Category Archives: Metagenomics & Bioinformatics

January 16, 2026

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Human Microbiome

The testobolome in microbial testosterone metabolism and human health – Liisa Veerus –  
npj biofilms and microbiomes 

Multi-omic definition of metabolic obesity through adipose tissue–microbiome interactions – Rima M. Chakaroun – Nature Medicine

Gut microbiome

The microbiome at the centre of NAD+ supplementation – Youngjae Jo – Nature Metabolism

Meta-analysis of H. pylori and the gut microbiome interactions and clinical outcomes – Xiongjian Wu – Frontiers in Cellular and Infection Microbiology

Environmental Microbiome

High microbial diversity in glacial habitats uncoupled from the specialized microbiomes of resident chironomid fauna – Valeria Lencioni – PLOS One

Bacterial communities show distinctive spatial diversity patterns in productive truffle orchards amended with peat-based substrate – Pedro Marco –  Environmental Microbiome

Plant Microbiome

Root Triterpenoid Metabolites Drive the Assembly and Feedback Regulation of the Rhizosphere Microbiome During Flowering to Senescence in Rhododendron hybridum – Fei Shan – Frontiers in Microbiology

Drought-Tolerant Rhizobacterial Consortia Enhance Grapevine Growth and Tolerance to Water Deficit – Ginevra Canavera – Frontiers in Plant Science

Bioinformatics

Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study – Tanya T. Karagiannis – PLOS Computational Biology

Novel artificial selection method improves function of simulated microbial communities – Bjorn Vessman – PLOS Computational Biology

January 14, 2026

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See you at MVIF next week!

Start 2026 with us! Join us in discussing microbiome science: register here → cassyni.com/s/mvif-45

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2026-01-08T08:16:08.069Z


Gut microbiome

Early-life colonization by aromatic-lactate-producing bifidobacteria lowers the risk of allergic sensitization – Pernille Neve Myers – Nature Microbiology 

Improving operative outcomes in patients with stomas – Stella M. Dilke – medRxiv

🎉🎉🎉 New preprint to start the new year 🎉🎉🎉Patients recovering from bowel surgery may have stomas formed to divert the flow of faeces to the opening on the skin, away from healing intestinal tissue. The visible sign of this process is an ileostomy or colostomy bag. /1#surgerysky #medsky

— Professor Lesley Hoyles (@bugsinyourguts.bsky.social) 2026-01-07T11:02:35.631Z

Gut microbiota induces mammary gland sIgA production to alleviate S. aureus mastitis – Zhaoqi He – Cell Reports

Microbial signature of pediatric Crohn’s disease: Differentiation from functional gastrointestinal disorders and relationship with increased disease activity – Jeremiah Levine – Physiological Reports

Gut micro-organisms associated with health, nutrition and dietary interventions – Francesco Asnicar – Nature

I'm very happy to share our latest manuscript published today in @nature.com !! ➡️ doi.org/10.1038/s415…We analyzed data from over 34,000 participants in the US and UK, revealing strong associations between specific gut bacteria and markers of cardiometabolic health and dietary habits.

— Francesco Asnicar (@fasnicar.bsky.social) 2025-12-10T17:26:39.522Z

Oral microbiome

Are you involved in oral microbiome research? 🧬We’re conducting a brief survey to understand how researchers report metadata for their oral microbiome studies. You must be 18 or older. To be eligible, you must have conducted research on the oral microbiome (past or currently).

— Sterling L. Wright (@anthbyte.bsky.social) 2026-01-07T04:03:01.699Z

Animal microbiome

Impact of sequencing approach on ecological inference from highly variable bat gut microbiomes – Ostaizka Aizpurua – bioRxiv

Animal experiments

Primate gut microbiota induce evolutionarily salient changes in mouse neurodevelopment – Alex R. DeCasien – PNAS

The maternal microbiome influence on pregnancy success: breeding comparison of germ-free and conventionalized mice – Chudan Xu – Gut Microbes

Our first paper of 2026 is outWhen we began this project, this was not the paper we set out to publishBut science has a way of redirecting us toward the questions we should be asking#Microbiome researchers-this one’s for youwww.tandfonline.com/doi/full/10….🧵

— Prof Francine Marques (@fzmarques.bsky.social) 2026-01-13T00:45:36.844Z

Plant, soil, root microbiome

Bark microbiota modulate climate-active gas fluxes in Australian forests – Pok Man Leung – Science 

In this week’s @science.org cover article, we discover tree bark is a hidden habitat for abundant, diverse, and specialized microbial life that actively regulate our climate 🦠. Bark isn't just an inert armor of tree but an active interface for climate and biodiversitywww.science.org/eprint/7H9PX…

— Bob Leung (@bobpmleung.bsky.social) 2026-01-08T20:37:13.725Z

Translational microbiomes in agriculture: microbial communities as tools to effect host and system health for improved crop production – Alex D. Vompe – Applied and Environmental Microbiology 

Extreme environments

Microbial Community Metagenomics in the Eastern Tropical North Pacific Oxygen Minimum Zone Reveals Functional Differences Along Biogeochemical Gradients – F. Gutierrez – Environmental Microbiology 

Bioinformatics

LAMPP: A benchmark for continuous evaluation of host phenotype prediction from shotgun metagenomic data – Netta Barak – bioRxiv

January 13th , 2026

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Environmental & Wastewater Microbiomes

Viral and eukaryotic drivers of prokaryotic and antibiotic resistance gene diversity in wastewater microbiomes – Antonia Weiss – Springer nature

Correction: Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants – Huifeng Hu – Springer nature

Ruminant & Livestock Gut Microbiomes

The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows – Jianhao Yang – Springer nature

Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation – Moli Li – Springer nature

Rumen microbiota inoculation indicates collaborative mechanisms enhancing propionate supply to alleviate weaning stress in lambs – Tianrong Chen – Springer nature

Host-Associated Gut Microbiomes (Non-Human Models)

Ningxiang pig-derived Enterococcus hirae protects against E. coli-induced gut dysbiosis and inflammation via acetate/propionate-MyD88-NF-κB axis in piglets – Longlin Zhang – Springer nature

Insect & Evolutionary Microbiomes

Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera Pentatomidae) –Jingjing Sun – Springer nature

December 05, 2025

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See you at MVIF next week!

Join us in December for #MVIF 44!We will discuss diverse #microbiome topics:human urinary, gut, oral and nasal microbiomes, extreme environments, anda new sequence alignment tool.

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-11-24T10:34:26.363Z

General microbiome

Consensus Statement: STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies – Julia M. Kelliher – Nature Microbiology

Urinary microbiome

Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection – Michael L. Neugent – NPJ Biofilms and Microbiomes

Thrilled to share that our recent work is out in npj Biofilms and Microbiomes. 🧵 (1/4)www.nature.com/articles/s41…

— Mike Neugent PhD (@mikeneugent.bsky.social) 2025-11-24T17:49:26.272Z

Vaginal microbiome

Microbial and seminal traces of sexual intercourse and forensic implications – Sarah Ahannach – Microbiome

Ambient temperature affects the composition of the vaginal microbiome, and temperature-sensitive vaginal microbes influence assisted reproductive technology outcomes – Zheng Liu –  – Microbiome

Gut microbiome

HGMT: a database of human gut microbiota for tumors and immunotherapy response – Jinxin Liu – Genome Biology

Review: Circadian rhythms as a modulator of gut microbiota-tumor microenvironment crosstalk – Qinglong Xu – Cellular and Molecular Life Sciences

Dynamics of gut metabolome and microbiota maturation during early life – Anna-Katariina Aatsinki – iScience

Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk – Pamela Ferretti – Nature Communications

Animal microbiome

Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function – Omar E. Tovar-Herrera – Nature Ecology & Evolution

Longitudinal changes in gut microbiota across reproductive states in wild baboons – Chelsea A. Southworth – bioRxiv

Probiotic effect of B. subtilis PS-216 in broiler chickens: modulation of weight, feed conversion, short chain fatty acids, microbiota and meat quality – Katarina Šimunović – Animal Microbiome

Animal experiments

The microbial metabolite imidazole propionate modulates hypothalamic activity and stress-induced behaviors – Gulistan Agirman – Cell Host & Microbe

Excited to share new work by Guli Agirman + co that identifies a direct mechanism linking gut microbial imidazole propionate to stress! 🧠🦠 Btw this image was made by Nano Banana Pro 🍌. First time I've gotten a model to accurately generate a science graphic 🤯 authors.elsevier.com/a/1mA5M6t8JE…

— Elaine Hsiao (@pipethero.bsky.social) 2025-11-25T17:45:03.571Z

Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function – Yi Wang – PNAS

Selection and transmission of the gut microbiome alone can shift mammalian behavior – Taichi A. Suzuki – Nature Communications

Postbiotics

Review: Postbiotics as microbial-derived therapeutics for wound healing disorders: from molecular mechanisms to future application – Miroslav Dinić – Home  Cell Communication and Signaling

Phages and viruses

Unveiling the global urban virome through wastewater metagenomics – Nathalie Worp – Nature Communications 

Soil, root and plant microbiome

Rare taxa modulate the emergence of dominants in microbial communities – Jianing Wang – mBio

Integrated effects of anaerobic soil disinfestation and beneficial microbes in strawberry production – Baker D. Aljawasim – PlosOne

Food microbiome

Exploring diversity and functional contribution of the microbiome of traditional Italian dry-cured hams – Giulia Longhi – Current Research in Microbial Sciences

Environmental microbiome

The Microflora Danica atlas of Danish environmental microbiomes – C. M. Singleton – Nature

Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬www.nature.com/articles/s41…

— Morten Kam Dahl Dueholm (@mkddueholm.bsky.social) 2025-12-03T20:50:16.284Z

Bioinformatics

TAGINE: Fast Taxonomy-based Feature Engineering for Microbiome Analysis – Shiri Baum – bioRxiv

Creating unity: linking 16S rRNA gene sequence information to the core taxonomy of genomes – Hilde Vinje – Environmental Microbiome

LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation – Wei Xue – Nature Communications

cFMD v1.3.0 is here! 🚀We're thrilled to announce the release of the latest version of the curatedFoodMetagenomicData (cFMD) github.com/SegataLab/cFMDWhile we're keeping the same core datasets & samples, we've packed this release w/ significant improvements under the hood.1/4

— Segata Lab (@cibiocm.bsky.social) 2025-11-26T13:09:52.484Z

November 28, 2025

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Human Microbiome

Awareness of human microbiome may promote healthier lifestyle and more positive environmental attitudes – Olga Rook – Nature

Viruses and Phages

Long-read metagenomics reveals phage dynamics in the human gut microbiome – Jakob Wirbel- Nature

Gut microbiome

Association Between Gut Microbiota Diversity and Body Mass Index (BMI) in Healthy Young Adults in the United States: Insights Into the Gut-Brain-Metabolic Axis Using the Curated Metagenomic Data – Nenrot S. Gopep – Cureus

Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro – Indra Roux – Nature

Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson’s disease – Rémy Villette – Microbiome

Respiratory Microbiome

Whole genome sequencing of the pulmonary microbiome in interstitial lung disease subtypes – Kristel S. Knudsen – Respiratory Research

Enrichment of Streptococcus oralis in respiratory microbiome enhance innate immunity and protects against influenza infection– Xiaohui Zou –  Signal Transduction and Targeted Therapy

Animal microbiome

Non-pasteurized milk enhances early colonization and persistence of Lactobacillus species in dairy calves promoting a stable hindgut microbiome – Shengnan Qiu – Animal Advances

The interaction of microplastics with the ruminal ecosystem in vitro – J. Eichinger – Journal of Hazardous Materials

Bacterial predation in a marine host-associated microbiome – Rory M Welsh – The ISME Journal

Water Microbiome

Spontaneous fermentation of raisin water to form wine – Mamoru Hio – Scientific Reports

Nasal Microbiome

Comparative meta-transcriptomic analysis of nasal and anal microbiota in respiratory syncytial virus mono and co-infected children – Iman Dandachi – Microbiology

Bioinformatics

SHAP-based binarization enhances metataxonomic machine learning with application to gut microbiota of inflammatory bowel disease – Youngro Lee – Scientific Reports

November 21, 2025

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prepared by Bugembe Allan

Human gut microbiome

Effects of ascorbic acid on intestinal flora and metabolites of C57 mice exposed to formaldehyde in the digestive tract – Xin Ling – PLOS ONE

Consumption of non-sugar sweeteners by Brazilian adolescents and adults in 2017–2018: Socioeconomic distribution and food sources – Luisa Gazola Lage – PLOS ONE

The impact of day care attendance on antibiotic use among children aged 0–12 years: A population-based register study – Tapio Räsänen – PLOS ONE

Continuous Glucose Monitoring under standardised conditions regarding diet, exercise and stress in Healthy Young People (CGM-HYPE study) – Florian Kinny – PLOS Digital Health

Animal microbiome

Triadic relationships between pasture exposure, gastrointestinal parasites, and hindgut microbiomes in grazing lambs – Jack Jefferson – PLOS ONE

Prevalence and antimicrobial resistance of multidrug-resistant Staphylococcus epidermidis from raw milk of dairy cattle and ewes – Inamullah – PLOS ONE

Fate of Trypanosoma cruzi in bed bugs after oral ingestion or intrathoracic injection – Sanam Meraj – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Salmonella enterica exploits the auxin signaling pathway to overcome stomatal immunity – Brianna Fochs – PLOS Pathogens

Microbial Ecology

Bacterial immune systems as causes and consequences of microbiome structure – Rafael Custodio – PLOS Biology

Human respiratory microbiome

Non-canonical metatranscriptomic analysis of COVID-19 and Dengue reveals an expanded microbial and AMR landscape in COVID-19 mortality patients – Aanchal Yadav – PLOS Pathogens

Metagenomics & Bioinformatics

tvsfglasso: Time-varying scale-free graphical lasso for network estimation from time-series data – Markku Kuismin – PLOS Computational Biology

Quantifying microbial interactions based on compositional data with generalized Lotka-Volterra equations – Yue Huang – PLOS Computational Biology

Water microbiome

Diverse biophysical and molecular mechanisms drive phytoplankton sinking in response to starvation – Yanqi Wu – PLOS Biology

Phages & Viruses

ATG-3 limits Orsay virus infection in C. elegans and regulates collagen pathways – Gowri Kalugotla – PLOS Pathogens

Animal experiments

Antioxidant and antidiabetic effects of Angylocalyx oligophyllus leaves aqueous extract in pregnant diabetic rats – Christian Tenezogang Takoukam – PLOS ONE

November 14, 2025

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Gut Microbiome & Host Health

Sleep deprivation disrupts diurnal rhythmicity of gut microbiota and blood inflammatory cytokines in mice — Weiran Shan et al. (PLOS ONE)

Chemical modulation of gut bacterial metabolism induces colanic acid and extends the lifespan of nematode and mammalian hosts — Guo Hu et al. (PLOS Biology)

The role of hypothyroidism in cirrhosis pathogenesis: A retrospective cohort study and multi-omics integration analysis — Ziyang Yang et al. (PLOS Genetics)

Multi-omics analysis reveals metabolic regulation of phosphatidylcholine, triglycerides, phosphatidylethanolamine, and cardiolipin metabolism in mouse liver with MASLD — Hong Liang & Kang Song (PLOS ONE)

Metabolomics and glucose tolerance in pregnancy and postpartum: The PONCH study — Ulrika Andersson-Hall et al. (PLOS ONE)

Microbial Pathogens, Immunity & Infection

Exploring the gut microbiota of Pacific white shrimp suffering pale shrimp disease — Lalitphan Kitsanayanyong et al. (PLOS ONE)

Dominance of Zygosaccharomyces and shifts in bacterial pathways under antimicrobial pressure — Maria Cecilia Rasuk et al. (PLOS ONE)

How transcriptional networks control Verticillium plant infection — Ying-Yu Chen et al. (PLOS Pathogens)

Integrative machine learning and multi-omics framework identifies shared biomarkers for rheumatoid arthritis and ulcerative colitis — Meili Liu et al. (PLOS ONE)

The cervicovaginal microbiome associates with spatially restricted host transcriptional signatures throughout the ectocervical epithelium — Vilde Kaldhusdal et al. (PLOS Pathogens)

Characterization of ORF19.7608 (PPP1), a biofilm-induced gene of Candida albicans — Nmerichukwu C. Iwuchukwu et al. (PLOS ONE)

Differential regulation of the eicosanoid biosynthesis pathway during Enterocytozoon hepatopenaei infection in shrimp — Wananit Wimuttisuk et al. (PLOS ONE)

Animal, Environmental & Soil Microbiomes

Cuts or carcasses? Diet form affects fecal microbial and fiber fractions in Asiatic lions — Mengmeng Sun et al. (PLOS ONE)

From pre-oral secretions to gut digestion: How Lucilia sericata larvae handle Leishmania major — Azam Malekian et al. (PLOS ONE)

Targeted pathogen profiling of ancient feces reveals common enteric infections (725–920 CE) — Drew Capone et al. (PLOS ONE)

Starve or share? Phosphate availability shapes plant–microbe interactions — Maja Schmidt et al. (PLOS Pathogens)

Pathogenicity and transmission of Morganella morganii in honey bees — Yijun Chen & Qiang Huang (PLOS Pathogens)

Mitogenomics of the tropical bont tick reveals vertical and horizontal transmission of Rickettsia africae — Elisha Chatanga et al. (PLOS NTDs)

Differentiation of bacterial communities in the coral Orbicella faveolata across life-cycle stages — Amanda Pérez-Trejo et al. (PLOS ONE)

Insect-derived polymer hydrogel based on fibroin matrix from whole silkworm larvae — Maki Yamazaki et al. (PLOS ONE)

Thermophilic microbiome acclimation improves anaerobic digestion of food waste — Hengxuan Shao et al. (PLOS ONE)

Epidemiology, Public Health & Clinical Microbiology

Assessing piperacillin/tazobactam vs. ceftriaxone + metronidazole for children with perforated appendicitis — Daniel Briatico et al. (PLOS ONE)

Prevalence and antimicrobial resistance of multidrug-resistant Staphylococcus epidermidis in raw milk — Inamullah et al. (PLOS ONE)

Hematological ratios, immune-related adverse events, and mortality in patients receiving immune checkpoint inhibitors — Sophie Lekkerkerker et al. (PLOS ONE)

Geographical and climatic risk factors for COVID-19 in southwest Iran — Koorosh Nikaein et al. (PLOS ONE)

Anthropometric and neurocognitive consequences of Campylobacter, ETEC, and norovirus infections: A systematic review — Patricia B. Pavlinac et al. (PLOS NTDs)

Neuroscience, Immunology & Molecular Networks

Skin melanin is associated with body temperature regulation in humans and mice — Kale S. Bongers et al. (PLOS ONE)

Oxytocin neurons drive melanocortin circuit maturation via vesicle release — Pierre-Yves Barelle et al. (PLOS Biology)

Elucidation and application of the neuroimmune axis between depression and autoimmune diseases — Fu Sun et al. (PLOS ONE)

Quantifying microbial interactions using an iterative generalized Lotka–Volterra approach — Yue Huang et al. (PLOS Computational Biology)

November 7, 2025

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General Microbiome

Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes – Ricardo Leon-Sampedro – Nature

Gut microbiome

Pushing the frontier of gut microbiome health cross-kingdom and cross-organ – Tao Zuo  (左涛) – Nature

The early-life gut microbiome in common pediatric diseases: roles and therapeutic implications – Taiwo Bankole – Frontiers in Nutrition

The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals – Christophe Boetto – Communications Biology

Respiratory Microbiome

Oral microbiome dysbiosis is associated with chronic respiratory diseases: evidence from a population-based study and a hospital cohort – Baolin Jia – Frontiers in Public Health

Distinguishing tuberculosis from non-tuberculous mycobacteria and other respiratory conditions by microbiome patterns – Jee Youn Oh –  Scientific Reports

Animal microbiome

Effects of avian Plasmodium exposure on the microbiota of Culex pipiens – Marta Garrigos – Nature

Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes – Georges P. Schmartz – Nature Communications

Animal Experiments

Fiber, microbiomes, and SCFAs: insights from companion animal models to inform personalized nutrition – Leigh A. Frame – mSystems

Water Microbiome

Microbiome of highly polluted coal mine drainage from Onyeama, Nigeria, and its potential for sequestrating toxic heavy metals – Ganiyu Oladunjoye Oyetibo – Scientific Reports

Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems – Congmin Zhu – Nature Communications

Bringing the uncultivated microbial majority of freshwater ecosystems into culture – Michaela M. Salcher – Nature Communications

Bioinformatics

Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand– Watchaporn Chuchaona – Scientific Reports

Uncovering the viral aetiology of undiagnosed acute febrile illness in Uganda using metagenomic sequencing – Shirin Ashraf – Nature Communications

Metaproteomics and metagenomics reveal microbial pathways of organic matter degradation and methanogenesis in a marginally producing natural gas well – Eli K. Moore – Communications Earth & Environment 

November 5, 2025

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See you next week at MVIF!

🆕 #MVIF 43 program is out! Free registration: cassyni.com/s/mvif-43⭐️ Highlights:🇵🇰 Muhammad Faheem Raziq🇺🇸 Fuqing Wu⭐️ Keynote:🇮🇳 Deepa Agashe @deepaagashe.bsky.social ‬⭐️ Talks:🇺🇸 Lukas Bethlehem🇵🇱 Kinga Zielinska🇸🇪 Eran Elhaik

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-10-28T12:40:43.755Z

Human gut microbiome

Associations Between Gut Microbiome and 24-Hour Blood Pressure Variability: A Cross-sectional Study Highlighting Sex Differences and Potential Therapeutic Targets – Preeti Dinesh Virwani – bioRxiv

Infant gut microbiota in multi-child families converges with adults without a sibling-specific signature – Eveliina Hanski – bioRxiv 

Shaping the future of probiotics, live biotherapeutic products, and fecal microbiota transplantation: 30 scientific recommendations from the CHINAGUT Conference – Weihong Wang – iMeta 

A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people – Caitlin Welsh – Nature Miicrobiology

Long-read metagenomics for strain tracking after faecal microbiota transplant – Yu Fan – Nature Microbiology

Excited to share our LongTrack study out in @natmicrobiol.nature.com today! Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/📄 rdcu.be/eL8mR

— Gang Fang (@gangfang.bsky.social) 2025-10-22T15:39:22.720Z

Host transcriptional responses to gut microbiome variation arising from urbanism – Sabrina Arif – bioRxiv

Soft Drink Consumption and Depression Mediated by Gut Microbiome Alterations – Sharmili  Edwin Thanarajah – JAMA Psychiatry

Oral microbiome

A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights – Jun Hyung Cha – Cell Host & Microbe

Urinary tract microbiome

Daily and Weekly Fluctuations in the Microbiome of the Urinary Tract of Postmenopausal Women with No History of Urinary Tract Infections – Jacob Hogins – bioRxiv

Animal experiments

Microbial succession at weaning is guided by microbial metabolism of host glycans – Jean-Bernard Lubin – Microbiome 

Animal microbiome

Temporal establishment of the colon microbiota in Angus calves from birth to post-weaning – Michelle M. Stafford – PlosOne

Viruses and phages

Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota – Malick Ndiaye – Nature Communications

Plant, root and soil microbiome

Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome – Robert M. Bowers – Microbiome

Soil bacterial, fungal, and protistan assembly processes across a 1300 km climate and land-use transect – Mingming Du – Catena 

Are you curious about the whether soil microbial distribution is predictable?🤔 The key takeaway:Bacteria 🦠→ predictable! 😊 Fungi & Protists 🍄💧 → harder to predict 😭 #SoilEcology #Microbiome #CommunityAssembly #SoilScience #Microbeswww.sciencedirect.com/science/arti…

— Mingming Du (@mingming0105.bsky.social) 2025-11-04T08:18:30.583Z

Drinking water microbiome

Microbial drinking water quality deterioration during distribution and household usage, determined together with citizen scientists – Paul W. J. J. van der Wielen – PlosOne

Bioinformatics

annoSnake: a Snakemake workflow for taxonomic and functional annotation of metagenomes and metagenome-assembled genomes (MAGs) – Bastian Heimburger  – bioRxiv

October 17, 2025

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Gut Microbiome & Health

Lactic acid produced by optimal vaginal Lactobacillus spp. potently and specifically inactivates HIV-1 in vitro by targeting the viral RNA genome and reverse transcriptase
– Muriel Aldunate – PLOS Pathogens

Differential composition of the pulmonary microbiome in HIV-positive versus HIV-negative patients with Pneumocystis jirovecii
– Chang-Run Zhang – PLOS ONE

Risk of atopic dermatitis in periodontitis patients with and without dental scaling: A retrospective cohort study
– Ming-Che Chiang – PLOS ONE

Fecal carriage and associated factors of extended-spectrum beta-lactamase-producing Enterobacteriaceae in children under five years old with diarrhea at a tertiary hospital in Tanzania
– Emily M. Jackson – PLOS ONE

Pathogens, Immunity & Host Interactions

Dietary tannic acid promotes intestinal clearance of Candida albicans by cross-linking hyphal chitosan
– Jia Feng – PLOS Pathogens

Trends in Clostridioides difficile infection prevalence among pediatric cancer patients: A systematic review and meta-analysis
– Muluneh Assefa – PLOS ONE

Multiplex serology for Streptobacillus moniliformis and other ‘rat bite fever-like’ microorganisms for seroprevalence studies in rodents
– Katja Schmidt – PLOS ONE

Animal & Environmental Microbiomes

Effects of rumen-protected or unprotected Clostridium butyricum on growth performance, rumen fermentation, immunity and antioxidation in fattening goats
– Caixia Zhang – PLOS ONE

The intracellular symbiont Wolbachia alters Drosophila development and metabolism to buffer against nutritional stress
– Amelia R. I. Lindsey – PLOS Genetics

Interactive effects of developmental and adult nutrition on lifespan and fecundity in a genetically diverse Drosophila population
– Andrew Jones – PLOS ONE

Metabolism, Health & Disease

Alterations in the serum metabolome in patients with the COVID-19 Omicron variant and in recovered cases
– Feng Gao – PLOS ONE

Humanized monoacylglycerol acyltransferase 2 mice on a high-fat diet exhibit impaired liver detoxification during metabolic dysfunction-associated steatotic liver disease
– J. Jose Corbalan – PLOS ONE

Current and future burden of gynecological cancers attributable to high body-mass index: A comprehensive global analysis and projection study
– Xuanyu Zhao – PLOS ONE

Developing and experimentally validating a glucocorticoid signaling-related gene signature to evaluate the prognosis and immunotherapeutic response in kidney renal clear cell carcinoma
– Yu Zhang – PLOS ONE

Computational & Bioinformatics Advances

ArcDFI: Attention regularization guided by CYP450 interactions for predicting drug–food interactions
– Mogan Gim – PLOS Computational Biology

Advanced deep learning-based brain tumor classification using a novel customized CNN and optimized residual network
– Mehwish Rasheed – PLOS ONE