November 21, 2025

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

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

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

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 13, 2025

General Microbiome

Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research – Imane Allali – Microbiome

Gut microbiome

Gut microbiota alterations are linked to COVID-19 severity in North African and European populations – Marius Bredon – Nature

Expanding the human gut microbiome atlas of Africa -Dylan G. Maghini – Nature

Vaginal microbiome

Changes in the vaginal microbiome in female patients with condyloma acuminatum and its impact on persistent HPV infection – Zhiyu Liu – Nature

Associations among HPV persistence, the vaginal microbiome, and cervical cancer recurrence – Despina Tsementzi – Journal of Translational Medicine

Respiratory Microbiome

Impact of RNA extraction on respiratory microbiome analysis using third-generation sequencing – Alice Michel – BMC Genomics

Animal microbiome

UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog – Shuang Liu – Nature

Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails – Yiyue Zhang – Microbiome

Water Microbiome

Decoding the genetic drivers of marine bacterial blooms through comparative genomics – Xavier Rey-Velasco – Microbiome

Bioinformatics

Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics – Kang Mao – BMC Microbiology

Computational microbiome pharmacology analysis elucidates the anti-cancer potential of vaginal microbes and metabolites – Damilola C Lawore  – Frontiers

October 10, 2025

Gut Microbiome & Health

Effects of ethnicity and geography on the fecal microbiota and dietary habits of Tibeto-Burman hill tribes in Northern Thailand – Tanapon Seetaraso – PLOS ONE

Relationship between Gut microbiome and brain volumes among Japanese Men – Sabrina Ahmed – PLOS ONE

Association of serum intestinal fatty-acid binding protein, inflammatory and oxidative stress markers with colorectal cancer among Ghanaian patients – Genevieve Kwao-Zigah – PLOS ONE

Trends in incidence, mortality and disability-adjusted life years of colorectal cancer in East Asia (1990–2021): An analysis of the Global Burden of Disease study 2021 – Yuanyi Cao – PLOS ONE

Pathogens, Immunity & Host Interactions

Host- and microbial-mediated mucin degradation differentially shape Pseudomonas aeruginosa physiology and gene expression – Sabrina J. Arif – PLOS Pathogens

Blockade of mTOR ameliorates IgA nephropathy by correcting CD89 and CD71 dysfunctions in humanized mice – Alexandra Cambier – PLOS ONE

Single-cell analysis reveals an important role of CD137L+ macrophages in the host response to uropathogenic Escherichia coli infection in the bladder – Yaxiao Liu – PLOS Pathogens

Intestinal inflammation induced by heat-labile toxin-producing enterotoxigenic E. coli infection and impact on immune responses in an experimental human challenge model – Xueyan Zhang – PLOS Neglected Tropical Diseases

Vector-Borne & Parasitic Infections

The effects of mating and blood feeding on the immune defense of female Aedes aegypti mosquitoes – Brendan J. Kelly – PLOS Neglected Tropical Diseases

Temporal and spatial profiling of Aedes albopictus immune responses to chikungunya virus infection – Maria Greta Dipaola – PLOS Neglected Tropical Diseases

Distribution of schistosomes and soil-transmitted helminth infections and their association with growth and nutritional status of school-aged children in Cameroon – Estelle Mezajou Mewamba – PLOS Neglected Tropical Diseases

Risk factors influencing Coxiella burnetii seropositivity in water buffalo populations of Egypt’s Nile Delta – Abdelfattah Selim – PLOS ONE

Global genomic and antimicrobial resistance profiling of Neisseria gonorrhoeae: Insights from whole genome sequencing and minimum inhibitory concentration analysis – Elaheh Ebrahimi – PLOS Neglected Tropical Diseases

Oral & Other Microbiomes

Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients – Duangnapa Roongpiboonsopit – PLOS ONE

Bacterial communities of fungus-growing ant queens are species-specific and suggest vertical transmission – Victoria A. Sadowski – PLOS ONE

Captivity-driven microbiota reshaping: A cross-species analysis of divergent patterns in the gut microbiota of giant pandas, red pandas, and Asiatic black bears – Lin Xu – PLOS ONE

Environmental & Soil Microbiomes

Microbiome characterization of a pre-Hispanic man from Zimapán, Mexico: Insights into ancient gut microbial communities – Santiago Rosas-Plaza – PLOS ONE

The spatial distribution of salt tolerant bacteria and other soil parameters under different agricultural systems of the Indian Sundarbans – Sreemoyee Mitra – PLOS ONE

Pilot-scale depuration demonstrates the suitability of non-pathogenic Vibrio parahaemolyticus as a surrogate for commercial-scale validation studies – Spencer L. Lunda – PLOS ONE

Public Health & Perception

Public perceptions and support for introduced microbes to combat hospital-acquired infections and antimicrobial resistance – Christopher L. Cummings – PLOS ONE

Nutritional status and bacteremia patterns in children with diarrheal diseases: A comparative analysis of bacteremia from Salmonella Typhi versus other pathogens – Md Rezaul Hossain – PLOS ONE

Exploration of common biomarkers and pathogenesis of primary Sjögren’s syndrome and interstitial lung disease by machine learning and weighted gene co-expression networks – Jingqi Dong – PLOS ONE

October 3, 2025

See you at the MVIF 42!

NEW #MVIF program is out! 🤩Free registration: cassyni.com/s/mvif-42⭐️ Highlights:🇦🇺 @gbouras13.bsky.social🇺🇸 Danica Schmidtke⭐️ Keynote:🇺🇸 Peter Turnbaugh⭐️ Talks: 🇸🇬 Minghao Chia🇺🇸 @arzamasovalex.bsky.social 🇳🇿 Brooke Wilson

Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-09-23T14:27:57.484Z

Human gut microbiome

Micro-scale spatial metagenomics: revealing high-resolution spatial biogeography of gut microbiomes – Carlotta Pietroni – bioRxiv

Animal microbiome

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort – Anna Cuscó – bioRxiv

Finally, the results of my postdoc at the @bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs.See our new preprint:www.biorxiv.org/content/10.1…

Anna Cusco (@annacusco.bsky.social) 2025-09-23T11:23:52.836Z

Genome-resolved metagenomics reveals microbiome diversity across 48 tick species – Li-Feng Du – Nature Microbiology

The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media – Alice M. Buckner – Microbiology Spectrum

Animal experiments

The microbiota extends the reproductive lifespan by safeguarding the ovarian reserve – Sarah K. Munyoki – bioRxiv

Comment: From gut to gamete: how the microbiome influences fertility and preconception health – Sarah K. Munyoki – Microbiome

Review: Microbiome in heritage: how maternal microbiome transmission impacts next generation health – Clara Delaroque & Benoit Chassaing – Microbiome

Water microbiome

Metagenomics reveal allopatric speciation and higher connectivity among coastal vs. inland hypersaline lakes and solar salterns – Tomeu Viver – bioRxiv

Bioinformatics

microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis – Haris Zafeiropoulos – Genome Biology

our software, microbetag, for the annotation of microbial co-occurrence networks with phenotypic traits & metabolic complementarities was just publishedA Cytoscape app is also available to make your life easier (and prettier)#microbiome #metabolic-modeling #networks

Haris Zafeiropoulos (@hariszaf.bsky.social) 2025-09-23T09:42:39.741Z

A roadmap for equitable reuse of public microbiome data – Laura A. Hug – Nature Microbiology

Reference-guided assembly of metagenomes with MetaCompass – Tu Luan – Cell Reports Methods

👏 “To promote more inclusive scientific discussions with international colleagues at our conferences, virtual delegates based in Lower and Middle-Income Countries can register for free”

Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2025-09-30T07:09:00.327Z

September 23, 2025

General Microbiome

Specialty grand challenge: how can we use integrative approaches to understand microbial community dynamics? – Umer Zeeshan Ijaz- Frontiers in Systems Biology

Gut microbiome

Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis – Sunhee Jung – nature metabolism

Repopulation of the gut microbiota after a screening colonoscopy – Yezaz A Ghouri – PLOS One

Leveraging the Role of Microbiome in Endometriosis: Novel Non-Invasive Diagnostic and Therapeutic Approaches – Eleni Andria Kalopedis – Frontiers in Immunology

Vaginal microbiome

Vaginal Lactobacillus crispatus in early pregnancy associates with favorable gestational outcomes in a Japanese maternal-neonatal microbiome cohort – Noriaki Oguri – Nature Communications

Animal microbiome

Bacterial assemblages on eggs reflect nesting strategies in wetland-associated birds – Wouter F. D. van Dongen – PLOS One

Whole-Genome Sequencing Uncovers Chromosomal and Plasmid-Borne Multidrug Resistance and Virulence Genes in Poultry-Associated Escherichia coli from Nigeria – Chika Ejikeugwu – bioRxiv

Virome

Duck Slurry as a Matrix for Avian Influenza Virus Surveillance and Genetic Characterization in Domestic Flocks – Clément Castille – bioRxiv

Bioinformatics

Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics – Banaz Star-Shirko – BMC research notes

Bioinformatics-based stereochemical elucidation of MM 46115: an unusual antiviral spirotetronate that inhibits clathrin-mediated endocytosis – Afifah Tasnim – bioRxiv

April 30, 2025

See you next week at MVIF! 

Just announced! #MVIF 39 featuring groundbreaking research on the role of the Nagoya Protocol in protecting microbial diversity through fair use! Don't miss this special event!Sign up now: cassyni.com/s/mvif-391/2

Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-04-24T13:46:23.487Z

Skin microbiome

Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites – Chengchen Li – bioRxiv

Super thrilled to share our labor of love from the Asian Skin Microbiome Program! We collected >3,500 skin samples, built metagenomic libraries w/ >70 billion reads and >10TB of data to study heterogeneity of the skin microbiome in the general population (200 adults, 18 sites) t.co/ZylbJMpvpw

Niranjan Nagarajan (@niranjantw.bsky.social) 2025-04-28T04:52:26.147Z

Oral microbiome

Toxic cultures: e-cigarettes and the oral microbial exposome – Michelle Lee-Scott Beverly – npj Biofilms and Microbiomes

Gut microbiome

The gut microbiota promotes pain in fibromyalgia – Weihua Cai – Neuron

Brief antibiotic use drives human gut bacteria towards low-cost resistance – Eitan Yaffe – Nature

Review: Implication of Gut Mycobiome and Virome in Type-2 Diabetes Mellitus: Uncovering the Hidden Players – Mona Kriti – Phenomics

Unravelling the causality between inflammatory bowel disease and polycystic ovary syndrome mediated by gut microbiota and blood metabolism: insights from two prospective cohort studies – Zhaoman Wan – Gut

Animal experiments

Enhanced propionate and butyrate metabolism in cecal microbiota contributes to cold-stress adaptation in sheep – Xindong Cheng – Microbiome

Animal microbiome

Social and environmental predictors of gut microbiome age in wild baboons – Mauna R Dasari – eLife

Effects of parental care on skin microbial community composition in poison frogs – Marie-Therese Fischer – eLife

Food microbiome

The effect of different milk pretreatment methods on microbiome community development during Herrgårds cheese production and ripening – Juan Antonio Rodríguez – bioRxiv

🧀 New preprint drop: adventures in the cheese microbiome! 📝We tracked microbiome dynamics across 14 production steps of industrial Herrgårds cheese (Swedish classic 🇸🇪🧐). http://www.biorxiv.org/cgi/content/…(1/7)

Juan Antonio Rodríguez (@jrotwitguez.bsky.social) 2025-04-24T07:50:58.839Z

Bioinformatics

Assemblies of long-read metagenomes suffer from diverse errors – Florian Trigodet – bioRxiv

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,www.biorxiv.org/content/10.1…and tell you just a little bit about it in the following 🧵

Florian Trigodet (@floriantrigodet.bsky.social) 2025-04-28T08:07:49.715Z

Enhanced semantic classification of microbiome sample origins using Large Language Models (LLMs) – Daniela Gaio – bioRxiv

argNorm is published now academic.oup.com/bioinformati…

Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2025-04-17T04:57:42.847Z

April 22, 2025


General microbiome

[Editorial] A blueprint for contemporary studies of microbiomes – Bindels et al. Microbiome

[Perspective] Moving from genome-scale to community-scale metabolic models for the human gut microbiome – Quinn-Bohmann et al. Nature Microbiology

[Review] Clinical translation of microbiome research – Gilbert et al. Nature Medicine

Gut microbiome

Antibiotic-induced gut microbiome perturbation alters the immune responses to the rabies vaccine – Feng et al. Cell Host & Microbe

Animal models

Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice – Zhang et al. Microbiome

Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model  – Cuisiniere et al. Microbiome

Virome

The T-series bacteriophages are reductionist models that continue to shape the field  – Barr. Nature Microbiology

Phollow reveals in situ phage transmission dynamics in the zebrafish gut microbiome at single-virion resolution  – Ortiz de ora et al. Nature Microbiology

Bioinformatics 

FGeneBERT: function-driven pre-trained gene language model for metagenomics – Duan et al. Briefings in Bioinformatics. 

TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases – Cong et al. Briefings in Bioinformatics.