Author Archives: Svetlana Ugarcina Perovic

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

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 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 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 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 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 11, 2025

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Happy Friday and see you next week at MVIF!

NEXT WEEK don't miss #MVIF 38 on Microbiome and Citizen Science👉https://cassyni.com/s/mvif-38& meet:🇫🇷 @patrickveiga.bsky.social & Mathieu Almeida🇮🇹Claudia Cappello 🇨🇦 @waldispuhl.bsky.social 🇺🇸Daniel McDonald🇺🇸Mikayla A. Borton🇧🇪Sarah Ahannach🇳🇱Saara Suominen🇺🇸 @gilbertjacka.bsky.social

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-04-07T14:59:29.156Z

Gut microbiome

The South American MicroBiome Archive (saMBA): Enriching the healthy microbiome concept by evaluating uniqueness and biodiversity of neglected populations – Benjamin Valderrama – bioRxiv

Excited to share our preprint on the South American MicroBiome Archive (saMBA)! 🌎🦠.We analysed one of the regions with the fewest microbiome samples but some of the highest biodiversities.📄: shorturl.at/Lmvp5 🧵: What did we find—and why? Find out 👇#microbiome #gut-microbiome (1/8)

— Ben Valderrama (@bvalderrama.bsky.social) 2025-04-09T12:50:10.653Z

Microbiome–metabolome dynamics associated with impaired glucose control and responses to lifestyle changes – Hao Wu – Nature Medicine

Gene-by-environment interactions modulate the infant gut microbiota in asthma and atopy – Sara A. Stickley – Journal of Allergy and Clinical Immunology

Mutualistic interactions between Escherichia coli and Bifidobacterium bifidum enable degradation of human milk oligosaccharides in healthy infants – David Seki – bioRxiv

Excited to finally share results from my first post-doc @halllab.bsky.social 🫡E.coli commonly occurs in infant gut microbiota, yet its role during healthy development has been disregarded. In our pre-print, we reveal its fundamental involvement in HMO-degradation.www.biorxiv.org/content/10.1…

— David Seki (@sekid.bsky.social) 2025-04-09T15:12:35.525Z

Delivery Mode Impacts Gut Bacteriophage Colonization During Infancy – Poorani Subramanian – Gut Microbes Report

Our paper on #bacteriophages in the infant gut #microbiome came out earlier this year.This work was a long time coming, and I'm super proud to be first author alongside Suchi Hourigan and Hector Romero Soto of the Clinical Microbiome Unit at NIAID.doi.org/10.1080/2993…

— poorani (@poorani.bsky.social) 2025-04-09T17:08:33.195Z

Animal microbiome

Humpback whales harbor a highly novel and endemic gut microbiome that adapts to periods of fasting during migration – Ryan Bos – bioRxiv

Wild house mice have a more dynamic and aerotolerant gut microbiota than laboratory mice – Eveliina Hanski – BMC Microbiology

Animal experiments

Acute stress enhances synaptic plasticity in male mice via a microbiota-dependent mechanism – Cristina Rosell-Cardona – Neuropharmacology

First paper from my PD at @apcmicrobiomeirel.bsky.social out! 🥳Do you want to know how acute stress enhances synaptic plasticity?Our latest study shows that the gut microbiota is essential.@jfcryan.bsky.social @kjdoriordan.bsky.socialsciencedirect.com/science/article/pii/S0028390825001406?s=08

— Cristina Rosell Cardona (@crosellcardona.bsky.social) 2025-04-05T15:13:41.606Z

Built environment

Assessing microbial diversity in open-pit mining: Metabarcoding analysis of soil and pit microbiota across operational and restoration stages – Priscila Heredia Reto – PlosOne

Bioinformatics

Commentary: Mixing microbiomes in vitro reveals rules of community assembly – Alyssa H. Mitchell and Tami D. Lieberman – PNAS

CoverM: Read alignment statistics for metagenomics – Samuel T N Aroney – Bioinformatics

Excited to introduce the preprint for CoverM: the Swiss Army knife of coverage calculators for metagenomics! 🧬🖥️ DOI: doi.org/10.48550/arX…@benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social

— Samuel Aroney (@aroneys.bsky.social) 2025-01-22T06:11:42.303Z

Investigating statistical power of differential abundance studies – Michael Agronah and Benjamin Bolker – PlosOne

MetaDAVis: An R shiny application for metagenomic data analysis and visualization – Sankarasubramanian Jagadesan and Chittibabu Guda – PlosOne 

Anita & I chatted abt #opensource tools, dbs and **community** around the microbiome science in #OpenSourceDiaries!I mentioned @bioconductor.bsky.social @microbiomevif.bsky.social & @merenbey.bsky.social’s anvi’o & other important tools for microbiome data analysis.www.youtube.com/watch?v=7yii…

— Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2025-04-07T17:17:29.063Z

March 14, 2025

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Happy Friday and see you next week at MVIF 37!

Just announced #MVIF 37 on Microbiomes in Extreme Environments!Don't miss this special event w/our guests🇩🇪 Nicole Dublier🇳🇱 Henk Bolhuis🇺🇸 Rachael Morgan-Kiss 🇺🇸 Kasthuri Venkateswaran 🇮🇹 Fabiana Canini 🇺🇸 Diana Ayala-Muñoz🇮🇹 Luca Tonietti cassyni.com/s/mvif-37

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-03-06T14:14:27.441Z

Women’s health

Vaginal microbiota changes during a natural menstrual cycle in the Women4Health cohort highlights specific features of the Italian population – Elena Vinerbi – bioRxiv

Review: Menopausal shift on women’s health and microbial niches – Maria R. Nieto – npj Women’s Health

1/ 🚨 🧪New Research: #Menopause, #Microbiome & #WomensHealth Menopause reshapes health through hormonal, microbial, and physiological changes. 🧪📖 Explore the study: rdcu.be/d5725⬇️ Let’s dive into the key insights:

— Aurea Simon-Soro (@aureasimon-soro.bsky.social) 2025-01-23T12:57:47.907Z

Gut microbiome

Review: The gut microbiota-immune-brain axis: Therapeutic implications – Kenneth J. O’Riordan – Cell Reports Medicine

Effects of oral supplementation of probiotics on body weight and visceral fat in obese patients: a meta-analysis and systematic review – Manhou Guo – Scientific Reports

Longitudinal phage–bacteria dynamics in the early life gut microbiome – Michael J. Tisza – Nature Microbiology 

Skin microbiome

Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers – Deepan Thiruppathy – Microbiome 

Animal experiments

Maternal undernutrition exacerbates microbiota-driven growth stunting through pre and postnatal effects – Yadeliz A. Serrano Matos – bioRxiv

Excited to share my lab's latest preprint and very proud of the whole team for their hard work. Check it out if you're interested in the #microbiome #maternalhealth or #undernutrition. http://www.biorxiv.org/content/10.1…

— Carrie Cowardin (@ccowardin.bsky.social) 2025-03-10T13:21:21.537Z

Animal microbiome

Rumen microbiome associates with postpartum ketosis development in dairy cows: a prospective nested case–control study – Fanlin Kong – Microbiome 

Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide – Ostaizka Aizpurua – Molecular Ecology

Endometrial microbiome in mares with and without clinical endometritis – Lulu Guo – bioRxiv

Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly – Lílian Caesar – bioRxiv

New preprint out! 🐝🦠 Among the incredible diversity of bees, only a few have evolved a highly social lifestyle—honey bees and stingless bees (Apidae). We characterize for first time, using metagenomics/microbial experiments, the microbiome of a stingless bee colony

— Lilian Caesar (@liliancaesar.bsky.social) 2025-03-11T08:00:43.662Z

Food microbiome

The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics – Samuel Breselge – Communications Biology

Fantastic to see this comprehensive study of water kefir pangenomes, led by Samuel Breselge, now published “The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics". @teagasc.bsky.social @apcmicrobiomeirel.bsky.social rdcu.be/ec7GT

— Paul Cotter (@pauldcotter.bsky.social) 2025-03-11T20:35:16.288Z

Antimicrobial resistance

Effects of cigarette-derived compounds on the spread of antimicrobial resistance in artificial human lung sputum medium, simulated environmental media and wastewater – Peiju Fang – Environmental Health Perspectives

🚬🧬🚬🧬🚬🧬Proud to present the newest study of my PhD students Peiju and Diala in Environmental Health PerspectivesEffects of cigarette-derived compounds on the spread of #AMR in artificial human lung sputum medium, simulated environmental media and wastewaterdoi.org/10.1289/EHP1…1/9#microsky

— Uli Klümper (@ulikluemper.bsky.social) 2025-03-04T15:03:48.183Z

Drinking water plumbing systems are a hot spot for antimicrobial resistant pathogens – Claire Hayward – Journal of Hospital Infection

DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data – Ella Rannon – Microbiome

Bioinformatics

LEMMIv2: Benchmarking Framework for Metagenomic and 16S Amplicon Profilers with a Catalogue of Evaluated Tools – M. Seppey – bioRxiv 

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

Microbial network inference for longitudinal microbiome studies with LUPINE – Saritha Kodikara, Kim-Anh Le Cao – Microbiome

Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases – Ekaterina Avershina – Microbiome

🥁We are happy to announce the release of a new version of curatedFoodMetagenomicData (cFMD)🔗 Get it here: github.com/SegataLab/cFMD🧵👇1/5

— Segata Lab (@cibiocm.bsky.social) 2025-03-12T13:56:24.948Z

February 14, 2025

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Check out my list of selected latest microbiome studies and see you next week at #MVIF!

It's Friday! …and a new #MVIF program is out! 🤩Registration here: cassyni.com/s/mvif-36⭐️ MicroTalks:🇯🇵 Nodoka Chiba 🇮🇩 Patsy Tasyana Fitri⭐️ Keynote: 🇯🇵 Ruixin Liu⭐️ Selected talks: 🇦🇺 @aroneys.bsky.social 🇬🇧 Maria Kardakova🇦🇺 Theo Portlock

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2025-02-07T12:39:31.099Z

Gut microbiome

Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses – Puspendu Sardar – Nature Microbiology 

Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome – Nicholas Pucci – PeerJ

Though it's already a weeks ago, the newest paper from the (old) lab came out.We explored the drivers of Bifidobacterium longum subspecies dynamics in the infant gut in detail. Still fascinated by the interplay of ecology, metabolic capacity and dietpeerj.com/articles/186…

— Daniel Mende (@pangenomics.bsky.social) 2025-02-12T06:54:25.656Z

Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition – Maria Luisa Savo Sardaro – Nutrients

Long-term yogurt intake and colorectal cancer incidence subclassified by Bifidobacterium abundance in tumor – Satoko Ugai – Gut Microbes

From sporulation to village differentiation: the shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia – Clarissa A. Febinia – bioRxiv

Urinary microbiome

The urinary microbiome in association with diabetes and diabetic kidney disease: A systematic review – Tiscar Graells – PlosOne

Vaginal microbiome

Quantitative profiling of the vaginal microbiota improves resolution of the microbiota-immune axis – Eric Armstrong – Microbiome

Migration and standing variation in vaginal and rectal yeast populations in recurrent vulvovaginal candidiasis – Abdul-Rahman Adamu Bukari – bioRxiv

Skin microbiome

A human skin microbiome reference catalog and the skin microbial landscape of plateau adults – Yi Liu – iMetsOmics

Animal microbiome

Exploring the impact of grazing on fecal and soil microbiome dynamics in small ruminants in organic crop-livestock integration systems – Sejin Cheong – PlosOne

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

Animal experiments

A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma – Mattia Ballerini – Nature Biomedical Engineering

Early-life gut mycobiome core species modulate metabolic health in mice – Mackenzie W. Gutierrez – Nature Communications

Microbiota governs host chenodeoxycholic acid glucuronidation to ameliorate bile acid disorder induced diarrhea – Zishen Lin – Microbiome

The bacterial microbiome modulates the initiation of brain metastasis by impacting the gut-to-brain axis – Matteo Massara – iScience

Excited to share a new paper from our lab 😀We investigate the tumor microenvironment – to reveal factors influencing cancer progression & therapy response 🔬🧪So we naturally wanted to ask – does the gut #microbiome influence brain #metastasis 🦠 🧠?Massara et al 2025www.cell.com/iscience/ful…

— Johanna Joyce (@johannajoyce.bsky.social) 2025-02-10T14:03:22.248Z

Bacterial community assembly of specific pathogen-free neonatal mice – Elizabeth A. Kennedy – Microbiome

Antibiotic-associated changes in Akkermansia muciniphila alter its effects on host metabolic health –Yumin Han – Microbiome

Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets – Shankumar Mooyottu – Microbiome

Bacterial profiles of the oral, vaginal, and rectal mucosa and colostrum of periparturient sows – Virpi Piirainen – PlosOne

Plant microbiome

Comparative analysis of grape berry microbiota uncovers sour rot associates from a Maryland vineyard – Blaise Jumbam – PlosOne

Drinking water microbiome

Building plumbing influences the microdiversity and community assembly of the drinking water microbiome – Huanqi He – Water Research

Bioinformatics

Intraspecies associations from strain-rich metagenome samples – Evan B. Qu – bioRxiv

Excited to share my preprint describing a new microbiome analysis method, PHLAME, for detecting strain-level associations in difficult sample types. 🧵www.biorxiv.org/content/10.1…This work was done with my great coauthors and my amazing advisor @contaminatedsci.bsky.social

— Evan Qu (@quevan.bsky.social) 2025-02-11T23:06:43.624Z

Techniques

De-biasing microbiome sequencing data: bacterial morphology-based correction of extraction bias and correlates of chimera formation – Luise Rauer – Microbiome

Internships

Outreachy–a 3 month paid internship in open source and open science–applications for the June 2025 cohort are ongoing.

It was an awesome #Outreachy chat! Thanks for all your (detailed) questions, hope I answered them all…Recording available here: I enjoyed it a lot!www.youtube.com/live/PiOm6nq…

— Svetlana Ugarcina Perovic (@svetlanaup.bsky.social) 2025-02-05T16:46:07.001Z