Very interesting strategy to sense infection!

The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology. I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬

Building inclusive microbial communities 🌍 @adjiep.bsky.social (@kuesellab.bsky.social, @uni-jena.de & Sullivan Lab) shares how mentorship & representation can shape a more inclusive future in microbial sciences. 🎤 Meet him at the #ISME Early Career Researchers event on 21 Oct: lnkd.in/dXeyvnZK

www.nature.com/articles/s41... #microsky #microbiome

www.cell.com/cell-systems... #phagesky #phage

Very excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

📸 ISME is calling all microbial ecologists! Send us your best photos & videos—lab, field, or under the microscope. Winners will be featured on journal covers or on ISME promotional materials! Deadline: 11 November 2025 Details 👉 isme-microbes.org/call-for-mic... #MicrobialEcology

Fascinating preprint. I've always been curious about genome stability of phages. 🧫🦠

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

The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes www.science.org/doi/full/10.... #jcampubs

Had a great time yesterday with Konstantinos Kormas (@kkormas.bsky.social), Irene Ramirez Hernandez & Akbar Adjie Pratama (@adjiep.bsky.social) at the professional pathway lunch, part of @mikrobiokosmos.bsky.social. Thanks to @isme-microbes.bsky.social for making it possible! #mbkceesme2025

In this new series, ISME would like to introduce the members of the Early Career Scientist Committee to you, starting with Chair Burak Avcı. Find out more at isme-microbes.org/meet-ecsc-bu...

Ann Gregory, Co-Chair of the ISME Early Career Scientist Committee, introduces herself and her work on viruses to the ISME community. Find out more at isme-microbes.org/meet-ecsc-an...

Learn more about new ISME Early Career Scientist Member Pam Engelberts's research, career, and the work she's been doing for BrisJAMS. isme-microbes.org/meet-ecsc-pa...

New ISME Early Career Scientist Committee Member Akbar Adjie Pratama @adjiep.bsky.social has a joint position in Germany and the U.S. Learn more about his career and interests at isme-microbes.org/meet-ecsc-ak...

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt

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

🚨 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...

“Hidden viral players: Diversity and ecological roles of viruses in groundwater Microbiomes” We uncover how viruses shape groundwater microbial communities and ecosystem function. www.biorxiv.org/content/10.1...

Phages as treatment for infections are coming. Lots of steps to get right first though. @cmijournal.bsky.social #IDSky #ClinMicro www.clinicalmicrobiologyandinfection.com/article/S119...

New paper out by former postdoc and Humboldt fellow, Luís Fernando Amato-Lourenço et al. with work done in Berlin community gardens Environmental factors influence airborne microplastic deposition in the soil of urban allotment gardens www.sciencedirect.com/science/arti...

Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research www.nature.com/articles/s41... #jcampubs

New paper out! We discovered a tiny archaeon with the smallest known archaeal genome — only 238 kbp! Candidatus Sukunaarchaeum mirabile has almost no recognizable metabolic pathways and may rely heavily on a host to survive. It also represents a novel, deep-branching lineage in the archaeal tree.

Another position within the PHYVIR project 😁. Are you looking for an interesting Postdoc (45 month!) on marine viral ecology? Check out the ad below. workingat.nioz.nl/o/postdoc-po...

Exploring the horizontal gene transfer potential of virus-like particles and extracellular vesicles in the pelagic marine environment - www.nature.com/artic...

ISME is looking for the next destination for its symposium! Interested scientists can now submit an Expression of Interest for their city to be the host for ISME22 in 2030. The deadline for Expressions of Interest is 1 April. isme-microbes.org/call-for-bid... #MicrobialEcology #microbes #isme22

🚨🚨🚨 New pre-print alert: "Stable states in an unstable landscape: microbial resistance at the front line of climate change" doi.org/10.1101/2025... Probably the most complex paper I have ever worked on. It took 4 (!) co-first authors to accomplish and literal years to decipher the story.

Published on my birthday 🎉 Another paper in collaboration with @themaxwelllab.bsky.social Phage reprogramming of Pseudomonas aeruginosa amino acid metabolism drives efficient phage replication doi.org/10.1128/mbio... 🦠🧫🧪🧬

My main PhD work is now out! We find that choice of antibiotic and the level of (sub-inhibitory) dose is important for combining with phages. Good combinations reduce resistance evolution and simple antibiotic susceptibility experiments can help us choose Co-authors not on bsky, brief thread below

The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate : doi.org/10.1101/2025... (for the very busy: 1-6% of gene gains) #MicroSky

Will always be our first #rust project, a special place.

New paper alert: Our 20-year study of viral ecology and evolution reveals viral roles in microbial dynamics, phage genome evolution over time, and key interactions with hosts. A big thank you to our awesome collaborators @quendi.bsky.social @archaeal.bsky.social www.nature.com/articles/s41...

Where the microbes aren't academic.oup.com/femsre/advan... #jcampubs

And I finally got round to updating the GitHub links... github.com/RyanCook94/i...

Is it “winner-takes all” when the simplest living things compete? Check out my fresh publication on phage coexistence in Science and a thread below🧵 www.science.org/doi/10.1126/...

A fantastic resource for early life microbiome: over 3K prokaryotes and 130K viral genomes constructed from 20K gut metagenomes. www.cell.com/cell-host-mi...

Excited to share our new study in @naturecomms.bsky.social showing that soil fungi, unlike bacteria, remain fully active under severe drought conditions, and also invest in synthesis of storage compounds. Led by the amazing @loutsi.bsky.social and Alberto Canarini. Thread 1/2 rdcu.be/d1Tyg

Excited to share “Bin Chicken”, substantially improving genome recovery through rational metagenomic assembly. Applied to public 🌍 metagenomes, it recovered 24,000 novel species 🦠, including 6 novel phyla. doi.org/10.1101/2024... @wwood @rhysnewell @CMR_QUT 🧵1/6

Hallo Bluesky. Please be nice!!