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...

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

Check our new preprint by Knopp M. et al.! Human gut microbiomes can impose strong +/- selection for resistant versions of resident opportunistic pathogens. In the case we follow up, selection is driven by altered carbohydrate utilisation that the resistant mutant evolves. doi.org/10.64898/202...

Now online! Engineered commensals for metabolic modulation of the gut-liver-brain axis

Check out our work on E. coli capsules! Including a 3x extended catalog of capsule loci from >37K genomes, a scalable tool to type them in silico (kTYPr) and new associations with ecology and disease! A joint effort from @microbiomeresearch.bsky.social @mucosalimmunology.bsky.social at @ethz.ch.

Out Now! In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules #MicroSky

Out Now! Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires #MicroSky

Cool paper👇 In a microbial community, each species changes its proteome (what proteins it expresses) to do a more specialised metabolic job, so overall functional overlap between species goes down...

Aging killifish show systemic inflammation and accumulating DNA damage in progenitor-like immune cells, offering a window into the evolutionarily conserved mechanisms of vertebrate immune aging. Great work from Gabriele, @mdonertas.bsky.social, and the whole team. www.nature.com/articles/s43...

Out now in @science.org Host-derived nitrate fuels indole production by Escherichia coli to drive chronic kidney disease progression | Science www.science.org/doi/10.1126/...

VIBRANT: Phase 1 trial of multi-strain L. crispatus for BV Women w/bacterial vaginosis receiving multi-strain vaginal L. crispatus live biotherapeutic 3–7 days post antibiotics showed vaginal colonization up to 12 wks, reducing risk of recurrent BV www.cell.com/cell-host-mi...

Out Now! Drought drives elevated antibiotic resistance across soils #MicroSky

How can we tap into the enormous functional diversity of microbes on this planet? Join us at EMBL Heidelberg (8–10 Dec 2026) to learn about ongoing efforts to decode gene function and organisation in human gut microbes, and present your science.

What happens if you knock down every metabolic gene in E. coli? We measured the metabolome of 1515 CRISPRi strains. Result: metabolism behaves like traffic. Block an enzyme and metabolites pile up upstream. 🚗🚗🚗 New paper 🧵

Out Now! Skin androgens regulate Staphylococcus aureus pathogenicity via quorum sensing #MicroSky

A study in Nature shows that the single-celled form of a tiny, aquatic organism can turn into a multicellular version by three different routes. The discovery adds insight to the possible origins of multicellular life, suggesting a previously unrecognized degree of flexibility. 🧪

Out Now! Tryptophanase disruption promotes insect–bacterium mutualism #MicroSky

Systematic discovery of a topical bacterial consortium that targets Staphylococcus aureus to treat atopic dermatitis https://www.biorxiv.org/content/10.64898/2026.02.13.705787v1

Low levels of metabolic auxotrophy among environmental Pseudomonas isolates https://www.biorxiv.org/content/10.64898/2026.02.13.705048v1

Rewiring of oncogenic signaling in #DrugResistance is a moving target. In our new study, we used biophysical phosphoproteomics to investigate #BRAF mutant cancer, linking phosphorylation changes to protein function and #MolecularMechanisms through #Multi-Omics integration. tinyurl.com/funsignaling

I am pleased to share that our paper is now published in Cell! www.cell.com/cell/fulltex... I am deeply grateful to all co-authors for making this possible. This work was made possible through the guidance of Dr. Peer Bork. I share this in grateful memory and with deep respect for his mentorship.

Just published: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" by @podlesny.bsky.social @chanyeong-kim.bsky.social and @jonas-bio.bsky.social www.cell.com/cell/fulltex... See the quoted post below for a thread on the preprint!

Excited to announce my upcoming @snsf.ch Ambizione research group at EPFL on bacteria-host interactions, combining systems approaches and microphysiological models. 🚨 We have an open PhD position! More info on projects and how to apply here: elisabettacacace.github.io/BHI-Lab/ 🧪

Protists shift bacterial interactions Soil protist predation shifts bacterial metabolic interactions from competitive to cooperative. Protist-driven microbial cross-feeding enhances plant-beneficial functions www.cell.com/cell-host-mi...

It has been two weeks since the unexpected death of Peer Bork, and all of us in his research group are deeply missing him. His scientific vision brought us together as a team, and we are immensely grateful for the time we spent together. 🧵

Now online! A Bacteroides synthetic biology toolkit to build an in vivo malabsorption biosensor

Peer Bork died yesterday 💔 which shocked me. In 2003 I did a short-term fellowship in Peer’s lab because I idolized him. I met Martin there & we wrote this paper together. Peer was great at bringing people together; a master collaborator with a rare ability to think up big ideas.

This is such hard news to process. Such an amazing scientist and inspiration for so many of us. www.embl.org/news/embl-an...

Nature research paper: Genetic switch between unicellularity and multicellularity in marine yeasts go.nature.com/4poZ9HP

"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXT

This broader metabolic capacity makes core microbes true functional generalist with far greater metabolic independence than non-core taxa, allowing them to thrive in the dynamic rumen environment. (4/8)

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...

Combining genome-scale metabolic modelling with in vitro and in planta experiments, the authors show that cross-feeding metabolites and substrate utilization synergistically determine microbial community resistance to pathogen invasion 🧪 www.nature.com/articles/s41...

Highlighting another recent paper from the lab in Science Advances on engineering a gut probiotic to modulate GLP-1 levels and ameliorating colitis. Led by Leonie Brockmann & @carlottaronda.bsky.social . @columbiasysbio.bsky.social @columbiauniversity.bsky.social 🧬🦠💊 www.science.org/doi/full/10....

Population genetics simulations and analysis of experimental datasets in yeast, Drosophila and E. coli show that beneficial mutations are abundant but transient, as they become deleterious after environmental turnover (antagonistic pleiotropy)🧪 www.nature.com/articles/s41...

Hmmm This work has so many implications on literature 😳😬 Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS www.pnas.org/doi/10.1073/...

Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut - @harriswang.bsky.social go.nature.com/4i7XnZR

Niche partitioning by resource size in the gut microbiome https://www.biorxiv.org/content/10.1101/2025.11.13.688124v1

When colonizing a new habitat, organisms adapt to maximize their reproductive success via #LifeHistory #evolution. @ecoevodevolab.bsky.social @cbank.bsky.social show that life history evolution facilitates niche diversification across a range of theoretical models @plosbiology.org 🧪 plos.io/4p7YT0a

Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️ www.science.org/doi/10.1126/...

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases | Science

@sacrozhangt.bsky.social and I wrote a commentary on Jordi van Gestel and Carol Gross's latest paper, check it out! www.pnas.org/doi/10.1073/... Sadly, the Editors at PNAS rejected our initial introduction, which was a David Attenborough style voice over of the microbial Serengeti (included below)

Let me use this as an opportunity to talk about Jordi et al's very cool paper, now out in PNAS 🧪: pmc.ncbi.nlm.nih.gov/articles/PMC... You can read our news and views here: www.pnas.org/doi/10.1073/...

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...

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...

Had to draw a cartoon for this fascinating finding! Defensive fungal symbiosis on insect hindlegs: www.science.org/doi/10.1126/... #SymbioSky

@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎 www.pnas.org/doi/10.1073/...

What makes PhD students happy? Good supervision Supportive and frequent supervision is a key factor that significantly enhances PhD students' satisfaction and well-being during their research journey. doi.org/10.1038/d415...

NEW publication from our lab: One of the first methodologies (FUGAsseM) for gene function prediction from microbial community multi-omics data! www.nature.com/articles/s41... 🧵⬇️ 1/8