Spontaneous aging-associated inflammation and genome instability in the immune system of turquoise killifish - Nature Aging Turquoise killifish are naturally short-lived vertebrates that serve as a model system for aging. The authors show that killifish exhibit age-related transformation in the immune system, which rapidly...

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...

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...

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: A phase 1 randomized trial of multi-strain vaginal L. crispatus live biotherapeutic products in people with bacterial vaginosis In this phase 1 randomized trial of women with bacterial vaginosis in South Africa and the United States, Potloane et al. show that a multi-strain vaginal Lactobacillus crispatus live biotherapeutic a...

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...

Drought drives elevated antibiotic resistance across soils Nature Microbiology, Published online: 23 March 2026; doi:10.1038/s41564-026-02274-xDrought conditions in soil systems lead to elevated concentrations of natural antibiotics, as well as the enrichment of antibiotic-resistant microorganisms, highlighting a link between climate and the spread of antimicrobial resistance.

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 🧵

Skin androgens regulate Staphylococcus aureus pathogenicity via quorum sensing Nature Microbiology, Published online: 27 February 2026; doi:10.1038/s41564-026-02261-2Testosterone produced by skin cells enhances Staphylococcus aureus pathogenicity by activating quorum sensing, and a stereoisomer of testosterone that blocks this interaction inhibits bacterial cytotoxicity towards human cells.

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

Clonal-aggregative multicellularity tuned by salinity in a choanoflagellate - Nature The choanoflagellate Choanoeca flexa forms motile and contractile cell monolayers purely clonally, purely aggregatively or through a combination of both processes depending on environmental conditions.

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. 🧪

Tryptophanase disruption promotes insect–bacterium mutualism Nature Microbiology, Published online: 27 February 2026; doi:10.1038/s41564-026-02264-zDisruption of a single gene encoding tryptophanase makes Escherichia coli mutualistic in a stinkbug model owing to the accumulation of tryptophan and a reduction in toxic indole. This gene is typically lacking in symbionts of wild stinkbugs.

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

Systematic discovery of a topical bacterial consortium that targets Staphylococcus aureus to treat atopic dermatitis www.biorxiv.org/content/10.64898/2026.02...

Low levels of metabolic auxotrophy among environmental Pseudomonas isolates www.biorxiv.org/content/10.64898/2026.02...

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/
🧪

Congratulations on receiving the Ambizione grant and establishing the new group Eli!!👏

Predation by soil protists shifts bacterial metabolism from competitive to cooperative interactions Chen et al. demonstrate that soil protist predation shifts bacterial metabolic interactions from competitive to cooperative. Integrating large-scale surveys, metabolic modeling, and control experiment...

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. 🧵

A Bacteroides synthetic biology toolkit to build an in vivo malabsorption biosensor Engineered repressible promoters enable tunable fluorescence outputs in Bacteroides and the development of biosensors that report on subclinical gut malabsorption.

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.

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.

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

Genetic switch between unicellularity and multicellularity in marine yeasts - Nature Myb1 functions as a switch-like regulator of state transitions in Hortaea werneckii, whereby its expression and degradation are coupled to nutrient conditions, stabilizing unicellular or multicellular growth.

Nature research paper: Genetic switch between unicellularity and multicellularity in marine yeasts

go.nature.com/4poZ9HP

The changing roles of Escherichia coli Nature Microbiology - Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.

"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 reveals phage dynamics in the human gut microbiome - Nature Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

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...

Substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion - Nature Ecology & Evolution 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 commun...

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...

Engineered probiotic restores GLP-1 signaling to ameliorate fiber-deficiency exacerbated colitis Engineered probiotic delivers bacterial peptide that enhances GLP-1 and restores barrier integrity in diet-modulated colitis.

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....

Adaptive tracking with antagonistic pleiotropy results in seemingly neutral molecular evolution - Nature Ecology & Evolution 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 envir...

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...

Fluorescein-based dyes are not valid reporters of oxidative stress in bacteria, and conclusions based on their use must be reconsidered | PNAS Dihydrodichlorofluorescein derivatives have been employed as reporters of intracellular reactive oxygen species (ROS) in innumerable studies. Their...

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/...