New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. https://doi.org/10.1038/s41564-026-02471-8

Excited to share the first paper from the Urtecho Lab! We built a framework to move fecal microbiota transplantation (FMT) from a black-box therapy to precision medicine for gut disorders 🧵 doi.org/10.1080/19490976.2026.2725403 #Microbiome. #OpenAccess

Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies

Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable and donor-selection strategies remai...

doi.org

Very happy that our paper Obligate cross-feeding of metabolites is common in soil microbial communities just came out in Nature Microbiology. See here 👇 Paywalled version: www.nature.com/articles/s41... Free read-only version: rdcu.be/fBHAb

Obligate cross-feeding of metabolites is common in soil microbial communities - Nature Microbiology

Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...

nature.com

📢 Flex Funds Call for 2027 is now open! Contribute to advancing #FAIRData, #OpenScience, infrastructure, workflows, or training in #microbiology! 💶 Funding: €10,000–€40,000/project 📅 Funding period: Apr–Dec 2027 📆 Application deadline: Oct 11 👉️ More details: nfdi4microbiota.de/newsroom/fle...

From @jfy133.genomic.social.ap.brid.gy @maxibor.bsky.social @christinawarinner.bsky.social et al., in @plos.org #Computational #Biology | De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag | #Education #Genomics #Microbes | 🧬🖥️🧪🔓 ⬇️ journals.plos.org/ploscompbiol...

De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag

Author summary Advancements in genomic sequencing analyses are increasingly allowing researchers to reconstruct the genomes of microbial ‘dark matter’—those microbial species that are difficult to iso...

journals.plos.org

Check out the MiDAS global genome catalog preprint! We applied Nanopore long-read metagenomics to 83 selected samples from the MiDAS 4 global survey of wastewater treatment plants to create a genome catalog covering all core genera in the activated sludge microbiome. www.biorxiv.org/content/10.6...

Absolutely bonkers how amazing this speaker lineup is. Can't make it myself, but this looks like a great conference here.

Typas Lab@typaslab.bsky.social · 2mo ago

Join us at EMBL Heidelberg from 8–10 Dec 2026 for the conference “Gut Microbe Function” and explore the latest advances in the field. Submit your abstract, register, and join the discussion! 📝Abstract deadline 15 Sep 2026 📍On-site registration deadline 27 Oct 2026 www.embl.org/about/info/c...

Proud to share our single-cell transcriptomics approach for the microbiome by instrument-free split-pool barcoding - metaSPLiT, developed by the incredible @monochamussutor.bsky.social together with @gibbological.bsky.social, @cdiener.com, et al. at @isbscience.org

Dmitry Sutormin@monochamussutor.bsky.social · 2mo ago

🚀 Thrilled to share our first metaSPLiT preprint from @annabiosys.bsky.social's lab in collaboration with @gibbological.bsky.social! Explore hidden bacterial phenotypic heterogeneity in the human gut microbiome and discover the concept of "physiological guilds": www.biorxiv.org/content/10.6...

Dear microbiome enthusiasts: I'm excited to be moving my lab to New York University this fall (& the NYU Institute for Engineering Health); with joint-appointment @isbscience.org I'm hiring a postdoc @ NYU to look at diet-driven evolution in the gut: apply.interfolio.com/189980 Please share! 🦠🤓

Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics https://www.biorxiv.org/content/10.64898/2026.07.30.741866v1

New reading list for July, before the summer break! ☀️ Some studies that caught my eye in the field of microbiome research, population health, microbial genomics, ecology, evolution and other topics. Comments my own. Hope this will be useful to some of you! mericlab.com/blog/2026-07/

I'm happy to announce the release of GlobDB r232! This version contains 346,233 bacterial and archaeal genomes, based on 26 datasets. More info globdb.org 🦠🖥️🧬

Interesting article by Glass et al. on using metabolic modeling to find new antibiotics for the vaginal microbiome.

Nature Microbiology@natmicrobiol.nature.com · 4mo ago

Out Now! Genome-scale metabolic modelling identifies vaginal microbiome members as potential probiotics #MicroSky

Milliardenkürzungen bei Unis? Das hätte massive Folgen für die Steiermark! Setzen wir bei den Demos ein Zeichen: 🟢 Wien: 27. Mai 2026, 13 Uhr, Hauptgebäude der Universität Wien, Universitätsring 1​ 🟢 Graz: 28. Mai 2026, 14.30 Uhr, Wilhelm-Fischer-Allee am Stadtpark, Graz #unisretten

New online! Sequencing what we eat

New online! Next-generation probiotics: an outlook into current applications and future developments

Next-generation probiotics: an outlook into current applications and future developments

Nature Reviews Microbiology, Published online: 08 May 2026; doi:10.1038/s41579-026-01311-0In this Review, Kern, Tofield, Frame and Elinav discuss recent advances in the design of next-generation probiotics, from identification of candidates to therapeutic applications across diverse disease contexts, and highlight major challenges and the potential of artificial intelligence to develop effective, personalized probiotics with therapeutic functions.

dlvr.it

Very excited to share our new paper out in Nature. Congrats to Xiaoqian (Annie) Yu and all the coauthors. www.nature.com/articles/s41...

I like how all the p-values are like 10^-300. Take that power analysis.

Theo Sanderson@theo.io · 6mo ago

Indeed.. here is "generate the first page of a great Nature paper that will get lots of citations. It must be very novel."

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...

Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study

The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

merenlab.org

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...

Paper out: Profiling of lytic phage infection in individual B. fragilis cells with bacterial scRNA-seq. Congratulations Anika Gupta, Norma Morella, @monochamussutor.bsky.social Dmitry Sutormin et al, in collaboration with Georg Seelig (UW) and Neel Dey (Fred Hutch). www.nature.com/articles/s41...

Mikrobiom: Hype oder klinische Evidenz? Am 20.05.2026 bietet die Fortbildung „Medizinische Mikrobiomforschung“ fundierte Einordnung, organsiert von @medunigraz.at, JKULinz & @fwf-at.bsky.social CoE MicroPlanet Aktuelle Forschung, Evidenzlage zu Diagnostik, FMT, Probiotika.

Out Now! Gut bacteria ammonia production restores acetylcholine neurotransmission and bowel motility #MicroSky

Gut bacteria ammonia production restores acetylcholine neurotransmission and bowel motility

Nature Microbiology, Published online: 26 February 2026; doi:10.1038/s41564-026-02292-9Acetylcholine levels are reduced in gut dysmotility conditions. We find that gut acetylcholine levels induce a compensatory increase in gut microbiota urease activity and ammonia production. By upregulating presynaptic Cav2.1 calcium channels in enteric neurons, ammonia enhances calcium influx and restores acetylcholine release neurotransmission, revealing a microbiota-driven mechanism that preserves gut motility.

go.nature.com

Our latest is out today in @plosbiology.org: "Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials" @isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social doi.org/10.1371/jour...

Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials

Prebiotic and probiotic interventions can induce therapeutically relevant shifts in the human microbiome, but their effects are variable across individuals. This study shows that metabolic models can ...

doi.org

I joined efforts with D.A. Lucassen, @cdiener.com @gibbological.bsky.social and T. Wilson and got a really nice paper out on how to best integrate modern dietary assessment technologies to improve the accuracy of the current tools. Have a look here 👇 www.nature.com/articles/s43...

Integration of modern technologies to advance dietary assessment

Nature Food - Accurately measuring dietary intake has long been a challenge in nutrition research. Integrating emerging tools with multisampling strategies and a dietary assessment methodology...

nature.com

Check out our review on emerging technologies for diet tracking in Nature Food. 👇 This paper was led by @catalinacuparencu.bsky.social, with @cdiener.com and others: www.nature.com/articles/s43... @isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social

Integration of modern technologies to advance dietary assessment - Nature Food

Accurately measuring dietary intake has long been a challenge in nutrition research. Integrating emerging tools with multisampling strategies and a dietary assessment methodology aligned with the rese...

nature.com

How do we really assess dietary intake—and where is the field heading next? This is the topic of the keynote lecture at #GMFH2026 by Lawrence David. 👉 Register now & join us https://www.gutmicrobiotaforhealth.com/porto-2026-fourteenth-edition/registration/ 📍Porto | March 14–15

We mourn the passing of Peer Bork, EMBO Member since 2000: https://www.embl.org/news/embl-announcements/in-remembrance-of-peer-bork/

In remembrance of Peer Bork  | EMBL

EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General. 

embl.org

So happy to host Dr. Xiaoqian (Annie) Yu - soon starting her lab at University of Montreal! She used population genomics and large data analysis to group gut microbiome into ecological units based on sweep events (major revision at Nature)! www.biorxiv.org/content/10.1... #microsky #microbiomesky 🧪🦠

📢 We are hiring 📢 1st round of recruiting for our ERC project BacImmune-Decode! @erc.europa.eu We are looking for a postdoc for wet-lab work on regulation of phage defence systems in bacteria using high-throughput microbial genetics. Check it out: lnkd.in/es7AE968 #Hiring #Postdoc #Microbiology