Category Archives: Food Microbiology

January 28th , 2026

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Reproductive / Urogenital Microbiome & Host–Pathogen Interactions

The interactive relationship between Fusobacterium necrophorum, Bacteroides pyogenes, and Porphyromonas levii in driving inflammatory uterine disease – Dianjun Cao – springer nature

 Gut Microbiome, Diet, and Host Health

Total and different types of olive oil consumption, gut microbiota, and cognitive function changes in older adults – Jiaqi Ni – springer nature

A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate – Lena-Sophie Paul – springer nature

Environmental Microbiome & Antimicrobial Resistance (Resistome)

Beyond borders: plasmids drive a shared antibiotic resistome in European urban water systems

– Wanli He – springer nature

Spatial and temporal patterns of public transit aerobiomes – Russell J. S. Or – springer nature

Food Chain, Meat Microbiome & Resistome Dynamics

Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life – Elena Fernández-Trapote – springer nature

Microbiome–Immune System Interactions

Commensal microbe-derived butyrate enhances T follicular helper cell function to boost mucosal vaccine efficacy – Haeun Ko – springer nature

January 16, 2026

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Human Microbiome

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

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

Gut microbiome

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

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

Environmental Microbiome

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

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

Plant Microbiome

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

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

Bioinformatics

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

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

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

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

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

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

November 8, 2024

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Get ready for #MVIF 33 & register here https://cassyni.com/s/mvif-33
See you next week!


Ecology and evolution

Community conservatism is widespread throughout microbial phyla and environments – Lukas Malfertheiner – bioRxiv 

Gut microbiome

Fecal microbiota transplantation alters the proteomic landscape of inflammation in HIV: identifying bacterial drivers – Claudio Díaz-García – Microbiome

Insights into the gut microbiome of vitiligo patients from India – Sudhir Kumar – BMC Microbiology

Design and reporting of prebiotic and probiotic clinical trials in the context of diet and the gut microbiome – Kevin Whelan – Nature Microbiology

Pregnancy and Early Life Gut Microbiome: Influencing Factors and Health Implications – Trishla Sinha – Research Square

Gut and oral microbial compositional differences in women with breast cancer, women with ductal carcinoma in situ, and healthy women – Emma McCune – mSystems

Gut microbiota regulates stress responsivity via the circadian system – Gabriel S.S. Tofani – Cell Metabolism

Link to the post: https://twitter.com/gabriel_tofani/status/1853862878870446530

Oral microbiome

The role of the oral microbiota in the causal effect of adjunctive antibiotics on clinical outcomes in stage III–IV periodontitis patients – Sven Kleine Bardenhorst – Microbiome

Vaginal microbiome

Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study – Chloe Hicks – BJOG: An International Journal of Obstetrics and Gynaecology

Evaluation of the Vaginal Panel Realtime PCR kit (Vircell, SL) for diagnosing vaginitis: A comparative study with routinely used diagnostics – Isabel Amor – PlosOne

Animal experiments

The gut microbiome in patients with Cushing’s disease affects depression- and anxiety-like behavior in mice – Ding Nie – Microbiome

Food microbiome

Review: Novel fermentations integrate traditional practice and rational design of fermented-food microbiomes – Dillon Arrigan – Current Biology

In-depth characterization of food and environmental microbiomes across different meat processing plants – Coral Barcenilla – Microbiome

Bioinformatics

Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases – Sriram Ramesh – PlosOne 

Techniques

DNA Extraction Protocols for Animal Fecal Material on Blood Spot Cards – Ann-Katrin Llarena – bioRxiv

Link to the post: https://twitter.com/svetlana_up/status/1854091197498683755
Link to the presentation: https://github.com/SvetlanaUP/presentations/blob/main/How_to_give_a_good_online_presentation_11_2024.pdf

October 4, 2024

Posted on by

Happy Friday! And see you next week at MVIF!

Plastisphere microbiome

What harmful microbes are lurking in the world’s 7 billion tonnes of plastic waste? – Changchao Li – Nature

Respiratory microbiome

Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis – Hongbin Chen – npj Biofilms and Microbiomes

Vaginal microbiome

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

Oral microbiome

The intensive physical activity causes changes in the composition of gut and oral microbiota – Szymon Urban – Scientific Reports
⚽ “Twenty professional football players and twelve amateurs were invited to the study groups.”

Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome – Yuya Kiguchi – bioRxiv

The association between mode of childbirth delivery and early childhood caries: A comprehensive systematic review and meta-analysis – Li Xiang – PlosOne

Gut microbiome

What’s GABA got to do with it? A potential link between the microbiome, schizophrenia, and the endo-cannabinoid system – Ayala Glinert – Psychiatry Research

Changes in intestinal permeability and gut microbiota following diet-induced weight loss in patients with metabolic dysfunction-associated steatohepatitis and liver fibrosis – Dimitrios A. Koutoukidis – Gut Microbes

Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis – Yan Jia – Scientific Reports

Detailed Analysis of Prebiotic Fructo- and Galacto-Oligosaccharides in the Human Small Intestine – Mara P. H. van Trijp – Journal of Agricultural and Food Chemistry

Dietary fibers boost gut microbiota-produced B vitamin pool and alter host immune landscape – Erica T. Grant – Microbiome

Human milk microbiome

Maternal HIV infection and the milk microbiome – Nicole H. Tobin – Microbiome

Viruses and phages

Genomic surveillance as a scalable framework for precision phage therapy against antibiotic-resistant pathogens – Mihály Koncz – Cell

Animals

Differential interactions of Rickettsia species with tick microbiota in Rh. sanguineus and Rh. turanicus – Apolline Maitre – Scientific Reports 

Animal experiments

Disruption of the intestinal clock drives dysbiosis and impaired barrier function in colorectal cancer – Rachel C. Fellows – Science Advances

Photoperiod effects on corticosterone and seasonal clocks in cafeteria-induced obese fischer 344 rats are influenced by gut microbiota – Verónica Arreaza-Gil – Scientific Reports 

Plant, root, soil microbiome

Closing the gap: examining the impact of source habitat proximity on plant and soil microbial communities in post-mining spoil heap succession – Lenka Mészárošová – Frontiers in Microbiology

Bacterial Communities from the Antique Roman City of Carnuntum (Austria):16S r-RNA-Based Comparison of Soil Samples from Different Archaeological Horizons – Johann Michael Köhler – preprints

Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient – Viviana Freire-Zapata – Nature Microbiology

Phosphorus availability influences disease-suppressive soil microbiome through plant-microbe interactions – Yifan Cao – Microbiome

Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils – Luiz A. Domeignoz-Horta – Nature Communications

Bacterial diversity of cantaloupes and soil from Arizona and California commercial fields at the point of harvest – Madison Goforth – Plos One

Drinking water microbiome

Making waves: From tap to gut- exploring the impact of drinking water on gut microbiota – Hanieh Shakeri Moghaddam – Water Research

Bioinformatics

Taxometer: Improving taxonomic classification of metagenomics contigs – Svetlana Kutuzova – Nature Communications

Jaeger: an accurate and fast deep-learning tool to detect bacteriophage sequences – Yasas Wijesekara – bioRxiv

Emergent ecological patterns and modelling of gut microbiomes in health and in disease – Jacopo Pasqualini – Plos Computational Biology

Technique

Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing – Harry T. Child – Access Microbiology

Microbial community interactions on a chip – Duane S. Juang – PNAS