📣 We’re hiring a postdoc for @hot-mes-asu.bsky.social ! 🦠🔬 We’re looking for someone excited about microbial interactions, ecology & evolution, and using molecular genetics and microfluidics to understand microbial communities. Come do fun science with us! apply.interfolio.com/190859

An active learning approach integrating explainable machine learning, Bayesian optimization, and high-throughput community construction designs microbial communities with desired functions in response to key nutrients www.nature.com/articles/s41...

Designing fiber–gut microbiome interactions with active learning - Nature Chemical Biology

Dietary fibers are a primary energy source for gut bacteria and shape the composition and function of the microbiome. Now, an active learning approach integrating explainable machine learning, Bayesia...

nature.com

Our new paper is out in Nature Ecology & Evolution. We show that increasing nutrient diversity can enhance microbial resource uptake, intensify competition, and ultimately reduce biodiversity. doi.org/10.1038/s415...

Out Now! Within-patient gene transfer between transiently and chronically infecting bacteria causes extreme antibiotic resistance during lung infections #MicroSky

Within-patient gene transfer between transiently and chronically infecting bacteria causes extreme antibiotic resistance during lung infections

Nature Microbiology, Published online: 23 July 2026; doi:10.1038/s41564-026-02414-3Antibiotic resistance gene acquisition by Pseudomonas aeruginosa and Achromobacter from transiently infecting bacteria drives rapid and extreme resistance to tobramycin during chronic lung infection within patients.

go.nature.com

Out Now! Klebsiella pneumoniae inhibits vasodilation through capsule and T6SS-dependent pathways #MicroSky

Klebsiella pneumoniae inhibits vasodilation through capsule and T6SS-dependent pathways

Nature Microbiology, Published online: 21 July 2026; doi:10.1038/s41564-026-02425-0Vasodilation is inhibited by Klebsiella pneumonia through a multipronged approach involving type VI secretion system activity and the VgrG4 effector, plus capsule, to limit eNOS-dependent and endothelial hyperpolarization routes to vasodilation.

go.nature.com

Excited that this is finally out, led by @jhuisman.bsky.social with Jeff Gore, combining experiments, theory and natural microbiome data! As salinity rises, diversity and individual species growth rates fall, yet community's overall growth stays robust: faster growers take over and keep it going.

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

Out Now! Predictable shifts in microbial species composition lead to community-wide robustness to environmental stress #MicroSky

Environmental stress triggers predictable changes in species composition, which in turn make microbial communities more robust at the community level.

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

Out Now! Predictable shifts in microbial species composition lead to community-wide robustness to environmental stress #MicroSky

Out Now! Non-canonical gene amplifications facilitate adaptive evolution in bacteria #MicroSky

Non-canonical gene amplifications facilitate adaptive evolution in bacteria

Nature Microbiology, Published online: 06 July 2026; doi:10.1038/s41564-026-02415-2Transposon-associated amplifications are dominated by a previously underappreciated architecture, where the transposon is found only between, not flanking, the amplicons. These amplifications facilitate the evolution of bacteria and their adaptation to antibiotics.

go.nature.com

Excited to share that I've been awarded a 5-year NIH MIRA (R35) from the National Institute of General Medical Sciences! The lab is growing! We're recruiting postdocs and research techs interested in microbial ecology, quantitative microscopy, microfluidics, and molecular biology. Please share!

Advances & challenges in microbiome transplantation Review examines FMT for established & emerging disorders, focusing on mechanisms, clinical applications, donor selection, safety & standardization, w/aim of enabling durable, safer interventions www.cell.com/cell-host-mi...

Advances and challenges in microbiome transplantation

Fecal microbiome transplantation restores disrupted microbial ecosystems and is established for recurrent Clostridioides difficile infection, with expanding investigation across diverse diseases. This...

cell.com

Predicting antimicrobial resistance for precision medicine Perspective proposing precision-medicine for patient-specific anti-infective therapy based on AI and ML-based predictions of antimicrobial susceptibility & pathogen vulnerabilities. www.cell.com/cell-host-mi...

Predicting antimicrobial resistance for precision medicine

Fink et al. outline a precision-medicine strategy for patient-specific anti-infective therapy based on predicting antimicrobial susceptibility and pathogen vulnerabilities to improve existing treatmen...

cell.com

After nearly two years reporting almost exclusively on the dismantling of American science and public health, this piece - on the triumphs and travails of basic research - was a delight to report and write. www.nytimes.com/2026/07/08/m...

Our Bacteria Are Talking. We’ve Just Begun to Understand What They’re Saying.

nytimes.com

Check the conference link: www.embl.org/about/info/c... Abstract deadline 15 Sep 2026 & Registration (on-site) 27 Oct 2026, don’t miss out! #EMBLGutMicrobeFunction

Unlocking the functional diversity of gut microbiomes

embl.org

How can we harness the vast functional diversity of microbes on our planet? Join us at EMBL Heidelberg from 8–10 December 2026 to hear about ongoing efforts to decode gene function and organisation in human gut microbes, and to present your own research. www.embl.org/about/info/c...

I really value: the dynamics of community assembly on 2 contrasting C sources. Daily sampling of communities derived from compost & maintained over 8 wks. No difference in diversity maintained on simple or complex C. AmaZinG. 🙏 all enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources

Taxonomically and functionally distinct communities assemble on cellulose and its monomer, glucose. Although single carbon sources were provided, high and comparable diversity was maintained in both ...

enviromicro-journals.onlinelibrary.wiley.com

Evolutionary rescue in a phage community! New paper from former PhD student, Sam Greenrod, with brilliant colleague @craigmaclean.bsky.social : academic.oup.com/ismej/advanc...

Rapid adaptation accelerates competitive suppression in a parasite community

Abstract. Environmental stress leads to changes in community composition by altering competitive hierarchies and pushing taxa towards extinction. Parasites

academic.oup.com

🔥 Published today, and just in time for summer conferences, here are your guidelines for presenting badly www.nature.com/articles/s41... rdcu.be/fqa92

Out Now! Enteropathy produced in mice by intergenerational transmission of small intestinal microbiota from undernourished children #MicroSky

Enteropathy produced in mice by intergenerational transmission of small intestinal microbiota from undernourished children

Nature Microbiology, Published online: 16 June 2026; doi:10.1038/s41564-026-02394-4In mouse models, small intestine microbiota of children suffering from environmental enteric dysfunction is transmitted maternally and recapitulates growth defects by modulation of inflammatory pathways

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A phase 1b clinical trial compared fecal #microbiome transplant or a 15-strain live biotherapeutic product derived from the same donor & found similar efficacy & engraftment between treatments.

15-strain live biotherapeutic product or same donor fecal microbiota transplant for recurrent Clostridioides difficile infection: a randomized phase 1b trial - Nature Medicine

A randomized, single-blind, parallel-group, phase 1b clinical trial compared fecal microbiota transplant or a 15-strain live biotherapeutic product (MTC01) derived from the same donor and found similar efficacy and engraftment between treatments.

dlvr.it

Interesting story: from FMT to LBP - 15-strain live biotherapeutic product or same donor fecal microbiota transplant for recurrent Clostridioides difficile infection: a randomized phase 1b trial @natureportfolio.nature.com Nature Medicine www.nature.com/articles/s41...

15-strain live biotherapeutic product or same donor fecal microbiota transplant for recurrent Clostridioides difficile infection: a randomized phase 1b trial - Nature Medicine

A randomized, single-blind, parallel-group, phase 1b clinical trial compared fecal microbiota transplant or a 15-strain live biotherapeutic product (MTC01) derived from the same donor and found simila...

nature.com

Nutrient environments shape amino acid auxotrophy and cross-feeding https://www.biorxiv.org/content/10.64898/2026.05.20.726445v1

Strategies for maintaining weight lost following injectable treatment or via dieting are described in two unrelated randomised controlled trials published in Nature Medicine. go.nature.com/4tAkDUq go.nature.com/4fgodiL #medsky 🧪

The version of record of our revised preprint is finally out today. In it, we introduce a fast and reliable methdology for the full factorial design of microbial communities, i.e. constructing every monoculture, pair, trio, four-member,... n-member co-culture of N strains. doi.org/10.7554/eLif...

Full factorial construction of synthetic microbial communities

A rapid, inexpensive, and easy to implement experimental protocol enables the construction of combinatorially complete sets of microbial consortia.

doi.org

Glad that our paper is out today in @cp-cellhostmicrobe.bsky.social A baby received a routine course of amoxicillin. In that infant's #gut 💩, we could see something remarkable, already present **before** the antibiotic arriveda single strain 🦠 of #Akkermansia muciniphila was already running 1/n

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation

Ni et al. show that epigenetic phase variation (ePV)—gene expression changes mediated by bacterial DNA methylation—is prevalent in the human gut microbiome and associated with fluctuating environments...

cell.com

After 7 years at Cambridge, EMBL, and ETHZ building & applying computational tools for microbiome science, I'm pivoting to industry. Available starting October 2026 for senior comp-bio roles in Switzerland 🇨🇭 Open to agtech, microbial biotech, AI-for-biology. Portfolio 👉 franciscozorrilla.github.io

A short piece about what "the pangenome" is and is not. open.substack.com/pub/profmcin...

The Pangenome Is Not a Parts List

The pangenome is the total genetic repertoire of a group of organisms. It is a property of populations, maintained by evolutionary processes.

open.substack.com

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

Yesterday, EMBO was visited by the delegation of the Department of Biotechnology of the Government of India. During the meeting, the EMBO Programmes and the future of the #cooperation between EMBO and #India were discussed. 🧪 #LifeSciences #research

Simons Graduate Fellowships in Ecology & Evolution are open! Our lab is open to hosting applicants. We link cell-level decision making to ecological outcomes and evolutionary trajectories in microbiomes. Interested or know someone who might be? Let's chat! www.simonsfoundation.org/grant/simons...

Simons Graduate Fellowships in Ecology and Evolution

The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...

simonsfoundation.org

Eubiota: Modular Agentic AI for Autonomous Discovery in the Gut Microbiome https://www.biorxiv.org/content/10.64898/2026.02.27.708412v1