How diverse is bacterial immunity ?

We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems.
👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie...

Explore them here defensefinder.mdmlab.fr/wiki/refseq_...

A new paper in Science measured the prevalence of social sycophancy across 11 leading large language models. The model’s responses were nearly 50% more sycophantic than humans’, even when users engaged in unethical, illegal, or harmful behaviors.
www.science.org/doi/10.1126/...

The ERC's new white paper examines the gap in participation and success rates between Europe’s strongest research systems and a group of countries performing less well. It also calls for coordinated efforts at national and European level.

Read more: erc.europa.eu/news-events/...

Hedging their bets: how bacterial pathogens diversify to survive infection Phenotypic heterogeneity within isogenic bacterial populations represents a fundamental adaptation strategy that enables pathogen survival across the …

New review out! Bacterial pathogens diversify to survive during infection - using bet-hedging and division of labor to generate specialized subpopulations. We explore how host signal actively drive this process

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

Framework for microbiome-inspired functional synthetic communities

One of the biggest challenges in microbial biotechnology? Unlocking the potential of non-model microbes and synthetic communities! Glad to share our review @sonjablasche.bsky.social @simonemozzachiodi.bsky.social @kiranrpatil.bsky.social @cambridgebiosci.bsky.social🧵(1/7) doi.org/10.1016/j.co...

Exapted CRISPR–Cas12f homologues drive RNA-guided transcription - Nature Specialized σ factors interact with nuclease-dead, CRISPR–Cas12f proteins to form potent, RNA-guided gene activation systems that function independently of fixed promoter motifs.

Just amazing what evolution can come up with. Naturally occurring nuclease deficient Cas12 family members use gRNAs to bind DNA and recruit sigmaE family members that drive txn initiation proximally. 2 papers! 1- describes 2- structure!
www.nature.com/articles/s41... www.nature.com/articles/s41...

Excited to share a preprint from my postdoc work in
Shipman’s lab!

We developed Detectrons — programmable biosensors that convert RNA signals into stable DNA barcodes inside living cells, enabling multiplexed RNA sensing. 🧵👇

biorxiv.org/content/10.6...

Slowpoke: An Automated Golden Gate Cloning Workflow for Opentrons OT-2 and Flex In synthetic biology, DNA assembly is a routine process where increasing demands for standardization, high-throughput capacity, and error-free execution are driving the development of accessible, auto...

🤖 Announcement for Opentrons users - OT-2 & Flex 🤖
We developed Slowpoke, an open-source, automated Golden Gate cloning tool with Fankang Meng & @proftomellis.bsky.social at @imperialcollegeldn.bsky.social
Flex-optimisation by @gregorybatt.bsky.social at @pasteur.fr
👉 pubs.acs.org/doi/10.1021/...

what a time to be alive

The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...

Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!

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

A Bacteroides synthetic biology toolkit to build an in vivo malabsorption biosensor
doi.org/10.1016/j.ce...

Can @cultivarium.bsky.social please stop churning out amazing papers please

A genetic platform for a biocementation bacterium www.biorxiv.org/content/10.64898/2025.12...

A commensal bacterium secretes effector proteins to establish population heterogeneity in the gut Zagieboylo and colleagues demonstrate that the human commensal Bacteroides thetaiotaomicron secretes two self-targeting proteins that induce heterogeneity within its own population. Differential expre...

An unexpected mechanism for population heterogeneity in the gut microbiome:

www.cell.com/cell-host-mi...

How does linguistic bias reinforce privilege in science? #AppEnvMicro Editor in Chief @microgem.bsky.social offers insights and discusses how reviewers can identify it to support a more equitable review process. Read the article: asm.social/2Hp #COPE #PublicationIntegrity

Pretty science and pretty colours is a combination hard to beat

Now that we understood neutral dynamics, we turned to competition. What could cause one plasmid to replicate better than another? Our first thought was transcription might interfere with replication, and it turns out there was a much larger tradeoff than we expected! 7/

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge.

Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...

In the UK, SUVs accounted for 63% of new sales in 2024.

The proliferation of SUVs is one aspect of “carspreading,” whereby cars are becoming steadily larger over time and with this comes potential harms to health 🧵

www.bmj.com/content/391/...

A new review paper from our lab courtesy of @jazzsynbio.bsky.social is published in Trends in Biotechnology
In this review, we look at the many opportunities for synthetic biology to be used in the research and applications of Holobionts.

The logic of sabotaging the ability to hire trained researchers from abroad while simultaneously sabotaging the ability of US universities to train American researchers is truly baffling.

Translational coupling of neighboring genes in prokaryotes | Journal of Bacteriology Prokaryotic genes are arranged in operons, with functionally related genes often located adjacent to one another (1). There are several ways in which the operonic organization of genes facilitates the...

Check out our new paper: a review of translational coupling, the phenomenon where translation of one prokaryotic gene can promote translation of the gene downstream. We cover the history, and delve into the mechanism, which is still not fully understood. journals.asm.org/doi/10.1128/...

Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes - Nature Biotechnology Append editing of ADP-ribosyl to thymine is used for precise modifications in bacteria and eukaryotes.

🚀 New publication alert! 🚀

We just published in @natbiotech.nature.com:
👉 Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes
doi.org/10.1038/s415...

I love this diagram

New paper from our lab on synthetic genome work in yeast is out - Iterative SCRaMbLE for Engineering Synthetic Genome Modules and Chromosomes. Exciting project led by Jane (Xinyu) Lu in our group, now online. t.co/0LuGwgAWlA

Photo: HIRI / Luisa Härtig

The Friends of the @helmholtzhzi.bsky.social have awarded Gianluca Prezza the HZI PhD Award for his outstanding doctoral thesis. In #HIRI's @westermannlab.bsky.social, he investigated #sRNAs in the gut bacterium B. theta. 🦠👨🎓 Congrats, @gprezza.bsky.social!
www.helmholtz-hiri.de/en/newsroom/...

Engineering yeast multicellular behaviors via synthetic adhesion and contact signaling By designing synthetic toolkits for contact-based signaling (MARS) and cell-cell adhesion (SATURN), we program yeast to form multicellular structures and perform complex tasks, like building logic cir...

Online now @ Cell is the yeast multicellular engineering paper from Fankang Meng - the fruits of his productive PhD in our group. He developed modular synthetic biology tools to bring multicellular behaviours to yeast - specific adhesion, juxtacrine signalling and more. www.cell.com/cell/fulltex...

While writing my thesis, I kept wondering why I was putting so much effort in something that "nobody will ever read". Well, someone did and thought it deserved a prize! 🤯
Many thanks to people @westermannlab.bsky.social and Alex in particular for the support, supervision and, eventually, nomination.

Fantastic to see this work published, and the interest it has sparked! A tour de force by Anna Lindell and a interdisciplinary team I was honoured to contribute to.👉 PFAS are already in our environment and bodies, we urgently need ways to mitigate their impact 🧫🧪 www.nature.com/articles/s41... 1/2

We're hiring for 2 postdocs to work in our lab in London on the newly announced Wellcome Trust SynHG project. If you know people looking to work on big-scale ambitious science like this, please RT and share this with them. Apply by 7/20, interviews in Aug. imperial.ac.uk/jobs/search-...