October 13, 2025

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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

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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

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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 26, 2025

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Posted on September 26, 2025 by Bugembe Allan

Gut Microbiome & Human Health

Combined effect of probiotics and omega-3 fatty acids on blood and liver function biomarkers and gut microbiota diversity in male mice with high fat diet-induced obesity – Kwang Hee Son – PLOS ONE

Development and validation of a machine learning-based predictive model for clinical remission in Crohn’s disease patients receiving Adalimumab therapy – Pianpian Xia – PLOS ONE

Molecular mechanisms of dragon’s blood in treating ulcerative colitis based on NF-κb/NLPR3/Caspase-1 pyroptosis signaling pathway – Bilian Cai – PLOS ONE

Antimicrobial Resistance & Pathogens

Perinatal colonization with extended-spectrum beta-lactamase-producing and carbapenem-resistant gram-negative bacteria among home births in Bangladesh – Gregory S. Wu – PLOS ONE

Isolation, purification, and phenotypic characterization of virulent Klebsiella pneumoniae phages from environmental samples in Addis Ababa, Ethiopia – Assefa Asnakew Abebe – PLOS ONE

Other Microbiomes (Marine & Environmental)

Effects of repeated hemolymph sampling from adductor muscles of relaxed Pacific oysters (Magallana gigas) – Jingwei Song – PLOS ONE

Morphological differences in populations of Jacobaea erucifolia: Genetic differentiation, phenotypic plasticity or ecotypes? – Barbara Gawrońska – PLOS ONE

Reviews & Systematic Studies

Infection and telomere length: A systematic review – Louis Tunnicliffe – PLOS ONE

Cardiovascular & Comorbidities

Stratifying atherosclerotic cardiovascular disease by SMuRF burden in a Middle-Eastern country: A multiregistry study – Osama Alkouri – PLOS ONE

September 23, 2025

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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

September 19, 2025

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prepared by Bugembe Allan

Gut microbiome

Iron-saturated bovine lactoferrin preserves microbiota diversity and healthy ageing-associated taxa in an in vitro colon model of elderly gut microbiota – María Ruiz-Rico – PLOS ONE

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

Gut microbiome signatures in iNPH: Insights from a shotgun metagenomics study – Rahel Park – PLOS ONE

Animal microbiome

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

Substrate degradation and black soldier fly larvae bioconversion performance profile on co-digested oil palm biomass-based feedstock – Mulki Salendra Kusumah – PLOS ONE

Soil microbiome

Mycelial traits and GRSP in enhancing soil stability on cold region highway slopes: Comparative effects of three shrub species – Yibo Li – PLOS ONE

Food microbiome

Investigation of bacterial community and histamine production in fresh mackerel at low temperature storage – Grace Margareta – PLOS ONE

Combinatorial effects of Zingiber officinale and Citrus limon juices: Hypolipidemic and antioxidant insights from in vivo, in vitro, and in silico investigations – Oussama Bekkouch – PLOS ONE

Human Health & Disease

Maternal-infant rotavirus-specific antibody kinetics to inform timing of vaccine boosting in Malawi: An observational study – Jonathan Mandolo – PLOS Medicine

Mother-child autonomic nervous system interaction as an indication of parental stress: 24-hour cross recurrence plot analysis – Jiarui Li – PLOS ONE

Pre-infection cerebral cortex structure predicts murine sepsis outcome – Robert M. Gallant – PLOS ONE

Optimized processing of Gardenia Fruits with ginger juice: Unveiling therapeutic mechanisms for cholestatic liver injury through TLR4/NF-κB, FXR/PPAR-α, and PI3K/AKT/GSK-3β – Chenzi Lyu – PLOS ONE

Pathogens & Virulence

How Klebsiella pneumoniae controls its virulence – To Nguyen Thi Nguyen – PLOS Pathogens

Coronavirus M protein impairs cilium during early infection by enhancing the AurA-HDAC6 axis – Tenghan Zhuang – PLOS Pathogens

Virulence gene profile and antimicrobial resistance patterns of Aeromonas hydrophila in farmed catfishes – Farjana Ferdousi – PLOS ONE

Chimeric PRR T-cell-engager targeting cell surface β-1,3-glucan for invasive candidiasis – Yu Fang Sun – PLOS Pathogens

September 10, 2025

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General Microbiome

The multi-kingdom cancer microbiome – Anders B. Dohlman – Nature Microbiology

Gut microbiome

Influence of dietary components on the gut microbiota of middle-aged adults: the gut-Mediterranean connection – Shrushti Shah – BMC Microbiology

Gut microbial production of imidazole propionate drives Parkinson’s pathologies – Hyunji Park – nature communications

Vaginal microbiome

Identifying a Vaginal Microbiome-Derived Selective Antibiotic Metabolite via Microbiome Pharmacology Analysis – Smrutiti Jena – bioRxiv

Animal microbiome

Longitudinal Long-Read Microbiome Profiling in a Canine Model Reveals How Age, Diet, and Birth Mode Shape Gut Community Dynamics – Md Asaduzzaman – bioRxiv

Water microbiome

Net rate of lateral gene transfer in marine prokaryoplankton – Ramunas Stepanauskas – The ISME Journal

Virome

Spatio-temporal factors shape mosquito virome diversity and composition in a host and virus phylogeny-dependent manner – Cassandra Koh – bioRxiv

Bioinformatics

Dietary Protein Source Shapes Gut Microbial Structure and Predicted Function: A Meta-Analysis with Machine Learning – SAMSON A. ADEJUMO – bioRxiv

Distinct Microbial Communities Within and On Seep Carbonates Support Long-term Anaerobic Oxidation of Methane and Divergent pMMO Diversity – Magdalena J Mayr – The ISME Journal

Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson’s disease – Stefano Romano – nature communications

Microbes on the market

Microbiome Manufacturing Market Size to Hit USD 130.37 Billion by 2034 – Deepa Pandey – Precedence Research

September 5, 2025

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See you next week at #GloMiNe2025!

Program for #GloMiNe2025 "Preservation of microbial diversity” by @microbiotavault.bsky.social ‬and #MVIF is OUT:cassyni.com/s/mvif-glomi…1/3

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-08-22T11:42:37.937Z

Gut microbiome

Gut fungi are associated with human genetic variation and disease risk – Emily P. Van Syoc – Plos Biology

The resident gut microbiome modulates the effect of synbiotics on the immunogenicity after SARS-COV-2 vaccination in elderly and diabetes patients – Lin Zhang – npj Biofilms and Microbiomes

Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research – Matija Tričković – Cell Host & Microbe

New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.

— Silas Kieser (@silask.bsky.social) 2025-08-29T10:06:18.408Z

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants – Raymond Kiu – Nature Communications

A defined microbial community reproduces attributes of fine flavour chocolate fermentation – David Gopaulchan – Nature Microbiology

Gut microbiome alterations precede graft rejection in kidney transplantation patients – Johannes Holle – American Journal of Transplantation

Adolescent girls at familial risk for depression with more advanced adrenarche have altered gut microbiota – A. Kolobaric – bioRxiv

Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial – Russell G. Davies – The Journal of Physiology

Resistome

Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort – Katariina Pärnänen – Nature Communications

Oral microbiome

Complementary Predictors for Asthma Attack Prediction in Children: Salivary Microbiome, Serum Inflammatory Mediators, and Past Attack History – Shahriyar Shahbazi Khamas – Allergy

Profiles of oral microbiota and metabolites in periodontitis and benign prostatic hyperplasia patients: a pilot study – Cong Zhu – Microbiology Spectrum

SANA-Biome: A Protocol for a Cross-Sectional Study on Oral Health, Diet, and the Oral Microbiome in Romania – Sterling L. Wright – Healthcare 

🧬🪥 Just published! Our new paper introduces the SANA-biome, a biocultural study exploring how diet, lifestyle, and the oral microbiome shape periodontal health in Romania.📰 Read the open-access protocol in Healthcare: 👉 http://www.mdpi.com/2227-9032/13…

— Sterling L. Wright (@anthbyte.bsky.social) 2025-08-27T16:01:43.887Z

Animal microbiome

Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota – Anum Ali Ahmad – BMC Microbiology

Thrilled that our new paper on the Red Grouse microbiota has now been published in BMC Microbiology: doi.org/10.1186/s128…! A really rewarding collaboration between our team and Nick Hesford and Kathy Fletcher from the Game & Wildlife Conservation Trust @gwct.org.uk.

— Laura Glendinning (@microbes4ever.bsky.social) 2025-08-19T14:12:37.569Z

Establishment of the early gut microbiota in vaginally delivered infants: the influence of maternal gut microbiota outweighs vaginal microbiota – Haishan Xie – Microbiology Spectrum

Integrative multi-omics analysis of dietary fibre-induced modulations in the composition and function of chicken caecal microbiota – Anum Ali Ahmad – bioRxiv

Vaginal microbiome

Degradation of Resistant α-1,4-glucan by Vaginal Gardnerella Species is Associated with Bacterial Vaginosis – Rosanne Hertzberger – Current Microbiology 

Animal experiments

The microbiome is associated with obesity-related metabolome signature in the process of aging – Dana Binyamin – npj Biofilms and Microbiomes

Evidence for an indigenous female mouse urobiome – Sidra Sohail – bioRxiv 

Food microbiome 

Microbiome profiling of Grana Padano and Parmigiano Reggiano cheeses reveals cheese-specific biomarkers, psychobiotic potential, and bioprotective activities – Vincenzo Valentino – npj Biofilms and Microbiomes

Metabolomics

Microbes release lower-value metabolites at higher rates – Snorre Sulheim – bioRxiv

So excited to share this new paper by @sulheim.bsky.social and others! It's rare that you find a pattern, propose a hypothesis and the more you look, the more data you find that fits! Snorre's intuition, hard work and rigour to put it all together have been inspiring! Let us know what you think…

— Sara Mitri (@saramitri.bsky.social) 2025-08-22T14:05:47.584Z

Soil microbiome

236 metagenome-assembled microbial genomes from rivers along a latitudinal gradient – Xiang Xiong – Scientific Data 

Bioinformatics

StrainFacts accurately quantifies both endogenous and live biotherapeutic product strain abundances in simulated and clinical vaginal microbiota samples – Johnathan Shih – bioRxiv

Comparison of iSeq and Miseq in 16S rRNA sequencing-based human gut microbiome analysis – Yanling Wang – bioRxiv 

Podcast

Biopolis – into the microbiome A young scientist is looking for answers in the human microbiome.

Food systems are teeming with complex microbial networks, carried from soil and water to crops, animals, and humans. Can we better track and steer these networks to enhance ecosystem health and food security? Find out more at this #FrontiersForum webinar ➡️ fro.ntiers.in/NfcCnmIEkWb

— Paul Cotter (@pauldcotter.bsky.social) 2025-09-05T13:25:35.039Z

April 30, 2025

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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

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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.