, including probiotics and fecal microbiota transplantation. This study outlines the evolving landscape of microbiota research and provides valuable insights to inform future investigations within the field.},
}

Humans
*Microbiota
*Biomedical Research
Bibliometrics
Gastrointestinal Microbiome

@article {pmid40314024,
year = {2025},
author = {Malwe, AS and Longwani, U and Sharma, VK},
title = {XenoBug: machine learning-based tool to predict pollutant-degrading enzymes from environmental metagenomes.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf037},
pmid = {40314024},
issn = {2631-9268},
mesh = {*Machine Learning ; *Metagenome ; *Xenobiotics/metabolism ; Biodegradation, Environmental ; *Environmental Pollutants/metabolism ; *Bacteria/enzymology/genetics ; Metagenomics/methods ; },
abstract = {Application of machine learning-based methods to identify novel bacterial enzymes capable of degrading a wide range of xenobiotics offers enormous potential for bioremediation of toxic and carcinogenic recalcitrant xenobiotics such as pesticides, plastics, petroleum, and pharmacological products that adversely impact ecology and health. Using 6814 diverse substrates involved in ∼141 200 biochemical reactions, we have developed 'XenoBug', a machine learning-based tool that predicts bacterial enzymes, enzymatic reaction, the species capable of biodegrading xenobiotics, and the metagenomic source of the predicted enzymes. For training, a hybrid feature set was used that comprises 1603 molecular descriptors and linear and circular fingerprints. It also includes enzyme datasets consisting of ∼3.3 million enzyme sequences derived from an environmental metagenome database and ∼16 million enzymes from ∼38 000 bacterial genomes. For different reaction classes, XenoBug shows very high binary accuracies (>0.75) and F1 scores (>0.62). XenoBug is also validated on a set of diverse classes of xenobiotics such as pesticides, environmental pollutants, pharmacological products, and hydrocarbons known to be degraded by the bacterial enzymes. XenoBug predicted known as well as previously unreported metabolic enzymes for the degradation of molecules in the validation set, thus showing its broad utility to predict the metabolism of any input xenobiotic molecules. XenoBug is available on: https://metabiosys.iiserb.ac.in/xenobug.},
}

*Machine Learning
*Metagenome
*Xenobiotics/metabolism
Biodegradation, Environmental
*Environmental Pollutants/metabolism
*Bacteria/enzymology/genetics
Metagenomics/methods

@article {pmid40313842,
year = {2025},
author = {Lu, X and Du, X and Zhong, D and Li, R and Cao, J and Huang, S and Wang, Y},
title = {Nanopore Environmental Analysis.},
journal = {JACS Au},
volume = {5},
number = {4},
pages = {1570-1590},
pmid = {40313842},
issn = {2691-3704},
abstract = {As global pollution continues to escalate, timely and accurate monitoring is essential for guiding pollution governance and safeguarding public health. The increasing diversity of pollutants across environmental matrices poses a significant challenge for instrumental analysis methods, which often require labor-intensive and time-consuming sample pretreatment. Nanopore technology, an emerging single-molecule technique, presents a promising solution by enabling the rapid identification of multiple targets within complex mixtures with minimal sample preparation. A wide range of pollutants have been characterized using natural biological nanopores or artificial solid-state nanopores, and their distinct advantages include simple sample preparation, high sensitivity, and rapid onsite analysis. In particular, long-read nanopore sequencing has led to dramatic improvements in the analyses of environmental microbial communities, allows species-level taxonomic assignment using amplicon sequencing, and simplifies the assembly of metagenomes. In this Perspective, we review the latest advancements in analyzing chemical and biological pollutants through nanopore sensing and sequencing techniques. We also explore the challenges that remain in this rapidly evolving field and provide an outlook on the potential for nanopore environmental analysis to transform pollution monitoring, risk assessment, and public health protection.},
}

@article {pmid40313750,
year = {2025},
author = {Ndione, MHD and Ndiaye, EH and Dieng, M and Diouf, B and Sankhé, S and Diallo, D and Kane, M and Sene, NM and Mbanne, M and Sy, FA and Diop, SMBS and Doukanda, SFM and Sall, AA and Faye, O and Dia, N and Weaver, SC and Faye, O and Diallo, M and Fall, G and Gaye, A and Diagne, MM},
title = {Mosquito-Based Detection of Endogenous Jaagsiekte Sheep Retrovirus in Senegal: Expanding the Scope of Xenosurveillance.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-5951454/v1},
pmid = {40313750},
issn = {2693-5015},
abstract = {Background Mosquitoes are well-known vectors for arthropod-borne viruses, yet their role as passive carriers of non-arthropod-borne viruses remains underexplored. Xenosurveillance, a method that utilizes blood-feeding arthropods to sample host and pathogen genetic material, has emerged as a valuable tool in viral ecology. In this study, we report the first identification of Jaagsiekte Sheep Retrovirus (JSRV)-related sequences in blood-fed mosquitoes collected in Senegal. JSRV, a betaretrovirus responsible for ovine pulmonary adenocarcinoma, is typically found in sheep, but its genetic trace in mosquitoes offers a novel perspective on host-vector contact and surveillance. Our study aimed to investigate whether mosquitoes can serve as sentinels for detecting both pathogens and host-derived markers in complex ecosystems. Methods Mosquitoes were collected between 2016 and 2019 from three ecologically significant regions in Senegal (Louga, Barkedji, and Kedougou). Blood-fed mosquitoes were pooled and subjected to RNA extraction and metagenomic sequencing using Illumina NextSeq550. Sequencing data were analyzed with CZ-ID and BLAST for viral identification. RT-qPCR assays were designed to validate the presence of JSRV-related sequences, targeting conserved regions of the envelope gene and 3' untranslated region. Phylogenetic analysis was conducted using MAFFT and IQ-TREE to compare the detected sequence with global exogenous and endogenous JSRV references. Results A diverse array of viruses across mosquito species, including both arboviruses and non-arthropod-borne viruses. A JSRV-related sequence was detected in a single blood-fed mosquito pool collected in Barkedji (2019). The RT-qPCR assay confirmed JSRV presence, validating the sequencing results. Phylogenetic analysis revealed strong similarity to known endogenous JSRV (enJSRV) sequences integrated in the sheep genome, indicating that the detected material likely originated from host DNA ingested during blood feeding. Discussion This study presents the first report of endogenous retroviral sequences detected in mosquitoes, alongside the identification of actively circulating viruses, highlighting the broader potential of mosquitoes as environmental sentinels. While mosquitoes are not biological vectors for JSRV, their ability to capture both host-derived retroviral material and pathogenic viral genomes through bloodmeals reinforces the value of xenosurveillance for monitoring livestock-vector-environment interactions. These findings contribute to broader efforts in integrated disease surveillance and underscore the utility of combining metagenomics with molecular diagnostics to detect diverse viral signals in high-risk ecological settings.},
}

@article {pmid40313611,
year = {2025},
author = {Ren, X and Sun, H and Cheng, Y and Zhang, Y and Gao, D},
title = {Neurocysticercosis detected by targeted next-generation sequencing of cerebrospinal fluid: a case report.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1504348},
pmid = {40313611},
issn = {1664-2295},
abstract = {The patient, a middle-aged male with a long history of the disease, had experienced recurrent headaches for 26 years and episodic shaking of the right limb with slurred speech for the past month. He was previously diagnosed with cerebral cysticercosis and had shown improvement after anthelmintic treatment. In recent years, he noted a resurgence of headaches. One month prior, he developed right limb shaking and occasional slurred speech. A clinical neurological examination was unremarkable, but cranial MRI and cerebrospinal fluid sequencing confirmed a diagnosis of cerebral cysticercosis. Anthelmintic treatment was administered, resulting in symptom improvement.},
}

@article {pmid40313603,
year = {2025},
author = {Pu, Y and Zhou, X and Cai, H and Lou, T and Liu, C and Kong, M and Sun, Z and Wang, Y and Zhang, R and Zhu, Y and Ye, L and Zheng, Y and Zhu, B and Quan, Z and Zhao, G and Zheng, Y},
title = {Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {76-90},
pmid = {40313603},
issn = {2730-5848},
abstract = {UNLABELLED: In gut microbial research, DNA extraction remarkably influences study outcomes and biological interpretations. Rapid advancements in the research scale and technological upgrades necessitate evaluating new methods to ensure reliability and precision in microbial community profiling. We systematically evaluated the performance of eight recent and commonly used extraction methods using a microbial mock community (MMC) and fecal samples from two healthy volunteers, incorporating bacterial, archaeal, and fungal constituents. Performance metrics included nucleic acid assessment, microbial profile assessment, and scalability for large-scale studies, leveraging shotgun metagenomics for in-depth analysis. Despite variations in DNA quantity and quality, all methods yielded sufficient DNA for shotgun metagenomic sequencing. In the MMC microbial profile assessment, the QIAamp PowerFecal pro Kit (PF) and DNeasy PowerSoil HTP kit (PS) methods exhibited higher similarity with the theoretical composition and lower variability across technical replicates compared to other methods. For fecal samples, the extraction method accounted for 21.4% of the overall microbiome variation and significantly affected the abundances of 32% of detected microbial species. Methods using mechanical lysis with small beads, such as PF and PS, demonstrated better efficiency, indicated by increased microbial diversity in extracting DNA from Gram-positive bacteria. Furthermore, the PF and PS methods are notably simple to execute and automation-friendly, though relatively costly. Our study underscores the importance of maintaining consistency in DNA extraction methods for reliable comparative metagenomic analyses. We recommend PF and PS methods as optimal for expansive gut metagenomic research, emphasizing the critical role of mechanical lysis in DNA extraction.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00232-x.},
}

@article {pmid40313600,
year = {2025},
author = {Tang, M and Zhang, Z and Lin, L and Niu, J and Meng, G and Wang, W and Wang, J and Wang, Y},
title = {Comparative Analysis of Growth Dynamics and Relative Abundances of Gut Microbiota Influenced by Ketogenic Diet.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {65-75},
pmid = {40313600},
issn = {2730-5848},
abstract = {UNLABELLED: Although the compositional alterations of gut bacteria in ketogenic diet (KD) have been intensively investigated, the causal relationship between this extreme diet and the microbiota changes is not fully understood. Here, we studied the growth dynamics of intestinal bacteria in KD. We used the CoPTR method to calculate the peak-to-trough ratio (PTR) based on metagenomic sequencing data, serving as an indicator of bacterial growth rates. Notably, Akkermansia muciniphila, a bacterium strongly linked to the therapeutic benefits of KD, exhibited one of the highest growth rates, aligning with its markedly elevated abundance. Our findings also revealed discrepancies in the change patterns of CoPTR values and relative abundances for various bacteria across different diet groups, some of which might be attributed to the exceptionally high or low growth rates of specific species. For some of the species demonstrating obvious differences in growth rates between KD and standard diet, we conducted in vitro culture experiments, supplementing them with diverse nutritional sources to elucidate the underlying mechanisms. The integrative analysis of bacterial abundance and growth dynamics can help deepen our understanding of the gut microbiota changes caused by KD and the therapeutic effects of this special diet.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00228-7.},
}

@article {pmid40313461,
year = {2025},
author = {Bessa, LJ and Egas, C and Pires, C and Proença, L and Mascarenhas, P and Pais, RJ and Barroso, H and Machado, V and Botelho, J and Alcoforado, G and Mendes, JJ and Alves, R},
title = {Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1543100},
pmid = {40313461},
issn = {2235-2988},
mesh = {Humans ; *Peri-Implantitis/microbiology ; *Saliva/microbiology ; Pilot Projects ; Cross-Sectional Studies ; *Microbiota ; *Dental Implants/microbiology ; Male ; Female ; Biofilms/growth & development ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: The rising use of dental implants is accompanied by an expected increase in peri-implant diseases, particularly peri-implantitis (PI), which poses a significant threat to implant success and necessitates a thorough understanding of its pathogenesis for effective management.

METHODS: To gain deeper insights into the role and impact of the peri-implant microbiome in the pathogenesis and progression of PI, we analyzed 100 samples of saliva and subgingival biofilm from 40 participants with healthy implants (HI group) or with co-occurrence of diagnosed PI-affected implants and healthy implants (PI group) using shotgun metagenomic sequencing. We identified the most discriminative species distinguishing healthy from diseased study groups through log ratios and differential ranking analyses.

RESULTS AND DISCUSSION: Mogibacterium timidum, Schaalia cardiffensis, Parvimonas micra, Filifactor alocis, Porphyromonas endodontalis, Porphyromonas gingivalis and Olsenella uli were associated with the subgingival peri-implant biofilm. In contrast, Neisseria sp oral taxon 014, Haemophilus parainfluenzae, Actinomyces naeslundii, Rothia mucilaginosa and Rothia aeria were more prevalent in the healthy peri-implant biofilm. Functional pathways such as arginine and polyamine biosynthesis, including putrescine and citrulline biosynthesis, showed stronger correlations with PI-affected implants. In contrast, peri-implant health was characterized by the predominance of pathways involved in purine and pyrimidine deoxyribonucleotide de novo biosynthesis, glucose and glucose-1-phosphate degradation, and tetrapyrrole biosynthesis. Our findings reveal that healthy implants in PI-free oral cavities differ significantly in microbial composition and functional pathways compared to healthy implants co-occurring with PI-affected implants, which more closely resemble PI-associated profiles. This pattern extended to salivary samples, where microbial and functional biomarkers follow similar trends.},
}

Humans
*Peri-Implantitis/microbiology
*Saliva/microbiology
Pilot Projects
Cross-Sectional Studies
*Microbiota
*Dental Implants/microbiology
Male
Female
Biofilms/growth & development
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Aged
Metagenomics
Adult

@article {pmid40313410,
year = {2025},
author = {Liu, J and Zhou, Y and Feng, J and Cai, C and Zhang, S},
title = {Comparative metagenomic analysis reveals the adaptive evolutionary traits of siboglinid tubeworm symbionts.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1533506},
pmid = {40313410},
issn = {1664-302X},
abstract = {Tubeworms flourish in marine cold seeps and hydrothermal vents through the establishment of symbiotic relationships with chemosynthetic bacteria. However, the environmental adaptations and evolutionary relationships of tubeworm symbionts across diverse habitats and hosts remain largely unknown. In this study, we characterized the genomes of 26 siboglinid tubeworm symbionts collected from deep-sea hydrothermal vents, cold seeps, and deep-sea mud, including two sequenced in this study and 24 previously published. Phylogenetic analysis classified the 26 symbiont genomes into five distinct clusters at the genus level. The findings highlight the remarkable diversity in symbiont classification, influenced by the habitat and species of tubeworm, with the symbiont genome characteristics of various genera revealing unique evolutionary strategies. Siboglinid symbionts exhibit functional metabolic diversity, encompassing chemical autotrophic capabilities for carbon, nitrogen, and sulfur metabolism, hydrogen oxidation, and a chemoorganotrophic ability to utilize various amino acids, cofactors, and vitamins. Furthermore, the symbiont's homeostatic mechanisms and CRISPR-Cas system are vital adaptations for survival. Overall, this study highlights the metabolic traits of siboglinid symbionts across different genera and enhances our understanding of how different habitats and hosts influence symbiont evolution, offering valuable insights into the strategies that symbionts use to adapt and thrive in extreme environments.},
}

@article {pmid40313389,
year = {2025},
author = {Yu, D and Liu, Y and Cai, H and Huang, W and Wu, H and Yang, P},
title = {Metagenomic investigation of bacterial laccases in a straw-amended soil.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19327},
pmid = {40313389},
issn = {2167-8359},
mesh = {*Laccase/genetics/metabolism ; *Metagenomics ; *Soil Microbiology ; Phylogeny ; *Bacteria/enzymology/genetics ; *Soil/chemistry ; Escherichia coli/genetics ; *Bacterial Proteins/genetics/metabolism ; },
abstract = {BACKGROUND: Bacterial laccases play a crucial role in the degradation of lignin and the turnover of soil organic matter. Their advantageous properties make them highly suitable for a wide range of industrial applications. However, the limited identification of these potential enzymes has impeded their full utilization. The straw-amended soil provides materials for the development of bacterial laccases.

METHODS: Metagenomic sequencing of a straw-amended soil was conducted to explore novel bacterial laccases. The putative bacterial laccases were then screened using profile hidden Markov models for further analysis. The most abundant gene, lacS1, was heterologously expressed in Escherichia coli and the recombinant laccase was purified for enzymatic characterization.

RESULTS: A total of 322 putative bacterial laccases were identified in the straw-amended soil. Among them, 45 sequences had less than 30% identity to any entries in the Carbohydrate-Active Enzyme database and only 4.66% were more than 75% similar to proteins in the NCBI environmental database, exhibiting their novelty. These enzymes were found across various bacterial orders, demonstrating substantial diversity. Phylogenetic analysis revealed a number of the bacterial laccase sequences clustered with homologs characterized by favorable enzymatic properties. Five full-length representative bacterial laccase genes were obtained by modified thermal asymmetric interlaced PCR. The laccase activity of lacS1 was validated. It was a mesophilic enzyme with alkaline stability and halotolerance, indicating its promise for industrial applications.

IMPLICATIONS: These findings highlight novel bacterial laccase resources with potential for industrial applications and enzyme engineering.},
}

*Laccase/genetics/metabolism
*Metagenomics
*Soil Microbiology
Phylogeny
*Bacteria/enzymology/genetics
*Soil/chemistry
Escherichia coli/genetics
*Bacterial Proteins/genetics/metabolism

@article {pmid40313234,
year = {2025},
author = {Leibovitzh, H and Fliss Isakov, N and Werner, L and Thurm, T and Hirsch, A and Cohen, NA and Maharshak, N},
title = {A Mushroom Based Prebiotic Supplement Pilot Study Among Patients with Crohn's Disease.},
journal = {Journal of dietary supplements},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/19390211.2025.2498127},
pmid = {40313234},
issn = {1939-022X},
abstract = {Data on a mushroom based prebiotic supplementation in patients with Crohn's disease (CD) in western population is scarce. In this pilot trial, we aimed to assess the clinical efficacy and fecal microbial compositional and functional alterations associated with 'Mycodigest,' a commercial prebiotic supplement composed of three mushroom extracts. Patients with mild to moderate CD were recruited to a single center, randomized, double-blind, placebo-controlled pilot induction trial. Clinical efficacy using the Harvey-Bradshaw index and biochemical response using C-reactive protein and fecal calprotectin were assessed at week 8 post-intervention. Fecal samples were assessed by DNA shotgun metagenomic sequencing. A multivariable linear mixed effects model was used to assess alteration in fecal microbiome composition and function pre- and post-'Mycodigest' intervention. Clinical response was higher in the 'Mycodigest' intervention (N = 10) compared to the placebo (N = 6) group (80 vs. 16.7%, respectively, p = 0.035). There were no differences in terms of biochemical response within each group pre- and post-intervention. Post-'Mycodigest' intervention, 25 species were found to be differentially abundant compared to baseline, including increase in short chain fatty acid producing bacteria, such as Parabacteroides distasonis (Beta coefficient 0.92, 95% Confidence interval [CI] 0.36-1.47) and Faecalimonas umbilicata (Beta coefficient 0.57, 95% CI 0.23-0.90). Two microbial pathways related to the metabolism of isoprenoid compounds were increased post-'Mycodigest' intervention. Mushroom based prebiotic supplementation in subjects with CD resulted in clinical improvement which may be related to post-intervention favorable compositional and functional microbial alterations.},
}

@article {pmid40313154,
year = {2025},
author = {Abiola, C and Gwak, JH and Lee, UJ and Adigun, AO and Rhee, SK},
title = {Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {4},
pages = {e2502002},
doi = {10.71150/jm.2502002},
pmid = {40313154},
issn = {1976-3794},
support = {//National Research Foundation of Korea/ ; 2021R1A2C3004015//Ministry of Science and ICT/ ; RS-2023-00213601//Ministry of Science and ICT/ ; 2020R1A6A1A06046235//Ministry of Education/ ; //Korea Institute of Marine Science & Technology Promotion/ ; RS-2024-00436293//Ministry of Oceans and Fisheries/ ; },
mesh = {*Soil Microbiology ; Phylogeny ; *Nitrification ; *Archaea/genetics/classification/metabolism/isolation & purification ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Ammonia/metabolism ; Oxidation-Reduction ; Soil/chemistry ; Metagenomics ; Filtration ; Nitrites/metabolism ; },
abstract = {Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FF_bin01 and FF_bin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FF_bin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FF_bin01 and FF_bin02 are identified as novel species within the genera "Candidatus Nitrosocosmicus" and Nitrososphaera, respectively, while FF_bin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FF_bin01 and FF_bin02 harbor a gene encoding manganese catalase and FF_bin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.},
}

*Soil Microbiology
Phylogeny
*Nitrification
*Archaea/genetics/classification/metabolism/isolation & purification
*Bacteria/genetics/classification/metabolism/isolation & purification
Ammonia/metabolism
Oxidation-Reduction
Soil/chemistry
Metagenomics
Filtration
Nitrites/metabolism

@article {pmid40313146,
year = {2025},
author = {Jeong, H and Choe, Y and Nam, J and Ban, YH},
title = {A guide to genome mining and genetic manipulation of biosynthetic gene clusters in Streptomyces.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {4},
pages = {e2409026},
doi = {10.71150/jm.2409026},
pmid = {40313146},
issn = {1976-3794},
support = {//Ministry of Science and ICT/ ; IITP-2025-RS-2023-00260267//Institute for Information & communications Technology Planning & Evaluation/ ; 202305080001//Kangwon National University/ ; //National Research Foundation of Korea/ ; 2021R1C1C2006260//Ministry of Science and ICT/ ; RS-2023-00301850//Ministry of Education/ ; },
mesh = {*Streptomyces/genetics/metabolism ; *Multigene Family ; *Biosynthetic Pathways/genetics ; *Genome, Bacterial ; Secondary Metabolism/genetics ; Biological Products/metabolism ; *Genomics/methods ; },
abstract = {Streptomyces are a crucial source of bioactive secondary metabolites with significant clinical applications. Recent studies of bacterial and metagenome-assembled genomes have revealed that Streptomyces harbors a substantial number of uncharacterized silent secondary metabolite biosynthetic gene clusters (BGCs). These BGCs represent a vast diversity of biosynthetic pathways for natural product synthesis, indicating significant untapped potential for discovering new metabolites. To exploit this potential, genome mining using comprehensive strategies that leverage extensive genomic databases can be conducted. By linking BGCs to their encoded products and integrating genetic manipulation techniques, researchers can greatly enhance the identification of new secondary metabolites with therapeutic relevance. In this context, we present a step-by-step guide for using the antiSMASH pipeline to identify secondary metabolite-coding BGCs within the complete genome of a novel Streptomyces strain. This protocol also outlines gene manipulation methods that can be applied to Streptomyces to activate cryptic clusters of interest and validate the functions of biosynthetic genes. By following these guidelines, researchers can pave the way for discovering and characterizing valuable natural products.},
}

*Streptomyces/genetics/metabolism
*Multigene Family
*Biosynthetic Pathways/genetics
*Genome, Bacterial
Secondary Metabolism/genetics
Biological Products/metabolism
*Genomics/methods

@article {pmid40312907,
year = {2025},
author = {Zheng, CM and Kang, HW and Moon, S and Byun, YJ and Kim, WT and Choi, YH and Moon, SK and Piao, XM and Yun, SJ},
title = {Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer.},
journal = {Investigative and clinical urology},
volume = {66},
number = {3},
pages = {272-280},
doi = {10.4111/icu.20240454},
pmid = {40312907},
issn = {2466-054X},
support = {2020R1I1A3062508/NRF/National Research Foundation of Korea/Korea ; RS-2023-00245919/NRF/National Research Foundation of Korea/Korea ; RS-2024-00342111/NRF/National Research Foundation of Korea/Korea ; 5199990614277/NRF/National Research Foundation of Korea/Korea ; /KHIDI/Korea Health Industry Development Institute/Korea ; },
mesh = {Humans ; *Microbiota/genetics ; *Urinary Bladder Neoplasms/microbiology/urine ; *DNA, Bacterial/isolation & purification/urine ; Male ; Female ; Middle Aged ; *Urine/microbiology ; Aged ; RNA, Ribosomal, 16S ; Reproducibility of Results ; },
abstract = {PURPOSE: This study aimed to evaluate and optimize microbial DNA extraction methods from urine, a non-invasive sample source, to enhance DNA quality, purity, and reliability for urinary microbiome research and biomarker discovery in bladder cancer.

MATERIALS AND METHODS: A total of 302 individuals (258 with genitourinary cancers and 44 with benign urologic diseases) participated in this study. Urine samples were collected via sterile catheterization, resulting in 445 vials for microbial analysis. DNA extraction was performed using three protocols: the standard protocol (SP), water dilution protocol (WDP), and chelation-assisted protocol (CAP). DNA quality (concentration, purity, and contamination levels) was assessed using NanoDrop spectrophotometry. Microbial analysis was conducted on 138 samples (108 cancerous and 30 benign) using 16S rRNA sequencing. Prior to sequencing on the Illumina MiSeq platform, Victor 3 fluorometry was used for validation.

RESULTS: WDP outperformed other methods, achieving significantly higher 260/280 and 260/230 ratios, indicating superior DNA purity and reduced contamination, while maintaining reliable DNA yields. CAP was excluded due to poor performance across all metrics. Microbial abundance was significantly higher in WDP-extracted samples (p<0.0001), whereas SP demonstrated higher alpha diversity indices (p<0.01), likely due to improved detection of low-abundance taxa. Beta diversity analysis showed no significant compositional differences between SP and WDP (p=1.0), supporting the reliability of WDP for microbiome research.

CONCLUSIONS: WDP is a highly effective and reliable method for microbial DNA extraction from urine, ensuring high-quality and reproducible results. Future research should address sample variability and crystal precipitation to further refine microbiome-based diagnostics and therapeutics.},
}

Humans
*Microbiota/genetics
*Urinary Bladder Neoplasms/microbiology/urine
*DNA, Bacterial/isolation & purification/urine
Male
Female
Middle Aged
*Urine/microbiology
Aged
RNA, Ribosomal, 16S
Reproducibility of Results

@article {pmid40312727,
year = {2025},
author = {Wang, L and Wu, Y and Zhao, ZB and Jia, T},
title = {Small-scale heterogeneity of soil properties in farmland affected fava beans growth through rhizosphere differential metabolites and microorganisms.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {45},
pmid = {40312727},
issn = {2524-6372},
support = {52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; 52100207//The Youth Program of the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Soil heterogeneity has been acknowledged to influence plant growth, with the small-scale soil heterogeneity always being overlooked in practice. It remains unclear how rhizosphere soil biotics and abiotics respond to soil heterogeneity and how rhizosphere interactions influence crop growth.

RESULTS: In this study, we planted fava beans in a farmland around an e-waste dismantling site, and a distinct boundary (row spacing is 30 cm) was observed in the field during the flowering stage, which divided fava beans phenotypes into two distinct groups (Big vs Little) based on the differences in biomass and height. Soil total concentrations of As, B, Co, Cr, Cu, Pb, Sr, Zn, Ni, Cd and soil pH significantly differed in the rhizosphere of fava beans in the two adjacent rows, which were located on either side of the boundary, with a row-spacing of 30 cm. Random Forest analysis demonstrated that these differentiated soil properties (soil pH, total As, B, Cd, Co, Cr, Cu, Mo, Ni and Zn) substantially influenced fava beans growth (height and biomass). Metagenomic sequencing showed that microbial taxa were significantly enriched their abundance in rhizosphere soils between the two groups of fava beans, with eukaryotic taxa being more sensitively affected. A total of 20 metabolites including coniferyl alcohol, jasmonic acid, resveratrol, and L-aspartic acid, etc. were significantly correlated with fava beans growth. These metabolites were significantly enriched in 15 metabolic pathways (nucleotide metabolism, pyrimidine metabolism, purine metabolism, biosynthesis of plant secondary metabolites, lysine biosynthesis, etc.). Furthermore, 11 microbial genera involved in these metabolic pathways, and these genera were differentially enriched between the two groups and significantly correlated with fava beans growth.

CONCLUSIONS: Overall, the integrated analysis of multi-omics revealed that soil properties heterogeneity at small-scale altered the rhizosphere differential microorganisms and metabolites, which functionally influenced fava beans growth and tolerance to environmental stress. Notably, even soil heterogeneity at such a small spatial scale can cause significant differences in plant growth, and the comprehensive explorations utilizing multi-omics techniques provide novel insights to the field management, which is crucial for the survival and sustainable development of humanity.},
}

@article {pmid40312673,
year = {2025},
author = {Qin, X and Song, Y and Ding, J and Qin, X and Chen, K and Wang, H},
title = {Symptomatic central nervous system infections in kidney transplant recipients: a 20-years multicenter observational study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {641},
pmid = {40312673},
issn = {1471-2334},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; Male ; Female ; *Central Nervous System Infections/epidemiology/microbiology/etiology/diagnosis/mortality/cerebrospinal fluid ; Retrospective Studies ; Middle Aged ; Adult ; *Transplant Recipients/statistics & numerical data ; China/epidemiology ; Aged ; Young Adult ; },
abstract = {BACKGROUND: Central nervous system (CNS) infections in kidney transplant recipients (KTRs) remain poorly characterized, with current evidence largely derived from isolated case reports over the past two decades. This multicenter study aims to systematically delineate the epidemiology, clinical profiles, and outcomes of CNS infections in a large KTR cohort.

METHODS: We conducted a retrospective analysis of 3,602 KTRs across three transplant centers in China (May 2004-July 2024). CNS infections were defined by: 1) neurological symptoms/signs, and 2) microbiological confirmation via cerebrospinal fluid (CSF) analysis, including metagenomic next-generation sequencing (mNGS) and routine microbiologic testing (bacterial and fungal cultures).

RESULTS: CNS infections were diagnosed in 0.53% of KTRs (19/3602), with symptom onset occurring 2-121 months post-transplantation. Etiologies included bacterial (47%, 9/19), viral (32%, 6/19), and fungal (21%, 4/19) pathogens. Notably, 79% of cases (15/19) were exclusively identified by mNGS, whereas conventional cultures failed detection. Presenting symptoms included headache (79%) and altered mental status (42%). Mortality reached 42% (8/19) within 9-22 days of diagnosis; among survivors, 73% (8/11) exhibited neurological sequelae.

CONCLUSIONS: CNS infections in KTRs are rare but characterized by rapid progression and high fatality rate. While the risk of CNS infections persists throughout the post-transplant period, 1-6 months after transplantation is a higher-incidence period of CNS infections. KTRs with neurological symptoms (particularly headache and elevated CSF pressure) should undergo CSF mNGS which is critical in diagnosing such infections.},
}

Humans
*Kidney Transplantation/adverse effects
Male
Female
*Central Nervous System Infections/epidemiology/microbiology/etiology/diagnosis/mortality/cerebrospinal fluid
Retrospective Studies
Middle Aged
Adult
*Transplant Recipients/statistics & numerical data
China/epidemiology
Aged
Young Adult

@article {pmid40312516,
year = {2025},
author = {Kim, DD and Swarthout, JM and Worby, CJ and Chieng, B and Mboya, J and Earl, AM and Njenga, SM and Pickering, AJ},
title = {Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40312516},
issn = {2058-5276},
support = {n/a//Tufts University/ ; U19AI110818//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5R21AI171890//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5R21AI171890//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Identifying bacterial transmission pathways is crucial to inform strategies that limit the spread of pathogenic and antibiotic-resistant bacteria. Here we assessed Escherichia coli strain-sharing and overlap of antibiotic resistance genes (ARGs) across humans, poultry, canines, soil, and drinking water within and between households in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households with half having access to chlorinated water. We performed Pooling Isolated Colonies-seq, which sequences pools of up to five E. coli colonies per sample to capture strain diversity. Pooling Isolated Colonies-seq captured 1,516 colonies and identified 154 strain-sharing events, overcoming limitations of single-isolate sequencing and metagenomics. Within households, strain-sharing rates and resistome similarities across sample types were strongly correlated, suggesting clonal transmission of ARGs. E. coli isolated from the environment carried clinically relevant ARGs. Strain-sharing was rare between animals and humans but frequent between humans and drinking water. E. coli-contaminated stored drinking water was associated with higher human-human strain-sharing within households. These results suggest that contaminated drinking water facilitates human to human strain-sharing, and water treatment can disrupt transmission.},
}

@article {pmid40312036,
year = {2025},
author = {Patangia, DV and Grimaud, G and Lyons, K and Dempsey, E and Ryan, CA and O'Shea, CA and Ross, RP and Stanton, C},
title = {Influence of feeding habit and duration on infant gut microbiome - a 6 month pilot study.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-15},
doi = {10.1163/18762891-bja00075},
pmid = {40312036},
issn = {1876-2891},
abstract = {While the importance of breastfeeding on the developing infant gut microbiota has been established, few studies have compared the effect of breastfeeding duration on infant gut microbiota development. In this pilot study, we included 23 infants, divided into 4 groups to compare the effect of breastfeeding duration for first 4 (BreastFed_4) or 8 weeks (BreastFed_8) compared to exclusive breast (Exc Breast Fed) or formula feeding (Formula Fed) for 6 months. We used metagenomics shotgun sequencing of 88 infant stool samples and 64 corresponding maternal milk samples to examine the microbial composition. Breast milk samples showed the presence of previously defined core bacteria including spp. belonging to Staphylococcus, Streptococcus, Corynebacterium, Cutibacterium, Rothia and Pseudomonas. We report that the Exc Breast Fed infant group had the lowest alpha diversity and a distinct microbial composition compared to the Formula Fed group. BreastFed_4 clustered distinctly from all other groups, indicating the impact of duration and time of feeding on infant microbiota. Certain Bifidobacterium spp. were more associated to certain groups, in particular, B. infantis was more associated to Exc Breast Fed while Bacteroides/Phocaeicola with BreastFed_8. Exc Breast Fed showed the highest frequency of persisters with B. infantis being the dominant persister, while B. bifidum was the dominant persister in Formula Fed group. Persisters showed significantly higher abundance of several glycoside hydrolases (GH) important in early life across all groups compared to non-persisters. This study highlights infant gut microbiota changes associated with breastfeeding duration, warranting more detailed studies on the impact of breastfeeding duration on long-term health outcomes.},
}

@article {pmid40311978,
year = {2025},
author = {Wang, YX and Dong, BX and Liu, YJ and Tan, YQ and An, YT and Lin, LH and Li, G},
title = {Molecular cloning, characterization, and structural stability analysis of a rare acidic catechol 2,3-dioxygenase from the metagenome of coal-polluted soil.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {143652},
doi = {10.1016/j.ijbiomac.2025.143652},
pmid = {40311978},
issn = {1879-0003},
abstract = {Polycyclic Aromatic Hydrocarbons (PAHs) are ubiquitous environmental pollutants that pose substantial health hazards, especially in coal-mining areas. This study presented the metagenomic identification and comprehensive characterization of a novel acidic catechol 2,3-dioxygenase, C23O927, derived from a coal-contaminated soil metagenome. Optimal enzymatic activity for C23O927 was observed at pH 4.0 and 55 °C, with remarkable stability across a wide pH spectrum (2.0-10.0) and temperature range (30 °C-60 °C). The enzyme displayed robust tolerance to various organic solvents and salts, and its activity was notably activated by diverse metal ions. Distinct from other catechol 2,3-dioxygenases, C23O927 exhibited oxygen tolerance and maintained robust activity after purification at 4 °C for up to three days. The structural stability of C23O927 is attributed to its unique extended β-sheet structure and increased α-helices. These characteristics help enhance rigidity and reduce the exposure of the hydrophobic core, thereby conferring greater stability on C23O927. The unique properties of C23O927, which include an optimal pH for acidic environments, salt tolerance, resistance to metal ions and organic solvents, and thermal stability, render it a promising candidate for industrial waste management and soil bioremediation.},
}

@article {pmid40311618,
year = {2025},
author = {Andreu-Sánchez, S and Blanco-Míguez, A and Wang, D and Golzato, D and Manghi, P and Heidrich, V and Fackelmann, G and Zhernakova, DV and Kurilshikov, A and Valles-Colomer, M and Weersma, RK and Zhernakova, A and Fu, J and Segata, N},
title = {Global genetic structure of human gut microbiome species is related to geographic location and host health.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.04.014},
pmid = {40311618},
issn = {1097-4172},
abstract = {The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have associated microbial relative abundances with human-health-related phenotypes, the substantial intraspecies genetic variability of gut microbes has not yet been comprehensively considered, limiting the potential of linking such genetic traits with host conditions. Here, we analyzed 32,152 metagenomes from 94 microbiome studies across the globe to investigate the human microbiome intraspecies genetic diversity. We reconstructed 583 species-specific phylogenies and linked them to geographic information and species' horizontal transmissibility. We identified 484 microbial-strain-level associations with 241 host phenotypes, encompassing human anthropometric factors, biochemical measurements, diseases, and lifestyle. We observed a higher prevalence of a Ruminococcus gnavus clade in nonagenarians correlated with distinct plasma bile acid profiles and a melanoma and prostate-cancer-associated Collinsella clade. Our large-scale intraspecies genetic analysis highlights the relevance of strain diversity as it relates to human health.},
}

@article {pmid40311598,
year = {2025},
author = {Hong, Y and Cui, J and Xu, G and Li, N and Peng, G},
title = {Intestinal IL-17 family orchestrates microbiota-driven histone deacetylation and promotes Treg differentiation to mediate the alleviation of asthma by Ma-Xing-Shi-Gan decoction.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {142},
number = {},
pages = {156656},
doi = {10.1016/j.phymed.2025.156656},
pmid = {40311598},
issn = {1618-095X},
abstract = {BACKGROUND: Gut microbiota imbalance is well-known as one important trigger of allergic asthma. Ma-Xing-Shi-Gan decoction (MXSG) is a traditional Chinese medicine prescription with ideal clinical efficacy on asthma. However, whether and how MXSG exerts its efficacy on asthma through gut microbiota remains unclear.

PURPOSE: To investigate the underlying mechanism of MXSG against asthma using multi-omics technologies.

METHODS: An asthma model was established using 8-week-old C57BL/6 J mice, after which they were daily administrated with high-, medium- and low-dose MXSG for 7 days. Histopathological examinations and flow cytometry were performed to evaluate the effects of MXSG on lung immune injury. Key regulatory pathways were predicted via network pharmacology and verified using 16S rRNA sequencing, metagenomics, metabolomics, and in vivo experiments including the knockout of the targeting gene.

RESULTS: MXSG alleviated asthma symptoms, elevated intestinal microbial diversities, and enriched potential beneficial microbes such as Lactococcus, Lactobacillus, and Limosilactobacillus. Network pharmacology and experimental validation highlighted the IL-17/Treg signaling as crucial for asthma treatment. IL-17 knockout experiments revealed its necessity for Treg differentiation during asthma. Moreover, IL-17-deficient asthmatic mice exhibited lower levels of Lactobacillus and significant changes in microbial genes involving histone deacetylases (HDAC) and short-chain fatty acids (SCFAs). Finally, MXSG significantly boosted SCFA production and reduced HDAC9 expression, which were correlated with Treg cell ratios.

CONCLUSION: Our study delineates a novel mechanism where MXSG synergizes with the IL-17 family to enrich intestinal beneficial microbes (e.g. Lactobacillus) and SCFAs. This inhibits the expression of SCFA-downstream HDAC9 to promote Treg differentiation, and thus potentially alleviates asthma.},
}

@article {pmid40311430,
year = {2025},
author = {Chen, Z and Hu, Y and Qiu, G and Liang, D and Cheng, J and Chen, Y and Wang, G and Zhu, X and Xie, J},
title = {Inoculation with Acinetobacter indicus CZH-5 in internal circulation airlift zeolite spheres sequencing batch reactor to augment simultaneous removal of nitrogen, phosphorus, and tetracycline.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138384},
doi = {10.1016/j.jhazmat.2025.138384},
pmid = {40311430},
issn = {1873-3336},
abstract = {Inoculating functional bacterial strains is a cost-effective strategy for enhancing treatment of anaerobic digestion liquids in swine wastewater. This study systematically evaluated inoculation of heterotrophic nitrification aerobic denitrification strain Acinetobacter indicus CZH-5 in an internal circulation airlift zeolite sphere-based sequencing batch reactor (IR) for aerobic removal of nitrogen (N), phosphorus (P), and tetracycline (TEC). Inoculation with CZH-5 promoted secretion of quorum sensing signaling molecules, specifically N-acyl-homoserine lactones (C6-HSL and C10-HSL). These signaling molecules enhance quorum sensing and reinforce cooperation among functional bacteria. Under optimal conditions, average removal efficiencies of total nitrogen, total phosphate, and TEC were 92.8 %, 88.4 %, and 93.1 %, respectively. The removal performance in IR exceeded that of the control by 26 %-71 %. N removal involved complete nitrification-denitrification, while accumulated P was transformed into phosphate monoesters within biofilm. Metagenomic analysis identified Thauera and Acinetobacter as the dominant genera, and Acinetobacter indicus as predominant species. Inoculation enhanced microbial richness and diversity to improve system operational stability. The abundance of functional genes associated with N, P, and TEC transformations significantly increased compared to the control. This study aimed to investigate the characteristics and mechanisms of inoculating a heterotrophic nitrification aerobic denitrification strain into an aerated biofilm system for swine wastewater remediation.},
}

@article {pmid40311350,
year = {2025},
author = {Monge-Olivares, L and Peñalva, G and Pulido, MR and Garrudo, L and Ángel Doval, M and Ballesta, S and Merchante, N and Rasero, P and Cuberos, L and Carpes, G and López-Cerero, L},
title = {Quantitative study of ESBL and carbapenemase producers in wastewater treatment plants in Seville, Spain: a culture-based detection analysis of raw and treated water.},
journal = {Water research},
volume = {281},
number = {},
pages = {123706},
doi = {10.1016/j.watres.2025.123706},
pmid = {40311350},
issn = {1879-2448},
abstract = {Antibiotics can modify populations of multidrug-resistant microorganism (MDRO) in urban wastewater. Our objectives were to quantify the differences in MDR Gram-negative bacteria between influents and effluents of WWTPs of a Spanish city and to evaluate the influence of human antibiotic prescriptions, as well as the persistence of these bacteria after treatment and their genetic relatedness to clinical isolates. The mean count of ESBL producers and carbapenemase producers were 3.77 and 2.74 log 10 CFU/ml, respectively. The reduction achieved by water treatment of ESBL-producing organisms was 1.4-log (96.11 %), whereas a 1.8-log reduction (98.36 %) was obtained regarding carbapenemase producing organisms. Aeromonas spp. predominated among MDROs and blaKPC-2 was the main carbapenemase detected in the influent wastewater samples. Among Escherichia coli and Klebsiella pneumoniae influent isolates, 44 % and 30 %, respectively, belonged to high-risk clones. Regarding Enterobacteriaceae, 10.6 % matched clinical isolates and one strain from an ongoing hospital outbreak was identified among raw samples. New MDROs and persistence of certain strains were detected in effluent samples. Quinolone and third-generation cephalosporin prescriptions, flow rate and population density were associated with higher OXA-48 producer counts. Despite reductions, additional technologies should be implemented in WWTPs receiving hospital discharges. Given the prevalence of environmental species, culture-based and metagenomic approaches should be combined to distinguish between human and sewage sources for antibiotic resistance monitoring. Overall, this study shows that WWTPs with secondary treatment are effective at removing MDRO, and antibiotic stewardship is a potential strategy to reduce the release of MDROs.},
}