Love seeing some @natureportfolio.nature.com journals allow author names in non-Roman characters. Such a simple change, but huge for representation and proper attribution!

Viral "dark matter" dominates the virosphere. In this review by me & @karthik-a.bsky.social, we synthesize what's known, highlight major gaps, and outline paths forward for illuminating viral protein functions in diverse ecosystems.

Breaking news: Democratic socialist Zohran Mamdani is elected as the next mayor of New York City, defeating former New York governor Andrew Cuomo and becoming the first Muslim and first of Indian descent to hold the office. https://wapo.st/47rlrDf

Microbes without borders: uniting societies for climate action @femsjournals.bsky.social Microbiol Ecol by @jaytlennon.bsky.social et al @leonorabit.bsky.social @vscooper.micropopbio.org @gilbertjacka.bsky.social academic.oup.com/femsec/artic...

Why are some species widespread while others are found only in small, isolated areas? A study in Nature Communications shows that species with narrow ranges, and thus higher extinction risk, are often island-restricted, poor dispersers, and have evolved relatively recently. #evosky 🧪

🚨 We’re hiring! 🚨 The Integrative Viromics Lab @UCalgary 🇨🇦 is looking for a Lab Technician! 🔬 Phage isolation & culture 🧫 Anaerobic chamber work 📦 Lab management & student mentoring Apply now & help us explore the virosphere! You must have work authorization to work in Canada already.

Thrilled to share our two latest papers with the @tcostalab.bsky.social lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species. @imperialcollegeldn.bsky.social www.cell.com/cell/fulltex...

📢Preprint out! Excited to share my final work from the @soreklab.bsky.social! We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery. Found 3 new families targeting immune signaling!

#phage #phagesky

Big Fantastic Virus Database (BFVD) version 2 improves 31% of predictions through 12 ColabFold recycles. PAEs and MSAs now also available for download and in the webserver. 🌐https://bfvd.foldseek.com 💾https://bfvd.steineggerlab.workers.dev/ 1/3

Last day back at home in the USA #internationalwomensday #tucson #arizona #womensrightsarehumanrights #notmypresident

1/46 Hey folks, we have a new paper out on the MuLTEE. Strap in and I’ll tell you the story of how this “little paper on polyploidy” turned into the most data rich paper our lab has produced, largely thanks to the leadership and work ethic of @kaitong25.bsky.social. www.nature.com/articles/s41...

Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42... #metagenomics #microbiome #microbiomesky So what is MEDI? A combination of two things:

Delighted to share this paper out via Virus Evolution: academic.oup.com/ve/advance-a... in which we develop and assess a quantitative method to infer phage and bacterial mutations driving changes in infection phenotypes arising in coevolutionary dynamics. a 🧵 about people (and some science)

We interrupt your regularly-scheduled chaos to bring you some cool microbiome science. 🦠 🖥️ 🧬 "Longitudinal phage–bacteria dynamics in the early life gut microbiome" now out in Nature Microbiology. We wanted a way to measure bacteria and phage in metagenomes 1/ www.nature.com/articles/s41...

Characteristics of Phages and Their Interactions With Hosts in Anaerobic Reactors enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs

Today we report a new compendium of human gut microbiomes with >168,000 samples By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria Now out in Cell: www.cell.com/cell/fulltex...

Excited to introduce the preprint for CoverM: the Swiss Army knife of coverage calculators for metagenomics! 🧬🖥️ DOI: doi.org/10.48550/arX... @benjwoodcroft.bsky.social @viralinstruction.bsky.social @apcamargo.bsky.social

RNA control of reverse transcription in a diversity-generating retroelement www.nature.com/articles/s41...

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

Blood DNA virome associates with autoimmune diseases and COVID-19 www.nature.com/articles/s41...

OUT NOW: Metagenomic immunoglobulin sequencing (MIg-seq) reveals IgA coating of microbial strains in the healthy human gut by Justin Sonnenburg, Matt Olm, Sean Spencer & co #microsky www.nature.com/articles/s41...

Unicore identifies single-copy protein structures across genomes using Foldseek, bypassing slow structure predictions by utilizing 3Di predictions from ProstT5, enabling rapid phylogenetic inference at the tree-of-life scale. 1/n 📄 www.biorxiv.org/content/10.1... 💾 github.com/steineggerla...

Delighted that @tarnopol.bsky.social’s paper (dissertation ch.) is online @currentbiology.bsky.social! “Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids.” Phage toxin genes became a feature of insect immune systems millions of years ago…👇🏼

I’m so excited to share that some of my grad work in the @aaronwhiteley lab is now available on bioRxiv! We used an AlphaFold-multimer screen to uncover how a bacterial NLR-related proteins senses multiple phage-encoded proteins to confer phage protection. Link: www.biorxiv.org/content/10.1...

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/...

It’s hard to believe the Integrative Viromics Lab is close to wrapping up its first year! This December has been full of celebrations—three birthdays, a festive winter holiday party, and so many milestones to reflect on and be proud of. Here’s to an even more exciting 2025! 🎉✨

EvoMIL uses protein language models & deep learning to predict virus-host associations with improved accuracy & highlights critical viral proteins. #VirusHostInteractions #DeepLearning #Bioinformatics 📄 doi.org/10.1371/jour... EVBC👤: @davidlrobertson.bsky.social

All cells are encapsulated by a membrane of complex lipidic composition, right? Not anymore! @JamesSaenz.bsky.social et al. show that a ‘minimal’ bacterial cell only needs 2 lipid species #microNatComms #Microbiology #CellBiology #lipids Read the paper: www.nature.com/artic...#microNatComms

Women are under-represented at senior levels in #academia globally, & across all #science 🧪 disciplines, as shown by these "scissor-shaped curves" ✂️ So how can we ever achieve #gender #equality? We discuss various strategies in this #Cell Commentary #WomeninSTEM www.cell.com/cell/fulltex... 🧵 1/

Our Big Fantastic Virus Database (BFVD) is now published NAR! It contains protein structure predictions of major viral clades, enhanced by petabase-scale homology search and it's explorable on the web. 🌐 bfvd.foldseek.com 💾 bfvd.steineggerlab.workers.dev 📄 academic.oup.com/nar/advance-...

Yet more evidence that transfer learning of sequence-only PLMs does not benefit from scale beyond 650M params 🧵

1/ Keen to share the story of my postdoc research out in @natureportfolio.bsky.social! We built a massive resource characterizing the spatial landscape of the gut—and yes, we dug deep into the biology too. If you’ve got a minute, let me walk you through the story. 🧵👇 www.nature.com/articles/s41...

This morning #Klebsiella2024 @olayarendueles.bsky.social is presenting work on the interactions between capsule, fitness and Horizontal Gene Transfer in Klebsiella pneumoniae. Great story, some of it published journals.plos.org/plosbiology/...

📢 REMINDER: The CSV Early Career Researcher Virtual Seminar Series on Friday, Nov 22 @ 10:30 AM PST / 1:30 PM EST! 📢 Featuring talks from Bryce Warner and Mariya Goncheva. A Zoom link has been sent to CSV members! Don't miss out and come support your fellow Canadian virologists!

Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination www.nature.com/articles/s41... #jcampubs

New paper from the lab out in Cell Systems. “Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut” www.cell.com/cell-systems...

Metabolites from intact phage-infected Synechococcus chemotactically attract heterotrophic marine bacteria www.nature.com/articles/s41... #jcampubs

Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use! www.biorxiv.org/content/10.1...

Happy to see our paper out @ Nat Comm We discovered a bacterial NLR-like pattern recognition receptor that can sense 3 different viral proteins as a signature for infection. This explains its broad defense against different phage families Congrats Nathalie Béchon! www.nature.com/articles/s41...

Join me at the Connecting Microbiome Communities (CMiC) meeting in San Diego for a one-of-a-kind opportunity for scientists to explore common challenges, create shared solutions, and establish new collaborations! #CMiC2024 simbhq.org/cmic/attend

Come join the Department of Biological Sciences at the University of Calgary. We're hiring an Assistant Professor in Molecular Genetics for Microbiome Editing! careers.ucalgary.ca/jobs/1422666... Applications are due May 17, 2024

CasPEDIA is live! We collected tons of information on important CRISPR enzymes, put it all in one place and provide a framework to compare diverse enzymatic activities. caspedia.org academic.oup.com/nar/article/...

Our News & Views (with @conmeehan.bsky.social ) out now on nature ecology & evolution : our introduction to an important paper on the evolution of pangenomes by @gmdouglas.bsky.social and @bjesseshapiro.bsky.social reacube open access: rdcu.be/du8Sd www.nature.com/articles/s41...

MicrobeMod 1.0.3 is released! It is now compatible with the dual 4mC and 5mC experimental all-context base calling model. 4mC calling seems to be working well for me so far, but want to see more tests! Excited to get all 3 major prokaryotic methylation types now. github.com/cultivarium/...

Shaping of the phyllosphere microbiome: we recently sought to manipulate plant #microbiome transmission over multiple generations to test how microbiome host specialization and generalism can arise without impacting plant fitness or gene expression. Check it out here: www.cell.com/cell-host-mi...

Viruses and autophagy: bend, but don’t break www.nature.com/articles/s41...

News on the Zorya defense system: anchors to the peptidoglycan and detects membrane disruption by phage. It has a flagella-motor-like device that rotates once activated. So cool! I've been waiting for insights on Zorya since we first described it 5 years ago. Congrats Tylor&co! t.co/WFvS9FePB5

Does anyone have any advice for where to purchase start-up equipment with a tight budget? (1)Class II Biosafety Cabinet (2)Benchtop Microcentrifuge (3)Anaerobic Chamber (4)Autoclavable Micropipettes sets (5)-80C Freezer #NewPI #Budget #ScienceSky #Culturing

I am excited to officially announce that I will be starting my own lab at the University of Calgary in January 2024 to study the human virome! I am recruiting grad students and postdocs. For more details, please check out my lab’s website: www.integrativeviromicslab.com