Indra Roux

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

Spatial transcriptomics maps host–gut microbiome biogeography at high resolution Nature Microbiology, Published online: 06 March 2026; doi:10.1038/s41564-026-02286-7Bulk polyadenylation improves the capture of microbial RNA, enabling host–microorganism interactions to be visualized at a high resolution when combined with commercially available spatial transcriptomics platforms.

Out Now! Spatial transcriptomics maps host–gut microbiome biogeography at high resolution #MicroSky

Our latest paper was just published. Will prepare a full thread very soon 🦠🧪🤖

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems MicrobeAtlas (www.microbeatlas.org) is an integrated, reference-based resource for truly planet-wide microbiomics, analyzing hundreds of thousands of microbial lineages across diverse environments, co...

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems: Cell www.cell.com/cell/fulltex...

#microsky

A new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...

Why are most metabolites barely detectable in wild-type cells — biology or technology?

A new study from the Link lab shows it's biology: cells actively maintain minimal metabolite pools to avoid unwanted effects.

www.cmfi.uni-tuebingen.de/en/news-even...

Our March #EngBio newsletter is out!

This month we are delighted to introduce the EngBio IRC's new Coordinator and Events Manager, Dr Francis Krampa. We are also sharing more details about the forthcoming EngBio Symposium & Forum on 21 May...

Read it here 👉🏼 mailchi.mp/519dc97b6e60...

Genome modelling and design across all domains of life with Evo 2 - Nature Evo 2 is an artificial intelligence-based biological foundation model trained on 9 trillion DNA base pairs spanning all domains of life that predicts functional properties from genomic sequences and p...

First released one year ago, Evo 2 predicts variant effects & generates functional DNA across all domains of life, from bacteria to humans, from a single set of weights, with no fine-tuning required.

www.nature.com/articles/s41...

Evolution navigated billions of challenges to get to us to where we are today. Directed evolution compresses this to a 1D axis.

Imagine if you could sample 200 dimensions at once, with data to boot 📈

First @chorylab.bsky.social PACE preprint on our new system to tackle this: bit.ly/turboprance

Out now! In collaboration with Leifu Chang, we uncover the molecular and structural underpinnings of CRISPR-Cas12f-like RNA-guided transcription systems!

Links to the published articles:
tinyurl.com/55kpavet
tinyurl.com/sk6djwx3

Previous thread for the preprint:
bsky.app/profile/did:...

New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome www.pnas.org/doi/10.1073/... @lauriebelch.bsky.social

Webinar Today!
Negotiating Your First Group Leader Position

Join us today to hear from three group leaders — including a co-author of a BMC Proceedings article on this topic — about their experiences and practical tips for negotiating your first group leader role.

👉 www.embl.org/about/info/e...

Linear-time prediction of proteome-scale microbial protein interactions https://www.biorxiv.org/content/10.64898/2026.03.01.708874v1

Highly mutagenic continuous evolution in E. coli using a Φ29-based orthogonal replication system - Nature Biotechnology Mutational rates of bacterial evolution are increased using an error-prone orthogonal system.

Very happy to see this work from Fabian Rehm, Jason Chin, and team on the development of a high error-rate orthogonal DNA replication system in E. coli, thus supporting continuous hypermutation and evolution of target genes in vivo. www.nature.com/articles/s41...

🔓Don't miss the #OpenAccess Highlight behind the cover of our latest issue by Francesco Del Carratore & Rainer Breitling @liverpooluni.bsky.social & @manchester.ac.uk on how microbiomes can be engineered for natural product discovery and production #secmet #natprod

pubs.rsc.org/en/content/a...

What questions currently beyond reach do you hope systems approaches will enable addressing in the next decade?

In a recent issue of Cell Systems, 13 scientists provide their insights into "𝗪𝗵𝗮𝘁 𝗾𝘂𝗲𝘀𝘁𝗶𝗼𝗻𝘀 𝗰𝘂𝗿𝗿𝗲𝗻𝘁𝗹𝘆 𝗯𝗲𝘆𝗼𝗻𝗱 𝗿𝗲𝗮𝗰𝗵 𝗱𝗼 𝘆𝗼𝘂 𝗵𝗼𝗽𝗲 𝘀𝘆𝘀𝘁𝗲𝗺𝘀 𝗮𝗽𝗽𝗿𝗼𝗮𝗰𝗵𝗲𝘀 𝘄𝗶𝗹𝗹 𝗲𝗻𝗮𝗯𝗹𝗲 𝗮𝗱𝗱𝗿𝗲𝘀𝘀𝗶𝗻𝗴 𝗶𝗻 𝘁𝗵𝗲 𝗻𝗲𝘅𝘁 𝗱𝗲𝗰𝗮𝗱𝗲?", including IMSB's Paola Picotti @picottilab.bsky.social
www.sciencedirect.com/science/arti...

Tryptophanase disruption promotes insect–bacterium mutualism - Nature Microbiology Disruption 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 typicall...

Disruption of a single gene, tnaA, encoding tryptophanase makes E. coli mutualistic to stinkbug, resulting in the accumulation of tryptophan and the reduction of toxic indole. www.nature.com/articles/s41...

New @plosbiology.org code sharing policy. In this Editorial, @npariente.bsky.social and Lauren Cadwallader explain the policy and offer guidance on compliance, noting that code sharing remains less well understood than equivalent requirements for data and ethics.

journals.plos.org/plosbiology/...

Now out in @natcomms.nature.com :
versions 2.0 of both BiG-SCAPE and BiG-SLiCE! With significant speed and accuracy increases, as well as new interactive functionalities.
Read the full paper here #openaccess:
www.nature.com/articles/s41...

What problem do you hope bioengineering or synthetic biology approaches will enable us to tackle in the next decade?
doi.org/10.1016/j.ce...

A portable orthogonal replication system enables continuous gene evolution near the biological speed limit https://www.biorxiv.org/content/10.64898/2026.02.20.706958v1

Interested in #SynBio #education? 🦠⚙️👩‍🎓
Together with @nevoti.bsky.social & @marcguellc.bsky.social at @melisupf.bsky.social we designed active learning activities 📚 to complement theoretical SynBio lectures, together with 3-day deductive lab session 🧑‍🔬 that combines mystery 🔍 and #CRISPR circuits.👇

Cancer therapies exploit DNA repair defects to kill tumours. We asked whether the same logic could constrain antibiotic resistance evolution...

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

Make sure to join us in the MIBiG Annotathons! The MITE database (mite.bioinformatics.nl) will join the efforts! If you are interested in tailoring enzymes/maturases, make sure to join us!

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0 Abstract. Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable compara

And the perspectives article about the strategies and lessons learned from the MIBiG 4.0 Annotathon here: academic.oup.com/bib/article/...

The MIBiG 5.0 Annotathon is coming soon, and registration is now open!

🧬 Does your research involve biosynthetic gene clusters? Do you love natural product biosynthesis? Do you have an interest in rare & exotic enzymes? We can use your help & expertise.

Register here 👉 forms.gle/C1cWcLHtrjT2...

☠️🍄The world's deadliest mushroom has been hiding a secondary metabolite secret! The Keller, Drott & Pringle Labs just published in @pnas.org: leaderless RiPPs, a peptide class never before seen in fungi, found in Amanita phalloides and linked to its Californian invasion. www.pnas.org/doi/10.1073/...

Figure 3F from https://www.biorxiv.org/content/10.64898/2026.02.12.705432v1. This shows a network of environmental meta-transcriptomics and TraDIS knockout results. Points are coloured based on gene function. Genes which are identified both by meta-t and TraDIS were associaetd with amino acid metabolism, nucleotide metabolism, biofilm and other.

What #Ecoli 🦠 genes enable environmental persistence?

Incredibly layered work in this study, spanning:
- Environmental meta-transcriptomics 📊
- Isolate culturing 🧫
- #metabolism ♻️
- Mouse survivability experiments 🐁
- TraDIS 🧬
- Isogenic mutant validation ∆

🧪

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

Growth-coupled evolution accelerates efficient biosynthesis of natural products Microbial natural product biosynthesis often suffers from metabolic burden and genetic instability. Bushin et al. introduce a synthetic C1 feedback loop that couples xanthommatin production to cell su...

Growth-coupled evolution accelerates efficient biosynthesis of natural products

@cp-trendsbiotech.bsky.social Spotlight from Dongsoo Yang

www.cell.com/trends/biote...

Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation - Nature Genetics Population-based studies from Sweden with replication in Norway identify associations between host genetic variants and gut microbial composition and implicate short-chain fatty acid chemosensors as m...

Delighted to have contributed to this impressive work led by @tovefall.bsky.social & many others👏 (w/ @gazollavolpiano.bsky.social from our side). This novel microbiome GWAS (n=~16k+12k valid) expands knowledge on genetic factors associated w/ gut microbiota variation.
www.nature.com/articles/s41...