Franklin Nobrega

Super excited to share our paper online 🚨today🚨 in Cell Host & Microbe‬! Xiaomei Ren @xiaomeiren.bsky.social and Mason Clark @rmasonclark.bsky.social‬ co-led discovery of ecological factors for Acinetobacter baumannii carriage in the gut, a reservoir for pathogen spread. 🎉

tinyurl.com/443kfefk

Open Call for Expressions of Interest in Max Planck Directorships: Expressions of interest can be submitted until 31 October 2025.

Director at Max Planck - a unique position! The Open Call for Expressions of Interest in Max Planck Directorships is open now and can be submitted by the 31st of October 2025. ➡️ mpg.de/directors - Please share the Open Call among potential candidates.

Escherichia coli with a 57-codon genetic code The near-universal genetic code uses 64 codons to encode the 20 canonical amino acids and protein synthesis. Here we designed and generated Escherichia coli with a 4 Mb synthetic genome in which we re...

Escherichia coli with a 57-codon genetic code | Science. Syn57, uses 55 codons to encode the 20 canonical amino acids. #rnasky #microsky 🦠 www.science.org/doi/10.1126/...

@isamirgiri.bsky.social
@shetoot.bsky.social

Group leader positions in @sangerinstitute.bsky.social Cellular Genomics, led by @mhaniffa.bsky.social, to decode and recode human tissues. Broad net - clinical research, in vitro models, single cell, AI. Vibrant, supportive community. Please share!

sanger.wd103.myworkdayjobs.com/en-GB/Wellco...

Thanks Kotaro!

Thank you Ariane

A family of linear plasmid phages that detect a quorum-sensing autoinducer exists in multiple bacterial species Temperate phages oscillate between lysogeny, a genomic maintenance state within a bacterial host, and lytic replication, in which the host is killed, and newly made phage particles are released. Successful transmission to new hosts requires that temperate phages appropriately time their transitions from lysogeny to lysis. It is well understood that temperate phages trigger lysis upon detection of host cell stress. Understanding of the breadth of cues that induce lysis expanded with the discovery of phages carrying quorum-sensing receptor genes that promote lytic induction exclusively at high host cell density. Bacteria engage in a cell-cell communication process called quorum sensing, which relies on the production, release, accumulation, and group-wide detection of extracellular signal molecules called autoinducers. Bacteria use quorum sensing to monitor changes in population density and synchronize collective behaviors. The temperate phage VP882 (jVP882) encodes VqmAj – a homolog of its host’s quorum-sensing receptor/transcription factor VqmA. VqmAj allows jVP882 to detect the accumulation of the host autoinducer called DPO. Presumably, launching the lytic induction program at high host cell density maximizes jVP882 transmission to new hosts. Here, by mining sequence databases for linear plasmid phages, we identify VP882-like phages in multiple DPO-producing bacterial species isolated at diverse times and geographic locations. We show that the VqmAj homologs can indeed detect DPO and, in response, activate the lytic pathway. Our observation indicates that jVP882 is a member of a large family of globally-dispersed quorum-sensing-responsive temperate phages.

A family of linear plasmid phages that detect a quorum-sensing autoinducer exists in multiple bacterial species | bioRxiv https://www.biorxiv.org/content/10.1101/2025.07.30.667625v1?rss=1

Group Leader – Molecular Systems Biology Unit Are you ready to lead groundbreaking research in Molecular Systems Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group, addressing original biological ...

Ready to lead pioneering research that bridges systems-level investigations of biological systems to molecular mechanism? The EMBL Molecular Systems Biology Unit in Heidelberg is hiring a Group Leader!

Synteny-aware functional annotation of bacteriophage genomes with Phynteny Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

🚨 New preprint 🚨

My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky

www.biorxiv.org/content/10.1...

Thank you Nonia!

Thank you David!

Thanks on this side 2 😉

Thanks Luuk!

Thanks Jens!

Thanks Ellinor

Thanks Fatima

Thanks Jay!

Manipulation of the nucleotide pool in human, bacterial and plant immunity - Nature Reviews Immunology Modification of the nucleotide pool is emerging as key to innate immunity in animals, plants and bacteria. This Review explains how immune pathways conserved from bacteria to humans manipulate the nuc...

Read my review with @soreklab.bsky.social on the nucleotide pool as a central playground in antiviral immunity across humans, bacteria and plants! 🧍‍♀️🦠🌿

& how viruses overcome these nucleotide-based immune mechanisms 🗡️

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

Recurrent acquisition of nuclease-protease pairs in antiviral immunity Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...

Excited to finally share this work!
We noticed a pair of genes - a nuclease and a protease - shuffles between antiviral systems. We show how proteolysis activates the nuclease, triggering defense in known and unknown immune contexts.
tinyurl.com/2uwwy4ty

Graph showing IS loads by Klebsiella sub-lineage

New preprint where we analysed IS loads in 🦠 #Klebsiella pneumoniae lineages and found they're inversely associated with nutrient usage. We propose an insertional tolerance model, whereby IS can only insert into metabolically-tolerable sites.

#IDSky #MicroSky 🧪

www.biorxiv.org/content/10.1...

Excited 🥳 to share our latest work on gut phages!
Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌
Out in Cell Reports @cp-cellreports.bsky.social
doi.org/10.1016/j.ce...
Here's what we found 🤓

Thanks Lingchen!!

Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites Zhang, Todeschini, and Wu et al. show that the bacterial defense system Kiwa senses phage attachment at the membrane and assembles a transmembrane complex that halts infection by blocking phage DNA re...

Thrilled to see our Kiwa story out today! A membrane-associated supercomplex that senses infection and blocks replication and transcription.

www.cell.com/cell/fulltex...

Huge congratulations to Yi and Zhiying for bringing it home, to Thomas for starting us off, and to all the collaborators.

PRISM: A platform for illuminating viral dark matter The exploration of bacteriophage diversity remains constrained by reliance on conventional plaque assays, which bias discovery toward phages that form visible plaques and propagate efficiently. The di...

#phage #phagesky

www.biorxiv.org/content/10.1...

🌟 Exciting news! We’re launching three fully-funded postdoc positions for "New Horizons for Synthetic Phages”

Join us in tackling antimicrobial resistance with cutting-edge synthetic biology + AI bioinformatics. Based at Flinders Uni in vibrant Adelaide.

👇 Read on for details!
#Phage

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats - Nature Microbiology Nanopore sequencing of Danish soils and sediments yields genomes from over 15,000 microbial species, expanding the phylogenetic diversity of prokaryotes by 8%.

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats www.nature.com/articles/s41... #jcampubs

Expression level of anti-phage defence systems controls a trade-off between protection range and autoimmunity - Nature Microbiology The authors examine several defense systems and find that increased expression enhances their protection range, albeit at a cost of autoimmunity.

Expression level of anti-phage defence systems controls a trade-off between protection range and autoimmunity
By Nitzan Aframian and Avigdor Eldar.
www.nature.com/articles/s41...

Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication. Asgard archaea hold a pivotal position in the tree of life as the closest known relatives to eukaryotes and are therefore crucial for understanding eukaryogenesis. Earlier genomic analyses revealed th...

Today is Asgard Friday! So happy that the project that has taken a big chunk of my PhD journey is out as a preprint (for now!)

“Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication”

www.biorxiv.org/content/10.1...

🦠🧍‍♀️From bacterial to human immunity.

We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social

www.science.org/doi/10.1126/...