Research linking gut microbes to autism is deeply flawed, critics say. Amid growing investment in the field, a new paper argues it rests on shaky foundations. | Science | AAAS www.science.org/content/arti...

Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...

Interested in #drugs, #microbiome and #antibiotic resistance, then check out our paper on the effects of over 300 drugs on the gut microbiome. Exciting results as well on the role of antibiotic resistance defining how microbiomes respond to drugs. @quadraminstitute.bsky.social rdcu.be/eMmcT

Looks interesting 👀: Distinguishing diet- and microbe-derived metabolites in the human gut microbiomejournal.biomedcentral.com/articles/10....

I welcome another promising tool to analyze strain-resolved WMS data! #microbiome

👀 What an interesting and under-explored idea!

SAVE THE DATE: 27 October, 2025 and join speakers from both illumina and #MVIF! Registration for the webinar is free: emea.illumina.com/events/webin...

👀 One of the first two articles published for the collection on #Microbiome and Reproductive Health! link.springer.com/collections/...

Happy to share this paper in final form rdcu.be/eH8tj, with more info on neuronal responses and potential mechanism of actions! The results suggest that there is neural interoception of microbial metabolic state 🧠🦠 We hope they can inspire more work in this area!

our software, microbetag, for the annotation of microbial co-occurrence networks with phenotypic traits & metabolic complementarities was just published A Cytoscape app is also available to make your life easier (and prettier) #microbiome #metabolic-modeling #networks

👀 This looks really interesting–being able to understand genomic context and assess species carriage of #ARGs from WMS data. #microbiome

We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome. We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated. Funded by a new grant from MIT-HEALS.

🧬 Research from the American Gut Project shows that people who eat 30+ different plants per week tend to have a more diverse gut #microbiome than those eating under 10. At Tiny Health, we're running a fun 7-day challenge to help you get there—plus one winner gets a gut health test ($199 value)!

MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes genomebiology.biomedcentral.com/articles/10.... #jcampubs

Authors argue that integrating metagenomics, culturing, and experimental validation to study hidden yet ecologically significant microbial species will advance our understanding of the microbiome in health and disease, and inform next-gen therapeutics leveraging the full diversity of the gut.

There are two recent papers that use sourmash in creative ways - and it gladdens my heart! pubmed.ncbi.nlm.nih.gov/40812187/ by @silask.bsky.social et al looks cleverly at human gut subspecies. www.biorxiv.org/content/10.1... by @rayanchikhi.bsky.social et al counts billions of k-mers. Super neat!

A Nature Outlook article reports on the preliminary evidence that microbiota-based treatments can be beneficial for people with mood disorders, such as depression and anxiety. But how these interventions work is not clear, and human trials are needed. #microbiome #medsky 🧪

1/3 🧬 Exciting news from my colleagues at Tiny Health! New study: A personalized #microbiome program helped C-section babies develop more normal gut microbiomes AND showed 83% lower odds of atopic dermatitis!

Just came across this preprint: groups at @broadinstitute.org and MGH developed a low-cost, #CRISPR based diagnostic for pathogenic bacteria and #AMR genes from blood cultures.

The potential relevance of FMT as a #microbiome augmenting intervention for #obesity management and metabolic health www.nature.com/articles/s41...

This looks really promising! It’s a step in the right direction to drill down to a more function based microbiome analysis while still maintaining taxonomic information.

Congrats to postdoc Zhe Zhou on her paper out today in @cp-cellhostmicrobe.bsky.social showing that gut bacteria cross-feed a common dietary antioxidant to produce energy under anaerobic conditions. Thanks to collaborators Angela Jiang and Xiaofang Jiang at NIH. www.sciencedirect.com/science/arti...

Is the gut microbiota composition in the 1st week of life linked to viral lower respiratory tract infections (vLRTIs) in early childhood? Here, work using the BBS birth cohort identifies Bifidobacterium longum-dominated cluster linked to lowest vLRTI rates 🔗 www.sciencedirect.com/science/arti...

This study published today finds "a more diverse gut microbiome is generally associated with healthier glucose spike metrics." It's certainly not implying causality, but it is very interesting to see the association!

#WeekendRead! #EveryCellIsAnImmuneCell! #TollPower! Kaelberer Bohorquez &co show @nature.com that #TLR5 signaling in response to flagellin drives neuropeptide PYY release by gut colonic neuropod cells, activating vagal neurons that signal to #brain, reducing feeding via a “neurobiotic sense”!

The Lynch lab’s latest research delves into the gut microbiome’s influence on peanut oral immunotherapy outcomes. The study identifies specific bile acids and microbial metabolic signatures that predict treatment success. #Microbiome #AllergyResearch #UCSF rdcu.be/ewbEn

Our lab just completed a +6 year #marathon, describing for the first time that the #microbiome is critical for #exercise - induced increases in antitumor CD8 T cell immunity and improved of #cancer #immunotherapy. www.cell.com/cell/fulltex...

Widespread Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis www.nature.com/articles/s42... Missing beneficial bacteria in infant guts linked to rising asthma and allergy cases medicalxpress.com/news/2025-07... Fecal samples from participants in 48 of 50 US states

Excellent review by @erikbakkeren.bsky.social et al in @cp-cellhostmicrobe.bsky.social Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering www.cell.com/cell-host-mi...

This month's editorial is an invitation to submit papers on clinical and translational aspect of the microbiome. This collection is a joint effort with @naturemedicine.bsky.social @natcomms.nature.com and @commsbio.nature.com #MicroSky #MicrobiomeSky 🦠⚕️🧪⚕️ www.nature.com/articles/s41...

Thrilled to share that our manuscript on strain-level gut microbiome variation across diverse populations and human phenotypes is out today in @cellpress.bsky.social Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n) www.sciencedirect.com/science/arti...

OPEN CALL for PhD positions in our lab through the semm_it program: 1️⃣ Microbiome signatures of early on-set colorectal cancer 2️⃣ High-resolution computational metagenomics for the study of human microbiome transmission More info: www.semm.it/education/op... Apply by June 9!

argNorm looks like a promising tool to analyze antimicrobial resistance genes from metagenomic data. Having tested and benchmarked different ARG databases and software suites in the past, argNorm would have come in handy. #microbiomesky #idsky #AMR

Exciting research out of Dan Littman’s group! Dan serves on our SAB. #immunosky #microbiomesky #allergysky #foodallergy

Microbial community-scale metabolic models (MCMMs) map gut microbiome composition & dietary context to functional outputs, at scale. Here, we describe these emerging tools & their utility to both basic & translational microbiome research. @natmicrobiol.nature.com www.nature.com/articles/s41...

This review touches on a lot of aspects of clinical #microbiome research. Solid read.

Welcome to Bluesky @foodallergyscience.org! #foodallergies

Nice study showing that 6-wk HAMSAB intervention in adults with T1D impacts gut mucosal immunity & host-microbiome metabolism. Some participants (2 responders/2 non-resp) then used as FMT donors in NOD mice to identify SCFA producers linked to anti-inflam + IgA prod. 🔗 www.nature.com/articles/s41...

Human microbiome acquisition and transmission www.nature.com/articles/s41... #jcampubs

We are still accepting registrations for this event! Please come join us and hear about cutting edge microbiome research.

📢Excited to announce a new collection open for submission - The Clinical Microbiome. 💉🦠 Led by @naturecomms.bsky.social with participation from @naturemedicine.bsky.social, @naturemicrobiol.bsky.social, and @commsmed.bsky.social Details: www.nature.com/collections/... #Microsky #MicrobiomeSky

New research into how the gut #microbiome interacts with and alters dietary plant small molecules

Come join us in Boston for this year's HCMPH Symposium on May 19th! This year's theme is "microbiome in food systems", however, any and all microbiome research is welcome!

Nice to see good methods being developped for long-reads metagenomic sequencing analyses. This one focuses on attempting to use coverage of long reads to assign AMR genes to host microbial species, something that's pretty hard to do with Illumina atm. Looks promising! www.nature.com/articles/s41...

Learn more & register at this link - huttenhower.sph.harvard.edu/biobakery2025/ #Microbiome #Metagenomics #bioinformatics 2/2

Wang et al. present a latent diffusion framework that rapidly generates diverse antimicrobial peptides. Of 40 candidates tested, 25 were active, with several showing in vivo efficacy, marking a promising AI approach to address drug-resistant pathogens. www.science.org/doi/10.1126/...

Always appreciate an ode to #Wolbachia, a fascinating bacteria that inhabits the reproductive tract (among other areas) of many insects. #Mosquito #Microbiome

Super proud of this paper on infant gut microbiome age coming from my lab. The paper has just been published with @springernature.bsky.social in @naturecomms.bsky.social. Read about it here: rdcu.be/d6cCw.

New study links #Microbiome to creeping fat in #CrohnsDisease via #Kynurenine metabolism Highlights: Commensal A. pulmonis drives CrF via macrophage-derived L-kynurenine Kynurenine activates AHR in adipocytes, promoting fat formation Blocking IDO1 or degrading kynurenine reduces CrF in mice

🧵 How does being a #vegan, #vegetarian or omnivore impact your gut #microbiome? 🥦 Find out in our new paper on gut microbiome signatures of vegan, vegetarian & omnivore diets & associated health outcomes across 21,561 individuals in @naturemicrobiol.bsky.social!🎉 1/10 www.nature.com/articles/s41...