@article {pmid39422492,
year = {2024},
author = {Lu, F and Huang, T and Chen, R and Yin, H},
title = {Multi-omics analysis reveals the interplay between pulmonary microbiome and host in immunocompromised patients with sepsis-induced acute lung injury.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0142424},
pmid = {39422492},
issn = {2165-0497},
support = {2024A04J4179//GDSTC | Basic and Applied Basic Research Foundation of Guangdong Province ()/ ; },
mesh = {Humans ; *Sepsis/complications/microbiology/immunology ; *Immunocompromised Host ; *Microbiota/genetics ; Female ; Male ; Middle Aged ; *Lung/microbiology/immunology ; *Acute Lung Injury/microbiology/immunology/etiology ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Adult ; Transcriptome ; Gene Expression Profiling ; Multiomics ; },
abstract = {UNLABELLED: The mechanisms behind the high inflammatory state and immunocompromise in severe sepsis remain unclear. While microbiota's role in immune regulation is known, the impact of pulmonary microbiota on sepsis progression is not fully understood. This study aims to investigate pulmonary microbial characteristics in septic patients and their relationship with host immune-related genes and clinical features. Fifty-four sepsis patients were divided into the immunocompromised host (ICH) group (n = 18) and the control group (n = 36). Bronchoalveolar lavage fluid (BALF) was analyzed using metagenomic next-generation sequencing (mNGS) to assess the pulmonary microbiome, and transcriptomic sequencing evaluated host gene expression. The pulmonary microbiota network in the ICH group showed notable alterations. Symbiotic bacteria like Streptococcus salivarius and Streptococcus oralis were key taxa in the control group. In contrast, opportunistic pathogens such as Campylobacter concisus and Prevotella melaninogenica, typically linked to infections in various body sites, dominated in the ICH group. Transcriptomic analysis revealed differential genes between the two groups. The downregulated differential genes in the ICH group were primarily enriched in pathways related to T-cell activation and the Type I interferon signaling pathway, both crucial for the immune system. Further correlation analysis identified significant associations between certain microbes and host genes, as well as clinical indicators, particularly with species like Campylobacter concisus, Streptococcus salivarius, Streptococcus oralis, and several species of Veillonella. These findings suggest that alterations in the pulmonary microbiome, especially the presence of opportunistic pathogens, may contribute to immune dysregulation in immunocompromised septic patients, warranting further research to explore causal relationships.

IMPORTANCE: Recent research has substantiated the significant role of microbiota in immune regulation, which could influence high inflammatory state and immunocompromise in patients with severe sepsis, as well as provide new opportunities for acute lung injury induced by sepsis diagnosis and treatment. Our study identified some potential critical microbes (Campylobacter concisus and several species of Veillonella), which were correlated with immune-related genes and might be the novel target to regulate immunotherapy in sepsis.},
}

Humans
*Sepsis/complications/microbiology/immunology
*Immunocompromised Host
*Microbiota/genetics
Female
Male
Middle Aged
*Lung/microbiology/immunology
*Acute Lung Injury/microbiology/immunology/etiology
Aged
Bronchoalveolar Lavage Fluid/microbiology
Bacteria/classification/genetics/isolation & purification
Metagenomics
High-Throughput Nucleotide Sequencing
Adult
Transcriptome
Gene Expression Profiling
Multiomics

@article {pmid39472002,
year = {2024},
author = {Yang, B and Zhang, C and Guan, C and Feng, X and Yan, D and Zhang, Z and Qin, Y and Xiong, S and Zhang, W and Cai, X and Hu, L},
title = {Analysis of the composition and function of rhizosphere microbial communities in plants with tobacco bacterial wilt disease and healthy plants.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0055924},
pmid = {39472002},
issn = {2165-0497},
support = {D2021194//Jiangxi Tobacco company/ ; D2019052//Shanghai Tobacco Group Co. Ltd/ ; 2020-079//Shanxi Scholarship Council of China (SSCC)/ ; 201901D111194//Shanxi Province Natural Science Foundation/ ; XD1807//Science Research Start-up Fund for Doctors of Shanxi Medical University/ ; },
mesh = {*Rhizosphere ; *Nicotiana/microbiology ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Soil/chemistry ; *Microbiota ; Nitrogen/analysis ; Ralstonia solanacearum ; Plant Roots/microbiology ; China ; Potassium/analysis ; Phosphorus/analysis ; },
abstract = {To explore the factors influencing the occurrence of bacterial wilt, the differences in the physicochemical properties, microbial community composition and function between rhizosphere soil of tobacco plants with bacterial wilt and healthy plants in the tobacco planting area of Fuzhou City, Jiangxi Province were analyzed and compared. The results showed that the rhizosphere soil of diseased tobacco exhibited significantly reduced levels of exchangeable potassium, water-soluble potassium, nitrate nitrogen, total nitrogen and pH, in comparison to the rhizosphere soil of healthy plants. Conversely, the available phosphorus content of the rhizosphere soil of diseased tobacco was significantly increased. The amount of Ralstonia solanacearum in soil was negatively correlated with pH, nitrate nitrogen and total nitrogen, and positively correlated with exchangeable potassium and water-soluble potassium. A total of 43 genera were significantly different between the two groups of rhizosphere soil, of which 24 genera were enriched in the rhizosphere of healthy plants, including Ideonella, Rhizophagus, Rhizobacter, Altererythrobacter and Ignavibacterium associated with plant disease resistance, Thermodesulfovibrio, Syntrophorhabdus, Syntrophus, Chlorobium, Hydrogenophaga and Limnohabitans associated with soil sulfur metabolism, as well as Ignavibacterium, Ideonella, Derxia and Azohydromonas associated with soil nitrogen cycling. Kyoto Encyclopedia of Genes and Genomes functional analysis of the unigenes obtained by metagenomic sequencing also showed that the differential unigenes were significantly enriched in the sulfur metabolism pathway. In addition, the rhizosphere soil of diseased tobacco plants exhibited a higher abundance of antibiotic-producing actinomycetes and an increased load of antibiotic resistance genes compared to that of healthy plants. In general, lower pH value, less content of nitrate nitrogen and total nitrogen, and more content of exchangeable potassium and water-soluble potassium could contribute to onset of bacterial wilt. Twenty-four genera, including Ideonella and Rhizophagus, may construct a healthy microecological network in the rhizosphere of tobacco plants. All these factors may interact with each other to control the development of bacterial wilt. This complicated interaction network needs to be explored further. IMPORTANCE Previous studies have mainly focused on the differences in microbial species composition between healthy and diseased soils, but the differences in microbial community functions between two types of soil have not been well characterized. In this study, soil samples in diseased and healthy plant rhizospheres were collected for physicochemical property testing and metagenomic sequencing. We focused on analyzing the differences in physicochemical properties and microbial community functions between these soils, as well as the correlation between these factors and pathogen content. The results of this study provide a theoretical basis for further understanding the occurrence of tobacco bacterial wilt in the field.},
}

*Rhizosphere
*Nicotiana/microbiology
*Soil Microbiology
*Plant Diseases/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
Soil/chemistry
*Microbiota
Nitrogen/analysis
Ralstonia solanacearum
Plant Roots/microbiology
China
Potassium/analysis
Phosphorus/analysis

@article {pmid39475247,
year = {2024},
author = {Xu, Z and Yeoh, YK and Tun, HM and Fei, N and Zhang, J and Morrison, M and Kamm, MA and Yu, J and Chan, FKL and Ng, SC},
title = {Variation in the metagenomic analysis of fecal microbiome composition calls for a standardized operating approach.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0151624},
pmid = {39475247},
issn = {2165-0497},
support = {//InnoHK/ ; },
mesh = {Humans ; *Feces/microbiology ; *Metagenomics/methods/standards ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; Female ; Male ; Middle Aged ; DNA, Bacterial/genetics/isolation & purification ; Adult ; Specimen Handling/methods/standards ; Reproducibility of Results ; Aged ; Colorectal Neoplasms/microbiology ; Inflammatory Bowel Diseases/microbiology ; Diabetes Mellitus, Type 2/microbiology ; },
abstract = {The reproducibility in microbiome studies is limited due to the lack of one gold-standard operating procedure. The aim of this study was to examine the impact of protocol variations on microbiome composition using metagenomic data sets from a single center. We assessed the variation in a data set consisted of 2,722 subjects, including 9 subcohorts harboring healthy subjects and patients with various disorders, such as inflammatory bowel disease, colorectal cancer, and type 2 diabetes. Two different DNA extraction kits, with or without lyticase, and two sample storage methods were compared. Our results indicated that DNA extraction had the largest impact on gut microbiota diversity among all host factors and sample operating procedures. Healthy subjects matched by age, body mass index, and sample operating methods exhibited reduced, yet significant differences (PERMANOVA, P < 0.05) in gut microbiota composition across studies. The variations contributed by DNA extraction were primarily driven by different recovery efficiency of gram-positive bacteria, e.g., phyla Firmicutes and Actinobacteria. This was further confirmed by a parallel comparison of fecal samples from five healthy subjects and a standard mock community. In addition, the DNA extraction method influenced DNA biomass, quality, and the detection of specific lineage-associated diseases. Sample operating approach and batch effects should be considered for cohorts with large sample size or longitudinal cohorts to ensure that source data were appropriately generated and analyzed. Comparison between samples processed with inconsistent methods should be dealt with caution. This study will promote the establishment of a sample operating standard to enhance our understanding of microbiome and translating in clinical practice.IMPORTANCEThe reproducibility of human gut microbiome studies has been suboptimal across cohorts and study design choices. One possible reason for the disagreement is the introduction of systemic biases due to differences in methodologies. In our study, we utilized microbial metagenomic data sets from 2,722 fecal samples generated from a single research center to examine the extent to which sample storage and DNA extraction influence the quantification of microbial composition and compared this variable with other sources of technical and biological variation. Our research highlights the impact of DNA extraction methods when analyzing microbiome data and suggests that the microbiome profile may be influenced by differences in the extraction efficiency of bacterial species. With metagenomics sequencing being increasingly used in clinical biology, our findings provide insight into the challenges using metagenomics sequencing in clinical diagnostics, where the detection of certain species and its abundance relative to a "healthy reference" is key.},
}

Humans
*Feces/microbiology
*Metagenomics/methods/standards
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/isolation & purification
Female
Male
Middle Aged
DNA, Bacterial/genetics/isolation & purification
Adult
Specimen Handling/methods/standards
Reproducibility of Results
Aged
Colorectal Neoplasms/microbiology
Inflammatory Bowel Diseases/microbiology
Diabetes Mellitus, Type 2/microbiology

@article {pmid39475249,
year = {2024},
author = {Liang, Y and Huang, Z and Fan, S and Li, C and Huang, L and Huang, C and Hutchins, AP and Fang, C and Zhang, X},
title = {Highlight signatures of vaginal microbiota and metabolome contributed to the occurrence and recurrence of vulvovaginal candidiasis.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0152124},
pmid = {39475249},
issn = {2165-0497},
support = {JCYJ20190809101409603//Science and Technology Planning Project of Shenzen Municipality (Science and Technology Planning Project of Shenzhen of China)/ ; JCYJ20220530160206014//Science and Technology Planning Project of Shenzen Municipality (Science and Technology Planning Project of Shenzhen of China)/ ; 82201793//National Natural Science Foundation of China (NSFC)/ ; KYQD2022145, KYQD202211//Scientific Research Foundation of PEKING UNIVERSITY SHENZHEN HOSPITAL/ ; YBH2019-260//Shenzhen High-level Hospital Construction/ ; no. SZXK027//Shenzhen Key Medical Discipline Construction/ ; no. SZSM202011016//Sanming Project of Medicine in Shenzhen/ ; },
mesh = {Female ; Humans ; *Candidiasis, Vulvovaginal/microbiology/metabolism ; *Vagina/microbiology ; *Microbiota ; Adult ; *Metabolome ; Recurrence ; Lactobacillus/isolation & purification/genetics/metabolism ; Young Adult ; *Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {UNLABELLED: Vulvovaginal candidiasis (VVC) is a common vaginal infectious disease caused by Candida. The high recurrence rate of VVC is a great clinical challenge, with recurrent VVC (RVVC) defined as four or more episodes within a year. In this study, we recruited 31 RVVC patients, 28 VVC patients, and 29 healthy women. Vaginal samples were collected for metagenomic and metabolic analysis. RVVC and VVC groups presented similar clinical symptoms, with only a significantly increased incidence of swelling in the VVC group. Vaginal microbiota in VVC/RVVC exhibited a decreased abundance of Lactobacillus and increased bacterial vaginosis-associated bacteria, such as Gardnerella, Prevotella, and Atopobium. Notably, Lactobacillus iners was higher in RVVC, suggesting not all Lactobacillus species are protective. Healthy women showed lower overall microbiota diversity, emphasizing single-species dominance for stability. Glycogen metabolism pathways were enriched in RVVC/VVC, and were correlated with Atopobium vaginae, Prevotella bivia, and Lactobacillus jensenii. Peptidoglycan synthesis pathways, associated with P. bivia, were enriched, with the substrate L-glutamate elevated in RVVC, possibly promoted by L. iners. These findings shed light on potential therapeutic targets for recurrent VVC, contributing to the understanding of the intricate interplay between the metabolism of vaginal microbiome and disease.

IMPORTANCE: This study enhances our knowledge of the vaginal microbiota dynamics and the role of associated metabolites in individuals with vulvovaginal candidiasis (VVC) and recurrent vulvovaginal candidiasis through shotgun sequencing and multi-omics analysis. The relationship between metabolites and vaginal microbiota and disease state was revealed. The accumulation of L-glutamate generated in glycogen metabolism, which is governed by Lactobacillus iners or bacterial vaginosis-associated bacteria, may contribute to the incidence and recurrence of VVC. Such insights have the potential to impact the treatment and prevention strategies for these common yet distressing conditions, potentially leading to targeted therapies and improved patient outcomes.},
}

Female
Humans
*Candidiasis, Vulvovaginal/microbiology/metabolism
*Vagina/microbiology
*Microbiota
Adult
*Metabolome
Recurrence
Lactobacillus/isolation & purification/genetics/metabolism
Young Adult
*Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid41123352,
year = {2025},
author = {Akinsola, OA and Dahunsi, SO and Odekanle, EL},
title = {Metagenomic study of food waste anaerobic digestion.},
journal = {Microbiology spectrum},
volume = {13},
number = {12},
pages = {e0208725},
pmid = {41123352},
issn = {2165-0497},
mesh = {Anaerobiosis ; *Metagenomics ; Methane/metabolism/biosynthesis ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Archaea/metabolism/genetics/classification ; Biofuels ; Fermentation ; Microbiota/genetics ; Food ; Food Loss and Waste ; },
abstract = {This study explores anaerobic digestion of food waste to understand the microbial community dynamics and metabolic pathways that drive the conversion of organic waste into biogas. Sampling was done at multiple time points during those 4 weeks (weekly) to capture microbial succession/changes over time. The microbial profile was evaluated using QIIME2 and BV-BRC, while functional annotation tools (PICRUSt2) were used to identify dominant pathways. The results reveal a temporal shift in microbial communities, with fermentative bacteria, such as Lactobacillus and Clostridia, dominating the early stages of digestion, followed by methanogenic archaea like Methanomicrobia in the later stages. Pathway analysis showed that fermentation, aromatic compound degradation, and methanogenesis were the primary metabolic processes, with methanogenesis becoming more prominent by week 3 (FW3_S162_R1). The study highlights the critical role of microbial community adaptation in maximizing methane production and offers new insights into optimizing anaerobic digestion for more efficient food waste biogas generation. By combining metagenomic and metabolomic approaches, this research provides a comprehensive understanding of the microbial and metabolic factors that shape the anaerobic digestion process, contributing to the development of sustainable waste management practices.IMPORTANCEThis study employs a metagenomic approach to elucidate the intricate microbial communities and metabolic processes involved in the anaerobic digestion of food waste. It highlights microbial interactions that influence biogas production, offering insights for optimizing waste-to-energy conversion. Understanding these dynamics is key to improving digestion efficiency, reducing environmental impacts, and advancing sustainable waste management and circular economy strategies. The findings provide a valuable foundation for future innovations addressing global waste and energy challenges.},
}

Anaerobiosis
*Metagenomics
Methane/metabolism/biosynthesis
*Bacteria/metabolism/genetics/classification/isolation & purification
Archaea/metabolism/genetics/classification
Biofuels
Fermentation
Microbiota/genetics
Food
Food Loss and Waste

@article {pmid41143528,
year = {2025},
author = {Mukherjee, SD and Adler, A and Dang, T and Taylor, EN and Curhan, G and Miller, AW},
title = {Evaluating the use of biobanked urine specimens for human urobiome studies.},
journal = {Microbiology spectrum},
volume = {13},
number = {12},
pages = {e0216424},
pmid = {41143528},
issn = {2165-0497},
support = {R01 DK121689/DK/NIDDK NIH HHS/United States ; //Lerner Research Institute, Cleveland Clinic/ ; },
mesh = {Humans ; *Biological Specimen Banks ; *Microbiota/genetics ; Male ; Female ; *Urine/microbiology ; *Urinary Tract/microbiology ; Metagenomics/methods ; Middle Aged ; Specimen Handling/methods ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Aged ; },
abstract = {Case-control studies focused on the urinary tract microbiome, or urobiome, have consistently reported significant associations with disease. However, clinical urobiome studies have typically been small, averaging ~50 patients per study. While these sample sizes are sufficient to detect large effect sizes, they have not been able to differentiate disease phenotypes within a larger disease complex (e.g., different types of kidney stones), which have unique etiological origins. Biobanked urine specimens can help fill this void. However, since these specimens were not collected specifically for urobiome studies, they must be validated before drawing any strong conclusions. The objective of this study was to evaluate microbiome data derived from metagenomic analysis of biobanked urine specimens against the following criteria: (i) level of contaminants; (ii) retention of high-quality DNA; (iii) overgrowth of a few dominant bacteria; and (iv) preservation of sex-specific taxa. A total of 174 samples were assessed from biobanked or freshly collected specimens (N = 118 patients total), in addition to multiple positive and negative controls. While there were significant differences in diversity (alpha/beta; P < 0.001) based on whether or not samples were biobanked, these differences can largely be explained by study-specific variation. With these criteria, we find that biobanked urine specimens provide similar data to fresh specimens collected using standardized protocols and can be used for clinical urobiome studies.IMPORTANCEThe urinary tract microbiome, or urobiome, is an emerging field of study that has shown promise as an important contributor to urologic health and disease. However, since this field is relatively new, clinical studies to evaluate the urobiome in the context of urologic disease have been relatively small. The use of biobanked urine specimens would allow for much larger studies to be conducted in a relatively short period of time. However, the use of biobanked urine specimens must first be validated. In this study, we sought to evaluate the use of biobanked urine specimens through multiple metrics, compared to previous studies conducted specifically to assess the impact of the urobiome. Results of our study suggest that biobanked urine specimens produce similar data to urine samples collected under rigorously controlled conditions and can be used in casecontrol studies of urologic conditions.},
}

Humans
*Biological Specimen Banks
*Microbiota/genetics
Male
Female
*Urine/microbiology
*Urinary Tract/microbiology
Metagenomics/methods
Middle Aged
Specimen Handling/methods
*Bacteria/classification/genetics/isolation & purification
Adult
Aged

@article {pmid41196055,
year = {2025},
author = {Plaza Oñate, F and Quinquis, B and Thirion, F and Gilles, M and Morabito, C and Valeille, K and Martin, R and Guidet, B and Kern, C and Pécastaings, S},
title = {Assessment of protocols for characterization of the human skin microbiome using shotgun metagenomics and comparative analysis with 16S metabarcoding.},
journal = {Microbiology spectrum},
volume = {13},
number = {12},
pages = {e0173225},
pmid = {41196055},
issn = {2165-0497},
support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; },
mesh = {Humans ; *Skin/microbiology/virology ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; *DNA Barcoding, Taxonomic/methods ; Viruses/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; Forehead/microbiology ; Adult ; DNA, Bacterial/genetics ; Male ; Sequence Analysis, DNA ; Female ; Skin Microbiome ; },
abstract = {The skin microbiome includes bacteria, fungi, and viruses, with composition varying significantly across body sites. Although 16S rRNA gene sequencing is common, it excludes non-prokaryotic taxa and offers limited functional data. Shotgun metagenomics provides broader taxonomic and functional insights but is challenging for low-biomass skin samples due to limited microbial DNA and high host contamination. In this study, we characterized the microbiome of the forehead and armpits in healthy individuals using shotgun metagenomics and assessed the strategies to improve sequencing success. We compared collection kits, DNA extraction protocols, and tested multiple displacement amplification (MDA). We found that sampling with D-Squame discs followed by an in-house DNA extraction protocol was the most effective combination to maximize DNA yields. MDA introduced significant compositional biases and is not recommended. Shotgun sequencing, without MDA, produced microbial compositions and diversity indices broadly consistent with 16S rRNA metabarcoding, although it showed discrepancies in the relative abundance of some genera. Consistent with prior studies, the armpit microbiome was dominated by Staphylococcus spp., whereas the forehead microbiome was dominated by Cutibacterium spp. Critically, shotgun sequencing provided additional insights into viral and eukaryotic microorganisms and revealed the functional potential of microbial communities, demonstrating its clear advantages over 16S rRNA metabarcoding for comprehensive skin microbiome research.IMPORTANCEWith growing evidence of the role of microorganisms in maintaining healthy skin, accurately characterizing the skin microbiome remains a significant challenge. In this study, we demonstrate that shotgun sequencing, carried out with adapted wet lab protocols, provides deep insights into the microbiome composition of specific areas, such as the forehead or the armpits. Notably, it enables the characterization of fungi and viruses while offering direct functional insights into microbial communities, providing a clear advantage over 16S ribosomal RNA gene sequencing. Our findings highlight the potential of shotgun metagenomics as a powerful tool for comprehensive skin microbiome analysis. They emphasize the importance of tailored protocols for low-biomass samples, improving the reliability of shotgun sequencing and paving the way for more robust clinical studies focused on the skin microbiome.},
}

Humans
*Skin/microbiology/virology
*Metagenomics/methods
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
*DNA Barcoding, Taxonomic/methods
Viruses/classification/genetics/isolation & purification
Fungi/classification/genetics/isolation & purification
Forehead/microbiology
Adult
DNA, Bacterial/genetics
Male
Sequence Analysis, DNA
Female
Skin Microbiome

@article {pmid41196057,
year = {2025},
author = {Fait Kadlec, T and Ilett, EE and da Cunha-Bang, C and Sengeløv, H and Brieghel, C and Gulay, A and Rafiq, S and Ravn, HB and Zheng, C and Nielsen, RV and Sørensen, SS and Zargari Marandi, R and Niemann, CU},
title = {Explainable machine learning to identify chronic lymphocytic leukemia and medication use based on gut microbiome data.},
journal = {Microbiology spectrum},
volume = {13},
number = {12},
pages = {e0094425},
pmid = {41196057},
issn = {2165-0497},
mesh = {Humans ; *Leukemia, Lymphocytic, Chronic, B-Cell/microbiology/drug therapy/diagnosis ; *Gastrointestinal Microbiome/drug effects ; *Machine Learning ; Male ; Female ; Aged ; Middle Aged ; Denmark ; Aged, 80 and over ; Adult ; Anti-Bacterial Agents/therapeutic use ; Cohort Studies ; Metagenomics ; },
abstract = {Medication, particularly antibiotics, significantly alters gut microbiome composition, often reducing microbial diversity and affecting host health. Given that the gut microbiome may influence cancer progression, we integrated clinical, shotgun metagenomic, and medication data to assess microbiome composition across diseased and healthy cohorts, as well as the impact of medication on microbiome variation. The study cohorts included patients with chronic lymphocytic leukemia (CLL, n = 85), acute myeloid leukemia (AML, n = 61), myeloid dysplastic syndrome (MDS), and other severe hematological malignancies (n = 104); patients scheduled for elective cardiac surgery (n = 89); and kidney donors (n = 9), all collected as part of a consecutive microbiome sampling effort at Copenhagen University Hospital, Denmark; and healthy individuals (N = 59). First, our analyses revealed similarities in both diversity and composition between microbiomes of patients with CLL and patients prior to elective cardiac surgery, whereas patients with AML and MDS exhibited the least diverse and most distinct microbiomes. Second, when we quantified sources of microbiome variation, the combination of medication, disease, age, and sex accounted for 4% of variation between all cohorts and 10.4% of variation between CLL and pre-cardiac surgery patients only; the two cohorts selected for comparison due to their similar microbiomes. Notably, this left 90%-95% of the variation unexplained, emphasizing the need for better identification of the parts of the microbiome variation impacting health and disease. Third, using a machine learning approach, we validated and further refined the CLL-associated microbiome pattern from our previous studies. Overall, our data provide a foundation for further investigation into disease-specific microbial signatures and the potential interactions between medication, underlying disease, and the microbiome, with the ultimate goal to improve our understanding and clinical management of CLL.IMPORTANCEThis study reveals how disease and medication influence the gut microbiome in patients with chronic lymphocytic leukemia (CLL) when compared to other more severe hematological malignancies, a cohort of patients scheduled for elective cardiac surgery representing a severely diseased nonhematological cohort, and a cohort of healthy individuals. We found that patients with CLL and those scheduled for cardiac surgery had the most similar microbiome diversity and composition. Similarities across very different disease contexts suggest that disease status alone has limited impact. Consistently, across all cohorts, medication, disease, age, and sex together explained only less of microbiome variation, leaving 90%-95% unexplained. This underscores the important need for better identification of factors shaping the microbiome. In addition, we validated a previously published, machine learning-based CLL-associated microbiome signature, demonstrating the robustness of our previous findings differentiating the microbiome signature for CLL as compared to healthy individuals. The findings expand knowledge on how disease states and medical treatments shape gut microbiome composition and diversity, potentially leading to new ways of managing CLL and improving patient outcomes through microbiome signatures.},
}

Humans
*Leukemia, Lymphocytic, Chronic, B-Cell/microbiology/drug therapy/diagnosis
*Gastrointestinal Microbiome/drug effects
*Machine Learning
Male
Female
Aged
Middle Aged
Denmark
Aged, 80 and over
Adult
Anti-Bacterial Agents/therapeutic use
Cohort Studies
Metagenomics

@article {pmid41802510,
year = {2026},
author = {Gou, X and Shen, Y and Liu, F and Wang, Y and Zong, Y and Qu, D and Ren Zeng, C and Nhamdriel, T and Kuang, T and Fan, G},
title = {Swertia chirayita ameliorates MAFLD by improving intestinal microenvironment and hepatic lipogenesis.},
journal = {Journal of ethnopharmacology},
volume = {364},
number = {},
pages = {121471},
doi = {10.1016/j.jep.2026.121471},
pmid = {41802510},
issn = {1872-7573},
mesh = {Animals ; *Lipogenesis/drug effects ; *Liver/drug effects/metabolism/pathology ; Male ; Rats ; *Swertia/chemistry ; *Plant Extracts/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Diet, High-Fat/adverse effects ; Intestines/drug effects ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Metabolic-associated fatty liver disease (MAFLD) is emerging as a very serious threat to human health. The search for effective remedies for MAFLD from natural herbs is gaining increasing attention. Swertia chirayita (SC) is a famous herb in China, India, and Nepal. It has long been employed within the traditional Tibetan medical system for managing hepatic disorders. Nevertheless, the therapeutic impacts and possible mechanisms of SC in the context of MAFLD are unclear.

AIM OF THE STUDY: This present investigation was designed to research the pharmacological influence and potential mechanisms of SC in MAFLD rats. We conducted a particular examination of its effects on the intestinal microenvironment and hepatic lipogenesis.

MATERIALS AND METHODS: The pharmacological effects of SC were evaluated in MAFLD rats established through a 12-week high-fat diet (HFD) feeding. After 8 weeks of SC administration, biochemical assessments were conducted for body fat, liver function, glucose metabolism, lipid parameters, and inflammatory factors. The main chemical constituents of SC and three short-chain fatty acids (SCFAs) in rat feces were quantitatively analyzed by HPLC. Furthermore, targeted metabolomics, transcriptomics, metagenomics, and Western blotting were employed to investigate possible mechanisms by which SC improves MAFLD.

RESULTS: Treatment with SC significantly ameliorated excessive fat accumulation and insulin resistance in MAFLD rats. It also improved hepatic enzyme activities (AST and ALT), several lipid metrics (TG, TC, and LDL-C), and liver histopathological changes. Moreover, SC attenuated systemic inflammation, as shown by decreased circulating IL-1β, TNF-α, LPS, and IL-6. Metagenomic profiling revealed that SC administration helped reestablish the dysregulation of multiple types of gut microbiota (bacteria, fungi, archaea, and viruses) in MAFLD rats. It improved microbial diversity, community composition, and transkingdom correlations. In addition, SC enhanced gut barrier function by raising the amount of butyric acid, acetic acid, and propionic acid and upregulating the expression of several ZO-1, occludin, and claudin-1. Liver transcriptomic analysis suggested that SC could regulate the metabolism of bile acids (BAs). Importantly, targeted metabolite analysis and western blotting demonstrated that SC improved bile acid dysfunction in MAFLD rats. In particular, SC increased TCDCA, TCA, and DCA, thereby activating the FXR/FGF15 signaling axis. This activation then controlled the production of SHP and SREBP-1c proteins in the hepatic, thereby inhibiting hepatic lipogenesis to improve MAFLD.

CONCLUSIONS: SC has shown a good therapeutic effect on MAFLD by improving intestinal microenvironment and hepatic lipogenesis. Specifically, it improves the imbalance of multiple types of gut microbiota, restores disrupted transkingdom interactions, promotes creation of beneficial SCFAs and bile acid, protects the intestinal barrier, and inhibits hepatic lipogenesis by regulating the BAs/FXR/FGF15 and SHP/SREBP-1c signaling pathways.},
}

Animals
*Lipogenesis/drug effects
*Liver/drug effects/metabolism/pathology
Male
Rats
*Swertia/chemistry
*Plant Extracts/pharmacology/therapeutic use
Rats, Sprague-Dawley
Diet, High-Fat/adverse effects
Intestines/drug effects
Gastrointestinal Microbiome/drug effects

@article {pmid41803907,
year = {2026},
author = {Fernández-de-Bobadilla, MD and Pérez-Cobas, AE and Andremont, A and Martínez, JL and Baquero, F and Lanza, VF and Coque, TM},
title = {The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the "robust-yet-fragile" architecture of human gut microbiomes.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41803907},
issn = {2049-2618},
support = {pFIS F19/00366//Instituto de Salud Carlos III/ ; CB21/13/00084//Instituto de Salud Carlos III/ ; CC23140547//Fundación Francisco Soria Melguizo/ ; MISTAR AC21_2/00041//Joint Programming Initiative on Antimicrobial Resistance/ ; "Ayudas de atracción de talento investigador César Nombela" 2023-T1/SAL-GL28953//Comunidad de Madrid/ ; FP7#282004//European Union/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; French Guiana ; Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Metals/pharmacology ; Male ; Female ; Adult ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Metagenome ; *Drug Resistance, Microbial/genetics ; },
abstract = {BACKGROUND: Metagenomics enables detailed profiling of genes encoding antimicrobial resistance. However, most studies focus exclusively on antibiotic resistance genes (ARGs), excluding those associated with non-antibiotic antimicrobials (metals, biocides), and often rely on methods with low-sensitivity and low-specificity. Furthermore, they rarely examine populations exposed to minimal anthropogenic pollution. We analyzed fecal resistomes of 95 Wayampi individuals, an Indigenous community in remote French Guiana, using a targeted metagenomic capture platform covering 8667 genes, including ARGs, metal resistance genes (MRGs) and biocide resistance genes (BRGs) (PMID: 29335005). Resistome profiles were compared with those of Europeans to assess population-level differences.

RESULTS: ARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs + BRGs gene richness was significantly higher in Wayampi (11,930 vs. 7419). Most genes appeared in a minority of individuals (mean 5% for ARGs, 2% for MRGs + BRGs), but several ARGs for tetracyclines [tet(32), tet(40), tet(O), tet(Q), tet(W), tet(X), tetAB(P)], aminoglycosides (ant6'-I, aph3-III), macrolides (ermB, ermF, mefA), and sulfonamides (sul2) were present in all individuals. Tetracycline resistance genes predominated overall, while beta-lactam resistance genes were more common in Wayampi, and genes conferring resistance to aminoglycosides, amphenicols, and folate inhibitors were more frequent in Europeans. Among MRGs, copper and arsenic resistance genes prevailed in both groups, followed by those for zinc, iron, cobalt, and nickel. Up to 76% of Wayampiis carried acquired MRGs for copper (pcoABCDRS and tcrB), silver (silACFPRS), arsenic (ars), and mercury (mer) detoxification. Shannon diversity indices were similar for ARGs, MRGs, and BRGs, but composition and evenness differed significantly. UMAP and ADONIS analyses distinguished cohorts based on ARG profiles (p < 0.001), but not on MRGs or BRGs. Correlation analysis revealed conserved gene-sharing networks and introgression of acquired ARGs and MRGs within both gut microbiomes.

CONCLUSIONS: The diverse and balanced Wayampi resistome reflects a less perturbed microbiome compared to industrialized populations, and reveals a background of "core" and "shell" acquired ARGs and MRGs, consistent with the "robust-yet-fragile" architecture of scale-free networks. The patchy yet resilient gene distribution suggests varying levels of conserved gene sharing highways among populations, likely shaped by long-term microbial-human evolution, and supports a broader view on acquired antimicrobial resistance. Video Abstract.},
}

Humans
*Gastrointestinal Microbiome/genetics/drug effects
*Anti-Bacterial Agents/pharmacology
French Guiana
Metagenomics/methods
Feces/microbiology
*Bacteria/genetics/drug effects/classification/isolation & purification
*Metals/pharmacology
Male
Female
Adult
*Drug Resistance, Bacterial/genetics
Genes, Bacterial
Metagenome
*Drug Resistance, Microbial/genetics

@article {pmid41879886,
year = {2026},
author = {Chen, W and Li, X and Zhao, X and Zuo, Z and Wang, D and Zhao, F},
title = {GMW: a hybrid graph-based approach for post-assembly metagenome analysis and decontamination.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41879886},
issn = {1869-1889},
abstract = {Accurate genome assembly from metagenomic sequencing data remains challenging, particularly in mixed infections involving multiple pathogens, due to data complexity and contaminant sequences. Here, we present GMW (Genomic Microbe-Wise), a novel computational tool that improves pathogen genome assembly accuracy and enhances contaminant removal capabilities by simplifying the post-assembly graph. GMW leverages community detection algorithms, sequence similarity analysis, and coverage patterns to resolve strain mixtures and improve assembly accuracy. Using datasets of influenza A virus subtypes, we demonstrate GMW's ability to disentangle mixed infections and reconstruct complete viral genomes with high precision. Additionally, GMW outperforms traditional sequence similarity methods in classifying target contigs from contaminants. This tool also provides interactive visualization modules to streamline the inspection of assembly outputs, including simplified representations of complex assembly graphs. By enhancing assembly quality and contamination filtering, GMW emerges as a versatile solution for applications in clinical diagnostics, microbial ecology, and pathogen surveillance.},
}

@article {pmid41881444,
year = {2026},
author = {Kringeland, GD and Tangedal, S and Julian, D and Paytuví-Gallart, A and Sanseverino, W and Bertelsen, RJ and Husebø, GR and Knudsen, KS and Lehmann, S and Nielsen, R and Eagan, TML},
title = {Antimicrobial resistance genes and antibiotic use in chronic lung disease: a bronchoscopy study of the lower airways microbiome.},
journal = {BMJ open respiratory research},
volume = {13},
number = {1},
pages = {},
doi = {10.1136/bmjresp-2025-003864},
pmid = {41881444},
issn = {2052-4439},
mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Bronchoscopy ; Middle Aged ; Aged ; *Anti-Bacterial Agents/therapeutic use ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy ; Case-Control Studies ; *Lung Diseases/microbiology/drug therapy ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Chronic Disease ; },
abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) in the respiratory microbiome are poorly characterised. We compared the presence of ARGs in healthy controls with patients with chronic lung disease in a cross-sectional study, adjusted for time since antibiotic use.

METHODS: Bronchoalveolar lavage was collected from 100 controls, and 93 patients with chronic obstructive pulmonary disease (COPD), 13 with asthma, 34 with sarcoidosis, 12 with idiopathic pulmonary fibrosis (IPF) and 11 patients with unclassifiable interstitial lung disease (uILD). Participants had not used antibiotics 14 days prior to sampling. Shotgun metagenomic sequencing was performed with Illumina NovaSeq. ARGs were identified using the National Database of Antibiotic-Resistant Organisms. Sample reads were normalised to counts per million.

RESULTS: In total, 38% of controls had at least one ARG, compared with 51%, 39%, 65% and 83% of patients with COPD, asthma, sarcoidosis and IPF, respectively (p=0.01). ARGs against tetracycline (33%) were the most common ARG class, followed by beta-lactam and macrolide resistance (both 26%). In a logistic regression analysis adjusted for sex, age, body composition, smoking and antibiotic use, the OR (95% CI) for having ARGs in the lower airways was 1.30 (0.70 to 2.41) in COPD, 1.00 (0.29 to 3.52) in asthma, 3.52 (1.40 to 8.83) in sarcoidosis, 6.40 (1.25 to 32.73) in IPF and 3.27 (0.76 to 14.16) in uILD compared with controls. Overall mean (SD) ARG counts per million were 403.8 (537.7) in the 35 subjects who had used antibiotics ≤3 months before bronchoscopy, compared with 197.6 (355.9) in the 228 subjects without (p=0.02).

CONCLUSION: The presence of ARGs in the lower airways microbiome was significantly higher in patients with sarcoidosis and IPF than in controls. The counts per million for ARGs were significantly associated with recent antibiotic use.},
}

Humans
Male
Female
Cross-Sectional Studies
Bronchoscopy
Middle Aged
Aged
*Anti-Bacterial Agents/therapeutic use
*Microbiota/genetics
Bronchoalveolar Lavage Fluid/microbiology
Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy
Case-Control Studies
*Lung Diseases/microbiology/drug therapy
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Chronic Disease

@article {pmid41881804,
year = {2026},
author = {Gutiérrez, J and Vergara-Amado, J and Martorell, C and Navedo, JG and Wille, M and Guajardo-Leiva, S and Castro-Nallar, E and Verdugo, C},
title = {Functional Shifts in the Gut DNA Virome in a Long-Distance Migratory Shorebird During the Pre-Migratory Fattening.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70315},
doi = {10.1111/mec.70315},
pmid = {41881804},
issn = {1365-294X},
support = {FONDECYT N°1191769//Agencia Nacional de Investigación y Desarrollo/ ; ANILLO ATE220062//Agencia Nacional de Investigación y Desarrollo/ ; Doctoral scholarship N°21201700//Agencia Nacional de Investigación y Desarrollo/ ; //The Pathogen Watchtower Program (Biotia Inc. & The Rockefeller Foundation)/ ; //Universidad Austral de Chile/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Charadriiformes/virology/physiology ; *Animal Migration ; *Virome/genetics ; Feces/virology ; Metagenomics ; Metagenome ; },
abstract = {Migration represents one of the most energetically demanding phases in the life cycle of long-distance migratory birds. Pre-migratory fattening is a critical preparatory stage characterized by hyperphagia, rapid fat accumulation, organ remodelling, and immune modulation. Although the gut microbiome has been recognized as a key contributor to these physiological adaptations, the role of the gut virome remains poorly understood. In this study, the diversity, functional potential, and temporal dynamics of the gut DNA virome in a trans-hemispheric migratory shorebird, the Hudsonian godwit (Limosa haemastica), were assessed during pre-migratory fattening. Adult individuals were maintained under controlled aviary conditions for 15 weeks during the preparation for northbound migration, and faecal samples were collected at two distinct physiological time points: at the beginning and the end of pre-migratory fattening. Shotgun metagenomic sequencing revealed 798 high-quality viral operational taxonomic units (vOTUs), the majority of which were bacteriophages (92%). Potential functional annotation identified auxiliary metabolic genes (AMGs) associated with nucleotide metabolism, redox balance, and host adaptation. Although overall gut virome diversity did not differ between stages, significant changes in potential functional profiles of phages were observed, especially during the final stage of fattening when energy demands are at their highest. In addition to bacteriophages, we report two divergent adenoviruses potentially associated with the Siadenovirus and Aviadenovirus genera. These findings suggest that dynamic viral communities may play underrecognized roles in supporting host physiology during energetically costly life stages.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Charadriiformes/virology/physiology
*Animal Migration
*Virome/genetics
Feces/virology
Metagenomics
Metagenome

@article {pmid41882399,
year = {2026},
author = {Çilkiz, M},
title = {Microbial Biotechnology in Agriculture.},
journal = {Progress in molecular and subcellular biology},
volume = {62},
number = {},
pages = {251-306},
pmid = {41882399},
issn = {0079-6484},
mesh = {*Agriculture/methods ; *Biotechnology/methods ; Soil Microbiology ; Metagenomics/methods ; Crops, Agricultural/growth & development/microbiology ; Metabolomics/methods ; Fertilizers ; },
abstract = {Global food security has become one of the greatest challenges of the twenty-first century due to the rapidly growing world population's food demands and environmental threats such as climate change, soil erosion, and the depletion of freshwater resources. The extensive use of chemical fertilizers and pesticides throughout conventional agriculture has increased productivity significantly, but it has additionally resulted in major ecological and socioeconomic problems, such as soil acidity, groundwater resource pollution, and decreased biodiversity. In this regard, microbial biotechnology is a particularly noteworthy technique that improves agricultural production while promoting environmental sustainability, maintaining ecological balance, and making effective use of resources. This application makes use of microorganisms to enhance soil health and structure, promote plant growth, and minimize both abiotic and biotic stresses. Microbial applications include nitrogen fixation, as well as biofertilizers that reduce the dependency on synthetic materials and biopesticides. Microbial consortia and biostimulants that improve plant physiology by producing phytohormones produce more dependable and durable consequences in the field. Metagenomics and metabolomics are the two types of omic technologies used in these areas of study that provide a thorough description of the variety and roles of microorganisms. Furthermore, the intentional production of microbes targeted at specific organisms has been made practical via synthetic biology and gene editing techniques. In-depth case studies performed in several countries reveal that microbial technologies significantly reduced expenses and improved soil production, advancing the sustainable development goals. Nevertheless, there are several barriers to the widespread use of microbial biotechnology in agriculture. These include unpredictable conditions in the fields, strict regulations, especially related to genetically modified organisms' problems with product quality, and farmers' insufficient understanding. Microbial biotechnology aims to accomplish its full potential as an advancement in technology and as an essential aspect of resource-efficient and environmentally friendly agricultural systems via responsible innovation, adaptable regulations, and worldwide cooperation.},
}

*Agriculture/methods
*Biotechnology/methods
Soil Microbiology
Metagenomics/methods
Crops, Agricultural/growth & development/microbiology
Metabolomics/methods
Fertilizers

@article {pmid39612216,
year = {2025},
author = {Wang, T and Luo, Y and Kong, X and Fang, L and Zhu, L and Yu, B and Zheng, P and Huang, Z and Mao, X and Jie, Y and Luo, J and Yan, H and He, J},
title = {Multiomics comparative analysis of feces AMRGs of Duroc pigs and Tibetan and the effect of fecal microbiota transplantation on AMRGs upon antibiotic exposure.},
journal = {Microbiology spectrum},
volume = {13},
number = {5},
pages = {e0198324},
pmid = {39612216},
issn = {2165-0497},
support = {No. U20A2056//MOST | National Natural Science Foundation of China (NSFC)/ ; 2020YFN0147//SPDST | Key Research and Development Program of Sichuan Province ()/ ; SCCXTD-2024-8//The Innovation Team of Sichuan Province/ ; },
mesh = {Animals ; Swine/microbiology ; *Feces/microbiology ; *Fecal Microbiota Transplantation ; *Anti-Bacterial Agents/pharmacology ; Tibet ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Gastrointestinal Microbiome ; Multiomics ; },
abstract = {UNLABELLED: Fecal matter is recognized as both a reservoir and a transmission source for various antimicrobial resistance genes (AMRGs). However, the transcriptional activity of AMRGs in swine feces is not well understood. In addition, the effect of fecal microbiota transplantation (FMT) on the excretion of AMRGs has rarely been reported. Our study explored the diversity, abundance, transcriptional activity, and bacterial hosts of AMRGs in Tibetan and Duroc pig feces using metagenomic and metatranscriptomic sequencing technologies. We discovered a significantly higher genomic abundance of AMRGs in the feces of Duroc pigs compared to Tibetan pigs (P < 0.001), although the transcript levels did not show a significant difference. The results showed that the core composition of AMRGs in pig feces varied considerably, with the most transcriptionally active AMRGs being oqxB, tetQ, Bla1, dfrA1, and amrB. Furthermore, the Firmicutes phylum is the main host of AMRGs. By transplanting fecal flora from Tibetan and Duroc pigs into the intestines of Duroc Landrace Yorkshire (DLY) piglets after acute antibiotic exposure, we found that only Tibetan pig fecal flora significantly reduced AMRGs in the feces of DLY piglets (P < 0.05). The effectiveness of Tibetan pig fecal microorganisms in removing AMRGs from DLY pig feces was mainly influenced by microbial communities, especially the Bacteroidota phylum. These findings offer valuable insights for the prevention and control of AMRG pollution.

IMPORTANCE: To the best of our knowledge, this study represents the first comprehensive analysis of antimicrobial resistance gene (AMRGs) expression in the fecal microbiota of Tibetan and Duroc pigs, employing an integrated metagenomic and metatranscriptomic approach. Our findings indicate a higher risk of AMRGs transmission in the feces of Duroc pigs compared to Tibetan pigs. Given the escalating antimicrobial resistance crisis, novel therapeutic interventions are imperative to mitigate gut colonization by pathogens and AMRGs. In this regard, we investigated the impact of fecal microbiota from Tibetan and Duroc pig sources on AMRGs excretion in Duroc Landrace Yorkshire (DLY) piglets' feces following acute antibiotic exposure. Remarkably, only fecal microbiota sourced from Tibetan pigs exhibited a reduction in AMRGs excretion in DLY piglets' feces. This underscores the significance of evaluating the presence of AMRGs within donor fecal microbiota for effective AMRGs decolonization strategies.},
}

Animals
Swine/microbiology
*Feces/microbiology
*Fecal Microbiota Transplantation
*Anti-Bacterial Agents/pharmacology
Tibet
*Bacteria/genetics/drug effects/classification/isolation & purification
*Drug Resistance, Bacterial/genetics
Metagenomics
Gastrointestinal Microbiome
Multiomics

@article {pmid40084855,
year = {2025},
author = {Brock, ML and Tavares-Reager, JF and Dong, J and Larkin, AA and Lam, T and Pineda, N and Olivares, CI and Mackey, KRM and Martiny, AC},
title = {Bacterial response to the 2021 Orange County, California, oil spill was episodic but subtle relative to natural fluctuations.},
journal = {Microbiology spectrum},
volume = {13},
number = {5},
pages = {e0226724},
pmid = {40084855},
issn = {2165-0497},
support = {T32 AI141346/AI/NIAID NIH HHS/United States ; 10.46936/10.25585/60001365//U.S. Department of Energy/ ; OCE-2135035//National Science Foundation/ ; 101813-Z7554214//National Oceanic and Atmospheric Administration/ ; 80NSSC21K1654/NASA/NASA/United States ; T32AI141346/NH/NIH HHS/United States ; 567367//Simons Foundation/ ; },
mesh = {California ; *Petroleum Pollution/analysis ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Seawater/microbiology/chemistry ; *Water Pollutants, Chemical/analysis/metabolism ; Polycyclic Aromatic Hydrocarbons/analysis/metabolism ; Petroleum ; Metagenome ; Microbiota ; },
abstract = {An oil spill began in October 2021 off the coast of Orange County, California, releasing 24,696 gallons of crude oil into coastal environments. Although oil spills, such as this one, are recurrent accidents along the California coast, no prior studies have been performed to examine the severity of the local bacterial response. A coastal 10-year time series of short-read metagenomes located within the impacted area allowed us to quantify the magnitude and duration of the disturbance relative to natural fluctuations. We found that the largest change in bacterial beta-diversity occurred at the end of October. The change in taxonomic beta-diversity corresponded with an increase in the sulfur-oxidizing clade Candidatus Thioglobus, an increase in the total relative abundance of potential hydrocarbon-degrading bacteria, and an anomalous decline in the picocyanobacteria Synechococcus. Similarly, changes in function were related to anomalous declines in photosynthetic pathways and anomalous increases in sulfur metabolism pathways as well as aromatic degradation pathways. There was a lagged response in taxonomy and function to peaks in total PAHs. One week after peaks in total PAH concentrations, the largest shifts in taxonomy were observed, and 1 week after the taxonomy shifts were observed, unique functional changes were seen. This response pattern was observed twice during our sampling period, corresponding with the combined effect of resuspended PAHs and increased nutrient concentrations due to physical transport events. Thus, the impact of the spill on bacterial communities was temporally extended and demonstrates the need for continued monitoring for longer than 3 months after initial oil exposure.IMPORTANCEOil spills are common occurrences in waterways, releasing contaminants into the aquatic environment that persist for long periods of time. Bacterial communities are rapid responders to environmental disturbances, such as oil spills. Within bacterial communities, some members will be susceptible to the disturbance caused by crude oil components and will decline in abundance, whereas others will be opportunistic and will be able to use crude oil components for their metabolism. In many cases, when an oil spill occurs, it is difficult to assess the oil spill's impact because no samples were collected prior to the accident. Here, we examined the bacterial response to the 2021 Orange County oil spill using a 10-year time series that lies within the impacted area. The results presented here are significant because (i) susceptible and opportunistic taxa to oil spills within the coastal California environment are identified and (ii) the magnitude and duration of the in situ bacterial response is quantified for the first time.},
}

California
*Petroleum Pollution/analysis
*Bacteria/classification/genetics/metabolism/isolation & purification
*Seawater/microbiology/chemistry
*Water Pollutants, Chemical/analysis/metabolism
Polycyclic Aromatic Hydrocarbons/analysis/metabolism
Petroleum
Metagenome
Microbiota

@article {pmid40130858,
year = {2025},
author = {Vaccaro, M and Pilat, AM and Gusmano, L and Pham, MTN and Barich, D and Gibson, A and Epalle, M and Frost, DJ and Volin, E and Slimak, ZC and Menke, CC and Fennessy, MS and Slonczewski, JL},
title = {Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins.},
journal = {Microbiology spectrum},
volume = {13},
number = {5},
pages = {e0303424},
pmid = {40130858},
issn = {2165-0497},
support = {1923077//National Science Foundation/ ; },
mesh = {*Tannins/analysis ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; *Ponds/microbiology/chemistry ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Seasons ; *Drug Resistance, Microbial/genetics ; Ohio ; Anti-Bacterial Agents/pharmacology ; *Water Microbiology ; Genes, Bacterial ; Metagenome ; Fresh Water/microbiology/chemistry ; },
abstract = {UNLABELLED: Microbial communities of small freshwater bodies interact dynamically with environmental factors in unknown ways. Longitudinal sampling of four ponds in Knox County, Ohio, revealed relationships among antibiotic resistance genes (ARGs) and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration, and metagenomes were analyzed by short-read sequencing. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database. The top 30 ARGs showed increased abundance at the end of the growing season. The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and acid stress response (mtrA). The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannic acids). Acidity amplifies the transmembrane pH difference component of the proton-motive force, thus increasing the cell's energy available for pump function and ARG expression. Association with microbial taxa was tested by the Kraken2/Bracken predictor of taxa profiles. The ARG profiles showed the strongest acid dependence in ponds with a high proportion of Proteobacteria, whereas a pond with high Cyanobacteria showed the lowest ARG counts. Efflux pumps such as SmeABC and transcriptional activation by MtrA incur large energy expenditures whose function may be favored at low external pH, where the cell's proton-motive force is maximal.

IMPORTANCE: Compared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes (ARGs). Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity of freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes how aquatic ARG prevalence may depend on environmental factors such as pH and tannic acid levels.},
}

*Tannins/analysis
Hydrogen-Ion Concentration
*Microbiota/genetics
*Ponds/microbiology/chemistry
*Bacteria/genetics/drug effects/classification/isolation & purification
Seasons
*Drug Resistance, Microbial/genetics
Ohio
Anti-Bacterial Agents/pharmacology
*Water Microbiology
Genes, Bacterial
Metagenome
Fresh Water/microbiology/chemistry

@article {pmid40197060,
year = {2025},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of the Neisseriaceae family in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {13},
number = {5},
pages = {e0327524},
pmid = {40197060},
issn = {2165-0497},
support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; R01 DE030136, R01 DE022586, 2R01 DE016937/NH/NIH HHS/United States ; },
mesh = {Humans ; *Mouth/microbiology ; Microbiota ; Dental Plaque/microbiology ; *Neisseria/genetics/classification/isolation & purification ; Metagenomics ; Ecosystem ; Genome, Bacterial ; Gingiva/microbiology ; Phylogeny ; },
abstract = {The human oral microbiome is a diverse ecosystem in which bacterial species have evolved to occupy specific niches within the oral cavity. The Neisseriaceae family, which includes human oral species in the genera Neisseria, Eikenella, Kingella, and Simonsiella, plays a significant role in both commensal and pathogenic relationships. In this study, we investigate the distribution and functional adaptations of Neisseriaceae species across oral habitats, focusing on their site tropisms and ecological roles. We employed a metapangenomic approach in which a curated set of reference genomes representing Neisseriaceae diversity was used for competitive mapping of metagenomic reads. Our analysis revealed distinct habitat preferences among Neisseriaceae species, with Kingella oralis, Neisseria elongata, and Neisseria mucosa primarily found in dental plaque; Neisseria subflava on the tongue dorsum; and Neisseria cinerea in the keratinized gingiva. Functional enrichment analyses identified genes and pathways underpinning habitat-specific adaptations. Plaque specialists showed metabolic versatility, with adaptations in nitrogen metabolism, including nitrate reduction and denitrification, lysine degradation, and galactose metabolism. Tongue dorsum specialists exhibited adaptations including enhanced capabilities for amino acid biosynthesis, short-chain fatty acid and glycerol transport, as well as lipopolysaccharide glycosylation, which may aid in resisting antimicrobial peptides and maintaining membrane integrity. These findings provide insights into the ecological roles and adaptive strategies of Neisseriaceae species within the human oral microbiome and establish a foundation for exploring functional specialization and microbial interactions in these niches.IMPORTANCEUnraveling the distribution and functional adaptations of Neisseriaceae within the human oral microbiome is essential for understanding the roles of these abundant and prevalent commensals in both health and disease. Through a metapangenomic approach, we uncovered distinct habitat preferences of various Neisseriaceae taxa across the oral cavity and identified key genetic traits that may drive their habitat specialization and role in host-microbe interactions. These insights enhance our understanding of the microbial dynamics that shape oral microbial ecology, offering potential pathways for advancing oral health research.},
}

Humans
*Mouth/microbiology
Microbiota
Dental Plaque/microbiology
*Neisseria/genetics/classification/isolation & purification
Metagenomics
Ecosystem
Genome, Bacterial
Gingiva/microbiology
Phylogeny

@article {pmid40231684,
year = {2025},
author = {Glenna, S and Birkeland, EE and Orr, RJ and Gilfillan, GD and Dalland, M and Økstad, OA and Voie, ØA and Rounge, TB},
title = {Skin bacterial community dynamics of hands and forearms before and after military field exercise.},
journal = {Microbiology spectrum},
volume = {13},
number = {5},
pages = {e0295324},
pmid = {40231684},
issn = {2165-0497},
support = {332591//Norges Forskningsråd/ ; //SoftOx Solutions/ ; },
mesh = {Humans ; *Military Personnel ; *Skin/microbiology ; *Microbiota/genetics ; *Forearm/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Hand/microbiology ; Male ; *Exercise ; Adult ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Norway ; },
abstract = {The human skin microbiome is crucial for health and immunity, especially under the extreme conditions military personnel face. Soldiers often encounter unique stressors and hygienic challenges that can alter their skin's microbial composition, particularly in field environments. In this study, we aimed to investigate the impact of military field exercises on the diversity and composition of the skin bacterial microbiota using 16S rRNA sequencing. We conducted a longitudinal study of Norwegian soldiers (n = 19) participating in outdoor training operations during the NATO winter exercise Cold Response 2022. Skin swabs were taken from soldiers' hands and forearms before and after the 10-day military exercise, and following a 3-week post-exercise leave. Our results reveal hand- and forearm-specific shifts in bacterial populations associated with the exercise, likely influenced by environmental exposure, reduced hygiene, and heightened social contact. Alpha diversity increased on forearms while remaining stable on hands, which appeared more resilient to perturbations. Both sites exhibited temporal changes in composition, with soil- and water-associated bacteria enriched post-exercise; most being transient on hands but more sustained on forearms. The soldiers' microbiomes converged during the exercise, then diverged in the post-exercise leave period, and neither skin site returned to baseline composition at follow-up. Our findings highlight the impact of collaborative outdoor activities on microbial communities and suggest that resilience and stability differ between skin sites.IMPORTANCEOptimizing soldier health and resilience is critical for maintaining military readiness and operational effectiveness. The skin, as the body's first line of defense, is subjected to numerous challenges in military environments. Unique environmental and hygiene challenges can disrupt the skin microbiome and increase susceptibility to skin and soft tissue infections. This longitudinal research provides valuable insights into the effects of military service on the bacterial dynamics of the skin microbiome but can also inform hygiene management and disease prevention in comparable situations.},
}

Humans
*Military Personnel
*Skin/microbiology
*Microbiota/genetics
*Forearm/microbiology
*Bacteria/classification/genetics/isolation & purification
*Hand/microbiology
Male
*Exercise
Adult
Longitudinal Studies
RNA, Ribosomal, 16S/genetics
Young Adult
Norway

@article {pmid41587946,
year = {2026},
author = {Quraishi, MN and Moakes, CA and Yalchin, M and Blackwell, C and Segal, J and Ives, NJ and Magill, L and Manzoor, SE and Gerasimidis, K and McMullan, C and Mathers, J and Horniblow, R and Loi, S and Kaur, M and Loman, NJ and Sharma, N and Hawkey, P and McCune, V and Quick, J and Nicholls, S and McMurray, C and Nichols, B and Svolos, V and Raguideau, S and Kerbiriou, C and Oo, YH and Beggs, AD and Crees, N and Hansen, R and Hart, AL and Gaya, DR and Quince, C and Iqbal, TH},
title = {Mechanistic insights into fecal microbiota transplantation for the treatment of ulcerative colitis: analysis of the STOP-Colitis trial.},
journal = {Journal of Crohn's & colitis},
volume = {20},
number = {3},
pages = {},
doi = {10.1093/ecco-jcc/jjag006},
pmid = {41587946},
issn = {1876-4479},
support = {13/179/01//National Institute for Health and Care Research/ ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Colitis, Ulcerative/therapy/microbiology/immunology ; Male ; Adult ; Female ; Middle Aged ; Prospective Studies ; Feces/microbiology/chemistry ; Pilot Projects ; Gastrointestinal Microbiome ; Colonoscopy ; Treatment Outcome ; Intubation, Gastrointestinal ; Fatty Acids, Volatile/metabolism ; },
abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) is a promising therapy for ulcerative colitis, but variable responses and unclear mechanisms limit its efficacy. We aimed to compare nasogastric versus colonic FMT delivery and define the microbial and immunological changes associated with clinical response.

METHODS: In this prospective, open-label, randomized pilot trial (STOP-Colitis), 30 adults with active ulcerative colitis were randomized to receive multidose FMT via nasogastric tube or colonoscopy with subsequent enemas. Key endpoints were clinical outcomes at week 8 and longitudinal multi-omic analyses of stool and biopsies to define changes in microbial composition (16S rRNA and shotgun metagenomics), short-chain fatty acids (SCFAs), mucosal T-cells, and host gene expression.

RESULTS: Colonic FMT was superior to nasogastric delivery, with a higher clinical response rate at week 8 (75% [9/12] vs 25% [2/8]; risk ratio 2.94, 95% CI 0.84-10.30-per protocol analysis). Response was underpinned by successful microbial engraftment, leading to significantly increased fecal microbial diversity and enrichment of SCFA-producing taxa, including Oscillospiraceae and Christensenellaceae. This correlated with reduced fecal calprotectin. Responders showed a significant increase in mucosal regulatory T cells (P = .01), with a concurrent decrease in Th17 (P = 0.03) and CD8+ T cells. This anti-inflammatory shift was confirmed by mucosal transcriptomics, which revealed upregulation of metabolic pathways and downregulation of proinflammatory defense pathways in responders. (Trial registration: ISRCTN74072945).

CONCLUSION: Colonic FMT is a more effective delivery route than nasogastric administration. Clinical response is driven by the engraftment of immunomodulatory bacteria that restore a healthy host-microbe dialogue, providing rationale for developing targeted microbial therapeutics.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Colitis, Ulcerative/therapy/microbiology/immunology
Male
Adult
Female
Middle Aged
Prospective Studies
Feces/microbiology/chemistry
Pilot Projects
Gastrointestinal Microbiome
Colonoscopy
Treatment Outcome
Intubation, Gastrointestinal
Fatty Acids, Volatile/metabolism

@article {pmid41870053,
year = {2026},
author = {Pasaribu, B and Vincent Mishael Dilens, C and Wahyudin Lewaru, M and Ayuningrum, D and Patria, MP and Juliandri Prihadi, D and Purba, NP and Untung Kurnia Agung, M and Maqbul, I and Sulistiowati, S},
title = {Shotgun metagenomic dataset of seawater bacterial communities from Pari Islands, Indonesia.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0147625},
doi = {10.1128/mra.01476-25},
pmid = {41870053},
issn = {2576-098X},
abstract = {Pari Island is located in Seribu Islands, Indonesia, and is well-known for its marine biodiversity. Shotgun metagenomic sequencing was performed using the DNaseq-G400 platform, and bioinformatics approaches were applied to analyze the sequence data.},
}

@article {pmid41872229,
year = {2026},
author = {Ji, M and Li, Y and Wang, M and Liu, X and Gong, X and Tu, Q},
title = {Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71095-7},
pmid = {41872229},
issn = {2041-1723},
abstract = {Large DNA viruses (LDVs) are unique members of the Earth's virosphere, remarkable for their extra-large genome sizes and broad metabolic potential. However, our knowledge of this viral group remains very limited, particularly in complex dynamic habitats. In this study, 237 metagenome-assembled LDV genomes are comprehensively recovered from intertidal mudflats using multiple sampling and sequencing strategies totaling 5.3 TB data. A phylogenetically distinct subgroup within Imitervirales is identified, showing broad associations with multiple eukaryotic lineages. Certain LDV populations can persist locally and exhibit significant genomic variations potentially driven by dynamic intertides. Ecological patterns are observed at both community and genetic levels, with giant viruses showing steeper community turnover but weaker nucleotide diversity variations than large phages. Moreover, LDVs exhibit similar macroecological patterns to their potential hosts, which substantially shape LDV community assembly. The intertidal LDVs encode diverse functional genes, most of which remain uncharacterized, with a 27.32% improvement for unknown phage genes using a protein language model. Although giant viruses and large phages share comparable functional gene composition, they exhibit distinct preferences for specific metabolic pathways, especially those associated with carbon and nitrogen cycling. This study broadens our understanding of the biodiversity and ecology of LDVs in the understudied intertidal ecosystems.},
}

@article {pmid41875072,
year = {2026},
author = {van der Heyde, M and Curran, M and Floeckner, S and Nevill, P and White, NE and Austin, AD and Guzik, MT},
title = {Validating COI eDNA Metabarcoding Primers for Detection of Subterranean Fauna.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70127},
pmid = {41875072},
issn = {1755-0998},
support = {LP190100555//Australia Research Council Linkage Project/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA Primers/genetics ; *DNA, Environmental/genetics ; *Electron Transport Complex IV/genetics ; Animals ; Biodiversity ; *Metagenomics/methods ; },
abstract = {Subterranean ecosystems host a diverse range of ancient fauna, but studying these ecosystems is challenging due to significant sampling difficulties. Environmental DNA (eDNA) metabarcoding offers a promising approach for monitoring subterranean biodiversity, yet issues such as primer bias and non-target amplification can complicate its effectiveness. Thus, thorough validation of metabarcoding primers is crucial for accurate and comprehensive assessments of subterranean faunal diversity. This study aimed to address the need for robust primer validation through in silico, in vitro and in situ analyses, shedding light on primer performance across various subterranean taxa. The primary objective was to evaluate the effectiveness of COI metabarcoding primers for assessing subterranean faunal diversity. In silico analyses involved curating COI sequences from the Barcode of Life Database (BOLD) and selecting 14 primer combinations for in vitro testing using mock communities. Results revealed varying primer performance in terms of PCR efficiency and detection limits across different taxa. One primer combination (BF1/jgHCO2198) detected 82% of taxa in the mock community, but only at high DNA concentrations of the target taxa. The highest proportion of subterranean taxa detected in a diluted mock community was 68% using the fwhF2/fwhR2n primer combination. For in situ field validation, this same primer set detected 13 out of 16 subterranean taxa identified in haul net samples, along with an additional four taxa not identified by haul net. These findings highlight the potential of COI metabarcoding and the critical importance of primer selection for eDNA studies aimed at conserving subterranean biodiversity.},
}

*DNA Barcoding, Taxonomic/methods
*DNA Primers/genetics
*DNA, Environmental/genetics
*Electron Transport Complex IV/genetics
Animals
Biodiversity
*Metagenomics/methods

@article {pmid41876513,
year = {2026},
author = {Jovicic, D and Anestis, K and Fiutowski, J and Jørgensen, BB and Kjeldsen, KU and Rotaru, AE},
title = {Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41876513},
issn = {2041-1723},
support = {1026-00159B//Natur og Univers, Det Frie Forskningsråd (Natural Sciences, Danish Council for Independent Research)/ ; 101045149//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Geologic Sediments/microbiology ; *Metagenomics/methods ; Acetates/metabolism ; Oxidation-Reduction ; Electron Transport ; Phylogeny ; *Microbial Consortia/genetics ; Methane/metabolism ; Methanosarcina/metabolism/genetics ; Charcoal ; Cytochromes/metabolism/genetics ; Genome, Bacterial ; },
abstract = {Conductive particles are common in coastal sediments, yet their role in shaping methane-producing communities and pathways remains unclear. We applied genome-resolved metagenomics to a sediment-derived consortium serially transferred for a decade and obligately dependent on granular activated carbon (GAC). We discovered a particle-obligate food web composed of electrogenic syntrophic acetate oxidizers (SAO), an electrotrophic methanogen, and necromass recyclers. The primary SAO electrogen, Candidatus Geosyntrophus acetoxidans, represents a new genus and possesses a complete acetate oxidation pathway and extracellular electron-transfer (EET) machinery, including two porin-cytochrome conduits, 43 additional multiheme cytochromes and conductive pili. A secondary SAO, a Lentimicrobium sp. with a giant PCC-cluster, supplies an alternative EET-linked acetate-oxidation route. Electrons from electrogens transfer via GAC to a Methanosarcina equipped with the heptaheme cytochrome MmcA and flagellin for electron uptake. These results provide a genomic blueprint of this particle-obligate environmental consortium and suggest an overlooked acetate-to-methane electron-transfer route in geoconductor-rich anoxic sediments.},
}

*Geologic Sediments/microbiology
*Metagenomics/methods
Acetates/metabolism
Oxidation-Reduction
Electron Transport
Phylogeny
*Microbial Consortia/genetics
Methane/metabolism
Methanosarcina/metabolism/genetics
Charcoal
Cytochromes/metabolism/genetics
Genome, Bacterial

@article {pmid41877461,
year = {2026},
author = {Tagliabue, A and Furfaro, G and Pallavicini, A and Martino, F and Zane, L and Sattin, E and Valle, G and Piraino, S and Turon, X},
title = {Comparative Multi-Marker Environmental DNA Metabarcoding of Marine Metazoan Communities: Water vs. Sediment.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70126},
doi = {10.1111/1755-0998.70126},
pmid = {41877461},
issn = {1755-0998},
support = {MCIU/AEI/10.13039/501100011033//BlueDNA PID2023-146307OB/ ; CCI 2014IT16M2OP005//Programma Operativo Nazionale Ricerca e Innovazione 2014-2020/ ; ECS00000043//Interconnected Nord-Est Innovation Ecosystem/ ; //European Regional Development Fund/ ; 2020J3W3WC//Italian Ministry of Education, Universities and Research/ ; D33C22000960007//National Recovery and Resilience Plan/ ; C93C22002810006//National Recovery and Resilience Plan/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; Animals ; *Geologic Sediments ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Electron Transport Complex IV/genetics ; *Metagenomics/methods ; *Seawater ; },
abstract = {This study investigates the metazoan biodiversity in the Southern Adriatic Sea using environmental DNA (eDNA) metabarcoding. Sediment and adjacent water samples were collected from three sites (one pristine, two impacted by human activities) at three distances from the coast across two seasons. The complex four-factor experimental design (576 samples) addresses key sources of eDNA variability and provides a valuable comparison of markers (COI and 18S) and sample types, which remain rare in the literature. Results showed differences in the number and type of taxa identified, taxonomic resolution, and number of amplicon sequence variants (ASV) per operational taxonomic unit (OTU) across markers. The obtained overall community structure (beta-diversity) was similar for both markers. Sediment samples had higher OTU richness, but lower diversity than water samples. The two sample types provided distinct and only partially overlapping views of biodiversity. Sediment samples were rich in benthic species, whereas water samples featured mostly planktonic and nektonic species. Biodiversity varied by site and season, with sediment samples showing less seasonal variability. The pristine site did not host higher biodiversity than impacted sites, likely because of the latter's habitat heterogeneity. This study confirms the effectiveness of eDNA metabarcoding for biodiversity assessment in coastal ecosystems and provides a foundational dataset for future monitoring. By highlighting the complementary nature of COI and 18S markers and the role of sample type, this research supports integrating eDNA metabarcoding into routine environmental monitoring programs while emphasising the need for further standardisation and improved reference databases.},
}

*DNA Barcoding, Taxonomic/methods
*DNA, Environmental/genetics
Animals
*Geologic Sediments
*Biodiversity
*Aquatic Organisms/classification/genetics
RNA, Ribosomal, 18S/genetics
Electron Transport Complex IV/genetics
*Metagenomics/methods
*Seawater

@article {pmid41878266,
year = {2026},
author = {Huang, J and Yan, X and Su, Q and Tu, H and Yu, Z and Liu, D and Wu, B},
title = {Temporal dynamics of gut microbiota and virome in preterm infants: insights from longitudinal metagenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1598786},
pmid = {41878266},
issn = {2235-2988},
mesh = {Humans ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Infant, Newborn ; *Metagenomics ; *Virome ; *Bacteriophages/genetics/isolation & purification/classification ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification ; Female ; Male ; Feces/microbiology/virology ; Enterococcus faecalis ; Gastrointestinal Tract/microbiology ; },
abstract = {INTRODUCTION: Preterm infants exhibit heightened vulnerability to morbidity and mortality due to their underdeveloped immune systems and immature gastrointestinal tract. The gut microbiota plays a pivotal role in neonatal health, yet its establishment is influenced by multiple factors, including prematurity, antibiotic exposure, and feeding modalities. This study aimed to examine the interactions among gut bacteriophages, bacterial communities, and clinical variables in preterm infants to identify potential microbial biomarkers associated with health outcomes.

METHODS: We employed metagenomic shotgun sequencing and co-occurrence network analysis to characterize the virome and bacterial communities in 12 preterm neonates at 14 and 28 days post-birth. This approach enabled the identification of dynamic microbial colonization patterns and key bacterial species and bacteriophages associated with clinical parameters.

RESULTS: Staphylococcus epidermidis exhibited a significant decline over time, whereas Enterococcus faecalis and its associated bacteriophages showed progressive enrichment, becoming predominant by day 28. In contrast, the relative abundances of Clostridioides difficile and Klebsiella pneumoniae remained statistically stable between the two time points (14 vs. 28 days).

DISCUSSION: These findings suggest that microbial changes during the first month of life may reflect a combination of host developmental processes and external influences, such as antibiotic exposure or delivery mode. The observed microbial signatures provide preliminary insights into early gut microbiota and virome development in preterm infants. However, their functional relevance and long-term stability require confirmation in larger, well-powered longitudinal studies with denser temporal sampling. The enrichment of Enterococcus faecalis may indicate its opportunistic colonization potential in the preterm gut and warrants further investigation regarding its role in gut homeostasis and immune system maturation.},
}

Humans
*Infant, Premature
*Gastrointestinal Microbiome/genetics
Infant, Newborn
*Metagenomics
*Virome
*Bacteriophages/genetics/isolation & purification/classification
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification
Female
Male
Feces/microbiology/virology
Enterococcus faecalis
Gastrointestinal Tract/microbiology

@article {pmid41603333,
year = {2026},
author = {Tiwari, P and Gupta, A and Kaushik, M and Dwivedi, R and Tripathi, M and Dada, R},
title = {Association of yoga with cognitive and gut microbiome changes in Alzheimer's disease: An exploratory case-control study.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {110},
number = {2},
pages = {562-575},
doi = {10.1177/13872877261415612},
pmid = {41603333},
issn = {1875-8908},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Alzheimer Disease/psychology/microbiology/therapy ; Male ; *Yoga/psychology ; Female ; Case-Control Studies ; Aged ; *Cognition/physiology ; Middle Aged ; Depression/psychology/therapy ; Cognitive Dysfunction ; },
abstract = {BackgroundAlzheimer's disease (AD) is marked by cognitive decline, depressive symptoms, and gut microbial dysbiosis. Yoga may support cognitive and emotional health while modulating gut microbiota, but integrative clinical evidence is limited.ObjectiveTo evaluate the effects of a 12-week yoga intervention on cognition, depressive symptoms, and gut microbial diversity, composition, and function in Indian patients with mild AD.MethodsIn this hospital-based case-control study, 16 AD patients and 17 cognitively healthy controls (HCs) were recruited at AIIMS, New Delhi. AD diagnosis followed NIA-AA criteria, supported by Montreal Cognitive Assessment (MoCA) and Patient Health Questionnaire-9 (PHQ-9) assessments. AD participants underwent 60-min supervised yoga sessions daily for 12 weeks. Cognitive performance, depressive symptoms, and stool microbiota were assessed pre- and post-intervention. Metagenomic sequencing enabled taxonomic and functional profiling, with alpha diversity, beta diversity (Bray-Curtis distance), and differential abundance analyses performed using standard bioinformatics tools.ResultsYoga was associated with improved cognition (MoCA: 22.33 ± 2.34 → 25.44 ± 2.01; p = 0.001) and reduced depressive symptoms (PHQ-9: 5.78 ± 3.11 → 2.22 ± 1.71; p = 0.007). Alpha diversity remained stable, while beta diversity shifted post-yoga AD samples toward the HC cluster. Beneficial taxa (Faecalibacterium prausnitzii, Roseburia intestinalis, Bifidobacterium, Akkermansia) increased, whereas pro-inflammatory taxa (Collinsella aerofaciens, Klebsiella spp.) decreased. Functional analysis showed partial recovery of metabolic and short-chain fatty acid pathways.ConclusionsA 12-week yoga intervention was associated with cognitive and mood improvements and partial normalization of gut microbial function in mild AD. Larger randomized trials with lifestyle monitoring and multi-omics integration are warranted to confirm causal mechanisms.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Alzheimer Disease/psychology/microbiology/therapy
Male
*Yoga/psychology
Female
Case-Control Studies
Aged
*Cognition/physiology
Middle Aged
Depression/psychology/therapy
Cognitive Dysfunction

@article {pmid41615149,
year = {2026},
author = {Mora-Martínez, C and Molina-Mendoza, G and Cenit, MC and Medina-Rodríguez, EM and Larroya-García, A and Sanchez-Carro, Y and Gonzalez-Blanco, L and Bobes, J and Lopez-Garcia, P and Zandio-Zorrilla, M and Lahortiga-Ramos, F and Gili, M and Garcia-Toro, M and Barcelo, B and Ibarra, O and Sanz, Y},
title = {Gut microbiome signatures associated with depression and obesity.},
journal = {mSystems},
volume = {11},
number = {3},
pages = {e0126325},
doi = {10.1128/msystems.01263-25},
pmid = {41615149},
issn = {2379-5077},
support = {EarlyCause 848158//Horizon 2020 Framework Programme/ ; Centro de Excelencia Severo Ochoa CEX2021-001189-S/MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; FPI PRE2018-083895//Ministerio de Ciencia e Innovación/ ; Miguel Servet CP22/00031//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology/complications ; Male ; Female ; Case-Control Studies ; *Major Depressive Disorder/microbiology ; Middle Aged ; Adult ; Body Mass Index ; Metagenomics/methods ; Metagenome ; },
abstract = {UNLABELLED: Depression and obesity are highly comorbid and likely involve common risk factors and pathophysiological mechanisms, which could crosslink to gut microbiome dysfunction. Here, we performed a case-control study with a total of 105 subjects, 43 with major depressive disorder (MDD) and 62 non-depressed controls free from psychiatric comorbidities, to identify gut microbiome signatures associated with MDD and dissect its relation to body mass index (BMI) and lifestyle (diet and exercise). We performed shotgun metagenomics, followed by taxonomic and functional annotations. Using different machine learning methods, we were able to classify subjects into depressed and non-depressed controls with a balanced accuracy of 0.90 and into depressed or non-depressed and normal weight or overweight with a balanced accuracy of 0.78 based solely on taxonomic profiles. We identify novel bacterial taxa associated with depression, including reductions in Butyrivibrio hungatei and Anaerocolumna sedimenticola, and also replicate previously reported associations, such as decreased Faecalibacterium prausnitzii in patients with MDD. Functional annotation of metagenomes shows differences in pathways linked to the synthesis of fundamental nutrients, which have been associated with diet, as well as inflammation. Strikingly, we found an increase in tryptophan degradation and a decrease in queuosine synthesis pathways, both of which are directly related to a decrease in monoaminergic neurotransmitter availability. Additionally, our functional analysis shows that most of the functions that are more abundant in controls than in depressed subjects are encoded by F. prausnitzii. These findings reveal distinct microbial and functional signatures associated with depression, including taxa and pathways linked to neurotransmitter metabolism and independent of other covariates. This suggests that gut microbiome profiling could support diagnosis and the development of gut-directed depression treatments.

IMPORTANCE: This study identifies gut microbiome signatures that are predictive of major depressive disorder (MDD) and explores their links to body mass index (BMI). We uncover bacterial species and metabolic pathways that are associated with MDD, some of them related to neurotransmitter metabolism and inflammation. Among the differences identified, depletion of Faecalibacterium prausnitzii stands out as an important feature in the MDD microbiome, which suggests the possible use of this species to improve depression symptoms. Importantly, we demonstrate shared microbiome features between MDD and BMI, suggesting common underlying mechanisms. This research not only provides a framework for developing microbiome-based diagnostics but also informs future stratified interventions targeting gut microbial functions to improve mental health outcomes.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Obesity/microbiology/complications
Male
Female
Case-Control Studies
*Major Depressive Disorder/microbiology
Middle Aged
Adult
Body Mass Index
Metagenomics/methods
Metagenome

@article {pmid41636510,
year = {2026},
author = {Anne Hallowell, H and Malogan, J and Suez, J},
title = {Tools and approaches to study the human gut virome: from the bench to bioinformatics.},
journal = {mSystems},
volume = {11},
number = {3},
pages = {e0100225},
doi = {10.1128/msystems.01002-25},
pmid = {41636510},
issn = {2379-5077},
mesh = {Humans ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Computational Biology/methods ; *Viruses/genetics ; Feces/virology ; Bacteriophages/genetics ; Genome, Viral ; Bacteria/virology/genetics ; },
abstract = {The human gastrointestinal tract is home to a diverse community of microorganisms from all domains of life, collectively referred to as the gut microbiome. While gut bacteria have been studied extensively in relation to human host health and physiology, other constituents remain underexplored. This includes the gut virome, the collection of bacteriophages, eukaryotic viruses, and other mobile genetic elements present in the intestine. Like gut bacteria, the gut virome has been causatively linked to human health and disease. However, the gut virome is substantially more difficult to characterize, given its high diversity and complexity, as well as multiple challenges related to in vitro cultivation and in silico detection and annotation. In this mini-review, we describe various methodologies for examining the gut virome using both culture-dependent and culture-independent tools. We highlight in vitro and in vivo approaches to cultivate viruses and characterize viral-bacterial host dynamics, as well as high-throughput screens to interrogate these relationships. We also outline a general workflow for identifying and characterizing uncultivated viral genomes from fecal metagenomes, along with several key considerations throughout the process. More broadly, we aim to highlight the opportunities to synergize and streamline wet- and dry-lab techniques to robustly and comprehensively interrogate the human gut virome.},
}

Humans
*Virome/genetics
*Gastrointestinal Microbiome/genetics
*Computational Biology/methods
*Viruses/genetics
Feces/virology
Bacteriophages/genetics
Genome, Viral
Bacteria/virology/genetics

@article {pmid41734043,
year = {2026},
author = {Thakur, M and Dolker, S and Wangmo, LK and Sharma, LK and Acharya, S and Mohapatra, P},
title = {Illumina-Based Metagenomic Insights into the Gut Microbiome of Amblyomma helvolum (Koch, 1844) Parasitizing Xenochrophis trianguligerus from Great Nicobar Island, India.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {26},
number = {4},
pages = {233-240},
doi = {10.1177/15303667261423035},
pmid = {41734043},
issn = {1557-7759},
mesh = {Animals ; India ; *Gastrointestinal Microbiome ; *Amblyomma/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics ; *Snakes/parasitology ; *Tick Infestations/veterinary/parasitology/epidemiology ; },
abstract = {During a faunal survey in Great Nicobar Island, we collected four Amblyomma helvolum ticks infesting the snake Xenochrophis trianguligerus and processed for gut-metagenomic analysis using Illumina paired-end sequencing. A total of 8.7 million high-quality reads were generated, revealing that the gut microbiome was dominated by Bacteria (∼99.9%), primarily represented by Proteobacteria (∼95.7%), followed by minor fractions of Firmicutes, Actinobacteria, and Bacteroidetes. The predominant bacterial families were Alcaligenaceae, Bradyrhizobiaceae, Boseaceae, and Rickettsiaceae, with Achromobacter xylosoxidans emerging as the most abundant species (∼30% of total reads). Species-level analyses revealed a complex microbial community dominated by Achromobacter, Brevibacillus, Stutzerimonas, and Aeromicrobium. Several putative opportunistic pathogens were detected, including Myroides sp., Sphingobacterium sp., Stutzerimonas stutzeri, Cutibacterium acnes, Mycobacterium abscessus, Staphylococcus hominis, Achromobacter xylosoxidans, and Pseudomonas otitidis. This study represents the first metagenomic characterization of A. helvolum from India and provides baseline data on reptile-tick-associated microbial diversity from Great Nicobar Island. The findings underscore the importance of molecular surveillance in remote ecosystems and highlight the potential of reptile ticks as reservoirs of opportunistic and zoonotic bacteria.},
}

Animals
India
*Gastrointestinal Microbiome
*Amblyomma/microbiology
*Bacteria/genetics/classification/isolation & purification
Metagenomics
*Snakes/parasitology
*Tick Infestations/veterinary/parasitology/epidemiology

@article {pmid41744504,
year = {2026},
author = {Firrman, J and Liu, L and Mahalak, K and Lemons, JMS and Narrowe, A and Friedman, ES and Wu, GD and Van de Weile, T},
title = {An in vitro model of the small intestinal microbiota provides key insights into interindividual variability in structure and function.},
journal = {mSystems},
volume = {11},
number = {3},
pages = {e0137325},
doi = {10.1128/msystems.01373-25},
pmid = {41744504},
issn = {2379-5077},
support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Metabolomics/methods ; Metagenomics/methods ; *Intestine, Small/microbiology ; Bacteria/classification/genetics/metabolism ; Male ; Female ; *Ileum/microbiology ; },
abstract = {UNLABELLED: Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of facultative and obligate anaerobic taxa typical of the SIM, such as Klebsiella, Escherichia, Streptococcus, and Enterococcus. Untargeted metabolomics revealed a high degree of similarity between communities in terms of which metabolites were produced. Combining metagenomics and metabolomics, a core set of genes, features, and metabolites was found shared across all communities despite the high degree of structural variability observed. These results indicated that while the taxonomic structure of the SIM was variable between individuals, there were similarities in functional outcome due to underlying gene representation in the microbiome. Moving forward, this model system may serve as a starting point to further elucidate the role of the SIM in nutrition and health.

IMPORTANCE: The small intestinal microbiota (SIM) plays a pivotal role in nutrient digestion and absorption and immune function, with researchers continuing to find connections between this community and human health. Expanding on the currently available methods within the field to study this community, here, an in vitro model of the SIM was developed and designed to mimic the terminal ileum. Metagenomic and metabolomic analysis confirmed that this model recapitulated the unique communities of four different donors while maintaining the interindividual variability canonical of the SIM. Despite variation in taxonomic structure, in-depth analysis found that there was a core set of genes shared among the four in vitro communities that correlated with a relatively consistent metabolomic signature. These significant findings provided unique insight into the relationship between structural and functional variability for the SIM and furthered the field's understanding of how such structurally variable communities have such similar physiological outcomes.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
Metabolomics/methods
Metagenomics/methods
*Intestine, Small/microbiology
Bacteria/classification/genetics/metabolism
Male
Female
*Ileum/microbiology

@article {pmid41789894,
year = {2026},
author = {Liu, M and Wang, L and Liu, J and Yuan, Q and Zhang, Y and Wu, S and Zhang, Y and Guo, R and Zhang, Y and Lu, T and Yan, Q and Li, S and Xing, G and Dong, B and Zheng, N},
title = {Gut virome and metabolic associations in patients with acute pancreatitis.},
journal = {mSystems},
volume = {11},
number = {3},
pages = {e0140025},
doi = {10.1128/msystems.01400-25},
pmid = {41789894},
issn = {2379-5077},
mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; Male ; Female ; *Pancreatitis/virology/metabolism/microbiology ; Middle Aged ; Adult ; Metagenomics ; Case-Control Studies ; Acute Disease ; Aged ; },
abstract = {Acute pancreatitis (AP) is a frequent inflammatory disorder with outcomes ranging from mild disease to severe forms marked by infection and organ failure. Gut microenvironment disruption and barrier dysfunction are increasingly recognized as key drivers of AP progression, yet most microbiome studies have focused on bacteria. The gut virome modulates bacterial ecology and host immune responses and remains poorly characterized in AP. We aimed to comprehensively profile virome alterations in AP and evaluate their associations with disease severity, etiology, and clinical parameters. Metagenomic sequencing data from AP patients and healthy controls (HCs) were analyzed using the viromic tools. Viral diversity, taxonomy, functional composition, and predicted viral-host linkages were profiled. Microbial-viral-metabolite networks were constructed, and classification performance was evaluated using random forest models. AP viromes exhibited significantly reduced Shannon and Simpson diversity and distinct β-diversity separation from HCs. AP-enriched phages predominantly targeted Parabacteroides, Escherichia, and Bacteroides, while HC-enriched phages were linked to SCFA-producing commensals. Functional analysis revealed enrichment of replication- and lysis-related auxiliary metabolic genes (AMGs) in AP-enriched viral operational taxonomic units (vOTUs), whereas HC-associated vOTUs carried stability-related functions. Severity- and etiology-stratified analyses indicated consistent enrichment of Peduoviridae infecting Enterobacteriaceae and higher prevalence of eukaryotic viruses in advanced stages. Network analyses revealed denser microbial-viral-metabolite interactions in AP, correlated with hepatobiliary and lipid metabolic markers. A minimal seven-virus panel achieved an AUC of 97.5% for AP classification. AP is characterized by profound gut virome remodeling reflecting disease severity and etiology, with diagnostic and mechanistic relevance for future therapeutic strategies.IMPORTANCEThis study highlights the gut virome as a previously underappreciated component of acute pancreatitis (AP)-associated dysbiosis and suggests that viral communities may influence disease severity and metabolic disturbances beyond bacterial effects alone. By demonstrating the diagnostic potential of virome-based signatures, our findings support expanding microbiome research in AP to include viral components, with implications for improved disease stratification and future therapeutic development.},
}

Humans
*Virome
*Gastrointestinal Microbiome
Male
Female
*Pancreatitis/virology/metabolism/microbiology
Middle Aged
Adult
Metagenomics
Case-Control Studies
Acute Disease
Aged

@article {pmid41818685,
year = {2026},
author = {Qu, Q and Jia, Y and Wang, S and Hu, K and Liu, C and Hu, X and Mu, L},
title = {Responses of Microbial Communities in River to Atmospheric Deposition.},
journal = {Environmental science & technology},
volume = {60},
number = {11},
pages = {8583-8592},
doi = {10.1021/acs.est.6c01648},
pmid = {41818685},
issn = {1520-5851},
mesh = {*Rivers/microbiology ; Atmosphere ; Bacteria ; Fungi ; Nitrogen ; China ; Microbiota ; Air Pollutants ; },
abstract = {Atmospheric deposition threatens aquatic ecosystems, yet its effects on the microbial diversity, composition, and function in rivers remain unclear. Here, we examined the responses of microbial communities to atmospheric pollutants across 105 Chinese rivers. We found that PM2.5 and PM10 were associated with reduced bacterial and fungal diversity and richness. Structural equation modeling revealed that atmospheric deposition (e.g., PM2.5, SO2, NO2, and organic matter aerosol) was directly and indirectly associated with bacterial and fungal community composition through cascading pathways mediated by dissolved oxygen, pH, Mn, inorganic nitrogen, nitrate nitrogen, ammonium nitrogen, and chlorophyll-a. Compared with fungal communities, bacterial communities exhibited broader environmental thresholds and greater sensitivity to atmospheric pollutants. Ecological network analysis further revealed that deposition preferentially disrupted mutualistic motifs in bacterial networks but intensified competitive interactions in fungal networks. Metagenomic analysis revealed that atmospheric pollution is significantly associated with key microbial functional genes involved in carbon degradation (e.g., glucoamylase, pullulanase, and β-glucosidase), nitrogen assimilation and reduction (e.g., nifD, narB, and nirS), and sulfur reduction (e.g., sat, aprA, and dsrA) in rivers. Our findings underscore the importance of air quality mitigation in terms of protecting river ecosystem health.},
}

*Rivers/microbiology
Atmosphere
Bacteria
Fungi
Nitrogen
China
Microbiota
Air Pollutants

@article {pmid41858257,
year = {2026},
author = {Geerts, MM and Curto, M and Alverson, AJ and Stone, J and Gante, HF},
title = {Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70128},
pmid = {41858257},
issn = {1755-0998},
support = {STG/21/044//KU Leuven Research Fund/ ; 11Q4724N//Fonds Wetenschappelijk Onderzoek/ ; UIDP/50027/2020//InBIO Programático FUI 2020-2023/ ; DEB-2331644//Division of Environmental Biology/ ; },
mesh = {*Metagenomics/methods ; *Diatoms/genetics/classification ; Phylogeny ; *Computational Biology/methods ; *DNA, Environmental/genetics ; *Eukaryota/genetics/classification ; Metagenome ; *Biodiversity ; Czech Republic ; Fresh Water/microbiology ; },
abstract = {Genome assembly graphs contain valuable yet frequently overlooked information that can enhance assembly completeness by revealing contig connectivity. Here, we demonstrate how leveraging these information-rich structures enables the discovery of hidden microeukaryotic diversity in environmental DNA shotgun metagenomic datasets. While GetOrganelle has previously been used for organellar genome assembly from isolated tissues, we present its first application to water eDNA metagenomic data, using diatoms as an example. We tested the efficiency of this organellar genome assembly tool on three freshwater eDNA metagenomic datasets with varying diatom abundances, finding that GetOrganelle alone yields fragmented scaffolds due to mixed-species complexity. By implementing manual disentanglement of assembly graphs, we successfully recovered complete organellar genomes from these assemblies. From high-abundance bloom samples, we recovered complete plastomes of Stephanodiscus hantzschii with 99.9% pairwise identity across distant geographical locations (USA and Czech Republic). From a lower abundance non-bloom sample, we reconstructed a potentially novel Cyclotella plastome with only 94.0% identity to its closest available reference, Cyclotella atomus. Our assembly quality assessment confirmed effective manual disentanglement even at low diatom abundances. By integrating sequence similarity, gene order conservation and phylogenetic analysis, we achieved robust species-level resolution and resolved previous taxonomic uncertainties. Our findings demonstrate that mining eDNA metagenomic data with GetOrganelle reveals previously hidden microeukaryotic diversity and provides higher taxonomic resolution than traditional binning methods. This approach proves especially valuable for microeukaryotes, where reference organellar genomes remain underrepresented in existing databases.},
}

*Metagenomics/methods
*Diatoms/genetics/classification
Phylogeny
*Computational Biology/methods
*DNA, Environmental/genetics
*Eukaryota/genetics/classification
Metagenome
*Biodiversity
Czech Republic
Fresh Water/microbiology

@article {pmid41863619,
year = {2026},
author = {Jonathan, AR and Balasubramanian, VK and Ho, ST and Chen, YP and Khunnamwong, P and Chou, JY},
title = {Next-generation strategies for PLA degradation: microbial consortia, metagenomics, enzyme engineering and AI-guided approaches.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41863619},
issn = {1432-072X},
support = {MOST 111-2621-B-018-001 to Jui-Yu Chou//Ministry of Science and Technology, Taiwan/ ; },
mesh = {*Metagenomics/methods ; *Microbial Consortia ; Biodegradation, Environmental ; *Polyesters/metabolism ; Artificial Intelligence ; Fungi/metabolism/genetics ; Bacteria/metabolism/genetics ; },
abstract = {Polylactic acid (PLA) is one of the most widely used biodegradable bioplastics; however, its slow degradation under natural conditions limits its environmental sustainability. This review summarizes recent advances in microbial and biotechnological strategies that enhance PLA biodegradation across diverse ecosystems. Emerging approaches include screening insect gut microbiota, isolating fungal species with strong adsorption or enzymatic capacities, and exploring soil, compost, and aquatic microbiomes using metagenomics and environmental DNA (eDNA) tools. Microbial consortia, thermophilic degraders, and co-culture systems are highlighted as effective solutions to overcome the intrinsic crystallinity and hydrolysis-dependent breakdown of PLA. Beyond natural systems, this review emphasizes the increasing role of synthetic biology, directed evolution, and artificial intelligence (AI) in engineering high-performance PLA-degrading enzymes. AI-driven structural prediction and machine-learning platforms offer new possibilities for designing robust depolymerases with improved specificity, thermostability, and catalytic efficiency. Collectively, these multidisciplinary strategies provide a roadmap for accelerating PLA degradation in industrial composting, wastewater treatment, and bioremediation. Future integration of ecological screening with computational enzyme engineering is expected to advance scalable and sustainable PLA waste management.},
}

*Metagenomics/methods
*Microbial Consortia
Biodegradation, Environmental
*Polyesters/metabolism
Artificial Intelligence
Fungi/metabolism/genetics
Bacteria/metabolism/genetics

@article {pmid41530018,
year = {2026},
author = {FitzGerald, JA and Lester, KL and O' Sullivan, N and Crispie, F and Lawton, EM and Cotter, PD and McNally, P and Cox, DW},
title = {Parallel metagenomic- and culture-based approaches show nasal swabs are a good proxy for broncho-alveolar lavage in children with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {25},
number = {2},
pages = {232-239},
doi = {10.1016/j.jcf.2025.12.011},
pmid = {41530018},
issn = {1873-5010},
mesh = {Humans ; *Cystic Fibrosis/microbiology/diagnosis ; *Bronchoalveolar Lavage/methods ; *Metagenomics/methods ; Child, Preschool ; Male ; Female ; Specimen Handling/methods ; Oropharynx/microbiology ; Microbiota ; Child ; *Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {BACKGROUND: Broncho-Alveolar Lavage (BAL) is the reference standard for airway surveillance in clinical management of cystic fibrosis (CF), but is invasive and requires general anaesthesia in children. Non-invasive alternatives can lack specificity (Oropharyngeal swabs; OPS), or evaluation in paediatric CF (Middle meatus sampling; MMS). We sought to determine if MMS via nasal-swabs performed better than OPS at representing the microbiological attributes of BAL.

METHODS: In a stable preschool CF cohort attending a single specialist centre, we evaluated the microbiological yield of BAL, MMS, and OPS sampling using both standard clinical culturing, and shotgun metagenomic sequencing (Illumina NextSeq 500).

RESULTS: Matched BAL, MMS, and OPS from 30 preschool children provided 88 samples. While both culture and metagenomic surveillance performed well at detecting S. pneumoniae in BAL, MMS performed better at detecting S. aureus, M. catarrhalis and Escherichia coli, while OPS performed better at detecting H. Influenzae. Metagenomics revealed a significantly more diverse microbiome in OPS than BAL or MMS. While agreement on pathogen profiles varied widely between metagenomics and culture methods, MMS more accurately represented BAL, particularly for Streptococcus, M. catarrhalis, and Escherichia.

CONCLUSIONS: MMS and OPS cultures performed well as proxies for BAL in relation to certain pathogens. Metagenomics detected pathogens in many samples that were unobserved in culture, and showed the oropharynx microbiome to be much more diverse. Lung and nares microbiomes were more similar in composition and diversity. Our data suggest that nasal sampling of the middle meatus may be a more accurate surrogate for lower airway samples.},
}

Humans
*Cystic Fibrosis/microbiology/diagnosis
*Bronchoalveolar Lavage/methods
*Metagenomics/methods
Child, Preschool
Male
Female
Specimen Handling/methods
Oropharynx/microbiology
Microbiota
Child
*Bronchoalveolar Lavage Fluid/microbiology

@article {pmid41560354,
year = {2026},
author = {He, N and Wang, H and Yang, Z and Li, H and Liu, B and Chen, K and Wu, Z and Zhao, X and Liang, H and Wang, M and Li, X and Zhong, Y and Zhang, H and Xiao, L and Kristiansen, K and Peng, J and Zou, Y and Li, S},
title = {The Gut Commensal Butyricimonas Virosa Modulates Gut Microbiota-Dependent Thiamine Metabolism and Attenuates Mouse Steatotic Liver Disease.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {17},
pages = {e17596},
doi = {10.1002/advs.202517596},
pmid = {41560354},
issn = {2198-3844},
support = {82470615//National Natural Science Foundation of China/ ; 2024KJJ042//Shandong Provincial Youth Entrepreneurship Program for Colleges and Universities/ ; ZR2022MH217//Shandong Provincial Natural Science Foundation/ ; 2023TD52//Central Public-interest Scientific Institution Basal Research Fund/ ; 2023TD76//Central Public-interest Scientific Institution Basal Research Fund/ ; KCXFZ20240903094006009//Shenzhen Municipal Government of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; No.25-1-5-smjk-13-nsh//Qingdao Municipal Demonstration Project for Science & Technology to Benefit the People/ ; 2025YFA1310200//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Thiamine/metabolism ; Male ; Mice, Inbred C57BL ; *Fatty Liver/metabolism/microbiology ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Liver/metabolism ; Prebiotics/administration & dosage ; *Eubacteriales/metabolism ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common chronic liver disease. This study investigates the anti-MASLD effects of dietary prebiotic stachyose (STA) on disease progression identifying Butyricimonas virosa as a key bacterium boosted by STA supplementation. Oral gavage of B. virosa to high fat diet (HFD)-fed mice significantly suppresses the progression of MASLD and modulates gut microbiota composition. Integration of metagenomic and metabolomic data demonstrates that B. virosa treatment significantly enhances the production of thiamine monophosphate (TMP), as well as its conversion to thiamine and subsequent accumulation in the liver. The accumulation of hepatic thiamine further leads to elevated thiamine pyrophosphate (TPP) concentrations enhancing the activity of branched-chain α-keto acid dehydrogenase E1 subunit α (BCKDHA) associated with augmented degradation of branched chain amino acids (BCAAs). Administration of B. virosa compensates via production of gut bacterial-derived TMP for hepatic TPP deficiency in mice fed a thiamine-deficient HFD. A population-based analysis reveals an inverse correlation between plasma thiamine levels, abundances of bacterial genes involved in thiamine synthesis and metabolism, and phenotypes associated with MASLD, suggesting that key genes involved in fecal thiamine metabolism, as well as serum thiamine determination, may potentially serve as biomarkers for the diagnosis of MASLD.},
}

Animals
*Gastrointestinal Microbiome/physiology
Mice
*Thiamine/metabolism
Male
Mice, Inbred C57BL
*Fatty Liver/metabolism/microbiology
Diet, High-Fat/adverse effects
Disease Models, Animal
Liver/metabolism
Prebiotics/administration & dosage
*Eubacteriales/metabolism

@article {pmid41747689,
year = {2026},
author = {Zhang, F and Zhou, T and Feng, Y and Chen, Y and Zhao, Q and Han, Q and Liu, J and Zhang, D and Jiang, H and Zhang, H},
title = {Metagenomic insights into the impacts of Vulcanococcus proliferation on microbial communities in a coastal bay.},
journal = {Marine environmental research},
volume = {217},
number = {},
pages = {107939},
doi = {10.1016/j.marenvres.2026.107939},
pmid = {41747689},
issn = {1879-0291},
mesh = {Metagenomics ; Seawater/microbiology ; Bays/microbiology ; *Metagenome ; *Microbiota ; *Enterococcaceae/genetics/physiology ; },
abstract = {Cyanobacterial blooms pose a major ecological challenge globally, with their outbreaks exerting profound effects on aquatic ecosystems. Vulcanococcus, a recently described cyanobacterial genus previously thought to be restricted to freshwater habitats, was documented in this study proliferation in seawater for the first time. Here, we reconstructed prokaryotic metagenome-assembled genomes (MAGs), including Vulcanococcus and the associated bacteria, enabling the assessment of their metabolic potential and influence of proliferation of Vulcanococcus on marine ecosystems. The proliferation of Vulcanococcus significantly altered the prokaryotic community compositions in the water, leading to a marked decline in the stability of prokaryotic co-occurrence networks. Comparative genomic analysis revealed that Vulcanococcus MAGs clustered within the freshwater Vulcanococcus clade, suggesting a possible freshwater origin. The high-quality Vulcanococcus MAG possess a complete set of urea transporter genes as well as urease genes, highlighting its potential for efficient urea utilization. The genome of Vulcanococcus encodes critical genes involved in vitamin B1 biosynthesis and is capable for de novo vitamin B12 synthesis, implying that proliferation of Vulcanococcus may serve as an important source of B vitamins for phytoplankton. Furthermore, Vulcanococcus exhibited significant correlations with eukaryotic phytoplankton, including diatoms and dinoflagellates, suggesting that Vulcanococcus may enhance B-vitamin availability for phytoplankton. Overall, these findings provide novel insights into the ecological roles and metabolic versatility of Vulcanococcus in marine environments, underscoring its potential impact on microbial community dynamics and nutrient cycling.},
}

Metagenomics
Seawater/microbiology
Bays/microbiology
*Metagenome
*Microbiota
*Enterococcaceae/genetics/physiology

@article {pmid41773424,
year = {2026},
author = {Valdés-Varela, L and Goyache, I and Virto, R and Sáinz, N and López-Yoldi, M and Sánchez-Vicente, A and López-Giral, N and Gil, AG and Milagro, FI and Aranaz, P},
title = {Companilactobacillus alimentarius CNTA 209 alleviates diet-induced obesity in mice through adipose tissue browning and gut barrier modulation.},
journal = {Food & function},
volume = {17},
number = {6},
pages = {2851-2870},
doi = {10.1039/d5fo04242a},
pmid = {41773424},
issn = {2042-650X},
mesh = {Animals ; *Obesity/metabolism ; *Probiotics/administration & dosage/pharmacology ; Mice ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Male ; *Adipose Tissue, Brown/metabolism ; Rats ; Rats, Wistar ; *Lactobacillaceae/physiology ; },
abstract = {The use of probiotics with health-promoting effects has emerged as a promising therapeutic strategy for managing obesity and metabolic syndrome. In this study, we characterized the probiotic properties of a novel strain, Companilactobacillus alimentarius CNTA 209, and investigated its potential anti-obesity effects and safety in rodent models. C. alimentarius exhibited sensitivity to all tested antibiotics, resistance to simulated gastric and intestinal conditions in vitro, and functional activities including β-galactosidase activity and short-chain fatty acid (SCFA) production. C. alimentarius supplementation mitigated liver damage induced by a high-fat, high-fructose diet and significantly reduced adiposity in obese C57BL/6 mice by enhancing brown adipose tissue metabolic activity. Metagenomic analysis revealed a beneficial modulation of gut microbiota composition, associated with improved intestinal barrier function. A comprehensive toxicological assessment conducted in Wistar rats confirmed the safety of the strain at a dose of 1 × 10[9] CFU per animal per day for oral administration. This study provides the first documented evidence of anti-obesity and metabolic benefits conferred by a strain of C. alimentarius, positioning CNTA 209 as a novel and safe candidate for the development of probiotic-based interventions targeting obesity and related metabolic disorders.},
}

Animals
*Obesity/metabolism
*Probiotics/administration & dosage/pharmacology
Mice
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Diet, High-Fat/adverse effects
Male
*Adipose Tissue, Brown/metabolism
Rats
Rats, Wistar
*Lactobacillaceae/physiology

@article {pmid41793958,
year = {2026},
author = {Li, X and Sun, Z and Lin, L and Deng, T and Xu, M},
title = {Attenuation of sulfamethoxazole and associated antimicrobial resistome by enriched electroactive microbial consortia.},
journal = {Environment international},
volume = {209},
number = {},
pages = {110182},
doi = {10.1016/j.envint.2026.110182},
pmid = {41793958},
issn = {1873-6750},
mesh = {*Sulfamethoxazole/metabolism ; *Microbial Consortia ; Biofilms ; Biodegradation, Environmental ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/metabolism ; },
abstract = {Electroactive biofilms with the capacity of extracellular electron transfer (EET) have shown great promise for mitigating antibiotics and antibiotic resistance genes (ARGs). However, detailed interactions between antibiotics and electroactive microorganisms, along with ARGs dissemination dynamics within the electroactive consortia, remained poorly understood. In this study, stable electroactive microbial consortia were enriched, and their influences on the fates of sulfamethoxazole (SMX) and associated ARGs were systematically investigated. The results showed the enriched consortia could degrade SMX effectively within a wide concentration range through co-metabolism which was stimulated by their electrogenic respiration. Moreover, with accelerated SMX removal, the abundances of associated ARGs including sul1 and sul2 in the consortia decreased significantly due to alleviated SMX-induced selective pressure and probably weakened horizontal gene transfer mediated by mobile genetic elements (e.g., IS91 and tnpA). Degrader isolation and metagenomic analysis identified the core EET-proficient genera (e.g., Geobacter and Alcaligenes) as essential for the accelerated co-metabolism biodegradation of SMX, whereas the proliferation of other bacteria with limited or no EET capacity (e.g., Hydrogenophaga, Burkholderia, Comamonas, Desulfovibrio and Pseudomonas) was closely linked to the ARGs dissemination. This work provides a mechanistic elucidation of how electroactive microbial consortia stimulate antibiotic degradation and attenuate ARGs proliferation, offering strategic insights for risk control of the resistome during wastewater treatment.},
}

*Sulfamethoxazole/metabolism
*Microbial Consortia
Biofilms
Biodegradation, Environmental
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/metabolism

@article {pmid41797015,
year = {2026},
author = {Jeon, J and Lee, DH and Kim, JH and Choi, Y and Jin, YK and Hong, JK and Lee, YM},
title = {Methanotrophic community structure and metabolic potential in the sulfate-methane transition zone of the ARAON mounds, Arctic Chukchi Sea.},
journal = {Marine environmental research},
volume = {217},
number = {},
pages = {107959},
doi = {10.1016/j.marenvres.2026.107959},
pmid = {41797015},
issn = {1879-0291},
mesh = {*Methane/metabolism ; Sulfates/metabolism ; Arctic Regions ; *Microbiota ; Archaea/metabolism ; Geologic Sediments/microbiology ; Bacteria/metabolism ; Oxidation-Reduction ; },
abstract = {Anaerobic oxidation of methane (AOM) mediated by archaea is a pivotal process for methane consumption in gas seepage-associated sediments. Despite its importance in regulating methane flux, the ecological roles and metabolic potential of microbial communities involved in AOM remain poorly understood in Arctic regions. In this study, we investigated the microbial community structures and methanotrophic signatures in sediments from gas hydrate-bearing and non-gas hydrate-bearing sites in ARAON Mounds (AMs) and reference sites. Microbial communities in AMs were distinct from those in reference sites, with high relative abundances of Euryarchaeota (45.5 ± 11%), Lokiarcheota (35 ± 6.1%), and Atribacterota (50.1 ± 23.3%). Anaerobic methanotrophic archaea (ANME) showed site- and depth-specific distributions, with ANME-1a, ANME-1b, and ANME-2c predominating the sulfate-methane transition zone (SMTZ) of the gas hydrate-bearing sites, and ANME-1a prevailing at non-gas hydrate-bearing sites. Sulfate-reducing bacteria (SRB) affiliated with Seep-SRB1 co-occurred with ANME-1a and ANME-1b within the AMs. Metagenome-assembled genomes (MAGs) of ANME-1b and ANME-2c recovered from the SMTZ of the gas hydrate-bearing site (AM6) harbored key AOM-related genes, and their putative syntrophic bacterial partner, ETH-SRB1, possessed essential genes for sulfate reduction. Additionally, Lokiarchaeota and Atribacterota MAGs encoded genes involved in protein degradation, fermentation, and hydrogen metabolism, indicating their possible roles in methane cycling. Collectively, these results reveal distinct microbial assemblages and their functional genomic traits, suggesting niche specialization associated with methane oxidation potential at the SMTZ of the gas hydrate-bearing site.},
}

*Methane/metabolism
Sulfates/metabolism
Arctic Regions
*Microbiota
Archaea/metabolism
Geologic Sediments/microbiology
Bacteria/metabolism
Oxidation-Reduction

@article {pmid41858251,
year = {2026},
author = {Morissette, O and Côté, G and Couillard, MA and Pouliot, R and Bernatchez, L},
title = {Trait-Based Biomonitoring Using eDNA Metabarcoding to Assess Anthropogenic Disturbances on Freshwater Fish Communities.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70131},
pmid = {41858251},
issn = {1755-0998},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/classification/genetics ; *DNA, Environmental/genetics ; Quebec ; Ecosystem ; Fresh Water ; Rivers ; *Biological Monitoring/methods ; Biodiversity ; *Environmental Monitoring/methods ; *Metagenomics/methods ; *Biota ; },
abstract = {Various anthropogenic disturbances affect the succession of aquatic habitats along dendritic river networks. Bioindicator taxa, such as fish, can be used to assess the effects of these disturbances on habitat quality. Environmental DNA (eDNA) metabarcoding offers a novel approach to complement traditional sampling and analysis of bioindicator taxa. Here, we apply a trait-based biomonitoring framework, focusing on fish tolerance to pollution, to assess habitat quality and fragmentation within two watersheds in southern Québec (Canada). We sampled 193 sites within the dendritic networks of the Châteauguay and St. François watersheds and estimated fish community tolerance indices on the basis of 12S metabarcoding. We found a significant correlation between the fish community tolerance index and environmental factors such as subwatershed land use, precipitation and elevation. We also found that river fragmentation caused by dams affected fish assemblages and native fish movement but also prevented the spread of the non-native common carp. Finally, we applied random-forest modelling to predict the tolerance of fish communities to disturbances in unsampled areas, providing a broader understanding of habitat quality within catchments. Our research highlights how eDNA metabarcoding for large-scale biomonitoring and river fragmentation studies provides a cost-effective and non-invasive method for assessing fish biodiversity and riverine ecosystem health.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Fishes/classification/genetics
*DNA, Environmental/genetics
Quebec
Ecosystem
Fresh Water
Rivers
*Biological Monitoring/methods
Biodiversity
*Environmental Monitoring/methods
*Metagenomics/methods
*Biota

@article {pmid41572814,
year = {2026},
author = {Fathima, N and Mascarenhas, R and Umar, D and Rekha, PD and Shetty, S and Amin, V},
title = {Impact of removing fixed orthodontic appliances on oral microbial dysbiosis: A longitudinal study and metagenomic sequencing analysis.},
journal = {Journal of orthodontics},
volume = {53},
number = {1},
pages = {34-44},
doi = {10.1177/14653125251408048},
pmid = {41572814},
issn = {1465-3133},
mesh = {Humans ; Longitudinal Studies ; *Orthodontic Appliances, Fixed/microbiology/adverse effects ; Male ; Female ; Metagenomics ; *Dysbiosis/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Adolescent ; DNA, Bacterial ; *Mouth/microbiology ; Young Adult ; Bacteria/classification ; },
abstract = {OBJECTIVE: To investigate the impact of appliance removal on oral microbial diversity, composition, and abundance using metagenomic sequencing. It aims to identify the core microbiome and assess changes between mid-treatment and 2 weeks after debonding to understand the relationship between orthodontic therapy and oral health better.

METHODS: This longitudinal cohort study recruited 26 patients undergoing fixed orthodontic treatment between January 2022 and June 2023. Saliva samples were collected at two predefined time points: mid-treatment (T0, defined as before appliance removal) and 2 weeks after debonding (T1). Microbial DNA was extracted and the V1-V3 hypervariable regions of the 16S rRNA gene were sequenced using Illumina NovaSeq. Bioinformatics analysis was performed using QIIME and the SILVA database to evaluate microbial diversity and composition at T0 and T1. Beta diversity metrics and statistical tests, including PERMANOVA and Wilcoxon signed-rank tests, were applied to identify significant differences (P < 0.05). Effect sizes with 95% confidence intervals (CIs) were reported.

RESULTS: The analysis revealed significant shifts in microbial diversity and composition between T0 and T1. A total of 189 species across 63 genera were identified, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria as dominant phyla. Genera such as Fusobacterium periodonticum (↑ 12.4%, 95% CI = 10.1-14.7) and Veillonella parvula (↑ 9.8%, 95% CI = 7.6-11.3) increased after debonding, while Prevotella melaninogenica (↓ 10.2%, 95% CI = 8.1-12.0) and Rothia dentocariosa (↓ 7.9%, 95% CI = 6.3-9.2) decreased. Beta diversity analysis confirmed a statistically significant microbial community shift (P < 0.05).

CONCLUSION: This study demonstrated significant microbial shifts between mid-treatment and 2 weeks after debonding, including increases in potentially pathogenic genera and alterations in the core microbiome. These findings indicate microbial changes persist for at least 2 weeks after appliance removal. Further research with pre-treatment baselines and extended follow-up is required to better define the long-term trajectory of these changes.},
}

Humans
Longitudinal Studies
*Orthodontic Appliances, Fixed/microbiology/adverse effects
Male
Female
Metagenomics
*Dysbiosis/microbiology
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Saliva/microbiology
Adolescent
DNA, Bacterial
*Mouth/microbiology
Young Adult
Bacteria/classification

@article {pmid41793822,
year = {2026},
author = {Li, P and Wang, Y and Bao, Z and He, X and Wang, S and Su, X and Nie, W and Xu, F and Zhou, H and Li, H and Xu, B},
title = {Metagenomics-based insights into the microbial community composition and quality characteristics development potentiality in traditional dry-cured ham.},
journal = {International journal of food microbiology},
volume = {453},
number = {},
pages = {111705},
doi = {10.1016/j.ijfoodmicro.2026.111705},
pmid = {41793822},
issn = {1879-3460},
mesh = {Animals ; Metagenomics ; Swine ; *Meat Products/microbiology/analysis ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Volatile Organic Compounds/analysis/metabolism ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; Food Microbiology ; Peptides ; },
abstract = {The objective of this study was to elucidate the formation mechanisms of quality characteristics in traditional dry-cured ham. The microbial community composition in three types of dry-cured ham was analyzed using metagenomics technology. Volatile flavor profiles were characterized via gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS), while peptide profiles were determined using liquid chromatography-mass spectrometry (LC-MS). Based on metagenomic data, biosynthetic pathways of volatile flavor compounds and bioactive peptides in dry-cured hams were reconstructed. Key microorganisms identified include Staphylococcus equorum, Staphylococcus saprophyticus, Aspergillus glaucus, Aspergillus ruber, Debaryomyces hansenii, and Debaryomyces fabryi. Using GC-MS and GC-IMS, 25 volatile compounds were identified in dry-cured ham, with branched-chain compounds exhibiting higher odor activity values (OAVs). LC-MS analysis identified 203 microbial-derived peptide fragments, predominantly possessing angiotensin-converting enzyme (ACE) inhibitory, dipeptidyl peptidase-IV (DPP-IV) inhibitory, and antioxidant activities. Further investigation into the contribution of microbial communities to the characteristic quality attributes revealed that Staphylococcus species promote the formation of 3-methyl-butanal via branched-chain amino acid transaminase (BCAT) and 3-hydroxy-2-butanone via acetolactate synthase (ALS). With regard to functional bioactive peptides, Staphylococcus indirectly contributes to the synthesis of NPPKFD, DLEE, and KRQKYD via glutamyl endopeptidase activity. Additionally, proteins derived from Aspergillus glaucus (actin-related protein 5) and Staphylococcus equorum (chromosome segregation protein) serve as direct precursors for bioactive peptides, yielding potential sequences such as KNSKDPVSI and LEDDI. This study provides evidence indicating the role of microbial communities in shaping the quality characteristics of dry-cured ham.},
}

Animals
Metagenomics
Swine
*Meat Products/microbiology/analysis
*Bacteria/genetics/classification/isolation & purification/metabolism
Volatile Organic Compounds/analysis/metabolism
*Microbiota
Gas Chromatography-Mass Spectrometry
Food Microbiology
Peptides

@article {pmid41825563,
year = {2026},
author = {An, M and Yu, J and Lin, X and Lu, Y and Li, X and He, J and Zhao, G},
title = {Multi-stage synthetic microbial consortia outperform single-stage augmentation by remodeling metabolism and mediating function-stability trade-off in anaerobic digestion.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134417},
doi = {10.1016/j.biortech.2026.134417},
pmid = {41825563},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Microbial Consortia/physiology ; Methane/metabolism/biosynthesis ; Bioreactors/microbiology ; Fatty Acids, Volatile/metabolism ; },
abstract = {Anaerobic digestion (AD) of food waste often suffers from low methane yield and volatile fatty acids (VFAs) accumulation, primarily due to inefficiencies or imbalances within the native microbial community. To address these metabolic and ecological limitations, we constructed two synthetic microbial communities (SynComs) using a function-driven strategy: a methanogen-only consortium (SynCom-J) and a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members (SynCom-YSJ). Both SynComs were introduced into semi-continuous reactors that already harbored a metabolically complete native microbiome, serving as bioaugmentation agents. When fed daily with partially hydrolyzed feedstock containing residual macromolecular organics and short-chain VFAs, SynCom-YSJ consistently outperformed SynCom-J during the entire hydraulic retention time. Compared to the non-bioaugmented control under identical operating conditions, SynCom-YSJ increased methane yield by 22% (vs. 8% for SynCom-J) and nearly eliminated the start-up lag phase, while both consortia reduced propionate accumulation by 1.6-fold. Successful colonization of the SynComs reshaped the AD microenvironment-characterized by elevated acetate, reduced propionate, and a moderate, non-inhibitory increase in total ammonia nitrogen-thereby imposing deterministic selection on the resident community. Metagenomic analysis revealed that SynCom-YSJ triggered broader metabolic reprogramming, upregulating genes involved in hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. Notably, a trade-off between microbial network stability and process performance emerged: SynCom-J promoted a more robust network, whereas SynCom-YSJ formed a more complex and high-efficiency network that prioritized methane yield. This study demonstrates that coordinated multi-stage bioaugmentation optimizes methanogenesis through targeted metabolic remodeling and provides an ecology-informed design principle for engineering SynComs that balance system performance with stability. These findings highlight the potential of multi-stage bioaugmentation to enhance both functional robustness and system resilience in food waste AD.},
}

Anaerobiosis
*Microbial Consortia/physiology
Methane/metabolism/biosynthesis
Bioreactors/microbiology
Fatty Acids, Volatile/metabolism

@article {pmid41831799,
year = {2026},
author = {Qi, H and Wu, R and Liao, J and Alvarez, PJJ and Yu, P},
title = {Longitudinal multi-omics reveal phase-dependent viral adaptive strategies and functional potential during formation of algal-bacterial granular sludge.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134410},
doi = {10.1016/j.biortech.2026.134410},
pmid = {41831799},
issn = {1873-2976},
mesh = {*Sewage/microbiology/virology ; *Bacteria/genetics/virology ; Symbiosis ; Metagenome ; Microbiota ; Bacteriophages/genetics ; Multiomics ; },
abstract = {Virus-prokaryote interactions within microbial aggregates critically influence microbiome function and stability, yet the interactive dynamics during microbial aggregation remain largely unexplored. Here, longitudinal multi-omics revealed that prokaryotic host community diversity underwent decline and subsequent recovery during algal-bacterial granular sludge (ABGS) formation from activated sludge. Declined host diversity in the collapse phase enriched for lysogenic viruses and facilitated virus-host mutualistic symbiosis, during which the proportion of lysogenic metagenome-assembled genomes (MAGs) peaked at 84% (841,649 TPM), with auxiliary metabolic genes (AMGs) primarily involved in genetic information processing and amino acid metabolism. Moreover, low host diversity increased viral microdiversity by 1.97-fold and selected for virion structure genes that were conducive to viral fitness and replication. As host diversity recovered during the recovery phase, viruses and hosts engaged in an evolutionary arms race, with both host defense systems (DS) (Spearman's Rho = 0.68, P < 0.05) and viral anti-defense systems (ADS) (Spearman's Rho = 0.51, P < 0.05) enriched along with granule maturation. Furthermore, active lysogenic infections were accompanied by the dissemination of AMGs predominantly associated with the metabolism of cofactors, vitamins, terpenoids, and polyketides. Despite their phase-dependent functional profiles, lysogenic phages with AMGs putatively enhanced the structural and functional stability of the microbiome during ABGS formation. Overall, our study unveils a phase-dependent co-evolutionary interplay between viruses and prokaryotic hosts during ABGS formation, providing insights into virus-mediated microbial structural and functional resilience in engineered ecosystems.},
}

*Sewage/microbiology/virology
*Bacteria/genetics/virology
Symbiosis
Metagenome
Microbiota
Bacteriophages/genetics
Multiomics

@article {pmid41839407,
year = {2026},
author = {Chen, S and Zhao, A and Zhang, W and Liu, Q and Li, D},
title = {Metabolic reprogramming disrupts the resistome-mobilome nexus and enhances bio-sanitization in synthetic microbial community-mediated composting.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134433},
doi = {10.1016/j.biortech.2026.134433},
pmid = {41839407},
issn = {1873-2976},
mesh = {*Composting/methods ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Lignin/metabolism ; Bacteria/metabolism/genetics ; Metabolic Reprogramming ; },
abstract = {The persistence of antibiotic resistance genes (ARGs) and pathogens during manure composting poses critical risks within the One Health framework. However, the ecological and metabolic mechanisms by which microbiome engineering disrupts the dissemination of these biohazards remain poorly understood. This study evaluated a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum) in mitigating these risks. KEGG analysis highlighted a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and enriched flagellar assembly. This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer (HGT) opportunities. Metagenomic analysis showed SynCom inoculation caused a transient ARG rebound followed by profound attenuation. While thermophilic hosts temporarily enriched specific ARGs, SynCom ultimately achieved a significant reduction in multidrug resistance genes and virulence factors by intensifying thermophilic fermentation. Mantel correlation analysis revealed the SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification were critical environmental drivers, restricting ARGs and alleviating co-selection pressure on metal resistance genes. Network analysis demonstrated SynCom induced a structural collapse of high-risk interactomes (reducing potential host-gene associations by 26.6%), effectively disrupting ARG and mobile genetic element connections by suppressing key recombinases (XerD, IntI1) and eliminating Pseudomonadota hub hosts. Consequently, deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g., Pseudomonas aeruginosa), phytopathogens, and specific virulence factors. These findings indicate that SynCom provides a robust microbiome engineering strategy to disrupt the genetic dissemination of biohazards and ensure organic fertilizer biosafety.},
}

*Composting/methods
*Microbiota/genetics
*Drug Resistance, Microbial/genetics
Lignin/metabolism
Bacteria/metabolism/genetics
Metabolic Reprogramming

@article {pmid41857857,
year = {2026},
author = {Ngoumou, GB and Ngandeu Schepanski, S and Blakeslee, SB and Diedering, A and Twal, E and Raue, SL and Schroeder, M and Wicaksono, WA and Stritter, W and Berg, G and Seifert, G},
title = {Effects of fermented versus unfermented red cabbage on symptoms, immune response, inflammatory markers and the gut microbiome in young adults with allergic rhinoconjunctivitis: a randomised controlled trial protocol.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e115290},
doi = {10.1136/bmjopen-2025-115290},
pmid = {41857857},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Adult ; Young Adult ; *Brassica ; Quality of Life ; *Fermented Foods ; Adolescent ; Randomized Controlled Trials as Topic ; *Conjunctivitis, Allergic/immunology/diet therapy ; *Rhinitis, Allergic/immunology/diet therapy ; Female ; Male ; Biomarkers ; },
abstract = {INTRODUCTION: Allergic rhinoconjunctivitis (ARC) is a highly prevalent immune-mediated condition associated with substantial symptom burden, impaired quality of life and increased healthcare use. Emerging evidence highlights the role of the gut microbiome in immune regulation and allergic disease. Fermented foods may contain live microbes (when unpasteurised or uncooked) and bioactive postbiotic metabolites that can modulate immune responses. Despite growing interest in dietary strategies targeting the microbiome, no randomised controlled trial has compared fermented versus unfermented red cabbage for ARC.

METHODS AND ANALYSES: This single-centre, randomised, controlled trial with a sensory-matched, unfermented cabbage comparator investigates the effects of daily consumption of fermented red cabbage for 8 weeks compared with an unfermented red cabbage control in young adults (18-35 years) with ARC. A total of 158 participants will be randomly assigned (1:1). The primary outcome is change in Total Nose and Eye Symptom Score from baseline to week 8. Secondary outcomes include daily symptoms and medication use captured via mobile ecological momentary assessments, quality of life, psychological well-being, gastrointestinal symptoms, systemic inflammatory markers, total IgE, immune cell profile and metagenomic characterisation of stool samples. A nested qualitative component explores participants' experiences and acceptability of the intervention. Analyses will include mixed-effects models, time-series analyses incorporating daily pollen counts and comprehensive microbiome statistics. Safety outcomes and adverse events will also be assessed.

ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charité-Universitätsmedizin Berlin (EA4/043/25) and is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Results will be disseminated through peer-reviewed publications, conference presentations and a lay summary provided to participants. Anonymised datasets and analysis scripts will be made available in public repositories, and metagenomic sequencing data will be deposited in an international sequence archive to ensure transparency and reproducibility.

TRIAL REGISTRATION NUMBER: DRKS00036475.},
}

Humans
*Gastrointestinal Microbiome/immunology
Adult
Young Adult
*Brassica
Quality of Life
*Fermented Foods
Adolescent
Randomized Controlled Trials as Topic
*Conjunctivitis, Allergic/immunology/diet therapy
*Rhinitis, Allergic/immunology/diet therapy
Female
Male
Biomarkers

@article {pmid41673004,
year = {2026},
author = {Niu, M and Fu, L and Yan, Q and He, Z and Li, D and Zhen, Y and Wang, M and Li, C},
title = {35 metagenomic datasets from the northern and southern parts of the Yap trench sediments.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41673004},
issn = {2052-4463},
mesh = {*Metagenome ; Metagenomics ; *Microbiota ; *Geologic Sediments/microbiology ; Bacteria/classification/genetics ; },
abstract = {The hadal trench is the deepest part of the global ocean and harbors highly abundant microbial cells. However, the diversity and function of the majority of microbial communities in this part of the ocean are still unclear. Here, we collected 35 metagenomes from three push cores across different sites in both the northern and southern Yap trench to construct a comprehensive gene and genome dataset. A total of 32 million non-redundant genes were predicted from the whole metagenome datasets, with 63% assigned to known functional groups based on currently available databases. A total of 404 metagenome-assembled genomes (MAGs) with completeness >50% and contamination <10% were retrieved, and their taxonomy was highly diverse across 26 phyla. Alpha- and Gammaproteobacteria, Phycisphaerae, Nitrospiria, and Dehalococcoidia were dominant classes across all samples. The nonredundant gene and MAG datasets are valuable resources for advancing our understanding of the diversity, composition, and functions of microbiota in the sediment of the hadal trench.},
}

*Metagenome
Metagenomics
*Microbiota
*Geologic Sediments/microbiology
Bacteria/classification/genetics

@article {pmid41776310,
year = {2026},
author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA},
title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.},
journal = {Nature aging},
volume = {6},
number = {3},
pages = {682-702},
pmid = {41776310},
issn = {2662-8465},
support = {#00034120//Pew Charitable Trusts/ ; T32 AG052374/AG/NIA NIH HHS/United States ; No. 58-1950-7-707//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; T32 AG052374/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; *Ovary/physiology ; *Fecal Microbiota Transplantation ; Mice ; *Aging/physiology ; Mice, Inbred C57BL ; Transcriptome ; *Menopause ; Metagenomics ; Fertility ; },
abstract = {The decline in ovarian function with age affects fertility and is associated with increased risk of age-related diseases, including osteoporosis and dementia. Notably, earlier menopause is linked to shorter lifespan, yet the molecular mechanisms underlying ovarian aging remain poorly understood. Recent evidence suggests the gut microbiota may influence ovarian health. Here we show that ovarian aging is associated with distinct gut microbial profiles in female mice and that the gut microbiome can directly influence ovarian health. Using fecal microbiota transplantation from young or estropausal female mice, we demonstrate that heterochronic microbiota transfer remodels the ovarian transcriptome, reduces inflammation-related gene expression and induces transcriptional features consistent with ovarian rejuvenation. These molecular changes are accompanied by enhanced ovarian health and increased fertility. Integrating metagenomics-based causal mediation analyses with serum untargeted metabolomics, we identify candidate microbial species and metabolites that may contribute to the observed effects. Our findings reveal a direct link between the gut microbiota and ovarian health.},
}

Animals
Female
*Gastrointestinal Microbiome/physiology
*Ovary/physiology
*Fecal Microbiota Transplantation
Mice
*Aging/physiology
Mice, Inbred C57BL
Transcriptome
*Menopause
Metagenomics
Fertility

@article {pmid41498484,
year = {2026},
author = {Huang, T and Ge, H and Wu, Z and Zhang, Y and Wang, L and Dang, C and Fu, J},
title = {Resistance of Microbial Community in Activated Sludge to Nano-Ag Stress Through Regulation of N-Acyl Homoserine Lactones-Mediated Quorum Sensing.},
journal = {Biotechnology and bioengineering},
volume = {123},
number = {4},
pages = {995-1010},
doi = {10.1002/bit.70155},
pmid = {41498484},
issn = {1097-0290},
support = {22306068//National Natural Science Foundation of China/ ; 42476142//National Natural Science Foundation of China/ ; //2022 HUST-UTS Key Partnership Research Seed Funding/ ; 2024AFD091//Hubei Provincial Natural Science Foundation of China/ ; },
mesh = {*Quorum Sensing/drug effects ; *Sewage/microbiology ; *Acyl-Butyrolactones/metabolism ; *Silver/toxicity ; Bioreactors/microbiology ; *Microbiota/drug effects ; Bacteria/drug effects/genetics/metabolism ; },
abstract = {Nano-Ag is increasingly detected in WWTP due to its widespread application, posing a significant threat to microbial communities responsible for wastewater treatment efficiency. Prior studies have demonstrated that quorum sensing (QS) can modulate bacterial tolerance to various environmental stressors in sludge systems. However, the feasibility and mechanisms of N-acyl homoserine lactones (AHLs)-mediated QS regulation to improve the resistance of microorganisms in WWTPs to nano-Ag shocks have been unexplored. Hence, we conducted sequencing batch reactor experiments, and as expected, nano-Ag significantly reduced the treatment performance of bioreactors. However, with the addition of AHLs (C6-HSL, C10-HSL, and C14-HSL) in the bioreactors, the microbial resistance in activated sludge to nano-Ag stress had been evidently enhanced, including the restoration of the sludge morphology, settleability, biomass and extracellular polymeric substances (EPS), as well as the treatment performance of bioreactors on removals of ammonium nitrogen (NH4 [+]-N), chemical oxygen demand (COD), and suspended solids. The joint analysis of metagenomics, metatranscriptomics, and metametabolomics indicated the multifunctional bacteria (e.g., Amaricoccus, Hydrogenophaga, and Brevundimonas) played a very important role during the regulation of AHLs-mediated QS, which harbored functional genes associated with nitrogen metabolism, carbon metabolism, silver resistance, and AHLs response. The upregulation on glutathione-dependent metabolisms (e.g., glutathione-oxidized glutathione redox cycle) and biosynthesis of EPS (e.g., poly-N-acetylglucosamine) were beneficial for the enhancement of microbial resistance to nano-Ag. This study provided a potentially feasible strategy and important theoretical basis to enhance the robustness and restore the function of microorganisms in wastewater treatment systems by using AHLs-mediated QS regulation.},
}

*Quorum Sensing/drug effects
*Sewage/microbiology
*Acyl-Butyrolactones/metabolism
*Silver/toxicity
Bioreactors/microbiology
*Microbiota/drug effects
Bacteria/drug effects/genetics/metabolism

@article {pmid41654729,
year = {2026},
author = {Wang, P and Yao, Y and Yan, K and Wang, S and Wang, M and Liu, X and Hu, C and Dong, Y and Li, J},
title = {A validation for sex differences in gut microbiome of essential hypertension based on cohort analysis.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41654729},
issn = {1471-2180},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; Feces/microbiology ; *Essential Hypertension/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Sex Factors ; Cohort Studies ; Metagenomics ; Aged ; Adult ; Fatty Acids, Volatile/metabolism ; China ; Hypertension/microbiology ; Sex Characteristics ; },
abstract = {BACKGROUND: Prior research has demonstrated sex-specific differences in hypertension (HTN). The gut microbiota (GM) and its metabolic functions have emerged as key players in the development of HTN. To explore potential sex-based heterogeneity in gut bacteria among hypertensive patients, we conducted this study with the aim of validating sex differences in the gut flora associated with HTN.

METHODS: Here, we leveraged a metagenomic dataset comprising 106 fecal samples from a Chinese cohort of individuals with essential HTN to systematically analyze and compare alterations in the gut microbiome between male and female patients, as well as relative to a healthy control group.

RESULTS: Our study confirmed a statistically significant difference in the β-diversity of GM between hypertensive patients and healthy controls. When the subjects were further stratified by sex, significant differences in the distribution of gut flora were observed exclusively in females, whereas none was noted between groups in males. It was observed that certain genera of GM exhibit negative correlations with blood pressure. Notably, the relative abundance of these bacterial genera, including Lachnospira, Faecalibacterium, and Roseburia, was significantly diminished in female hypertensive patients. These organisms are primarily involved in the biosynthesis of short-chain fatty acids (SCFAs), with a notable emphasis on butyrate production. Ruminococcus gnavus was specifically enriched in hypertensive males, whereas certain bacteria, such as Lactobacillus, were notably depleted. The abnormality of the SCFAs-producing flora in female hypertensive patients may be related to that women are more likely to develop hypertensive organ damage.

CONCLUSIONS: The findings of our study indicate that GM dysbiosis is more significantly associated with HTN in females. Consequently, sex constitutes a critical factor in evaluating the role of intestinal flora in the pathogenesis of HTN.},
}

Humans
*Gastrointestinal Microbiome
Female
Male
Middle Aged
Feces/microbiology
*Essential Hypertension/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
Sex Factors
Cohort Studies
Metagenomics
Aged
Adult
Fatty Acids, Volatile/metabolism
China
Hypertension/microbiology
Sex Characteristics

@article {pmid41713418,
year = {2026},
author = {Shao, Y and Wang, S and Gichuki, BM and Stares, MD and Rozday, TJ and Kumar, N and Browne, HP and Dawson, NJR and Njunge, JM and Tigoi, C and Ngao, N and Chisti, MJ and Singa, BO and Kariuki, S and Diallo, AH and Saleem, AF and Ali, SA and Mupere, E and Mbale, E and Tickell, KD and Voskuijl, WP and Lancioni, CL and Bandsma, RHJ and Ahmed, T and Walson, JL and Berkley, JA and Lawley, TD},
title = {Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design.},
journal = {Cell},
volume = {189},
number = {6},
pages = {1854-1873.e17},
doi = {10.1016/j.cell.2026.01.007},
pmid = {41713418},
issn = {1097-4172},
mesh = {*Probiotics ; Humans ; Infant ; *Genome, Bacterial/genetics ; *Bifidobacterium longum/genetics/classification ; Phylogeny ; *Bifidobacterium longum subspecies infantis/genetics/classification ; Genomics ; Gastrointestinal Microbiome/genetics ; Infant, Newborn ; Milk, Human/microbiology ; },
abstract = {Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genome-guided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.},
}

*Probiotics
Humans
Infant
*Genome, Bacterial/genetics
*Bifidobacterium longum/genetics/classification
Phylogeny
*Bifidobacterium longum subspecies infantis/genetics/classification
Genomics
Gastrointestinal Microbiome/genetics
Infant, Newborn
Milk, Human/microbiology

@article {pmid41785249,
year = {2026},
author = {Pucci, N and Kaan, AM and Ujčič-Voortman, J and Verhoeff, AP and Zaura, E and Mende, DR},
title = {Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1013185},
doi = {10.1371/journal.pcbi.1013185},
pmid = {41785249},
issn = {1553-7358},
mesh = {Humans ; *Mouth/microbiology ; Infant ; *Microbiota/genetics ; Female ; Phylogeny ; Metagenome/genetics ; Metagenomics ; Male ; Streptococcus/genetics/classification ; Longitudinal Studies ; Computational Biology ; },
abstract = {Early-life oral microbiome development is a complex community assembly process that influences long-term health outcomes. Nevertheless, microbial functions and interactions driving these ecological processes remain poorly understood. In this study, we analyze oral microbiomes from a longitudinal cohort of 24 mother-infant dyads at 1 and 6 months postpartum using shotgun metagenomics. We identify two previously undescribed Streptococcus and Rothia species to be among the most prevalent, abundant and strongly co-occurring members of the oral microbiome of six-month-old infants. By leveraging metagenome-assembled genomes (MAGs) and genome-scale metabolic models (GEMS) we reveal their genomic and functional characteristics relative to other infant-associated species and predict their metabolic interactions within a network of co-occurring oral taxa. Our findings highlight unique functional features, including genes encoding adhesins and carbohydrate-active enzymes (CAZymes). Metabolic modeling identified potential exchange of key amino acids, particularly ornithine and lysine, between these species, suggesting metabolic cross-feeding interactions that may explain their co-abundance across infant oral microbiomes. Overall, this study provides key insights into the functional adaptations and microbial interactions shaping early colonization in the oral cavity, providing testable hypotheses for future experimental validation.},
}

Humans
*Mouth/microbiology
Infant
*Microbiota/genetics
Female
Phylogeny
Metagenome/genetics
Metagenomics
Male
Streptococcus/genetics/classification
Longitudinal Studies
Computational Biology

@article {pmid41853717,
year = {2026},
author = {Matturro, B and Tucci, M and Firrincieli, A and Niccolini, L and Peña-Álvarez, V and Resitano, M and Trinchillo, M and Peláez, AI and Rossetti, S and Petruccioli, M and Viggi, CC and Aulenta, F},
title = {Multi-guild microbial cooperation sustains long-term anaerobic toluene degradation through sulfur cycling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1773863},
pmid = {41853717},
issn = {1664-302X},
abstract = {Anaerobic degradation of aromatic hydrocarbons such as toluene plays a critical role in the natural and engineered attenuation of contaminated environments. Here, we developed and characterized a microbial consortium enriched under strictly anoxic conditions, capable of sustained toluene degradation through sulfate reduction. By integrating biodegradation kinetics, long-read 16S rRNA profiling, and genome-resolved metagenomics, we elucidated the structure and function of a multi-guild community. The consortium was co-dominated by Desulfoprunum, a sulfate-reducing bacterium (SRB), and Sulfurovum-affiliated sulfur oxidizers (~34% each), with additional members including Stenotrophomonas, Achromobacter, and Stutzerimonas. Such co-dominance appears uncommon, as sulfate-reducing enrichments are often characterized by low diversity and the predominance of a single lineage, such as Desulfobacula or Desulfosarcina in marine systems. Genome-resolved analyses recovered seven metagenome-assembled genomes (MAGs) with distinct but complementary metabolic roles. Desulfoprunum encoded the fumarate-addition pathway (bss/bbs) for anaerobic toluene activation and dissimilatory sulfate reduction (aprAB, dsrAB). In contrast, Sulfurovum and several Gammaproteobacteria encoded sulfide:quinone oxidoreductase (sqr), coupling H2S detoxification to energy conservation, while a Moranbacterales MAG carried a putative sulfhydrogenase (hydAB) potentially catalyzing elemental sulfur (S°) reduction. Additional MAGs encoded assimilatory sulfate reduction (cys), suggesting integration of sulfur into biosynthetic pathways. Together, these features are consistent with the presence of a putative distributed sulfur redox loop, in which biogenic H2S may be recycled via oxidation and reduction reactions mediated by co-occurring taxa. This sulfur loop is hypothesized to contribute to buffering sulfide toxicity and stabilize redox dynamics, thereby potentially supporting long-term toluene degradation under sulfidic conditions. Our findings highlight anaerobic degradation as a community-driven process enabled by sulfur-cycling interactions. By revealing the role of cryptic sulfur cycling in stabilizing hydrocarbon degradation, this work offers a new framework for designing bioremediation strategies in contaminated anoxic environments.},
}

@article {pmid41853994,
year = {2026},
author = {Yang, Q and Aghdam, R and Tran, PQ and Anantharaman, K and Solís-Lemus, C},
title = {Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70245},
doi = {10.1111/1758-2229.70245},
pmid = {41853994},
issn = {1758-2229},
support = {506328//A Community Science Program New Investigator award/ ; //Natural Science and Engineering Research Council of Canada (NSERC)/ ; DBI-2047598//National Science Foundation/ ; DEB-2144367//National Science Foundation/ ; Hatch 1025641//USDA National Institute of Food and Agriculture/ ; //University of Wisconsin-Madison/ ; //Joint Genome Institute/ ; //Office of Science/ ; },
mesh = {*Ecosystem ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Metagenome ; *Lakes/microbiology ; *Fresh Water/microbiology ; Metagenomics ; Transcriptome ; },
abstract = {Freshwater lakes are dynamic ecosystems, with varying oxygen dynamics that influence microbiome structure, composition, and transcriptomic activity. In many freshwater studies, ecological function and abundance metrics are used to discover keystone species; however, it is well established that abundance does not equal activity. Despite the existence of long-term time series spanning multiple years, no previous study has looked at how microbial community and activity (metatranscriptomics) are influenced by shifting oxygen conditions across depths at the microbial network level. In this study, we leverage metagenome-assembled genomes and transcriptomic activity to identify keystone taxa in the ecosystem. Using the SPIEC-EASI and CARlasso methods, we mapped key microbial associations and used permutation-based analyses to assess the robustness of keystone identification. Our results reveal that a taxon's ecological centrality is context-dependent and that many species identified as keystone by abundance alone do not exhibit corresponding transcriptional activity. Notably, members of Bacteroidota and other lineages emerged as keystone taxa only when both abundance and activity were considered. Our study underscores the importance of combining metagenomic and metatranscriptomic approaches for accurate identification of functionally relevant keystone species in freshwater ecosystems, providing a framework for future microbial ecology studies.},
}

*Ecosystem
*Bacteria/genetics/classification/isolation & purification/metabolism
*Microbiota/genetics
Metagenome
*Lakes/microbiology
*Fresh Water/microbiology
Metagenomics
Transcriptome

@article {pmid41854683,
year = {2026},
author = {Wang, J and Shi, Y and Jia, Y and Peng, J},
title = {Effect of Diosmetin on Gut Microbiota and Serum Metabolites in Acute Pancreatitis Mice: A Metagenomic and Metabolomic Study.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {6},
pages = {e71679},
doi = {10.1096/fj.202503650RRR},
pmid = {41854683},
issn = {1530-6860},
support = {2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; 82170661//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Flavonoids/pharmacology ; Mice ; *Pancreatitis/drug therapy/metabolism/microbiology/blood/chemically induced ; Male ; Metabolomics/methods ; Metagenomics/methods ; Fecal Microbiota Transplantation ; Mice, Inbred C57BL ; *Metabolome/drug effects ; },
abstract = {Diosmetin is a bioactive flavonoid that exhibits well-documented antioxidant, anti-inflammatory, and anti-tumor properties. However, its potential to attenuate acute pancreatitis (AP) progression through gut microbiota modulation has not yet been elucidated. In this study, mice were pretreated with varying oral doses of diosmetin for 1 week before AP induction via intraperitoneal (i.p.) caerulein injections. The therapeutic efficacy and optimal dosage were determined through histopathological analysis of pancreatic tissue and serological biomarker assessment. Additionally, transcriptomic profiling and western blot were employed to elucidate the underlying signaling pathways. Furthermore, based on integrated metagenomic and metabolomic analyses, a core gut microbiota-metabolite-gene interaction network modulated by diosmetin was constructed. Finally, fecal microbiota transplantation (FMT) experiments validated the critical role of gut microbiota in the effects of diosmetin against AP. The results showed that medium-dose diosmetin treatment significantly attenuated pancreatic histopathological damage and acinar cell apoptosis in AP mice, while suppressing the activation of the MAPK inflammatory signaling pathway. Notably, diosmetin treatment was associated with restored microbial diversity, altered bacterial community structure, and changes in key metabolic pathways, reversing gut microbiota dysbiosis. Specifically, a diosmetin-responsive interaction network was constructed, highlighting associations between core bacterial taxa (Butyricimonas faecalis, Enterocloster bolteae, Roseburia intestinalis), key metabolites (3-indoleacrylic acid, 2-methoxy-4-vinylphenol, nitrite), and MAPK pathway-related genes. Finally, the protective effect of diosmetin was further substantiated by FMT, suggesting a potential role of the gut microbiota in this process. In conclusion, diosmetin ameliorated pancreatic injury in a murine model of caerulein-induced AP by modulating gut microbiota composition and associated metabolic profiles. These findings suggested that diosmetin represented a promising therapeutic option for AP, offering a scientific foundation for its clinical application and the underlying mechanisms involved.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Flavonoids/pharmacology
Mice
*Pancreatitis/drug therapy/metabolism/microbiology/blood/chemically induced
Male
Metabolomics/methods
Metagenomics/methods
Fecal Microbiota Transplantation
Mice, Inbred C57BL
*Metabolome/drug effects

@article {pmid41856620,
year = {2026},
author = {Lan, HY and Yang, XY and Zhang, YH and Lyu, YW and Bao, LL and Yu, YY},
title = {[Study on the characteristics and differences of intestinal microbiota in children with allergic diseases].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {60},
number = {3},
pages = {346-358},
doi = {10.3760/cma.j.cn112150-20251015-00988},
pmid = {41856620},
issn = {0253-9624},
support = {GSWS2024031//Research Project of the Gusu Talent Program of Suzhou City/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Child, Preschool ; *Hypersensitivity/microbiology ; Case-Control Studies ; Infant ; Dermatitis, Atopic/microbiology ; Female ; Food Hypersensitivity/microbiology ; Male ; Feces/microbiology ; Child ; Metagenomics ; },
abstract = {Objective: Based on metagenomic sequencing technology, this study aims to investigate the characteristics and differences of the intestinal microbiota in children with different allergic diseases, providing a theoretical basis for the early prevention and treatment of allergic diseases. Methods: The study adopted a case-control research method. 214 children with allergic diseases (Group A) who visited the Suzhou Hospital Affiliated to Nanjing Medical University from March 2023 to June 2024 were selected. According to age matching, 93 healthy controls (Group H) who participated in physical examinations during the same period were also included. Fecal samples and clinical data of the subjects were collected. The subjects were grouped according to age and type of allergic disease, and the fecal samples of the subjects were analyzed using metagenomic sequencing technology to study the characteristics and differences of the gut microbiota in different groups. The subjects were divided into 0-1 year old group (A1 and H1), 1-3 year old group (A2 and H2), and≥3 year old group (A3). According to the disease type, A1 was divided into food allergy without atopic dermatitis (F1) group and food allergy with atopic dermatitis (F2) group, A2 was divided into atopic dermatitis (AD) group, allergic rhinitis (AR) group and AD with AR group. A3 was divided into AR group, AD with AR group and AR with asthma (AS) group. Results: With age increase, the number of species annotated at the genus level in the microbiota showed a gradually increasing trend. There were significant differences in the diversity and composition of the intestinal microbiota between the allergic disease group and the control group. In the diversity analysis, it was found that there were differences in species richness between group A and group H (chao index, group A: 955.2±226.1, group H: 762.3±260.9, W=5 664, P<0.000 1), and significant differences in β-diversity between group A2 and group H2, and between group A3 and group AD-AR and group AR-AS (R=0.045, P=0.018, R=0.044, P=0.011). At the species level, the allergic disease group was mainly enriched with Bifidobacterium, Enterococcus, Escherichia, Mediterraneibacter and Blautia, while the control group was mainly enriched with Bifidobacterium. By age group analysis, the relative abundance of Mediterraneibacter and Blautia in group A1 (0-1 years old) was significantly higher than that in group H1 (Mediterraneibacter: A1: 5.2±9.4, H1: 0.9±2.1, W=718, P=0.000 8; Blautia: A1: 3.5±6.0, H1: 1.3±3.2, W=701, P= 0.000 5). In group A2 (1-3 years old), the relative abundance of Bacteroides and Faecalibacterium was significantly higher than that in group H2 (Bacteroides: A2: 5.6±8.7, H2: 3.1±5.8, W=456, P=0.020 8; Faecalibacterium: A2: 2.6±2.8, H2: 1.2±1.9, W=395, P=0.002 8). In the clinical subtype analysis, the relative abundance of Blautia and Fusicatenibacter was significantly increased in AR children (Blautia: AD: 8.0±7.9, AD-AR: 13.5±8.3, AR: 20.2±7.8, H=9.300 8, P=0.009 6; Fusicatenibacter: AD: 0.5±0.9, AD-AR: 1.2±1.6, AR: 2.2±2.4, H=7.878 3, P=0.019 5), and the relative abundance of Escherichia was significantly increased in AD children (AD: 3.3±4.3, AD-AR: 1.8±4.5, AR: 0.8±2.0, H=9.476 6, P=0.008 8). In group A3 (≥3 years old), Mediterraneibacter was significantly enriched (A3: 6.3±6.9, H3: 2.9±1.9, W=571, P=0.039 7), and the relative abundance of Anaerostipes was significantly increased in AR children (AD-AR: 2.9±2.9, AR: 5.2±4.9, AR-AS: 3.2±3.5, H=7.269, P=0.026 4). Conclusion: In infancy, the species of intestinal flora gradually increase with age. There are significant differences in the composition of intestinal flora among children with different allergic diseases. Bifidobacterium, as the main dominant species in infancy, has a lower relative abundance in the allergic disease group at different ages than in the healthy control group, suggesting that the lack of Bifidobacterium may be related to the occurrence and development of allergic diseases.},
}

Humans
*Gastrointestinal Microbiome
Child, Preschool
*Hypersensitivity/microbiology
Case-Control Studies
Infant
Dermatitis, Atopic/microbiology
Female
Food Hypersensitivity/microbiology
Male
Feces/microbiology
Child
Metagenomics

@article {pmid40064789,
year = {2026},
author = {Wang, H and Ma, H and Yan, H and Pei, Z and Zhao, J and Zhang, H and Zhang, Z and Lu, W},
title = {Study on the Effect of Bifidobacterium adolescentis CCFM1066 on Exercise Performance, Gut Microbiota, and Its Metabolites in Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {1},
pages = {54-67},
pmid = {40064789},
issn = {1867-1314},
support = {32172212, 32394052//National Natural Science Foundation of China/ ; 2022YFF1100403//National Key Research and Development Program of China/ ; WMCC202403//Cohort and Clinical Research Program of Wuxi Medical Center, Nanjing Medical University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Probiotics/administration & dosage/pharmacology ; *Physical Conditioning, Animal ; *Bifidobacterium adolescentis/physiology ; Male ; },
abstract = {Prolonged high-intensity exercise consumes significant energy, leading to fatigue and decreased performance. This study explores the effects of Bifidobacterium adolescentis CCFM1066 on exercise performance, gut microbiota, and its metabolites in mice. The results of the mouse experiments showed the mice which were intervened by Bifidobacterium adolescentis CCFM1066 have a significant increase in exercise performance, including forceful swimming time, fatigue baton turning time, and forelimb grip strength. Through metagenomic sequencing and differential metabolites, analysis indicated that the intervention of CCFM1066 increased Lachnospiraceae bacterium, Parabacteroides goldsteinii, Bacteroides xylanisolvens, and Bifidobacterium adolescentis and altered the key metabolic pathways including protein digestion and absorption and biosynthesis of amino acids. Supplementation with CCFM1066 modulates the production of short-chain fatty acids (SCFAs) and fatty acid amides (FAAs) by gut microbiota, decreasing levels of lactic acid (LA), blood urea nitrogen (BUN), lactate dehydrogenase (LDH), and creatine kinase (CK) while increasing muscle and hepatic glycogen content, thus reducing central nervous system fatigue and thereby improving exercise endurance and performance. These findings provide new insights into nutritional interventions for sports performance.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Probiotics/administration & dosage/pharmacology
*Physical Conditioning, Animal
*Bifidobacterium adolescentis/physiology
Male

@article {pmid40193036,
year = {2026},
author = {Kim, SY and Seol, D and Jeong, M and Kwak, W and Kim, H and Cho, S and Kim, TH},
title = {Assessing the Efficacy of Ligilactobacillus salivarius CLS0420 and Lacticaseibacillus paracasei CLPC0603 on Vaginal Well-Being in Healthy Women: A Pilot, Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {1},
pages = {368-380},
pmid = {40193036},
issn = {1867-1314},
mesh = {Humans ; Female ; *Probiotics/administration & dosage/pharmacology ; Adult ; Double-Blind Method ; *Vagina/microbiology ; Pilot Projects ; Middle Aged ; Young Adult ; *Vaginosis, Bacterial/prevention & control/microbiology ; *Lacticaseibacillus paracasei/physiology ; Gardnerella vaginalis/drug effects ; Microbiota ; Candida albicans/drug effects ; },
abstract = {Despite the growing development of probiotics for preventing bacterial vaginosis (BV), their effectiveness in women without BV has not been thoroughly investigated. This pilot, randomized, double-blind, placebo-controlled study aims to assess the impact of orally administered probiotic strains, exhibiting in vitro antimicrobial activity against Gardnerella vaginalis and Candida albicans, on vaginal well-being in women without preexisting health conditions. Healthy women (n = 30, aged 19-50) were enrolled and randomly assigned using simple randomization to receive either probiotic or placebo capsules. After excluding dropouts, 26 participants (15 in the probiotic group, 11 in the placebo group) completed the study, undergoing a 3-week intervention. Vaginal well-being was assessed before and after the intervention using self-assessed health on a 5-point Likert scale, along with analysis of the vaginal microbiome by targeting the 16S-ITS-23S rRNA operon region with the Nanopore sequencing platform and MIrROR database. Notably, only the probiotic group exhibited a significant improvement in self-assessed overall gut and vaginal health following the intervention (p = 0.009 and p = 0.003, respectively). Nevertheless, no significant changes were observed in the vaginal bacterial community following the intervention and confirming the vaginal colonization of orally ingested probiotic strains through metagenome sequencing proved challenging. In summary, these findings suggest that while oral probiotics may improve perceived vaginal well-being, their role in modulating the vaginal microbiome in healthy women remains inconclusive. Additional research with a larger sample size is necessary to substantiate the endorsement of oral probiotic consumption for preventing BV or maintaining vaginal health in healthy women. This study was retrospectively registered at Clinical Research Information Service (CRIS) (KCT0008957, November 15, 2023).},
}

Humans
Female
*Probiotics/administration & dosage/pharmacology
Adult
Double-Blind Method
*Vagina/microbiology
Pilot Projects
Middle Aged
Young Adult
*Vaginosis, Bacterial/prevention & control/microbiology
*Lacticaseibacillus paracasei/physiology
Gardnerella vaginalis/drug effects
Microbiota
Candida albicans/drug effects

@article {pmid40423879,
year = {2026},
author = {Zhao, Y and Dai, Z and Lang, Y and Li, R and Zheng, H and Mi, J and He, X and Liu, J and Xiang, R and Mei, X and Liu, Y and Wang, Y and Guo, H and Yang, Q and Ren, K and Yang, T},
title = {Screening of Fecal Bacteroides Strains and Discovery of Bacteroides eggerthii S13-F8 with Protective Effects Against Chemotherapy-Induced Diarrhea.},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {1},
pages = {1003-1019},
pmid = {40423879},
issn = {1867-1314},
support = {2024NSFSC0044//the Natural Science Foundation of Sichuan province/ ; No. 2024kjTzn04//CMC Excellent-talent Program/ ; },
mesh = {Animals ; *Diarrhea/chemically induced/prevention & control/microbiology ; Mice ; Fluorouracil/adverse effects ; *Feces/microbiology ; *Bacteroides/isolation & purification/genetics/classification/physiology ; Humans ; Male ; Gastrointestinal Microbiome ; *Probiotics/administration & dosage ; Female ; },
abstract = {Chemotherapy-induced diarrhea (CID) is a frequent gastrointestinal side effect in cancer patients, particularly associated with the use of 5-fluorouracil (5-FU). This study aimed to isolate multiple Bacteroides strains from the feces of healthy individuals and identify Bacteroides eggerthii (B. eggerthii) S13-F8 as the optimal candidate for alleviating CID. Whole-genome sequencing of B. eggerthii S13-F8 was conducted to uncover its functional characteristics and explore the potential mechanisms underlying its protective effects against CID. The anti-CID efficacy of B. eggerthii S13-F8 was assessed using multiple parameters, including diarrhea severity, food intake, and body weight changes. Comprehensive analyses, including blood tests, intestinal histopathology, colon transcriptomics, and fecal metagenomics, were performed to elucidate its underlying mechanisms. In a 5-FU-induced mouse model, B. eggerthii S13-F8 significantly alleviated weight loss and diarrhea. Histological examination revealed that B. eggerthii S13-F8 preserved the villus height-to-crypt depth (V/C) ratio and protected goblet cells in colonic tissues. Gene expression analysis showed that B. eggerthii S13-F8 upregulated protective markers, such as Aqp8, Slc26a3, and mucin-related genes (TFF3, FCGBP, and Muc2), while downregulating pro-inflammatory mediators, including IL-1α, IL-22, and Cxcl2. Furthermore, B. eggerthii S13-F8 modulated gut microbiota composition by suppressing pathogenic bacteria (Pseudomonas aeruginosa, Salmonella, γ-Proteobacteria, and Shigella) and enriching beneficial taxa, such as Lactobacillus and Akkermansia muciniphila. In conclusion, B. eggerthii S13-F8 demonstrates significant potential in mitigating severe diarrhea caused by 5-FU chemotherapy, providing a strong foundation for its development as a live biotherapeutic for CID treatment.},
}

Animals
*Diarrhea/chemically induced/prevention & control/microbiology
Mice
Fluorouracil/adverse effects
*Feces/microbiology
*Bacteroides/isolation & purification/genetics/classification/physiology
Humans
Male
Gastrointestinal Microbiome
*Probiotics/administration & dosage
Female

@article {pmid40824425,
year = {2026},
author = {İstanbullugil, FR and Sanli, K and Ozturk, T and Keskin, BC and Düyşöbayeva, A and Risvanli, A and Acaröz, U and Acaröz, DA and Salykov, R and Sahin, M},
title = {Koumiss Microbiome: Investigation of the Microbial Composition and Functional Potential of a Unique Beverage of Fermented Milk Produced at Kyrgyz Mountains.},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {1},
pages = {18-34},
pmid = {40824425},
issn = {1867-1314},
support = {KTMU-BAP-2023.FB.15//KTMU Scientific Research Projects Unit/ ; },
mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Cultured Milk Products/microbiology ; Kyrgyzstan ; Yeasts/classification/isolation & purification/genetics ; Animals ; Bacteriophages/isolation & purification/classification/genetics ; Archaea/classification/isolation & purification/genetics ; Metagenomics ; },
abstract = {This study aims to investigate the microbial composition of koumiss made via traditional methods in Kyrgyz mountain pastures. We collected koumiss samples produced in plastic (P), wood (T), and leather (D) containers at household settings. These samples were subjected to shotgun metagenomic sequencing. As a result of the metagenome analyses, we identified a diversity of bacteria, yeasts, bacteriophages, and archaea in koumiss produced within different containers. Koumiss' microbial community was predominantly composed of lactic acid bacteria (LAB), particularly Lactobacillus helveticus and Lactococcus lactis. Additional LAB species such as Lactobacillus kefiranofaciens, Lactococcus raffinolactis, Lactiplantibacillus plantarum, and Lactococcus cremoris, as well as non-LAB taxa such as Kluyvera intermedia, Raoultella planticola, and Hafnia alvei were also identified as part of the koumiss microbiota. Nonetheless, the opportunistic pathogen, Enterobacter hormaechei, was among the detected species. The most abundant yeast species was identified as Brettanomyces bruxellensis. Other yeast species involving Monosporozyma unispora, Monosporozyma servazzii, and Yarrowia lipolytica were also detected within the metagenome. Despite the type of container material not significantly affecting the microbial diversity, Bifidobacterium spp. and bacteriophages were identified at higher levels in plastic containers. We detected various antimicrobial resistance genes and gene clusters that produce bioactive compounds within koumiss samples. This study highlights koumiss' rich microbial composition and its potential health impacts. It underscores the importance of effectively utilizing metagenomic and bioinformatics methods for better comprehension of the microbiota of koumiss.},
}

*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Cultured Milk Products/microbiology
Kyrgyzstan
Yeasts/classification/isolation & purification/genetics
Animals
Bacteriophages/isolation & purification/classification/genetics
Archaea/classification/isolation & purification/genetics
Metagenomics

@article {pmid41418935,
year = {2026},
author = {Chen, S and Li, W and Fan, L and Xu, C and Liu, S and Li, H and Liu, P and Zhu, W and Wu, X and Qin, P and Li, J and Ma, X and Wei, Y},
title = {Metatranscriptomics profiling reveals rodent- and shrew-borne viral diversity and evolutionary relationships in Guangzhou, China.},
journal = {Virologica Sinica},
volume = {41},
number = {1},
pages = {35-47},
doi = {10.1016/j.virs.2025.12.009},
pmid = {41418935},
issn = {1995-820X},
mesh = {Animals ; China/epidemiology ; *Shrews/virology ; *Rodentia/virology ; *Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Virome ; Rats ; Genetic Variation ; Evolution, Molecular ; Metagenomics ; Gene Expression Profiling ; },
abstract = {Emerging zoonotic infectious diseases, predominantly caused by viruses, pose increasing public health threats globally. Rodents and shrews are natural hosts for a variety of zoonotic viruses. Guangzhou is one of China's most densely populated cities and experiences frequent international and domestic population movements, making it a hotspot for infectious diseases. This study reports the metatranscriptomics virome of 208 rodents and shrews collected between June 2023 and December 2024 from four main urban areas (Tianhe, Baiyun, Liwan, Yuexiu) and five non-main urban areas (Zengcheng, Huadu, Conghua, Panyu, Nansha) in Guangzhou. Individual libraries were constructed from mixed tissue samples (liver, spleen, lung, and kidney) of each animal. Metatranscriptomics sequencing revealed diverse viral communities, identifying 24 viral strains across eight mammalian-associated viral families. Notably, we identified 17 known viruses and seven potentially novel viruses, including Seoul virus (5.2% prevalence in Rattus norvegicus from Panyu), Wenzhou mammarenavirus (13.2% in Rattus norvegicus from Conghua and Huadu), Jeilongvirus (29.4% in Rattus andamanensis from Panyu), and a divergent lineage of arteriviruses that may represent a new genus (maximum positivity rates of 2.9% in Rattus norvegicus and 5.7% in Rattus tanezumi). Phylogenetic analysis elucidated evolutionary relationships within key families such as Hantaviridae, Arenaviridae, Flaviviridae, and Parvoviridae, revealing distinct viral carriage patterns in Guangzhou City that are shaped by host species and geographical location. This is the first macro-level study of rodent and shrew viromes in Guangzhou and provides a scientific basis for strengthening surveillance of mammalian-associated viruses and preventing emerging zoonotic infectious diseases in the region.},
}

Animals
China/epidemiology
*Shrews/virology
*Rodentia/virology
*Viruses/genetics/classification/isolation & purification
Phylogeny
*Virome
Rats
Genetic Variation
Evolution, Molecular
Metagenomics
Gene Expression Profiling

@article {pmid41690672,
year = {2026},
author = {Zhang, Y and Bai, Y and Ni, J and Shi, J and Zhang, Y and Bell-Sakyi, L and Wu, X and He, C and Deng, F and Yin, F and Shen, S and Fang, Y},
title = {Evidence of human exposure to tick-borne viruses based on viromes of ticks and presence of specific antibodies among patients in Hainan Island, southern China.},
journal = {Virologica Sinica},
volume = {41},
number = {1},
pages = {70-83},
doi = {10.1016/j.virs.2026.02.008},
pmid = {41690672},
issn = {1995-820X},
mesh = {Animals ; China/epidemiology ; Humans ; *Tick-Borne Diseases/virology/epidemiology ; *Antibodies, Viral/blood ; *Viruses/classification/genetics/isolation & purification/immunology ; *Ticks/virology ; Middle Aged ; *Virome ; Male ; Adult ; Female ; Phylogeny ; Aged ; Young Adult ; Islands ; Metagenomics ; *Virus Diseases/epidemiology/virology ; Adolescent ; },
abstract = {Hainan Island, located in the South China Sea, is known as an area with diseases related to Rickettsia spp. or spirochete infection; however, the potential threat there from infection with tick-borne viruses (TBVs) remains obscure. In the present study, the dominant tick species, including Rhipicephalus sanguineus and Rhipicephalus microplus, were collected in Hainan Island, and tick viromes were investigated by metagenomic sequencing. In total, 27 viral species were identified belonging to the families Orthomyxoviridae, Flaviviridae, Nairoviridae, Phenuiviridae, Totiviridae, Chuviridae, Rhabdoviridae, and Parvoviridae, amongst which one novel virus and 13 new strains were discovered. Subsequently, individual ticks were screened for seven TBVs, Huanggang Rhabd tick virus 1 (HRTV1), Lihan tick virus (LHTV), Mivirus (MIV), Guangdong tick quaranjavirus (GTQV), Wenchang Ephemerovirus (WEPMV), Jingmen tick virus (JMTV), and brown dog tick phlebovirus (BDPTV), resulting in high prevalence rates of 16.97%, 9.59%, 10.33%, 7.38%, 7.01%, 6.27%, and 3.69%, respectively. While co-infection with multiple viruses was more frequent in R. sanguineus, R. microplus ticks generally had higher viral loads. Four febrile patients showed antibody responses to three TBVs, one each to LHTV and JMTV, and two to GTQV; the patient with antibodies to JMTV also showed neutralizing activity against this virus. This study promoted our understanding of the diversity and complexity of the TBV community in Hainan Island. The results provide serological evidence that human exposure to TBVs like JMTV may have occurred in Hainan, raising concern about potential risks from TBVs and the need to perform further surveys of TBVs among ticks, animals and humans.},
}

Animals
China/epidemiology
Humans
*Tick-Borne Diseases/virology/epidemiology
*Antibodies, Viral/blood
*Viruses/classification/genetics/isolation & purification/immunology
*Ticks/virology
Middle Aged
*Virome
Male
Adult
Female
Phylogeny
Aged
Young Adult
Islands
Metagenomics
*Virus Diseases/epidemiology/virology
Adolescent

@article {pmid41699049,
year = {2026},
author = {Wu, LL and Liao, YJ and Peng, WH and Chen, LK and Huang, YC and Chen, CY and Juan, CC},
title = {FK506-binding protein-5 in high-fat diet-induced metabolic dysfunction-associated steatotic liver disease.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41699049},
issn = {2045-2322},
support = {108-2320-B-010-045-MY3, 110-2320-B-002-080-MY3, MOST 111-2314-B-A49-072, NSTC 112-2314-B-A49-028-MY3, NSTC 112-2740-B-A49-002, NSTC 113-2740-B-A49-003, NSTC 113-2321-B-A49-014-, NSTC 114-2321-B-A49-004 -, NSTC 114-2740-B-A49-003//Ministry of Science and Technology, Taiwan/ ; MOST 106-2320-B-010-009-MY3//Ministry of Science and Technology, Taiwan/ ; CI-110-22 and CI-111-24//Yen Tjing Ling Medical Foundation/ ; },
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Tacrolimus Binding Proteins/metabolism/genetics ; Mice ; Gastrointestinal Microbiome ; Mice, Knockout ; *Fatty Liver/metabolism/etiology ; Male ; Obesity/metabolism ; Mice, Inbred C57BL ; Liver/metabolism/pathology ; *Non-alcoholic Fatty Liver Disease/metabolism/etiology ; Dysbiosis ; Disease Models, Animal ; Inflammation ; },
abstract = {A high-fat diet (HFD) alters the gut microbiota (GM), impairs metabolic efficiency, and increases gut permeability and inflammation. Obesity and insulin resistance are associated with GM dysbiosis. The GM is strongly associated with metabolic disorders and fatty liver disease. The co-chaperone protein FK506-binding protein-5 (FKBP5) regulates several vital cellular processes. Although FKBP5 has been implicated in stress-related disorders, it has not been directly linked to HFD-induced metabolic fatty liver disease. This study aimed to elucidate how FK506 binding protein 5 impairment affects the GM in HFD-induced metabolic dysfunction-associated fatty liver disease and metabolic dysfunction-associated steatotic liver disease (MASLD). Wild-type and FKBP5-knockout (FKKO) mice were fed a normal chow diet or a high-fat diet for 16 weeks. Mouse GM was examined using 16 S rRNA metagenomic analysis. The number of gut-liver immune cells was measured using flow cytometry. HFD-induced hepatic steatosis and inflammation were prevented in FKBP5-deficient mice. FKKO animals showed higher butyric acid levels and GM resistance to diet-induced obesity alterations according to 16 S ribosomal rRNA gene analysis and displayed an HFD-specific gut-liver immunological response that maintained gut barrier failure and mucosal immunity, which are important for GM homeostasis. FKBP5 helps the GM address inadequate immunological responses, including lower gut and liver CD11b[+]Ly6C[+] monocytes and neutrophils, and protects against obesity by improving the GM response to HFD-induced MASLD. FKBP5 protects against HFD-induced MASLD through metabolic coordination between the gut barrier and intrahepatic immunity.},
}

Animals
*Diet, High-Fat/adverse effects
*Tacrolimus Binding Proteins/metabolism/genetics
Mice
Gastrointestinal Microbiome
Mice, Knockout
*Fatty Liver/metabolism/etiology
Male
Obesity/metabolism
Mice, Inbred C57BL
Liver/metabolism/pathology
*Non-alcoholic Fatty Liver Disease/metabolism/etiology
Dysbiosis
Disease Models, Animal
Inflammation

@article {pmid41707175,
year = {2026},
author = {Huang, X and Deng, K and Zhu, G and Huang, W and Gong, G and Liu, H and Yang, T and Gui, Y and Li, W},
title = {Dynamics of soil microbiome throughout the cultivation life cycle of Phallus rubrovolvatus.},
journal = {Canadian journal of microbiology},
volume = {72},
number = {},
pages = {1-14},
doi = {10.1139/cjm-2025-0279},
pmid = {41707175},
issn = {1480-3275},
mesh = {*Soil Microbiology ; *Microbiota ; China ; Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; Metagenomics ; Metagenome ; },
abstract = {Phallus rubrovolvatus is a valuable edible fungus extensively cultivated in Guizhou Province, China. However, the changes in the soil microbiome throughout its growth cycle remain poorly understood. In this study, we collected 35 casing soil samples across five growth stages covering the entire 120-day cultivation cycle of Phallus rubrovolvatus and conducted metagenomic sequencing to examine alterations in soil microbial composition, diversity, key biomarkers, and functional potential. Our analyses revealed significant stage-dependent shifts in microbial community structure, with alpha diversity reaching its lowest at the primordium stage (Shannon of 5.12) and network complexity peaking at harvest stage (1.8-fold increase in connectivity). Through LEfSe analysis, we identified 37 stage-specific microbial biomarkers primarily affiliated with Actinomycetota and Acidobacteriota. Notably, Acidobacteriota biomarkers dominated at the primordium stage, while Nitrospirota enrichment characterized the harvest stage. Functional analyses revealed that membrane transport and energy metabolism pathways were enriched during early mycelial colonization, whereas secondary metabolite biosynthesis and signaling pathways became prominent during fruiting body maturation. Correlation analyses identified available nitrogen as the primary soil variable associated with microbial community composition. These findings provide foundational knowledge of microbiome dynamics during Phallus rubrovolvatus cultivation and suggest that microbiome-based management strategies may benefit from stage-specific interventions synchronized with fungal developmental transitions.},
}

*Soil Microbiology
*Microbiota
China
Bacteria/classification/genetics/isolation & purification
Soil/chemistry
Metagenomics
Metagenome

@article {pmid41775266,
year = {2026},
author = {Han, Z and Sun, Z and Zhao, Q and Du, L and Zhen, D and Liu, X and Jiang, S and Liu, YY and Zhang, J},
title = {Competition and compromise between exogenous probiotics and native microbiota.},
journal = {Cell systems},
volume = {17},
number = {3},
pages = {101516},
doi = {10.1016/j.cels.2025.101516},
pmid = {41775266},
issn = {2405-4720},
mesh = {*Probiotics/pharmacology ; Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; Feces/microbiology ; Bifidobacterium animalis ; Mice, Inbred C57BL ; Dietary Fiber ; Male ; Bifidobacterium ; },
abstract = {Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic, Bifidobacterium animalis subsp. lactis V9 (BV9), to mechanistically investigate its competitive strategies. We perform metagenomic and whole-genome sequencing of stool samples and isolated BV9, longitudinally collected from 24 mice orally administered with BV9 and different diets. Results show that a high-fiber diet most effectively supports the colonization of BV9, where BV9 selectively competes with Parabacteroides distasonis (P. distasonis), rather than extensively with other gut bacteria. By comparing the genomic structures of BV9 and P. distasonis isolated during the washout period, we infer their co-evolution mechanisms, highlighting their competition and compromise in utilizing inulin-derived glucose. Finally, our in vitro co-culture experiments validate such competitive dynamics. This study fills a critical gap in our understanding of niche competition in colonization.},
}

*Probiotics/pharmacology
Animals
*Gastrointestinal Microbiome/physiology
Mice
Feces/microbiology
Bifidobacterium animalis
Mice, Inbred C57BL
Dietary Fiber
Male
Bifidobacterium

@article {pmid41845564,
year = {2026},
author = {Zhang, Y and Wang, DD},
title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644682},
doi = {10.1080/19490976.2026.2644682},
pmid = {41845564},
issn = {1949-0984},
mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Animals ; *Diet ; Metabolomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Proteomics ; Multiomics ; },
abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.},
}

*Diabetes Mellitus, Type 2/microbiology/metabolism
Humans
*Gastrointestinal Microbiome
Metagenomics
Animals
*Diet
Metabolomics
Bacteria/classification/genetics/metabolism/isolation & purification
Proteomics
Multiomics

@article {pmid41846126,
year = {2026},
author = {Wang, X and Zhao, L and Teng, Y and Hu, W and Xu, Y and Ma, J and Song, J and Ren, W and Zhang, J and Zhu, H and Wang, X and Wang, Y and Luo, Y and Kuramae, EE},
title = {Decoding the adaptive strategies of versatile diazotrophs to multi-metal(loid) stress in mercury-mining impacted farmland soils.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141760},
doi = {10.1016/j.jhazmat.2026.141760},
pmid = {41846126},
issn = {1873-3336},
abstract = {Diazotrophs are crucial for Earth's nitrogen cycle via biological nitrogen fixation, while also modulating other elemental cycles and exhibiting bioremediation potential. However, their responses to co-occurring heavy metal(loid) (HM) contaminants in polluted soils remain poorly understood. Using combined nifH (encoding nitrogenase) amplicon and metagenomic sequencing, we characterized the taxonomic structure and metabolic potential of diazotrophic community across multi-HM contamination gradients in mercury-mining impacted farmlands (paddy vs. upland). Results identified selenium (upland soils: 0-3.08 mg kg[-1]) and arsenic (paddy soils: 5.38-17.1 mg kg[-1]) as the primary HMs shaping diazotrophic diversity, whereas mercury (0.067-99.6 mg kg[-1]) showed a significant but weak correlation. Selenium and mercury correlated positively with diversity in upland soils (arsenic negatively), whereas all three HMs correlated negatively in paddy soils. Diazotrophic indicator taxa varied by HM type, yet certain taxa tolerated all three HMs simultaneously-notably Chromatiaceae/Pseudomonadaceae in upland soils and Xanthobacteraceae in paddy soils. Moreover, diazotrophs in upland soils exhibited synergistic associations with functional guilds involved in HM resistance and element cycling (e.g., carbon fixation and hydrogen metabolism), contrasting with the negative correlations in paddy soils. Metagenomic binning indicated that dominant diazotrophs were primarily aerobic heterotrophs with versatile metabolic potentials, including multi-HM resistance (e.g., arsenic/mercury reduction, efflux, and antioxidation) and energy acquisition via trace gas (CO, H2), manganese, and sulfide oxidation. These findings provide novel insights into diazotrophic adaptive strategies under multi-HM stress, advancing our understanding of their ecological and environmental functions.},
}

@article {pmid41849467,
year = {2026},
author = {Ferreira, LDS and Silva, JFBR and Vilhena, MPSP and Alegria, OC and Ramos, RTJ and Sousa, MPA},
title = {Bacterial diversity of lowland soils under cocoa cultivation in Amazon.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {86},
number = {},
pages = {e295836},
doi = {10.1590/1519-6984.295836},
pmid = {41849467},
issn = {1678-4375},
mesh = {*Cacao/growth & development ; *Soil Microbiology ; Brazil ; *Biodiversity ; *Bacteria/classification/genetics ; },
abstract = {This study investigated bacterial diversity in soils from six cacao-producing islands in Mocajuba, Pará, Brazil. Using next generation sequencing shotgun metagenomic DNA, we characterized the microbial composition and ecological structure of floodplain soils cultivated with Theobroma cacao. Taxonomic classification revealed a rich bacterial community encompassing 21 phyla, 54 classes, 121 orders, 240 families, 604 genera, and 2,289 species. The dominant phyla, Actinomycetota and Pseudomonadota, are known for their ecological roles in organic matter decomposition, antibiotic production, nitrogen cycling, and plant growth promotion. Alpha diversity metrics varied among samples, with P3 showing the highest species richness and P5 exhibiting the highest Shannon, Simpson, and evenness indices, suggesting a more balanced community. Beta diversity analysis based on Bray-Curtis dissimilarity under Total Sum Scaling (TSS) normalization revealed ecological gradients ranging from 0.228 to 0.527. Spatial ordination and hierarchical clustering indicated gradual shifts in community composition, supporting the concept of a compositional continuum shaped by environmental gradients. Functionally, Burkholderia lata was dominant in P1, reflecting its role in potassium solubilization, while Streptomyces species-detected in five of the six samples-contribute to biogeochemical cycling and pathogen suppression. Bradyrhizobium and Paraburkholderia, identified in P3, P5, and P6, are associated with nitrogen fixation and plant hormone regulation. These findings reveal the ecological complexity and functional potential of cacao soil microbiomes, providing insights for sustainable management of Amazonian floodplain agroecosystems.},
}

*Cacao/growth & development
*Soil Microbiology
Brazil
*Biodiversity
*Bacteria/classification/genetics

@article {pmid41852102,
year = {2026},
author = {Qu, X and Liao, Y and Muthuri, CW and Winowiecki, LA and Zi, H and Zhang, Y and Li, X},
title = {Soil Functionality Undermined by Symbiotic Fungal Decline Following Forest Conversion.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70268},
doi = {10.1111/1462-2920.70268},
pmid = {41852102},
issn = {1462-2920},
support = {W2412011//National Natural Science Foundation of China/ ; 32430069//National Natural Science Foundation of China/ ; jxsq2023102214//Double Thousand Plan of Jiangxi Province/ ; },
mesh = {*Soil Microbiology ; *Forests ; *Symbiosis ; *Soil/chemistry ; *Fungi/genetics/classification/physiology ; China ; Phosphorus/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Biodiversity ; Bacteria/genetics/classification ; Ecosystem ; },
abstract = {The conversion of native forests to other terrestrial ecosystems represents a profound form of land-use change, threatening aboveground biodiversity and biomass. However, its impact on soil ecological functions remains uncertain, particularly the regulatory role of soil microbial communities. To address this, we evaluated soil functionality related to carbon, nitrogen and phosphorus cycling by measuring nine enzyme activities in soils from native forests, plantations and croplands in subtropical China. Our results demonstrated a significant decline in soil functionality following the conversion of native forests, with the most pronounced reductions observed in croplands. This decline in soil functionality was strongly associated with a decrease in fungal richness but was independent of bacterial alpha-diversity. Specifically, the reduction in the abundance of symbiotic fungi, including key taxa such as Lactifluus and Tomentella, was identified as a primary driver of the functional impairment. Metagenomic analyses further confirmed that the loss of microbial functional genes was linked to the observed decline in soil functionality. Our findings underscore the critical role of key fungal taxa in maintaining soil processes and highlight the importance of their conservation and restoration to ensure ecosystem functionality in managed landscapes.},
}

*Soil Microbiology
*Forests
*Symbiosis
*Soil/chemistry
*Fungi/genetics/classification/physiology
China
Phosphorus/metabolism
Carbon/metabolism
Nitrogen/metabolism
Biodiversity
Bacteria/genetics/classification
Ecosystem

@article {pmid41852435,
year = {2025},
author = {Trubl, G and Malard, L and Rahlff, J},
title = {Editorial: Ecology, evolution, and biodiversity of microbiomes and viromes from extreme environments.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1604002},
doi = {10.3389/frmbi.2025.1604002},
pmid = {41852435},
issn = {2813-4338},
}

@article {pmid41852664,
year = {2026},
author = {Shibata, N and Yoshifuji, A and Oyama, E and Komatsu, M and Azegami, T and Hayashi, K and Ishii, Y and Hasegawa, N and Namkoong, H},
title = {Urinary microbiota and bacterial membrane vesicles in chronic kidney disease: contribution to antimicrobial-resistant urinary tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1748638},
pmid = {41852664},
issn = {2235-2988},
mesh = {Humans ; Male ; *Urinary Tract Infections/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology ; Middle Aged ; *Microbiota ; *Drug Resistance, Bacterial ; RNA, Ribosomal, 16S/genetics ; Aged ; *Urine/microbiology ; Metagenomics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Adult ; Microscopy, Electron, Transmission ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/chemistry/genetics ; *Extracellular Vesicles/ultrastructure ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Chronic kidney disease (CKD) is associated with an increased risk of severe urinary tract infections (UTIs), particularly those caused by antimicrobial-resistant bacteria. Although urinary microbiota and bacterial membrane vesicles (BMVs) are thought to contribute to UTI pathogenesis, their roles in CKD remain insufficiently understood. In this exploratory study, urine samples were collected from 10 male patients with CKD (eGFR <45 mL/min/1.73 m[2]) and 10 male non-CKD controls (eGFR ≥60 mL/min/1.73 m[2]). Urinary microbiota and BMV fractions were isolated and analyzed to compare microbial composition and antimicrobial resistance gene (ARG) profiles, and to evaluate their potential involvement in UTI development and the emergence of antimicrobial resistance in CKD. Both fractions were subjected to shotgun metagenomic sequencing; metagenomic analysis of BMVs was performed using pooled samples within each group. In addition, BMV fractions were characterized by transmission electron microscopy and 16S rRNA gene PCR. Urinary microbiota α-diversity was significantly lower in patients with CKD than in controls (ACE index, p = 0.04). Vesicle-like structures consistent with BMVs, with diameters of 20-200 nm, were detected in urine samples from both controls and patients with CKD. Principal coordinate analysis demonstrated that BMV fractions clustered within the corresponding urinary microbiota profiles. Furthermore, multiple antimicrobial resistance genes (ARGs), including ftsI and adeF, were identified in both urinary microbiota and BMV fractions. This study provides exploratory evidence of reduced urinary microbiota α-diversity in patients with CKD and the presence of ARGs in both urinary microbiota and BMV fractions from controls and patients with CKD. These findings suggest microbiological factors that may contribute to the high incidence of antimicrobial-resistant UTIs in this population. Future validation in larger cohorts with individual-level BMV profiling will be required to determine whether analyses focusing on urinary microbiota and BMVs can contribute to a better understanding of antimicrobial-resistant UTIs and to improved infection risk assessment in patients with CKD.},
}

Humans
Male
*Urinary Tract Infections/microbiology
*Renal Insufficiency, Chronic/complications/microbiology
Middle Aged
*Microbiota
*Drug Resistance, Bacterial
RNA, Ribosomal, 16S/genetics
Aged
*Urine/microbiology
Metagenomics
*Bacteria/genetics/drug effects/classification/isolation & purification
Adult
Microscopy, Electron, Transmission
Sequence Analysis, DNA
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal/chemistry/genetics
*Extracellular Vesicles/ultrastructure
Anti-Bacterial Agents/pharmacology

@article {pmid41852665,
year = {2026},
author = {Zhang, Y and Wang, H and Yan, R and Wang, K and Man, J and Yang, L},
title = {Research advances on the urinary microbiome in non-infectious urinary tract diseases: from community composition to clinical prospects.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1728182},
pmid = {41852665},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; Dysbiosis/microbiology ; *Urologic Diseases/microbiology/diagnosis ; *Urinary Tract/microbiology ; *Urine/microbiology ; Prostatic Neoplasms/microbiology ; },
abstract = {INTRODUCTION: With the rapid development of 16S rRNA sequencing and metagenomic technologies, the traditional concept of sterile urine has been completely overturned, and a diverse urinary microbiome has been identified even in healthy individuals. Increasing evidence indicates that dysbiosis of the urinary microbiome is closely associated with the onset and progression of various non-infectious urological diseases.

METHODS: This review systematically summarizes recent advances in the role of the urinary microbiome in non-infectious urological diseases, including bladder cancer, benign prostatic hyperplasia, prostate cancer, nephrolithiasis, interstitial cystitis/bladder pain syndrome, and urinary incontinence, with a focus on microbial dysbiosis, pathogenic mechanisms, and clinical applications.

RESULTS: Studies have shown that alterations in the composition and diversity of the urinary microbiome are closely related to chronic inflammation, immune dysregulation, metabolic disturbances, and changes in the local microenvironment. These alterations may contribute to disease pathogenesis through mechanisms such as persistent low-grade inflammation, abnormal metabolic activity, and biofilm formation. In recent years, non-invasive detection based on urinary microbial profiles has shown promising potential in the early diagnosis of bladder and prostate cancers, with some machine learning models achieving diagnostic accuracies above 80 percent. Furthermore, the urinary microbiome may influence the efficacy of immunotherapy, offering new insights for personalized precision medicine.

CONCLUSIONS: This review summarizes the mechanisms, research status, and clinical prospects of the urinary microbiome in non-infectious urological diseases, emphasizing the importance of methodological standardization and highlighting its potential applications in early screening, diagnostic stratification, and microbiome-targeted interventions.},
}

Humans
*Microbiota
Dysbiosis/microbiology
*Urologic Diseases/microbiology/diagnosis
*Urinary Tract/microbiology
*Urine/microbiology
Prostatic Neoplasms/microbiology

@article {pmid41852689,
year = {2026},
author = {Anandan, S and Ali, A and Selvarajoo, A and Supramaniam, CV},
title = {Trichoderma combined with palm kernel shell biochar promotes root health and rhizosphere biodiversity in young oil palm seedlings infected with Ganoderma boninense.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1742803},
pmid = {41852689},
issn = {2813-4338},
abstract = {Oil palm (Elaeis guineensis) contributes up to 3% of gross domestic product (GDP) in Malaysia. Long-term monoculture production reduced natural biodiversity and increased severe threat by Ganoderma boninense, a causal agent of basal stem rot (BSR) disease. BSR recorded projections of 860,610 hectares of plantations to be devastated by BSR by 2040. While disease management has prioritised good sanitation practices, Trichoderma spp. is a potential solution to combatting G. boninense. In this study, we determined the efficacy of Trichoderma spp. isolate 4A added to palm kernel shell (PKS) biochar (T-mix) to improve oil palm root health. Three-month-old seedlings were observed in control treatments, T1 to T4 and Trichoderma sp. treatments, T5 to 12 with Ganoderma added in T7,8, 11 and 12. Root development parameters such as root architecture, length, diameter, and surface area were observed every two months for six months. Root length of T5 (3.3 m) and T9 (4.4 m) was higher than no-treatment control, T1 (2.5 m) indicating Trichoderma sp. support of root health. T9 (T-mix) has significantly improved root architecture in root scan with denser and multiple root branches as while all other diseased oil palms exhibit stunted roots. The diameter of roots shows similar trend to root length of T9 roots with the highest reading at 5.4 mm. T11 showed the overall improved fungal biodiversity at 6 months post inoculation with potential disease suppressive effects against other common pathogens such as Fusarium sp. This study highlights a new perspective of Trichoderma spp. treatment with biochar to provide protection to growing young oil palm root health, beyond disease control, indicating a beneficial role for early application at seedling stage. For long term application, Trichoderma spp. combined with biochar support healthy fungal dynamics without over-dominating indigenous fungal inhabitants. This is the first study to highlight the role of combined Trichoderma spp. and biochar in influencing the root architecture and rhizosphere dynamics of a perennial oil palm at the seedling stage. Overall, this study presents an exciting opportunity to use a new Trichoderma sp.-biochar solution in the battle against G. boninense.},
}

@article {pmid41853343,
year = {2023},
author = {Ionescu, D and Zoccarato, L and Cabello-Yeves, PJ and Tikochinski, Y},
title = {Extreme fluctuations in ambient salinity select for bacteria with a hybrid "salt-in"/"salt-out" osmoregulation strategy.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1329925},
pmid = {41853343},
issn = {2813-4338},
abstract = {Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper "salt-in" and more expensive "salt-out" strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.},
}

@article {pmid38922826,
year = {2026},
author = {Parthasarathy, G and Malhi, H and Bajaj, JS},
title = {Therapeutic manipulation of the microbiome in liver disease.},
journal = {Hepatology (Baltimore, Md.)},
volume = {83},
number = {4},
pages = {948-969},
pmid = {38922826},
issn = {1527-3350},
support = {R01 DK111378/DK/NIDDK NIH HHS/United States ; U01 AA021788/AA/NIAAA NIH HHS/United States ; },
mesh = {Humans ; *Liver Diseases/therapy/microbiology ; *Gastrointestinal Microbiome/drug effects/physiology ; Probiotics/therapeutic use ; Animals ; Prebiotics ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Myriad associations between the microbiome and various facets of liver physiology and pathology have been described in the literature. Building on descriptive and correlative sequencing studies, metagenomic studies are expanding our collective understanding of the functional and mechanistic role of the microbiome as mediators of the gut-liver axis. Based on these mechanisms, the functional activity of the microbiome represents an attractive, tractable, and precision medicine therapeutic target in several liver diseases. Indeed, several therapeutics have been used in liver disease even before their description as a microbiome-dependent approach. To bring successful microbiome-targeted and microbiome-inspired therapies to the clinic, a comprehensive appreciation of the different approaches to influence, collaborate with, or engineer the gut microbiome to coopt a disease-relevant function of interest in the right patient is key. Herein, we describe the various levels at which the microbiome can be targeted-from prebiotics, probiotics, synbiotics, and antibiotics to microbiome reconstitution and precision microbiome engineering. Assimilating data from preclinical animal models, human studies as well as clinical trials, we describe the potential for and rationale behind studying such therapies across several liver diseases, including metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cirrhosis, HE as well as liver cancer. Lastly, we discuss lessons learned from previous attempts at developing such therapies, the regulatory framework that needs to be navigated, and the challenges that remain.},
}

Humans
*Liver Diseases/therapy/microbiology
*Gastrointestinal Microbiome/drug effects/physiology
Probiotics/therapeutic use
Animals
Prebiotics
Anti-Bacterial Agents/therapeutic use

@article {pmid41679688,
year = {2026},
author = {Tibi, MF and Argote, YM and Walker, AC and Pandey, S and Puente, C and Ellward, GL and Safwat, A and Rincon-Limas, DE and Czyż, DM},
title = {Modulation of host proteostasis by Prevotella corporis via induction of the heat shock response.},
journal = {Cell stress & chaperones},
volume = {31},
number = {2},
pages = {100150},
pmid = {41679688},
issn = {1466-1268},
support = {R01 AG077534/AG/NIA NIH HHS/United States ; },
mesh = {*Proteostasis ; Animals ; Caenorhabditis elegans/metabolism/microbiology ; *Prevotella/physiology/metabolism ; *Heat-Shock Response ; Gastrointestinal Microbiome ; Humans ; HSP70 Heat-Shock Proteins/metabolism ; },
abstract = {Neurodegenerative protein conformational diseases (PCDs) are progressive, currently incurable disorders driven by toxic protein aggregation that leads to neuronal death. Emerging evidence supports a microbial role in PCDs, including the most prevalent: Alzheimer's and Parkinson's disease. While metagenomic studies consistently associate gut dysbiosis with these disorders, the mechanisms by which microbes influence host proteostasis remain poorly understood. In particular, considerable attention has been given to proteotoxic bacteria, whereas the mechanisms by which commensal microbes confer proteoprotection have received comparatively little attention. We previously employed Caenorhabditis elegans models to characterize the role of over 220 bacterial isolates from the Human Microbiome Project on host proteostasis. Strikingly, members of the Prevotella genus exhibited proteoprotective effects. Most notably, transient exposure to Prevotella corporis uniquely induced Hsp70, a critical molecular chaperone that maintains proteostasis, and significantly reduced aggregation of polyglutamine (polyQ), Aβ42, and α-synuclein. In the present study, we expand on these findings, demonstrating that among 13 Prevotella species tested, P. corporis robustly activates the heat shock response (HSR) and confers conserved aggregate-suppressing activity in Drosophila melanogaster. We further demonstrate that transient exposure to P. corporis results in the activation of protective stress pathways and promotes disaggregation of existing intestinal polyQ aggregates in C. elegans, leading to a general enhancement of global proteostasis. This is supported by significantly improved survival and enhanced thermotolerance. Together, our findings reveal a beneficial niche for P. corporis in activating the HSR to enhance organismal proteostasis and support a microbe-mediated gut-proteostasis axis. This work underscores the therapeutic potential of targeting the gut microbiota for the management of PCDs, highlights the importance of species-level resolution in microbiome studies, and supports the emerging view of the intestine as a proteostasis-modulating organ.},
}

*Proteostasis
Animals
Caenorhabditis elegans/metabolism/microbiology
*Prevotella/physiology/metabolism
*Heat-Shock Response
Gastrointestinal Microbiome
Humans
HSP70 Heat-Shock Proteins/metabolism

@article {pmid41700856,
year = {2026},
author = {Zhang, R and Poulain, AJ and Pu, Q and Liu, J and Abdelhafiz, MA and Feng, X and Meng, B and Grégoire, DS},
title = {Methane cycling microbes are important predictors of methylmercury accumulation in rice paddies.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {3},
pages = {e0202825},
doi = {10.1128/aem.02028-25},
pmid = {41700856},
issn = {1098-5336},
support = {[2024]013//Guizhou Provincial Major Scientific and Technological Program/ ; RGPIN-2022-04891//Natural Sciences and Engineering Research Council of Canada/ ; 42394092//National Natural Science Foundation of China/ ; },
mesh = {*Methylmercury Compounds/metabolism/analysis ; *Oryza/growth & development/metabolism/microbiology ; *Methane/metabolism ; *Soil Microbiology ; Mercury/metabolism ; *Soil Pollutants/metabolism/analysis ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Rhizosphere ; Microbiota ; },
abstract = {Microbial production of methylmercury from inorganic mercury in rice paddies poses health risks to consumers of this essential dietary staple. Although mercury-methylating communities are well characterized, the microbial guilds contributing to methylmercury accumulation in rice paddies remain unclear. Here, we collected paddy soils across a mercury concentration gradient throughout the rice-growing season to identify microbial and environmental factors influencing methylmercury dynamics. We show that hgcA gene abundance, the key gene required for methylation, was not a significant predictor of methylmercury concentration in paddy soils. We also show that the merB gene abundance correlated with methylmercury in mercury-polluted rhizosphere samples. Methane cycling genes were actively expressed, and their beta-diversity was significantly associated with methylmercury levels. Methanogen abundance correlated with higher methylmercury under elevated total mercury concentrations. Analysis of the methanotroph-associated mbnT gene, implicated in demethylation, revealed an unexpected positive correlation with methylmercury. Multiple regression and machine learning models converged on mercury bioavailability and methanogen/methanotroph abundances as key predictors of methylmercury, with methanogen-associated hgcA gene abundance and methanogen-methanotroph interactions highlighted under flooded, low-redox conditions. These findings suggest that methane-cycling microbes play key roles in methylmercury cycling dynamics and point to management strategies that could simultaneously mitigate mercury pollution and greenhouse gas emissions.IMPORTANCEMethylmercury is a microbially derived neurotoxin that accumulates in the food staple rice (Oryza sativa). Mitigating the health effects of methylmercury exposure requires predicting mercury cycling dynamics in rice paddies. This task is challenging because of the complex interplay of microbial and environmental factors. Our study coupled genomic and geochemical measurements with machine learning models to identify the key biological indicators of methylmercury accumulation. We demonstrated that the abundance of methanogens and methanotrophs is a major microbial predictor of methylmercury variability. This predictive framework, which considers the interactions between these coupled microbial guilds, offers greater power than methods relying only on mercury methylation genes. These findings inform better management and remediation strategies for rice paddies, offering a path to reduce methylmercury exposure and mitigate greenhouse gas emissions.},
}

*Methylmercury Compounds/metabolism/analysis
*Oryza/growth & development/metabolism/microbiology
*Methane/metabolism
*Soil Microbiology
Mercury/metabolism
*Soil Pollutants/metabolism/analysis
*Bacteria/metabolism/genetics/classification/isolation & purification
Rhizosphere
Microbiota

@article {pmid41705822,
year = {2026},
author = {Guo, Z and Xiao, Y and Zhao, J and Tang, Z and Lin, Y and Yang, K},
title = {MetaRanker: precise profiling of antibiotic resistome risk in metagenomes by integrating abundance and genetic co-occurrence.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {3},
pages = {e0242225},
doi = {10.1128/aem.02422-25},
pmid = {41705822},
issn = {1098-5336},
support = {22176133//National Natural Science Foundation of China/ ; },
mesh = {*Metagenome ; *Anti-Bacterial Agents/pharmacology ; Microbiota ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; *Computational Biology/methods ; },
abstract = {The proliferation of antibiotic resistance genes (ARGs) in environmental microbiomes represents a major and growing threat to public health, creating a critical demand for precise and efficient tools to monitor resistance risk. Current approaches often depend on contig-based quantification or lack comprehensive risk indices, which compromises their accuracy and utility. To address this, we developed MetaRanker (https://github.com/SteamedFish6/MetaRanker), a computational pipeline that assesses resistome risk by integrating the abundance of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs)-calculated directly from sequencing reads-with their genetic co-occurrence on contigs into a unified risk index (RI). This index reflects the potential for horizontal transfer and pathogen emergence. Evaluated using in silico and diverse real-world metagenomes (n = 353), MetaRanker demonstrated superior accuracy and stronger discriminatory power than existing methods. Its optimized compact database (29.6 MB) and alignment strategy reduced runtime by over 50% in comparison to MetaCompare 2.0 under identical hardware configurations (32 CPU cores, 128 GB RAM). Practical applications confirmed that MetaRanker effectively discriminates risk levels across environments (e.g., hospital wastewater versus natural soil) and quantifies risk mitigation through wastewater treatment. As a robust, lightweight, and sequencing-platform-agnostic tool, MetaRanker offers a powerful solution for comprehensive environmental resistome surveillance and evidence-based risk management.IMPORTANCEThe environmental reservoir of antibiotic resistance is a key contributor to the global health crisis of antimicrobial resistance. Effective surveillance and risk assessment of complex microbial communities are essential for prioritizing interventions and safeguarding public health. However, existing methods often provide fragmented or computationally demanding analyses, limiting their practical application for large-scale environmental monitoring. The significance of our work lies in developing MetaRanker, which overcomes these barriers by delivering a fast, accurate, and integrated metric of resistome risk. By simultaneously accounting for the abundance, mobility potential, and pathogenicity linkage of resistance determinants, MetaRanker enables a more realistic threat assessment. This tool empowers researchers and public health officials to track resistance hotspots, evaluate the impact of human activities such as waste disposal, and monitor the effectiveness of mitigation strategies, ultimately supporting data-driven decisions to curb the environmental spread of resistance.},
}

*Metagenome
*Anti-Bacterial Agents/pharmacology
Microbiota
*Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
*Computational Biology/methods

@article {pmid41747700,
year = {2026},
author = {Zhang, H and Du, Y and Guan, E and Xu, X and Zhang, P and Gao, L},
title = {Microbial mechanisms of protein degradation and nicotine removal during aerobic composting of tobacco waste as the sole nitrogen source.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141461},
doi = {10.1016/j.jhazmat.2026.141461},
pmid = {41747700},
issn = {1873-3336},
mesh = {*Composting ; *Nicotiana/metabolism ; *Nicotine/metabolism ; *Nitrogen/metabolism ; Plant Leaves/metabolism ; Biodegradation, Environmental ; Aerobiosis ; Cattle ; Animals ; Microbiota ; Fermentation ; *Plant Proteins/metabolism ; Manure ; Peptide Hydrolases/metabolism ; Bacteria/metabolism ; },
abstract = {The massive accumulation of tobacco waste poses threats to environment safety and human health due to its high nicotine content. While aerobic composting represents an effective strategy for managing waste biomass, its application to fresh discarded tobacco leaves remains unreported. This study pioneered the use of tobacco leaves in aerobic composting and investigated the microbial mechanisms driving substrate transformation. Waste tobacco leaves are rich in protein and can be used as the sole nitrogen source of composting. The microbiota was characterized by a higher abundance of Bacillota and Pseudomonadota, but a lower abundance of Actinomycetota, compared with that during cattle manure composting as a control. The degradation of proteins in tobacco leaves was primarily mediated by proteases (e.g., families S8, S9, M42) secreted by Bacillota. Notably, a greater abundance of S8 family proteases was induced, of which two exhibiting larger substrate cavity volumes. Nicotine content decreased rapidly during initial fermentation, achieving a removal rate exceeding 97 % and meeting European Union safety standards. This degradation was primarily driven by the pyrrolidine pathway via Stutzerimonas stutzeri and Pseudomonas sp. Seed germination and pot experiments demonstrated the superior growth promoting effects of fermented tobacco leaves over cattle manure product. These findings elucidate the microbial mechanisms of tobacco waste fermentation and provide a theoretical basis for screening efficient nicotine-degrading strains and developing value-added fermentation products.},
}

*Composting
*Nicotiana/metabolism
*Nicotine/metabolism
*Nitrogen/metabolism
Plant Leaves/metabolism
Biodegradation, Environmental
Aerobiosis
Cattle
Animals
Microbiota
Fermentation
*Plant Proteins/metabolism
Manure
Peptide Hydrolases/metabolism
Bacteria/metabolism

@article {pmid41762461,
year = {2026},
author = {Shen, S and Wang, L and An, X and Liu, H and Shi, M and Tu, Y and Ji, W and He, Z and Li, A},
title = {Basin governance coincides with lower MGE loads yet rewired ARG mobility: a hazard‑oriented, platform‑centric assessment.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141608},
doi = {10.1016/j.jhazmat.2026.141608},
pmid = {41762461},
issn = {1873-3336},
mesh = {*Drug Resistance, Microbial/genetics ; *Rivers/microbiology ; China ; Environmental Monitoring ; *Genes, Bacterial ; Metagenomics ; Microbiota ; },
abstract = {Antibiotic resistance genes (ARGs) serve as critical indicators for evaluating the ecological success of river restoration policies. We investigated the restructuring of the riverine resistome in the Yangtze River following the implementation of the "Ten-Year Fishing Ban" and the Yangtze River Protection Law. Using basin-wide surveys in the Jiangsu reach (2021 vs. 2023), we integrated shotgun metagenomics and RT-qPCR functional validation with a noise-filtering sampling design to assess how the removal of anthropogenic pressures reshaped resistance dissemination. Results show that policy-driven ecological recovery significantly altered microbial assembly mechanisms. While total ARG abundance declined, microbial communities shifted toward a more dispersal-dominated regime, with neutral model fits increasing from 0.817 to 0.913. Crucially, RT-qPCR analysis confirmed that the transcriptional activity of key resistance elements remained significantly elevated relative to a pristine baseline, suggesting persistent functional risks despite lower overall abundance. As localized selective pressures relaxed, the resistome transitioned toward integrated genetic platforms, evidenced by a significant rise in the mosaic index (MGI) from 12.81% to 22.50% (p < 0.05). Structural equation modeling (R2 = 0.766) identified a dominant sequential pathway from environmental co-selectors to mobile genetic elements and subsequently to ARGs, with intensified roles for integrons and insertion sequences (intI1, IS26). These findings demonstrate that policy success requires evaluation through both abundance-based and structural indicators. We propose a platform-centric surveillance framework incorporating the mosaic index as an early-warning tool for environmental agencies.},
}

*Drug Resistance, Microbial/genetics
*Rivers/microbiology
China
Environmental Monitoring
*Genes, Bacterial
Metagenomics
Microbiota

@article {pmid41762466,
year = {2026},
author = {Ma, Q and López, MJ and Zhang, S and Jin, L and Wei, D and Yang, J and Liu, J and Ruan, Z},
title = {Carbon source-dependent activation of herbicide-mixture degradation in a synthetic microbial community enriched from black soil.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141615},
doi = {10.1016/j.jhazmat.2026.141615},
pmid = {41762466},
issn = {1873-3336},
mesh = {*Herbicides/metabolism ; *Soil Microbiology ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Carbon/metabolism ; *Microbial Consortia ; Cyclohexanones/metabolism ; Atrazine/metabolism ; Glucose/metabolism ; RNA, Ribosomal, 16S/genetics ; Sulfonylurea Compounds/metabolism ; Microbiota ; Pyridines ; },
abstract = {The extensive use of herbicides in agriculture has resulted in persistent soil contamination. Although microbial degradation of single herbicides has been extensively investigated, the responses and co-metabolism of microbial consortia to complex herbicide mixtures remain unclear. This study aimed to investigate the influence of a simple carbon source (glucose) on herbicide degradation by a natural microbial consortium (NMC) and identify key degraders for constructing an efficient synthetic microbial community (SynCom). An NMC enriched from herbicide-stressed agricultural black soil in Northeast China was inoculated into mineral salt media containing a mixture of herbicides (atrazine, nicosulfuron and mesotrione) as the sole carbon/nitrogen source, without (MSM) or with glucose supplementation (GSM). Significant herbicide degradation occurred only in the GSM system, with degradation rates of 97.27% for nicosulfuron, 68.00% for mesotrione, and 22.91% for atrazine after 8 days. Integrated 16S rRNA gene sequencing and metagenomic analysis linked the glucose amendment to a specific shift in the microbial community structure and activation of central carbon metabolism (tricarboxylic acid [TCA] and glycolytic), which enhanced cellular energy supply and environmental acidification for co-metabolic degradation of herbicides. In contrast, metabolism in the MSM system was biased toward biosynthesis. Combined random forest (RF) and co-occurrence network analyses identified the Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter as the keystone taxa. Metagenomic screening showed that these taxa were enriched for functional genes associated with herbicide degradation, including atzF (allophanate hydrolase) and gst (glutathione S-transferase). A simplified four-isolate SynCom, constructed based on these functional associations, degraded the herbicide mixtures more efficiently than either the individual isolates or the NMC in the GSM system. These findings elucidate the role of labile carbon in driving the co-metabolism of complex herbicides and provide direct candidate strains and a construction strategy, facilitating practical bioremediation applications.},
}

*Herbicides/metabolism
*Soil Microbiology
Biodegradation, Environmental
*Soil Pollutants/metabolism
*Carbon/metabolism
*Microbial Consortia
Cyclohexanones/metabolism
Atrazine/metabolism
Glucose/metabolism
RNA, Ribosomal, 16S/genetics
Sulfonylurea Compounds/metabolism
Microbiota
Pyridines

@article {pmid41775186,
year = {2026},
author = {Geromino, P and LeMoine, CM and Drahun, I and Cassone, BJ},
title = {Co-supplementation of a polyethylene diet for improved fitness of Galleria mellonella larvae.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141617},
doi = {10.1016/j.jhazmat.2026.141617},
pmid = {41775186},
issn = {1873-3336},
mesh = {Animals ; Larva/growth & development/drug effects ; *Moths/growth & development/physiology ; *Polyethylene/metabolism ; Diet ; Gastrointestinal Microbiome ; },
abstract = {A growing number of plastivore insects have been discovered that readily consume and biodegrade various petro plastics, including LDPE. The caterpillar larvae of Galleria mellonella are capable of breaking down the polymers at expedited rates; however, feeding on LDPE as a sole nutrient source is inefficient and detrimentally impacts larval survival, growth, and development. The objective of our study was to improve fitness parameters and feeding activities of LDPE-fed larvae through the addition of various macro- and micronutrients. Each co-supplementation recovered fitness and consumption to some extent in comparison to pure LDPE; however, artificial sources produced outcomes that were well below those of the caterpillar's natural diet, regardless of the combination. Co-supplementation of LDPE, honeycomb, and corn syrup was the most successful, with larval fitness and consumption approximating their natural diet. To provide mechanistic insights into this recovery, qPCR and metagenomics analyses indicated the co-supplementation promoted greater gut bacterial abundance and species richness and evenness. In addition, GC-MS analyses identified notable differences in their fat body metabolic profiles that may contribute to slower developmental rates. We also assessed the capability of the larvae to eliminate food wastes, which showed promise and could represent a potential co-supplement source for LDPE biodegradation.},
}

Animals
Larva/growth & development/drug effects
*Moths/growth & development/physiology
*Polyethylene/metabolism
Diet
Gastrointestinal Microbiome

@article {pmid41792922,
year = {2026},
author = {Mertz, CM and Mancuso, CJ and Robinson, DM and Yeboah, LD and Fogel, ML and Takacs-Vesbach, C and Newsome, SD},
title = {Microbially derived essential amino acids compensate for dietary deficiencies in an ecologically relevant mammalian host.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag044},
pmid = {41792922},
issn = {1751-7370},
support = {1755402//NSF Division of Integrative Organismal Systems/ ; 1755353//NSF Division of Integrative Organismal Systems/ ; 2439853//NSF Graduate Research Fellowship Program/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Amino Acids, Essential/metabolism/biosynthesis ; *Peromyscus/microbiology/metabolism ; Diet ; Muscle, Skeletal/metabolism ; Dietary Proteins/metabolism ; Mice ; Carbon Isotopes/analysis ; *Bacteria/metabolism/classification/genetics ; },
abstract = {Protein is the main structural and functional component of cells, making it crucial for the survival of all living organisms. Yet mammalian herbivores and omnivores often consume diets deficient in the amount of protein required for growth, homeostasis, and reproduction. To compensate, mammals likely rely on their gut microbiota to synthesize essential amino acids (AAESS), particularly during periods of dietary protein limitation. We quantified the contribution of microbially synthesized AAESS to skeletal muscle in captive, wild-derived deer mice (Peromyscus maniculatus) fed diets varying in macromolecular quantity and quality. Using amino acid carbon isotope (δ13C) analysis combined with genetic sequencing, we assessed the origin of AAESS incorporated into host muscle and identified gut microbial taxa with the genetic potential for AAESS biosynthesis. We estimate that up to 25% of host muscle AAESS were microbially derived, with greater microbial contributions in mice fed diets containing low protein or more complex macronutrients. Gut microbial populations with the genetic potential for AAESS biosynthesis were more abundant in mice with larger contributions of microbially-derived AAESS in their tissues. These results demonstrate the crucial and likely pervasive role the gut microbiome plays in host protein metabolism, especially in mammals facing seasonal or persistent dietary protein limitation.},
}

Animals
*Gastrointestinal Microbiome
*Amino Acids, Essential/metabolism/biosynthesis
*Peromyscus/microbiology/metabolism
Diet
Muscle, Skeletal/metabolism
Dietary Proteins/metabolism
Mice
Carbon Isotopes/analysis
*Bacteria/metabolism/classification/genetics

@article {pmid41842581,
year = {2026},
author = {Wang, X and Chen, J and Xia, J and Ma, T and Yang, W and Shan, T and He, W and Zhang, G and Xia, Z and Wang, W and Liu, Z and Zheng, Y and Nong, K and Niu, P and Chen, T},
title = {Brain-Targeted RVG-Liposomal Melatonin Ameliorates Manganese Neurotoxicity by Enhancing Neurogenesis and Modulating Systemic Amino Acid Profiles.},
journal = {Journal of pineal research},
volume = {78},
number = {2},
pages = {e70137},
doi = {10.1111/jpi.70137},
pmid = {41842581},
issn = {1600-079X},
support = {82173489//National Natural Science Foundation of China/ ; 7232234//Beijing Natural Science Foundation/ ; },
mesh = {Animals ; *Melatonin/pharmacology/administration & dosage ; Mice ; *Manganese/toxicity ; Liposomes ; *Brain/metabolism/drug effects ; *Neurogenesis/drug effects ; *Glycoproteins/pharmacology ; *Amino Acids/metabolism ; Male ; Mice, Inbred C57BL ; *Neurotoxicity Syndromes/drug therapy/metabolism ; *Neuroprotective Agents/pharmacology ; Gastrointestinal Microbiome/drug effects ; Peptide Fragments ; Viral Proteins ; },
abstract = {Chronic manganese (Mn) exposure induces severe neurotoxicity, characterized by impaired neurogenesis and disrupted metabolic homeostasis. Although melatonin (MT) possesses established neuroprotective properties, its clinical utility is hindered by poor bioavailability and limited brain delivery. Here, we developed a brain-targeted, rabies virus glycoprotein (RVG)-modified liposomal delivery system encapsulating melatonin (MT@RVG-Lip) to enhance therapeutic efficacy. Multi-omics analyses including brain and intestinal transcriptomics, serum metabolomics, and gut metagenomics were conducted to elucidate the underlying mechanisms. MT@RVG-Lip significantly improved motor deficits and enhanced neurogenesis while reducing neuroinflammation in Mn-exposed mice. Compared with regular MT and CaNa2-EDTA, MT@RVG-Lip more effectively alleviated Mn-disrupted gene expression in neurogenesis regions, particularly genes involved in amino acid metabolism. Additionally, MT@RVG-Lip demonstrated a regulatory effect on serum amino acid profiles and intestinal transporter gene expression. Gut microbiota analysis further revealed that MT@RVG-Lip partially reversed Mn-associated dysbiosis and promoted the improvement of key amino acid-related microbiota-mediated metabolic pathways. The RVG-modified liposomal formulation conferred sustained release and improved brain-targeting capability, prolonging MT bioavailability and enhancing therapeutic outcomes. These findings provide a new mechanistic framework for MT-based interventions in neurodegenerative diseases and highlight the therapeutic potential of multifunctional delivery strategies.},
}

Animals
*Melatonin/pharmacology/administration & dosage
Mice
*Manganese/toxicity
Liposomes
*Brain/metabolism/drug effects
*Neurogenesis/drug effects
*Glycoproteins/pharmacology
*Amino Acids/metabolism
Male
Mice, Inbred C57BL
*Neurotoxicity Syndromes/drug therapy/metabolism
*Neuroprotective Agents/pharmacology
Gastrointestinal Microbiome/drug effects
Peptide Fragments
Viral Proteins

@article {pmid41842880,
year = {2026},
author = {González-Mercado, VJ and Jean Lim, S and Kumar Singh, P and Sales-Martinez, S and Fernandez-Cajavilca, M and Marrero, LM and Pedro, E and D'Eramo Melkus, G},
title = {Dietary Quality and Microbiome Profiles among Rectal Cancer Patients: A Cross-Sectional Pilot Study.},
journal = {Puerto Rico health sciences journal},
volume = {45},
number = {1},
pages = {3-10},
pmid = {41842880},
issn = {2373-6011},
mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology ; Male ; Female ; Middle Aged ; Pilot Projects ; *Gastrointestinal Microbiome ; *Diet ; Cross-Sectional Studies ; Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Metagenomics ; Neoadjuvant Therapy ; },
abstract = {OBJECTIVE: Examining whether gut microbial taxa abundances and predicted functional pathways correlate with dietary quality scores at the end of neoadjuvant chemoradiotherapy (nCRT) for rectal cancer (RC); identifying differentially abundant bacterial species from the pantothenate and acetyl-coenzyme A biosynthesis pathways that differ among dietary quality groups in a subset of participants.

METHODS: RC patients (n = 30) provided stool samples for 16S rRNA gene sequencing. To validate pathway predictions from the 16S rRNA gene data, stool samples from a subset of 17 participants underwent shallow shotgun metagenomics sequencing (SMS). Dietary quality was calculated using the Prime Diet Quality Score (PDQS; 24-hour recall). 16S rRNA gene data were analyzed using QIIME2, and SMS data were analyzed using HUMAnN2.

RESULTS: At the genus level, Parvimonas, Caproiciproducens, and uncultured Eggerthellaceae abundances positively correlated (Spearman's rho = 0.36 to 0.50) with PDQS scores, whereas abundances of Prevotella, Rothia, Peptostreptococcus, Paeniclostridium, Enterococcus, and Howardella correlated negatively (Spearman's rho = -0.43 to 0.36). Predicted pathways, including those related to B-vitamin biosynthesis and enzyme cofactor biosynthesis (e.g., B5/pantothenate [phosphopantothenate biosynthesis I]), were correlated with higher PDQS scores. Mean abundances of species predicted to encode the vitamin B5-CoA pathway were greater in the high- diet-quality group.

CONCLUSION: Findings suggest important associations between the taxa abundances of gut bacteria and the abundances of predicted B-vitamin biosynthesis pathways and dietary quality at the end of nCRT. Three bacterial species encoding vitamin B5-CoA biosynthesis pathways were prominent in high-dietaryquality participants.},
}

Humans
*Rectal Neoplasms/therapy/microbiology
Male
Female
Middle Aged
Pilot Projects
*Gastrointestinal Microbiome
*Diet
Cross-Sectional Studies
Aged
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Metagenomics
Neoadjuvant Therapy

@article {pmid41843710,
year = {2026},
author = {Qian, C and Jeunen, GJ and Han, W and Chan, TY and Jiang, Y and Fu, W and Seymour, M},
title = {Developing and Evaluating Aquatic Passive Sampling of Environmental DNA for Microbial Community Profiling.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70121},
pmid = {41843710},
issn = {1755-0998},
support = {MCEF21003//Marine Conservation Enhancement Fund/ ; },
mesh = {*DNA, Environmental/isolation & purification/genetics ; Biodiversity ; *Specimen Handling/methods ; Bacteria/genetics/classification ; *Microbiota ; *Metagenomics/methods ; Phylogeny ; },
abstract = {Environmental DNA (eDNA) metabarcoding has transformed biodiversity monitoring across taxa from bacteria to mammals, yet sample collection remains a major bottleneck. Passive sampling via adsorption and entrapment has emerged as a promising alternative to overcome the limitations of conventional active filtration. However, the performance of passive sampling for microbial biodiversity monitoring remains unknown. Here, we developed passive sampling-based microbial community profiling by testing five submersion times and three common eDNA extraction methods in mesocosms, and comprehensively evaluated it by comparing results with active filtration in estuarine and coastal environments. We found that passive sampling for 24 h with enzymatic extraction yielded significantly more eDNA and higher biodiversity than shorter durations and mechanical extractions. Passive sampling consistently outperformed active filtration at every field site, with average increases of >100% in eDNA yields and >50% in taxonomic and phylogenetic diversities. Additionally, active filtration and passive sampling yielded significantly different prokaryotic and microeukaryotic community compositions, driven primarily by turnover rather than nestedness (on average 4-fold larger), implying that passive sampling is better suited for spatiotemporal detection than active filtration. Passive sampling showed greater sensitivity in identifying key environmental factors (3 vs. 2) and potential environmental bioindicators (40 vs. 20) compared with active filtration. Overall, this study establishes an efficient and practical passive sampling method for microbial biodiversity monitoring and environmental assessment in aquatic environments.},
}

*DNA, Environmental/isolation & purification/genetics
Biodiversity
*Specimen Handling/methods
Bacteria/genetics/classification
*Microbiota
*Metagenomics/methods
Phylogeny

@article {pmid41524860,
year = {2026},
author = {Parab, C and Yadav, KD and Prajapati, V},
title = {Metagenomic Insights into Microbial Community Succession and its Functional Changes during Natural Fermentation of Food Waste.},
journal = {Applied biochemistry and biotechnology},
volume = {198},
number = {3},
pages = {2053-2081},
pmid = {41524860},
issn = {1559-0291},
mesh = {*Fermentation ; *Metagenomics ; *Microbiota ; *Bacteria/genetics/metabolism ; *Food ; Food Loss and Waste ; },
abstract = {Food waste is a global concern, necessitating sustainable management strategies. While fermentation offers a promising approach to valorizing food waste, studies about microbial dynamics and functionality assessment of semi-controlled naturally fermented food waste are still seldom. This study employed whole-genome metagenomic sequencing to investigate the microbial succession and functional pathways during natural fermentation of food waste over 15 days. Physicochemical analysis revealed that pH decreased from 5.20 to 4.32 on day 3 and then neutralized. Protein, lipids, and carbohydrate were in the range of 4.03-4.90%, 9.99-17.78%, and 85.44-77.84%, respectively. Taxonomic profiling revealed clear community restructuring from an initially diverse consortium dominated by Enterobacter, Klebsiella, Pseudomonas, and Acinetobacter (collectively > 45% relative abundance at day 0) to a highly specialized lactic acid bacteria (LAB) community (> 80% by day 15). Lactobacillus helveticus and Limosilactobacillus panis emerged as the late-stage co-dominant species, together accounting for 60-75% of the total reads. Functional annotation based on the PFAM, eggNOG, GO, and EC databases revealed a progressive reduction in gene family richness and metabolic breadth, with early samples being enriched in carbohydrate-active enzymes, membrane transporters, and amino acid metabolism pathways. By contrast, late-stage communities were dominated by LAB-associated fermentative functions, including lactate and acetate production, stress-response modules, and transport systems supporting acid tolerance, driven mainly by Lactobacillus, Weissella, Streptococcus, Gluconobacter, Aeromonas, Saccharomyces, Klebsiella, and Cronobacter. These findings provide insights into the microbial dynamics and functional adaptations during natural fermentation of food waste, contributing to the development of optimized waste valorization strategies.},
}

*Fermentation
*Metagenomics
*Microbiota
*Bacteria/genetics/metabolism
*Food
Food Loss and Waste

@article {pmid41762508,
year = {2026},
author = {Zhang, L and Jiang, L and Zhang, Z and Wang, Y and Yao, C and Yu, K and Tao, H and Sun, W and He, X and Gu, J and Qian, X},
title = {Unraveling metal-organic frameworks impact on resistome and virome dynamics in swine manure anaerobic digestion via metagenomic.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129121},
doi = {10.1016/j.jenvman.2026.129121},
pmid = {41762508},
issn = {1095-8630},
mesh = {*Manure/microbiology ; Animals ; Swine ; Anaerobiosis ; *Metal-Organic Frameworks ; Drug Resistance, Microbial ; *Virome ; },
abstract = {Livestock manure is a major hotspot of antibiotic resistance genes (ARGs). However, the efficacy and mechanisms of anaerobic digestion (AD) in reducing ARGs, along with the ecological roles and risks of viral communities, remain poorly understood. This study demonstrates that AD significantly reduces total ARG abundance and diversity, with addition of metal-organic frameworks (MOFs) further enhancing the reduction of high-risk and clinically critical ARGs. ARG abundance decline was primarily driven by core ARGs, whereas diversity reduction was mainly attributed to the depletion of rare ARGs. ARGs exhibit a broad host distribution, alongside pervasive pathogenic host species. Viral communities display high diversity and novelty, with the Drexlerviridae family as the dominant virome. Viruses exhibit strong host specificity, with Actinobacteria (47.4%) and Atribacterota (12.7%) as primary hosts. Only eight viral contigs carried ANT(6)-Ia and lsa(B), indicating limited viral contribution to ARG horizontal transfer. Viruses enhance host metabolic capabilities by introducing diverse and unique auxiliary metabolic genes (AMGs). The AD process predominantly influences viral diversity, lifestyle, and AMG carriage. Mechanistically, AD reduces ARGs via decreasing co-occurrence frequencies of ARGs and plasmids, coupled with reduced abundances of ARG-hosting. These findings provide new insights for optimizing AD processes to control the diffusion of ARGs.},
}

*Manure/microbiology
Animals
Swine
Anaerobiosis
*Metal-Organic Frameworks
Drug Resistance, Microbial
*Virome

@article {pmid41835092,
year = {2026},
author = {Pérez, T and Vacelet, J and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the carnivorous sponge, Lycopodina hypogea (Vacelet & Boury-Esnault, 1996) (Poecilosclerida: Cladorhizidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {130},
pmid = {41835092},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Lycopodina hypogea (carnivorous sponge; Porifera; Demospongiae; Poecilosclerida; Cladorhizidae). The genome sequence has a total length of 235.10 megabases. Most of the assembly (98.85%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 31.1 kilobases. Gene annotation of this assembly by Ensembl identified 16 317 protein-coding genes. From the metagenome data we recovered 39 bins, of which 27 were high-quality MAGs, including four fully circularised genomes. The MAGs included archaea and bacteria involved in nitrification and sulfate-reduction as well as known sponge symbionts affiliated with Gammaproteobacteria (Candidatus Spongiihabitans, Porisulfidus) and Acidimicrobiales (Candidatus Poriferisodalaceae), among others.},
}

@article {pmid41836173,
year = {2026},
author = {Fuques, E and Massey, AL and Qureshi, F and Campos-Silva, JV and Ferreira da Silva, DJ and Peres, CA and Levi, T and Vega Thurber, RL},
title = {Large-scale metagenomic surveillance study expands the known diversity of RNA viruses in mosquito populations from the Amazon Basin.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20880},
pmid = {41836173},
issn = {2167-8359},
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification ; *Metagenomics ; *Culicidae/virology ; Brazil ; Phylogeny ; Female ; *Mosquito Vectors/virology ; Virome ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; },
abstract = {The Amazon Basin is one of the most biologically diverse regions on Earth, yet its viral diversity remains poorly characterized. Mosquitoes are important vectors and reservoirs of RNA viruses, but little is known about the composition and structure of their viromes in remote areas of the Amazon. In this study, we performed a large-scale metagenomics survey of RNA viruses associated with mosquito populations collected from the Jurua River region in the Western Amazon Basin of Brazil. We analyzed 211 pooled samples of adult female mosquitoes collected across thirty-seven sites, representing one of the most comprehensive mosquito virome studies conducted in this region to date. Utilizing high-throughput sequencing and de novo assembly, we identified over 500 viral sequences from 18 families, including 21 complete or nearly complete genomes. Our analysis revealed 18 putative novel viral species spanning diverse families and strains of nine previously described viruses. Phylogenetic analyses also revealed undocumented diversity within several virus families, including Iflaviridae, Mesoniviridae, Phasmaviridae, Phenuiviridae, Togaviridae, and Totiviridae, encompassing both novel species and previously known viruses detected for the first time in this region. Our findings highlight the immense, yet largely unexplored, diversity of RNA viruses circulating in mosquito populations in this ecologically rich but understudied region and provide critical insights into the evolutionary dynamics of mosquito-associated viruses. By leveraging high-throughput sequencing to uncover novel viral strains, this research demonstrates the value of metagenomic approaches in expanding the known diversity, distribution, and evolutionary relationships of RNA viruses, contributing to a broader understanding of virus-mosquito interactions and genome evolution.},
}

Animals
*RNA Viruses/genetics/classification/isolation & purification
*Metagenomics
*Culicidae/virology
Brazil
Phylogeny
Female
*Mosquito Vectors/virology
Virome
Genome, Viral
High-Throughput Nucleotide Sequencing

@article {pmid41837347,
year = {2026},
author = {Arnold, MJ and Bergner, LM and Malik, H and Ten Doeschate, M and Davison, NJ and Brownlow, A and Mollentze, N and Babayan, SA and Streicker, DG},
title = {Drivers of Viral Diversity and Sharing in Marine Mammals.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70294},
pmid = {41837347},
issn = {1365-294X},
support = {217221/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 218518/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BB/V003798/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DEB 2011069/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; PLP-2020-362//Leverhulme Trust/ ; NE/X01424X/1//Natural Environment Research Council/ ; INV-003079/GATES/Gates Foundation/United States ; INV-030025/GATES/Gates Foundation/United States ; MC_UU_00034/3/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Viruses/genetics/classification ; Scotland ; *Aquatic Organisms/virology ; *Cetacea/virology ; *Mammals/virology ; },
abstract = {Knowledge of viral infection in marine mammals, a group severely threatened by human activity, is largely limited to the pathology and epidemiology of few endemic viruses. The recent emergence in marine mammals of high-consequence viruses, such as H5N1 avian influenza and rabies, underscores the importance of understanding the ecology of viral transmission in these species. Metatranscriptomic approaches now enable relatively unbiased characterisation of full viral communities that can reveal ecological and evolutionary drivers of infection. We sequenced RNA from 15 marine mammal species (42 pools, 237 tissues, 128 animals) sampled in Scotland through the Scottish Marine Animal Strandings Scheme. Viral sequences were detected in 41 of 42 pools, representing more than 120 distinct viral taxonomic units (vOTUs). Virus host network analysis showed that viral communities were partly structured by host taxonomy, with clear differences between seals and cetaceans. However, vOTUs were frequently shared between species, mirroring reported ecological interactions, including cross-order sharing between seals and cetaceans. Generalised linear models showed no effect of host taxonomy on viral richness. Instead, age was the strongest predictor: juvenile pools contained roughly twice as many viral taxa as adults and more than neonates, indicating that changing population demography may impact viral transmission in marine mammals. These results provide a basis for understanding how anthropogenic stressors may exacerbate viral transmission in marine mammals and demonstrate the increasing practicality of using genomics to understand ecological and evolutionary drivers of virus infection in natural populations.},
}

Animals
*Viruses/genetics/classification
Scotland
*Aquatic Organisms/virology
*Cetacea/virology
*Mammals/virology

@article {pmid41841491,
year = {2026},
author = {Vidal, E and Phanthanourak, AL and Gharib, A and Webel, H and Assis, J and Ayala-Ruano, S and Cunha, AF and Santos, A},
title = {ABaCo: addressing heterogeneity challenges in metagenomic data integration with adversarial generative models.},
journal = {Nucleic acids research},
volume = {54},
number = {5},
pages = {},
doi = {10.1093/nar/gkag227},
pmid = {41841491},
issn = {1362-4962},
support = {NNF20CC0035580//Novo Nordisk Foundation/ ; Pasteur Network, Sep/2023//Calmette & Yersin PhD Grant/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Metagenome ; Algorithms ; },
abstract = {The rapid advancement of high-throughput metagenomics has produced extensive and heterogeneous datasets with significant implications for environmental and human health. Integrating these datasets is crucial for understanding the functional roles of microbiomes and the interactions within microbial communities. However, this integration remains challenging due to technical heterogeneity and the inherent complexity of these biological systems. To address these challenges, we introduce ABaCo, a generative model that combines a variational autoencoder with an adversarial discriminator specifically designed to handle the unique characteristics of metagenomic data. Our results demonstrate that ABaCo effectively integrates metagenomic data from multiple studies, corrects technical heterogeneity, outperforms existing methods, and preserves taxonomic-level biological signals. We have developed ABaCo as an open-source, fully documented Python library to facilitate, support and enhance metagenomics research in the scientific community.},
}

*Metagenomics/methods
Humans
*Software
Microbiota/genetics
Metagenome
Algorithms

@article {pmid41841524,
year = {2026},
author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, JM and Yin, Y},
title = {Limousia bacteria encode mucinolysome for mucin utilization in animal gut microbiomes.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2645267},
doi = {10.1080/19490976.2026.2645267},
pmid = {41841524},
issn = {1949-0984},
mesh = {*Mucins/metabolism ; Animals ; *Gastrointestinal Microbiome ; Humans ; Feces/microbiology ; Metagenome ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; },
abstract = {Mucins create a physical barrier that protects human and animal tissues from microbial pathogens. Here, we provide evidence that mucin degradation can be mediated by unique mucinolysomes, defined as extracellular cellulosome-like multi-enzyme complexes specializing in mucin degradation. We predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of three anaerobic species of Limousia, including seven MAGs from human gut microbiome samples from six countries. We validated that mucins can support the growth of the Limousia strain ET540 as its sole carbon source, triggering the upregulation of most mucinolysome-related genes in ET540. We modeled the mucinolysome assembly by predicting cohesin‒dockerin interactions among most of the mucinolysome proteins using AlphaFold3. We performed metagenomic read mapping of 2897 fecal samples from various human cohorts and wild/domesticated animals against Limousia MAGs. We found that Limousia has a greater abundance and prevalence in farm animals than in humans. This study characterizes and adds the Limousia bacteria as unique member to the list of human and animal gut mucin glycan-degrading bacteria. Overall, we discovered that this novel gut bacteria genus (Limousia) uses a previously unrecognized molecular mechanism for highly organized mucin glycan degradation, shedding new light on microbe‒host interactions in the gastrointestinal tracts of diverse animal hosts, including humans.},
}

*Mucins/metabolism
Animals
*Gastrointestinal Microbiome
Humans
Feces/microbiology
Metagenome
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenomics

@article {pmid41841712,
year = {2026},
author = {Oganesyan, EG and Zhuk, AS and Venchakova, VV and Dolgo-Saburova, YV and Zhorzh, ON and Zhang, FM and Vasilyeva, NV and Taraskina, AE},
title = {Microbiome associated with recurrent vulvovaginal candidiasis: key characteristics and potential therapeutic targets.},
journal = {Biomeditsinskaia khimiia},
volume = {72},
number = {1},
pages = {62-74},
doi = {10.18097/PBMCR1644},
pmid = {41841712},
issn = {2310-6972},
mesh = {Humans ; Female ; *Candidiasis, Vulvovaginal/microbiology/drug therapy ; *Microbiota ; Adult ; Case-Control Studies ; *Vagina/microbiology ; Recurrence ; Lactobacillus/genetics/isolation & purification ; Prevotella ; },
abstract = {Recurrent vulvovaginal candidiasis (RVVC) is one of the most complex forms of urogenital infection in terms of its clinical burden, impact on quality of life, and difficulty in preventing relapses. The aim of this study was to comprehensively characterize the taxonomic composition and functional potential of the vaginal microbiome associated with RVVC. This case-control study included patients with RVVC and conditionally healthy women. Vaginal samples were analyzed using shotgun metagenomic sequencing, followed by taxonomic and functional annotation of the microbiome using data quality control, taxonomic classification (Kraken2, MetaPhlAn4), and functional annotation (HUMAnN 3.9). At the community structure level, the RVVC microbiome exhibited pronounced interindividual variability and did not represent a uniform microbiota configuration. The taxonomic profile of the microbiome in RVVC was characterized by an increased relative abundance of Lactobacillus iners and anaerobic taxa (Prevotella bivia, Dialister microaerophilus), forming a compact "core" of intergroup differences. Functional analysis revealed a limited but reproducible set of metabolic pathways associated with RVVC; these included pathways of purine metabolism, central carbohydrate metabolism, and biosynthesis of cofactors and cell wall components. RVVC is associated not only with changes in the taxonomic composition of the microbiota but also with a stable reconfiguration of its functional potential. The identified shifts in metabolic pathway patterns reflect a transition of the vaginal microbial community to an alternative functional state, thus highlighting the need to develop new therapeutic strategies alternative to traditional antifungal-based approaches.},
}

Humans
Female
*Candidiasis, Vulvovaginal/microbiology/drug therapy
*Microbiota
Adult
Case-Control Studies
*Vagina/microbiology
Recurrence
Lactobacillus/genetics/isolation & purification
Prevotella