Category Archives: Human gut

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 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 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. 

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

April 3, 2025

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General microbiome

[REVIEW] The regulatory framework for microbiome-based therapies: insights into European regulatory developments – Rodriguez et al. npj Biofilms and microbiomes

Early life microbiome

Bifidobacteria support optimal infant vaccine responses – Ryan et al. Nature

Gut microbiome evolution from infancy to 8 years of age – Sawhney et al. Nature Medicine

Animal experiments

Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice – Litichevskyiy et al. Nature Microbiology

Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice – Sommer et al. Microbiome

Faecalibacterium prausnitzii-derived outer membrane vesicles reprogram gut microbiota metabolism to alleviate Porcine Epidemic Diarrhea Virus infection – Xing et al. Microbiome

Bioinformatics

Elementary methods provide more replicable results in microbial differential abundance analysis – Pelto et al. Briefings in Bioinformatics

DMoVGPE: predicting gut microbial associated metabolites profiles with deep mixture of variational Gaussian Process experts – Weng et al. BMC Bioinformatics

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

March 2, 2025

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Hello, have a nice Sunday! In this Digest, we have some highlights from the literature during this week. 

Human/General Microbiome

Gastrointestinal Tract

Microbiome analysis of gut microbiota in patients with colorectal polyps and healthy individuals – Dayi Deng – Scientific Reports

Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer – Ping Cai – mSystems

Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients – Yuling Qin – mSystems

Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages – Nejc Stopnisek – BMC Microbiology

Review: Helicobacter pylori, microbiota and gastric cancer – principles of microorganism-driven carcinogenesis – Jonas Wizenty – Nature Reviews. Gastroenterology & Hepatology

Skin

Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes – Diana M Proctor – Nature

Oral – Respiratory Tract

A gut Eggerthella lenta-derived metabolite impairs neutrophil function to aggravate bacterial lung infection – Le-Le Wang – Science Translational Medicine

Involvement of propionate, citrulline, homoserine, and succinate in oral microbiome metabolite-driven periodontal disease progression – Chikako Ishihara – Scientific Reports

Regulation of tryptophan-indole metabolic pathway in Porphyromonas gingivalis virulence and microbiota dysbiosis in periodontitis – Jing Ding – NPJ Biofilms and Microbiomes

Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis – Ying Liao – Cell Reports. Medicine

Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types – Zizheng Wang – Microbiology Spectrum

Other Sites

Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples – Hayden N Brochu – Microbiology Spectrum

Bacteria in the brain: do they have a role in the pathogenesis of Alzheimer’s disease? – Arnav Bhattacharya – Current Opinion in Psychiatry

Beneficial Microbes and Compounds

Microbiome modulation of implant-related infection by a novel miniaturized pulsed electromagnetic field device – João Gabriel S Souza – NPJ Biofilms and Microbiomes

Enterocloster clostridioformis protects against Salmonella pathogenesis and modulates epithelial and mucosal immune function – Benjamin S Beresford-Jones – Microbiome

Antibacterial activity and impact on keratinocyte cell growth of Cutibacterium acnes bacteriophages in a Cutibacterium acnes IA(1)- colonized keratinocyte model – Juan C Farfán-Esquivel – Current Research in Microbial Sciences

Microbiota-derived urolithin A in monoclonal gammopathies and multiple myeloma therapy – Alba Rodríguez-García – Microbiome

Environmental Microbiome / Ecology

The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns – Rodolfo A Salido – Cell

Residence Time Structures Microbial Communities Through Niche Partitioning – Emmi A Mueller – Ecology Letters

Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission – Reena Debray – Microbiome

Microbiome Analysis: Resources, Tools and Techniques

Tandem metabolic reaction-based sensors unlock in vivo metabolomics – Xuanbing Cheng – PNAS

Review: Antarctic bacterial natural products: from genomic insights to drug discovery – William Medeiros – Natural Product Reports