Very nice paper !

Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum - Nature Communications Escherichia coli is widespread in healthy breastfed infants, yet its ecological role is unclear. Here, the authors provide insights into the mechanisms supporting its persistence and co-existence with...

New paper out in Nature Comms 🎉

Congrats to first author @sekid.bsky.social & thanks team & collaborators

We show that B. bifidum & E. coli can cooperate in the breastfed infant gut through nutrient cross-feeding, helping shape early-life microbiome development 🦠👶

www.nature.com/articles/s41...

Cross-feeding enables robust coexistence between four bacterial species www.biorxiv.org/content/10.64898/2026.04...

Epigenetic fingerprints link early-onset colon and rectal cancer to pesticide exposure - Nature Medicine An analysis of exposome traits in patients with early-onset colorectal cancer (CRC) (<50 years) compared with late-onset CRC (≥70 years) based on epigenetic markers shows that pesticide usage, in p...

Delighted to share our new paper which has just been published in Nature Medicine. www.nature.com/articles/s41...

Microbiome signature of Parkinson’s disease in healthy and genetically at-risk individuals - Nature Medicine Microbiome analysis suggests that gut microbial changes in Parkinson’s disease evolve progressively from healthy individuals to genetically at-risk individuals to clinically affected patients, with th...

We've known the gut-brain axis is a key underpinning of Parkinson's disease. Today, for the 1st time, a gut microbiome signature denoting risk found in healthy individuals with genetic predisposition

nature.com/articles/s41...

Nutrient availability shapes the diversity and structure of microbial communities www.biorxiv.org/content/10.6... #jcampubs

Nutrient availability shapes the diversity and structure of microbial communities | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice Nature Microbiology, Published online: 17 April 2026; doi:10.1038/s41564-026-02326-2Phosphoribosyl pyrophosphate synthetase from Faecalibacterium prausnitzii inhibits PD-L1 trafficking to boost anti-tumour immunity and potentiate anti-PD-1 immune checkpoint inhibitor therapy during colorectal cancer.

Out Now! Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice #MicroSky

Predicting competition and substrate preferences for targeted microbiome alteration Microbiome science has greatly expanded our understanding of microbial life and its roles in the environment and human health. Yet microbiome science …

Congratulations to my colleague Karsten Zengler and coauthors on this exciting study, "Predicting competition and substrate preferences for targeted microbiome alteration". Our amazing co-mentored graduate student, Grant Norton, played a major role in the work.
www.sciencedirect.com/science/arti...

Truly honored and grateful 🙏 to be awarded the Gut Microbiota International Grant 2026 from the Biocodex Microbiota Foundation!

We are ready to explore some exciting fundamental microbial ecology questions regarding microbiome resilience.🦠

👉 www.biocodexmicrobiotafoundation.com/internationa...

How to measure microbiome health?

Commentary proposes adaptive coherence: capacity of host-microbiome systems to sustain integrated function via reorganization. Reframes health as emergent & relational, w/measurements of adaptability/functional integrity
www.cell.com/cell-host-mi...

Microbial communities can harbor many species that do not coexist in pairs, yet can coexist in the full community. Here we provide the mathematical foundations of emergent coexistence, and explain why it can't be predicted from pairwise tests journals.plos.org/ploscompbiol...

You need to make AI guidelines for your lab Here's why you should, and how to start

I wrote about why every lab should have AI use guidelines, and how to do it.

open.substack.com/pub/blekhman...

Diet–microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition - Nature Medicine Analyses of more than 10,000 participants from the Human Phenotype Project revealed distinct, persistent food–microbiome associations that can be used to simulate personalized dietary interventions to improve cardiometabolic health.

Diet is strongly associated with the gut microbiome 

Eran Segal & colleagues analyzed diet and microbiome data from 10,000+ people and found specific links between the microbiome and foods relevant for cardiometabolic health

@naturemedicine.bsky.social 

Micro-scale spatial metagenomics opens a new era in microbiome ecology Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, g...

Micro-scale spatial metagenomics opens a new era in microbiome ecology

@cp-trendsmicrobiol.bsky.social Opinion from @mizrahilab.bsky.social

www.cell.com/trends/micro...

Cool new paper just dropped from the @nanditagarud.bsky.social & @ctropini.bsky.social labs!

Looks like the gut is a (well) mixed bag! Strain frequencies were invariant throughout the gut, even if species abundances differ along the length of the (mouse) gut.

www.nature.com/articles/s41...

Interspecies interactions drive bacterial proteome reorganization and emergent metabolism - Nature Ecology & Evolution An analysis of the responses of 15 diverse human gut bacteria in more than 100 pairwise co-cultures reveals extensive remodelling of the bacterial proteome and metabolome in response to the presence o...

Check out our new paper applying fast DIA proteomics to bacterial co-cultures at scale. www.nature.com/articles/s41...
@kiranrpatil.bsky.social

Future events All future events of the Microbiome Virtual International Forum

Join the next #MVIF!

In April 2026 Gene Tyson will give a keynote talk,
the May 2026 event will be with Georg Zeller as a keynote,
and
in June 2026 we will welcome Julie Huber @julesdeep.bsky.social

Dates and details here: www.microbiome-vif.org/en-US/-/futu...

Image of the cover of the 1st volume of ISME Host Microbe a new official journal of the International Society for Microbial Ecology. Cover images shows a plant stomata with bacteria around and entering.

Excited to announce our new journal from @isme-microbes.bsky.social ISME Host Microbe is live and now accepting submissions. Look forward to receiving your papers! #Microsky 🧫 🦠

Host-derived nitrate fuels indole production by Escherichia coli to drive chronic kidney disease progression Chronic kidney disease (CKD) is linked to an elevated fecal abundance of Enterobacteriaceae, but the ecological drivers of this shift and its impact on disease progression remain unclear. The uremic t...

#NatMicroPicks

Host-microbe cycle in chronic kidney disease 🦠⚕️

Inefficient removal of indole derivatives due to kidney dysfunction in mice raises the levels of nitrate that in turn promote indole producing E. coli

#MicroSky

www.science.org/doi/10.1126/...

Gut motility as a driver of microbial community architecture and host–microbe evolution Digestive systems are dynamic, contractile ecosystems that continually shape the physical and chemical niches inhabited by gut microbes. Patterns of mixing and propulsion generate flow, shear, and nut...

Gut motility as a driver of microbial community architecture and host–microbe evolution

@cp-trendsmicrobiol.bsky.social from Sahar El Aidy

www.cell.com/trends/micro...

Blautia wexlerae Transforms Dietary Fatty Acids to Activate Enteroendocrine Signaling and Improve Metabolic Health in Mice and Humans www.biorxiv.org/content/10.64898/2026.03...

Announcing StrainVis! 🦠🧫🧪

www.biorxiv.org/content/10.6...

This nifty web-based tool allows you to visualize your strain level analyses. You can combine ANI and synteny based analyses and it will make all kinds of cool publication ready plots for you - examples follow. By Hagay Enav and Inbal Paz:

Even among healthy people, immune systems operate at different baseline levels.

In our new Cell paper, we show that these immune states are stable over time and are associated with the gut microbiome. 🧵
@cp-cell.bsky.social
#Immunology #SystemsImmunology

We combine spatial RNA-seq with enzymatic in situ polyadenylation to greatly improve bacterial RNA capture in intestinal tissue, generating high-res maps of microbiome biogeography and host–microbiome interactions.

A deeper-dive in our preprint thread:

bsky.app/profile/ntek...

Eubiota: Modular Agentic AI for Autonomous Discovery in the Gut Microbiome www.biorxiv.org/content/10.64898/2026.02...

Reflections on MVIF #46 (Feb. 9-11)

We brought together researchers across continents for an inspiring exploration of microbiome science. Whether joining from the Atlantic (ATL) or Pacific (PAC) regions, our community connected to advance knowledge that transcends borders.

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So thrilled to share episode 2 of #MVIFconversations with you all!

Getting to sit down with @bykriscampbell.bsky.social was such a privilege! If you're curious about where microbiome science is headed and why rigorous science communication matters more than ever, this one's for you.

1/2

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of gut health - Nature Reviews Gastroenterology & Hepatology This Consensus Statement provides a definition of the term ‘gut health’, as well as a discussion of the relevant domains that contribute to gut health and a framework for appropriate use of the term i...

Excited to share our latest publication! 🎉
This consensus statement, led by @isappscience.bsky.social, establishes an evidence-based definition of gut health relevant to clinical practice & dietary & biotic interventions.
www.nature.com/articles/s41...
#GutHealth #Microbiome #ISAPP #DigestiveHealth

Healthy dietary patterns, longevity genes, and life expectancy: A prospective cohort study Healthy dietary patterns are linked to longer life expectancy and can be adapted to personal preferences and cultural traditions.

"Healthy dietary patterns, longevity genes, and life expectancy: A prospective cohort study" www.science.org/doi/10.1126/...

TLDR:

Dietary component most associated with a longer life: dietary fiber

Dietary components most associated with shorter life: red meat and sugary drinks