GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio www.nature.com/articles/s41...

The excellence cluster Ocean floor @marumunibremen.bsky.social @icbm-uol.bsky.social @hifmb.de opens two strategic positions at the University of Oldenburg. Please distribute widely Scientific Coordinator: uol.de/job723en Data Steward: uol.de/job724en

ssDNA phage FLiP resides in dsDNA form in resistant Flavobacterium host https://www.biorxiv.org/content/10.1101/2025.09.12.675792v1

Nice summary from Songcan & Marc 🙏 on our discovery of a new microbial energy metabolism 🦠 🧫 ⚡ 🔌 Microbial Iron oxide respiration coupled to Sulfide Oxidation (MISO) @nature.com Research Briefing 😍 doi.org/10.1038/d415... 📰 Original paper www.nature.com/articles/s41... #microsky #microbiomesky

Please help me identify these. They are of freshwater origin and have chlorophyll.

Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...

We have several open positions in my group, funded from the ERC Grant on the Early Sequestered Germline of Fungi. We search broadly for applicants at both PhD and master-level, with a dedicated interest in fungal evolutionary biology. Please forward and RT! Find the positions here: su.varbi.com

I’m excited to share our effort to obtain one of the first estimates of the net rate, in physical time, of lateral gene transfer (LGT) – nature’s own genetic engineering - across a complex, global microbiome: doi.org/10.1093/isme...

Net rate of lateral gene transfer in marine prokaryoplankton #microbes #evolution #mevoSky #evoSky academic.oup.com/ismej/advanc...

Cyanophages: Billions of Years of Coevolution with Cyanobacteria | Annual Reviews https://www.annualreviews.org/content/journals/10.1146/annurev-micro-042924-095145?TRACK=RSS

Review. Marine Viruses and Their Role in Marine Ecosystems and Carbon Cycling www.annualreviews.org/content/jour...

At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social

CoCoBin: Graph–Based Metagenomic Binning via Composition–Coverage Separation www.biorxiv.org/content/10.1... #jcampubs

Preprint: De-novo design of proteins that inhibit bacterial defenses Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications Congrats Jeremy Garb! tinyurl.com/Syttt 🧵

The microscopic alliance between algae & bacteria offers rare, step-by-step snapshots of how bacteria lose genes and adapt to increasing host dependence. New study led by Wallenberg Academy Fellow Rachel Foster #research supported by Knut and Alice WallenbergFoundation #science tinyurl.com/yc2nw8r9

Partnership between #algae & #bacteria reveals secrets of evolution phys.org/news/2025-08... Stepwise genome #evolution from a facultative symbiont to an endosymbiont in the N2-fixing symbioses www.cell.com/current-biol... #protists by @vesnagrujcic.bsky.social, @mehrshmali.bsky.social, et al.

Check out our paper led by @vesnagrujcic.bsky.social on step by step symbiotic interactions of cyanobacteria with their diatom hosts!

How do microbes become permanent partners? 🌊🔬🦠 Check out our new study published in Current Biology showing how cyanobacterial genomes evolve step-by-step into endosymbionts of diatoms. www.sciencedirect.com/science/arti... @currentbiology.bsky.social @mehrshmali.bsky.social

Throwback to #ESEB2025: thank you for the memories 🌍

Very happy to see this one out: doi.org/10.1093/molbev/msaf192 Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio

www.nature.com/articles/s41... #phagesky #phage

I cannot fully put into words what publishing this Review has meant to me, so I leave you with how we closed the paper. "The humble bacterium is still a relevant tool for the study of the underlying mechanisms that are conserved throughout life." 🧪🧫🧬📚 doi.org/10.1093/gene...

New pre-print from Doudna lab members @erinedoherty.bsky.social & @jnoms.bsky.social ✨ Here we explore how recurrent adaptation of a single anti-defense protein fold enables evasion of distinct immune systems.

New in @asm.org #MMBR Computational function prediction of bacteria and phage proteins. How to annotate your #phage and #bacteria genomes by @susiegriggo.bsky.social @bedutilh.bsky.social @gbouras13.bsky.social and Bob #phagesky #microsky journals.asm.org/doi/epub/10....

I love the 3 boxes from #eseb2025 session 10! 🤩 Thank you Tilly!

Time for discussing Eco-evolutionary dynamics driven by Mobile Genetic Elements! Come to our session in room 123! #ESEB2025 @taylorpriest.bsky.social @eseb2025.bsky.social @eseb.bsky.social

😳 #phage #phagesky #microsky Pseudomonads coordinate innate defense against viruses and bacteria with a single regulatory system: www.cell.com/cell-host-mi...

Higher-order microbial interactions revealed by comparative metabolic modeling of synthetic communities with varying species composition #ISMEComms academic.oup.com/ismecommun/a...

We are happy to announce that our latest manuscript has been published in Nature Communications! We identified the highly abundant and prevalent (>70% in population) giant (Max. 395kb) extrachromosomal element in the human mouth, named "Inocle". www.nature.com/articles/s41...

#NewResearch Prion-like proteins in Escherichia coli trigger an abortive infection mechanism in response to phage infection—a process similar to amyloid-mediated immune signalling in fungi and animals. #MicroSky 🦠 www.nature.com/articles/s41...

www.biorxiv.org/content/10.1... #phage #phagesky

Arctic viruses follow the rhythm of the sea 🌊🦠 Just published in @natcomms.nature.com 🎯🙂 doi.org/10.1038/s414... Press release: www.geomar.de/en/news/arti... Great collaboration between @geomarkiel.bsky.social @awi.de @mpimarinemicrobio.bsky.social — our HAUSGARTEN Observatory goes viral 🙃

The JEDI marker - a new approach for measuring #biodiversity that captures all domains of life and is applicable across biological and ecological scales. It's time to change the way we perceive biodiversity - www.biorxiv.org/content/10.1...

Cell wall forming chitin synthases in a chytrid fungus https://www.biorxiv.org/content/10.1101/2025.08.12.668609v1

Longstanding collaboration with Scott Manalis where we have developed technology to measure single cell growth rates of bacteria in native seawater with some very surprising results. www.biorxiv.org/content/10.1...

#phage #phagesky Single cell viral tagging of Faecalibacterium prausnitzii reveals rare bacteriophages omitted by other techniques www.tandfonline.com/doi/full/10....

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...

Check out the new paper of my former lab about novel haloviruses infecting Haloquadratum walsbyi, the "square queen archaeon" of hypersaline systems 👑🟪 academic.oup.com/ismej/advanc...

This sounds super cool!

A novel mobile genetic element with virus-like characteristics is widespread in the world's oceans www.biorxiv.org/content/10.1...

Small uncultured viral-like entities redraw the origin of viruses and cellular compartments www.biorxiv.org/content/10.1...

our new paper on pelagic #Asgard archaea that use #rhodopsins with carotenoid antennas to harvest light energy in the oceans. Structural insights into light-harvesting by antenna-containing rhodopsins in marine Asgard archaea www.nature.com/articles/s41... @galitzlil.bsky.social

Happy to finally share this! Read here about the best strategy the the persistence of low-copy plasmids. @mariosanter.bsky.social @iwangtoknow.bsky.social doi.org/10.1038/s414...

PHACE: phylogeny-aware coevolution algorithm that maps amino acid substitutions onto a phylogenetic tree to detect molecular coevolution academic.oup.com/mbe/article/...

Very excited to host the GRS Marine Microbes next year, which we are centering on three key themes: diversification, adaptation and resilience! Applications are now open - www.grc.org/marine-micro...

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

Synteny-aware functional annotation of bacteriophage genomes with Phynteny https://www.biorxiv.org/content/10.1101/2025.07.28.667340v1

NEW Review from @soreklab.bsky.social @dinahoch.bsky.social explains how immune pathways manipulate the availability of nucleotides, chemically modify nucleotides to generate immune signalling molecules, and produce altered nucleotides that poison viral replication #immunosky #microsky #phagesky

#PhageSky #ProtistsOnSky endosymbionts have "their" phages, too. cyanos of sponges (below), 𝘞𝘰𝘭𝘣𝘢𝘤𝘩𝘪𝘢 of insects, and then we have the piñata 👇 schaechter.asmblog.org/schaechter/2...