Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them, or even how the few we have infect a cell. Our new preprint takes this on 🧵👇

RNA #VirusDiscovery gets a boost with RdRpCATCH, a unified framework combining multiple profile HMM resources to detect and taxonomically annotate #RNA viruses in (meta)transcriptomic data.🦠🔎 📄 https://doi.org/10.1093/nargab/lqag076 👤 EVBC: U. Neri, I. Olendraite, J. Charon, S. Sakaguchi, A. Kupczok

Machine learning prediction of eukaryotic hosts for giant viruses https://www.biorxiv.org/content/10.64898/2026.09.08.750034v1

A Global Catalog of Microbial Symbionts 🌍🦠🧬🫨 New resource from @jgi.doe.gov, led by @astrogenomics.bsky.social and @fmschu.bsky.social with contributions by @emileyeloe-fadrosh.bsky.social @miferg.bsky.social and many more 🔓 www.nature.com/articles/s41... @biosci.lbl.gov @berkeleylab.lbl.gov

A genomic catalog of Earth’s bacterial and archaeal symbionts - Nature Biotechnology

Symbiotic relationships of microorganisms are predicted and cataloged with a machine learning tool.

nature.com

Joint Genome Institute@jgi.doe.gov · last mo.

New AI Tool Maps the Global Catalog of Microbial Symbionts 🖥️ 🧬 🦠 Today in @natbiotech.nature.com: The publicly available Symbiont Genomes catalog is one of the most comprehensive guides to bacteria and archaea living in partnership with other organisms. Learn more ⬇️

New AI Tool Maps the Global Catalog of Microbial Symbionts 🖥️ 🧬 🦠 Today in @natbiotech.nature.com: The publicly available Symbiont Genomes catalog is one of the most comprehensive guides to bacteria and archaea living in partnership with other organisms. Learn more ⬇️

New AI Tool Maps the Global Catalog of Microbial Symbionts | Joint Genome Institute

The publicly available Symbiont Genomes catalog is one of the most comprehensive guides to bacteria and archaea living in partnership with other organisms.

jgi.doe.gov

Excited to be talking about my #phage #bioinformatics tool #Phables to study #viral #ecology in #IBD-associated #metagenomes. Come check out my talk in session AS13 at 2.30pm on Tuesday 18th Aug in room 303-305. #ISME20 GitHub: github.com/Vini2/phables Publication: academic.oup.com/bioinformati...

GitHub - Vini2/phables: 🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes - Vini2/phables

github.com

Our new paper just out @natmicrobiol.nature.com led by Yumary Vasquez & Frederik Schulz @jgi.doe.gov @norwichmicro.bsky.social Genomic catalogue of giant #viruses reveals expanded diversity and functional potential www.nature.com/articles/s41...

I am excited to share that our manuscript titled 'Defining the ESKAPE pathogen prophage repertoire with PHORAGER' is now available online as a preprint in BioRxiv! 🤩 (doi.org/10.64898/202...) Here we present PHORAGER, a Nextflow pipeline for the identification and quality assessment of prophages 🧬

If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out Thanks to @ardc.edu.au for making this possible!

🦠 #Bacteria organise themselves to hitchhike across large distances @susiegriggo.bsky.social @flinders.university.bsky.social #chemotaxis #metagenomics #EnvironmentalMicrobiology

Bacteria organise themselves to hitchhike across large distances

Microbes rarely travel alone. In any given environment, millions of microbial species compete with each other for resources while locked in an endless state of warfare […]

dlvr.it

1/4 Every good defence needs a backup! 🛡️⚔ Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 www.nature.com/articles/s41...

Immune safeguarding as a conserved principle of antiviral defence - Nature Reviews Microbiology

All organisms defend against viral infections through active immunity mechanisms that clear the virus or population-level mechanisms that cause regulated cell death. Recent research increasingly shows...

nature.com

Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time

🦠 #Bacteria organise themselves to hitchhike across large distances @susiegriggo.bsky.social @flinders.university.bsky.social #chemotaxis #metagenomics #EnvironmentalMicrobiology

Bacteria organise themselves to hitchhike across large distances

Microbes rarely travel alone. In any given environment, millions of microbial species compete with each other for resources while locked in an endless state of warfare […]

dlvr.it

Very excited to share our paper (and first for my PhD) on RdRpCATCH in NAR Genomics and Bioinformatics! doi.org/10.1093/narg... Co-authors: @urineri.bsky.social, @ingrida.bsky.social, Justine Charon, @sho1.bsky.social, @xinhou.bsky.social, Dick de Ridder, Mark P. Zwart, and @annecmg.bsky.social

RdRpCATCH: a unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov models

Abstract. Recent advances in large-scale sequence mining have expanded our knowledge of RNA virus diversity. Most genome mining approaches for detecting RN

doi.org

First community challenge for automated virus taxonomy https://www.biorxiv.org/content/10.64898/2026.07.04.736517v1

🚨 Registration for VEGA26 is 👏 officially open 👏 🚨 The 5th edition of our Viral EcoGenomics and Applications symposium will be held November 18-19, 2026, on the UC Berkeley campus 🧬 🦠 🔬 🧫 Event website ➡️ jgi.doe.gov/work-with-us... Registration link ➡️ cvent.me/e0RnA0

World-leading Aussie science fighting #AntimicrobialResistance! PhD student George Bouras added 17M bacterial protein predictions to the #AlphaFold database. This was made possible by a partnership between BioCommons & @pawseycentre.bsky.social to containerise #ColabFold on Setonix. Read more 🔗

World-leading Australian science: 17M protein structures added to the AlphaFold Database to accelerate the fight against antimicrobial resistance  — Australian BioCommons

Australian researcher, George Bouras, has recently contributed an extraordinary 17 million protein predictions to the AlphaFold Protein Structure Database. This work was possible thanks to the availability of the ColabFold tool on Setonix AMD, the result of collaboration between BioCommons and the P

biocommons.org.au

Language Modeling Materializes a World Model of Protein Biology https://www.biorxiv.org/content/10.64898/2026.06.03.729735v1

If you do any work with DNA sequencing at some point, you need to assemble the reads. Usually, we just use the contigs, but that ignores important evidence from your data, so @vijinim.bsky.social wrote agtools to explore the assembly graph and learn more! academic.oup.com/bioinformati...

agtools: a software framework to manipulate assembly graphs

AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info

academic.oup.com

Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! 🎉🦠🧬 www.science.org/doi/10.1126/... w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities

A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.

science.org

New preprint! 🚨 Phage proteins don't act alone. Phages rely on homooligomerisation to assemble identical protein subunits into functional forms. But figuring out those exact configurations experimentally is tough. Learn about our approach in our new preprint! 👇 (1/n) www.biorxiv.org/content/10.6...

New preprint! 🚨 Phage proteins don't act alone. Phages rely on homooligomerisation to assemble identical protein subunits into functional forms. But figuring out those exact configurations experimentally is tough. Learn about our approach in our new preprint! 👇 (1/n) www.biorxiv.org/content/10.6...

Beyond thrilled that our paper ‘Co-migration of hundreds of microbial species over metres drives selection and promotes non-motile hitchhikers’ has been accepted in Nature Communications! 🎉🦠 (1/n) www.nature.com/articles/s41...

🎊 New Preprint from phagefoundry.org ! Super excited to share our latest work on generating systematic phage-MDR P. aeruginosa interaction dataset & use of ML to predict phage susceptibility & phage cocktails from target genome sequences alone, w validations www.biorxiv.org/cgi/content/...

Beyond thrilled that our paper ‘Co-migration of hundreds of microbial species over metres drives selection and promotes non-motile hitchhikers’ has been accepted in Nature Communications! 🎉🦠 (1/n) www.nature.com/articles/s41...

5 Flinders researchers recognised in News Corp's Research Superheroes campaign, highlighting the life-changing impact of Australian research 👏 Chan: https://bit.ly/4nCQnqw Halsey: https://bit.ly/4tF6lBF Reynolds: https://bit.ly/3PP6Lrl Eckert: https://bit.ly/4fuNSEx Edwards: https://bit.ly/3RMNEyG

Proud of @ehauptfeld.bsky.social for receiving the Young Investigator Award by @biosb.bsky.social, in recognition to her PhD achievements in research and education! Very well deserved, and congratulations! @ubc-uu.bsky.social @utrechtuniversity.bsky.social

Mushuvirus is the most widespread phage genus in the human gut. 🌍 Together with other family members, these viruses occur in 89% of humans worldwide, including the Iceman Ötzi! How is it possible that they were hidden in previous metagenomic analyses? [1/7] Read: doi.org/10.64898/202...

During my PhD, @milja001.bsky.social and I started counting phage genomes, and tried to make them available in useful formats with useful metadata. We also described the extent of sequenced phage genomes at the time. Five years on, we've had a look at what's changed www.biorxiv.org/content/10.6...

🎉 Excited to share that our paper, “agtools: A Software Framework to Manipulate Assembly Graphs”, has been accepted in Bioinformatics Advances. (1/n) 🔗 GitHub: github.com/Vini2/agtools 📄 Paper: academic.oup.com/bioinformati... #bioinformatics #genomics #openscience

agtools: A Software Framework to Manipulate Assembly Graphs

AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info

academic.oup.com