Category Archives: Human reproductive or urinary

July 31, 2026

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Diet, Gut Health & Microbiome

Dietitian-led intervention to manage constipation in Parkinson’s disease: Study protocol for a parallel-group randomized controlled trial (NUTRI-GUT-PD) – Juliana Heitich Brendler – PLOS ONE

Efficacy and safety of prebiotics, probiotics, and synbiotics on hemoglobin and anemia in the pediatric population: A systematic review and meta-analysis – Gladys Estheysi Elías Solís – PLOS ONE

Pharmacokinetic model selection for infliximab based on inflammatory bowel disease phenotype and severity: Toward model-informed precision dosing – Ana Homšek Ilić – PLOS ONE

Pathogens, Infection & Host–Microbe Interactions

Neotropical bats as sentinels for emerging zoonoses in Central America: A case study identifying Trypanosoma cruzi in bats from Belize using metagenomic next-generation sequencing – Elissa G. Torgerson – PLOS Neglected Tropical Diseases

Viral replication dynamics: Coinfection and superinfection of Vero cells with Zika virus and West Nile virus or Zika virus and Mayaro virus – Larissa Krokovsky – PLOS ONE

Phenotypic and molecular characterization of Salmonella enterica isolated from retail beef in Peshawar, Pakistan – Muhammad Jawad Ullah – PLOS ONE

Longitudinal study of a rodent invasion reveals shifts in host pathogen interactions – Andrew McManus – PLOS ONE

Noncanonical bactericidal activity of teleost type I interferon is conferred by a membrane-targeting C-terminal peptide – Han Zhang – PLOS Pathogens

A single DNA methylation site regulates cell fate during Clostridioides difficile sporulation – Pola Kuhn – PLOS Genetics

Microbial Genomics & Systems Biology

A systems biology approach to find representative genes in Acute Myeloid Leukemia– Behnam Aghajan – PLOS ONE

Aquatic & Animal Microbiology

Influence of salinity on growth, nutrient utilization, and gene expression of giant freshwater prawn (Macrobrachium rosenbergii) – Farhana Ahamed Shanila – PLOS ONE

Metabolism, Inflammation & Human Health

Integrated computational analysis identifies FABP4, PTGS2, and HPGD as key molecular targets linking PET microplastic exposure to metabolic dysfunction-associated steatotic liver disease – Yi Zhang – PLOS ONE

Exploring the mechanism of Shuangyu Granule in regulating immune-inflammatory responses in influenza through UPLC-Orbitrap-MS/MS, GC-MS, and network target analysis – Ling Sun – PLOS ONE

Cardiometabolic risk pathways in adults with disabilities: A structural equation model of diet quality and functional ability – Radwan Qasrawi – PLOS ONE

Neuroscience & Neurodegeneration

Research advances in key genes and regulatory mechanisms of posttranslational modifications in Parkinson’s disease – Bangzhi Wang – PLOS ONE

Clinical & Healthcare Research

HF-OCAQ: Oral comfort assessment in heart failure patients – Mei Lu – PLOS ONE

Mental Health

Spirituality as a coping resource: Towards integration into mental health framework – Sajama Nepali – PLOS Mental Health

May 8, 2026

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See you next week at MVIF!

#MVIF 49 program is out! 🤩 Free registration: cassyni.com/s/mvif-49Highlights: 🇮🇱 Netta Barak 🇳🇬 Gandonu Selome Ruth⭐️ Sponsor spotlight by Dagmara Lewandowska #IntegraBiosciencesKeynote:🇩🇪 Georg ZellerTalks:🇲🇦 Suleiman Aminu🇨🇳 Hongbin Liu🇳🇱 Jiyang Chan

— Microbiome Virtual International Forum (@microbiomevif.bsky.social) 2026-04-30T09:34:17.767Z

Gut microbiome

Gut microbial diversity and inferred capacity to produce short-chain fatty acids are associated with acute stress reactivity in healthy adults – Thomas Karner – Neurobiology of Stress

In our new study at @univie.ac.at , gut microbiome composition was linked to stress reactivity. Higher microbial diversity and inferred butyrate-producing capacity were associated with stronger cortisol reactivity, which may reflect a more adaptive response. 🧠🦠

— Thomas Karner (@thomaskarner.bsky.social) 2026-04-22T15:08:33.422Z

Non-concussive head impacts sustained during American football correlate with changes in gut microbiome diversity and composition – Zachary J. Pelland – PlosOne

Gut microbiome is associated with recurrence-free survival in patients with resected high-risk melanoma receiving adjuvant immune checkpoint blockade – Mykhaylo Usyk – Cell

Genome-wide sweeps create ecological units in the human gut microbiome – Xiaoqian Annie Yu – Nature

Gut microbiome features associated with Bifidobacterium colonization predict personalized probiotic persistence patterns – Tarini Shankar Ghosh – Nature Communications

Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri – Youssef El Mouali – Cell Host & Microbe 

Review: The impact of artificial sweeteners on bacterial physiology and the microbiome – Ciaram Staber – Trends in Microbiology 

Habitual coffee intake shapes the gut microbiome and modifies host physiology and cognition – Serena Boscaini – Nature Communications

If you missed it earlier this week check out the video on new research led by APC's @jfcryan.bsky.social & @moloneyger.bsky.social where they reveal for the first time how #coffee influences communication between the gut and the brain. buff.ly/x884r4f #GutBrainAxis #Microbiome #CoffeeScience

— APC Microbiome Ireland (@apcmicrobiomeirel.bsky.social) 2026-04-24T12:54:33.975Z

Urinary microbiome

Fatty acid auxotrophy as driver of Lactobacillus symbiosis in the female urinary tract – Michael L. Neugent – BioRxiv

Oral microbiome

Integrative host–microbiome modeling uncovers the implication of oral–gut translocation in advanced cirrhosis – Yi Jin – iMeta

Strain-level translocation and enrichment dynamics of oral bacteria in the lower gastrointestinal tract of stunted children – Simon Yersin – Gut Microbes

📢 new paper alert! 📢Do we find the same #bacteria in the mouth and in the gut of stunded children?Go find out: doi.org/10.1080/1949…#microbiome #gut #gutmicrobes #metagenomicWith @vonaeschlab.bsky.social at @dmf-unil.bsky.social

— Simon Yersin (@yersim.bsky.social) 2026-04-07T12:42:09.651Z

Plant microbiome

The Anna Karenina principle in the assembly of plant microbiome under pathogen stress – Da Li – npj Biofilms and Microbiomes

Bioinformatics

Evaluating Reference-Independent Pipelines for the Detection of Spreading Organisms in Metagenomic Datasets – Nikolay Sergeevich Popov – BioRxiv

Learning the Language of the Microbiome with Transformers – Neythen J Treloar – BioRxiv

Holobiont

Viewing ourselves as nature: Holobiont literacy influences nature connectedness – Jake M. Robinson – Ambio

What happens when people learn that humans are not standalone organisms, but walking ecosystems?Our new paper explored whether learning about the #holobiont concept – humans are symbiotic assemblages of a host & trillions of microbes – influences nature connectedness.1/

— Jake Robinson (@jake1.bsky.social) 2026-05-06T22:07:54.693Z

April 29 , 2026

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Gut microbiome

Gut microbiota induces dysspermatogenesis via microbial-derived phenylacetylglycine in Ggt1-deficient mice – Jinhua Tang – Microbiome

Puerarin modulates the gut-liver-ovarian axis to ameliorate reproductive aging in breeder hens – Zhenwu Huang – microbiome

Gastrointestinal microbial nitrogen metabolic landscape underlies nitrogen utilization efficiency of goats fed distinct dietary protein sources – Yechan Zhao – microbiome

Environmental Microbiome

Unveiling microbial risks in Chinese household dust: a comprehensive analysis from absolute abundance to virulence unit – Lu Long – microbiome

Livestock Microbiome

Curcumin modulates hepatic pyroptosis-autophagy crosstalk induced by aflatoxin B1 via rumen microbiota-blood-liver axis – Tongwei Liu – microbiome

Plant Microbiome

Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot – Chuan You – microbiome

Microbiome & Cancer / Immunology

Trimethylamine-producing microbe Bacillus megaterium KCTC 3007 promotes antitumor immunity in endometrial cancer via type I interferon response pathways – Kyungchan Min – microbiome

March 19, 2026

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Gut microbiome

Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals – Gabriel Baldanzi – Nature Medicine

Spatial transcriptomics maps host–gut microbiome biogeography at high resolution – Ioannis Ntekas – Nature Microbiology

Respiratory Microbiome

Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19 – Abigail Glascock – Nature Microbiology

Dysbiosis of the nasal microbiome is associated with prospective acute exacerbation of COPD – Cristian Roca – Microbiome

Animal Microbiome

Towards standardization in pig microbiome research based on a comprehensive twenty-year review – Samuel Onyilokwu Enokela – Animal Microbiome

Longitudinal source-sink dynamics of fecal litter and farm indoor environmental resistomes in broiler chicken and Cherry Valley ducks – Peter Fauszt –  Animal Microbiome

Oral Microbiome

Denture-associated oral microbiome in dentate and edentulous older adults living in long-term care facilities – Muhammed Manzoor – Journal of Oral Microbiology

Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia – Jun Hyung Cha – Journal of Oral Microbiology

Water Microbiome

Water mass specific genes dominate the Southern Ocean microbiome – Emile Faure – Nature Communications

Plant Microbiome

Impacts of climate extremes on plant pathogens, microbiomes and plant health – Chao Xiong – Nature Reviews Microbiology

Heritability of the Pinus radiata root microbiome – Natalie Graham – Frontiers in Plant Science

Bioinformatics

DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models – Awais Qureshi – BMC Bioinformatics

RP3Net: a deep learning model for predicting recombinant protein production in Escherichia coli – Evgeny Tankhilevich – Bioinformatics

MetaFX: feature extraction from whole-genome metagenomic sequencing data – Artem Ivanov – Bioinformatics

January 28, 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 – microbiome

 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 – microbiome

Environmental Microbiome & Antimicrobial Resistance (Resistome)

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

– Wanli He – microbiome

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

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 – microbiome

Microbiome–Immune System Interactions

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

Animal microbiome

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

January 23, 2026

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Animal microbiome

Bacterial-archaeal co-occurrence in honey bee gut microbiomes across host species and management regimes -Jian-Ping Ying –PLOS ONE

Bacterial community associated with the surface and inside of centipede forcipules: Identification and characterization -Yasutaka Tanaka – PLOS ONE

Human reproductive & urinary microbiome

Vaginal chlorhexidine gluconate versus fluconazole for recurrent vulvovaginal candidiasis: A randomized noninferiority trial – Cathrin Alvendal – PLOS ONE

Infection and transplantation / Host–microbe interactions

DnaK supports intracellular persistence of Staphylococcus xylosus and confers mechanical resilience to a human breast cancer cell line – Lei Ye – PLOS ONE

Investigation of a viable but non-culturable state in Porphyromonas gingivalis and host cell invasion – Adenrele Oludiran – PLOS ONE

Microbial ecology & symbiosis

Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis – Sunnyjoy Dupuis – PLOS ONE

Oral microbiome & animal experiments

Effects of glycyrrhizin on healing and prevention of recurrent aphthous stomatitis in hamster models – Fumie Shiba – PLOS ONE

Plant, soil & ecological microbiome

Tree species-specific strategies of soil aggregation driven by SOC–GRSP coupling under nitrogen addition and precipitation reduction -Mingxin Zhou – PLOS ONE

Microbial genomics & bioremediation

Genomic analysis of Acinetobacter baumannii DUEMBL6 reveals diesel bioremediation potential and biosafety concerns – Nizam Uddin – PLOS ONE

Human gut & inflammatory disease

Identification of hypoxia- and mitophagy-related diagnostic biomarkers for ulcerative colitis based on bioinformatic analysis and machine learning – Zewei Sheng – PLOS ONE

Oral & dental archaeology / Ancient microbiome

Paleo-proteomic analysis of Iron Age dental calculus provides direct evidence of Scythian reliance on ruminant dairy – Jaruschka Pecnik – PLOS ONE

Cancer & clinical oncology

Radiomics profiling combined with clinical risk factors for preoperative lymphatic metastasis prediction in colorectal cancer: A multicenter study – Fangda Guo – PLOS ONE

Toxicology & respiratory health

Potential mechanisms and effects of AFB1-induced asthma: A comprehensive analysis based on network toxicology and molecular docking – Zhiyue Yu – PLOS ONE

Human development & diet (archaeology / isotopes)

Fed the same way? Exploring the influence of breastfeeding, weaning, and childhood diet on adult sex ratios through stable isotope analysis of incremental dentine in Medieval Tuscany – Alessio Amaro – PLOS ONE

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 13, 2025

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General Microbiome

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

Gut microbiome

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

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

Vaginal microbiome

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

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

Respiratory Microbiome

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

Animal microbiome

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

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

Water Microbiome

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

Bioinformatics

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

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

October 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

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