High-density microdroplet cultivation reveals the essential role of microbial interactions in the growth of environmental microbes | mBio The overwhelming majority of environmental microbes remain uncultured, limiting our understanding of their physiology and ecological roles. Although microbial interactions have been predicted as one o...

High-density microdroplet cultivation reveals the essential role of microbial interactions in the growth of environmental microbes.🦠🧫
journals.asm.org/doi/10.1128/...

We're in this week's Nature! We propose a model of how a cell learns by running an evolutionary algorithm: exploring different gene-regulatory combinations and using feedback responses to stabilize those combinations that reduce stress levels.
Full text: nature.com/articles/s41...

Dividing cells of Marchantia polymorpha near the apical meristem expressing a phase-specific marker (MpCDKB, yellow). Credit: Facundo Romani

Schematic model of the simple cell-cycle control system in Marchantia. Credit: Facundo Romani

Latest research from @jimhaseloff.bsky.social's lab @camplantsci.bsky.social sheds new light on the evolution of plant cell division & could unlock new ways to engineer crop growth.

👉 tinyurl.com/5n7h2n58

@fromani.bsky.social @ignacybo.bsky.social @cambridgebiosci.bsky.social 🧪

Out Now! Advancing microbiology through foundational science #MicroSky

A drug–microbiome–drug interaction impacts co-prescribed medications for Parkinson’s disease Nature Microbiology, Published online: 06 April 2026; doi:10.1038/s41564-026-02299-2Parkinson’s disease is managed through co-treatment with levodopa and tolcapone, with tolcapone altering the microbiome to increase its capacity to metabolize levodopa, implicating the gut microbiome in drug–drug interaction.

Out Now! A drug–microbiome–drug interaction impacts co-prescribed medications for Parkinson’s disease #MicroSky

A database of over 15,000 strain design publications reveals a conserved set of metabolic engineering targets across microbial hosts and products Microbial biotechnology has the potential to address several societal issues through the sustainable production of industrially relevant compounds. De…

New paper from our lab with a massive analysis of over 15.000 strain design publications by @emarquezz.bsky.social :)

www.sciencedirect.com/science/arti...

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

Awesome work by @skamrad.bsky.social & team 👏🏼

Researchers in the Patil lab found that co-culturing bacteria profoundly alters each species' behavior. Because the gut microbiome directly affects our health, understanding these interactions helps show how it responds to challenges (e.g. drugs)

Read the full story: buff.ly/dZ42Vnx

I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications! www.nature.com/articles/s41.... (1/n)

#microSky #MicrobiomeSky

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

Gut microbiota within-host evolution enforces colonization resistance against enteric infection www.biorxiv.org/content/10.64898/2026.03...

Multi-omics reveal vitamin D regulation of immune-gut microbiome interactions and tolerogenic pathways in inflammatory bowel disease Gubatan et al. demonstrate vitamin D’s immunoregulatory role on host immune-microbe interactions in patients with inflammatory bowel disease. Vitamin D alters the profiles of IgA- and IgG-bound gut ba...

Multi-omics reveal vitamin D regulation of immune-gut microbiome interactions and tolerogenic pathways in inflammatory bowel disease
www.cell.com/cell-reports...
Vitamin D Shows Promise in Resetting Immune System in Inflammatory Bowel Disease
www.sci.news/medicine/vit...

Bacteria covalently incorporate polyfluoroalkyl carboxylates into membrane lipids Nature Microbiology, Published online: 27 March 2026; doi:10.1038/s41564-026-02301-xBacteria are able to covalently incorporate n:3 polyfluoroalkyl carboxylates into phosphatidylethanolamine and phosphatidylglycerol, two major components of bacterial lipid bilayers.

Out Now! Bacteria covalently incorporate polyfluoroalkyl carboxylates into membrane lipids #MicroSky

Degradation of mucin O-glycans by a human gut symbiont requires a complex enzyme repertoire and promotes colonization www.biorxiv.org/content/10.64898/2026.03...

Immunometabolic gatekeeping: How tissue metabolism conditions tumor immunity Why the link between immune infiltration and tumor control varies so strongly across tissues remains unresolved. We propose the “immunometabolic gatekeeping” framework, whereby tissue-intrinsic metabo...

⚡Excited to share our new paper in Cancer Cell:
We propose immunometabolic gatekeeping: the idea that tissue metabolism constrains anti-tumour immunity, even pre-transformation.
Why does immune infiltration not always predict good outcomes? Tissue context may be key.
🔗 www.cell.com/cancer-cell/...

Join us at the yearly EngBio IRC Symposium, bringing together the Cambridge Engineering Biology community for an afternoon of cutting-edge science, collaboration, and networking. We are inviting abstract submissions for posters and short talks, with exciting prizes!🛠️🧬

Transposon mutagenesis in bacterial natural product discovery

-in Essays in Biochemistry @biochemsoc.bsky.social from Sacha Pidot
with @nodwell.bsky.social

portlandpress.com/essaysbioche...

Over 250 million protein sequences are known, but fewer than 0.1% have confirmed functions. Today, @genophoria.bsky.social, @bowang87.bsky.social & team introduce BioReason-Pro, a multimodal reasoning model that predicts protein function and explains its reasoning like an expert would.

Commensal-driven serotonin production modulates in vivo delivery of synthetic and viral vectors @science.org
www.science.org/doi/10.1126/...

New at Addgene!

Do you study non-model bacteria? Cultivarium has you covered with their JEROBA (Jumping Element libRaries with Broad hOst rAnge) Toolkit. Use this kit to screen different transposon configurations and find the optimal constructs for your unique bacteria 🦠

https://twp.ai/4ixKCP

Congratulations on the fantastic work! as someone from Mendoza, it is really moving to get to know more of the history of Huarpe people and their strategies for resilience. It is also great to see such quality transdisciplinary research performed, and together with the Huarpe communities.

Local agricultural transition, crisis and migration in the Southern Andes - Nature In the Uspallata Valley, agriculture was adopted by local populations, as evidenced by genetic continuity from earlier hunter-gatherers to farmers; maize-dependent groups from the same regional p...

How did farming reach the Southern Andes? Through migration or cultural transmission? Our new paper in @nature.com combines ancient DNA, isotopes, archaeology & paleoclimate to reconstruct 2,000+ years of history in Uspallata, Mendoza.
www.nature.com/articles/s41...
A Thread🧵 (1/25+)

Leveraging publicly available datasets and machine learning approaches for predicting the health benefits of fermented foods www.biorxiv.org/content/10.64898/2026.03...

Metabolic interactions shape ecosystems

Excited to share the upcoming EMBO | EMBL Symposium “Metabolic interactions shape ecosystems” 🧬🌍

📍 Heidelberg & online
📅 21–24 July 2026

Abstract deadline: 14 April!

More info & registration: www.embl.org/about/info/c...

#Metabolism #Microbiome #SystemsBiology #Ecology #EMBL #EMBO

Selection-free whole genome transplantation revives dead microbes www.biorxiv.org/content/10.64898/2026.03...

Bacteriophage data on capsular Klebsiella bacteria barcoded library

New paper 🔔

Collaboration
@sullivan-lab.bsky.social
Marissa Gittrich led the work

Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape

#microsky #phagesky #phage

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

Microbial secondary metabolites: advancements to accelerate discovery towards application Nature Reviews Microbiology - In this Review, Dinglasan and colleagues explore innovations that facilitate rapid microbial secondary metabolite discovery, focusing on recent techniques for the...

Our new review article "Microbial secondary metabolites: advancements to accelerate discovery towards application" in Nature Reviews Microbiology is now published!

rdcu.be/d6BHX