With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

Happy to announce the defense of PhD student Cody Martin tomorrow, May 1, at 3 pm CST for his thesis titled "Decoding the language of viral genomes with evolutionary-scale, context-aware genome language models". Talk is open to public - Email me for zoom link. #phagesky #microsky #Microbiomesky

I’ll be presenting at the next ECR Viromics Webinar on March 11 at 9 AM CT, highlighting a new tool I’ve been developing in the @karthik-a.bsky.social lab for scalable, automated discovery and curation of auxiliary viral genes: CheckAMG. Details and registration here: coms.osu.edu/webinars/ecr...

Join us for next week's MDTP student seminar, featuring James Kosmopoulos from Karthik Anantharaman's Lab! @kosmopoulos.bsky.social @karthik-a.bsky.social #UWMadison #viromics #MDTP

Excited to share that @michelle-hauer.bsky.social's paper with @katiekliermicrobe.bsky.social @maggielangwig.bsky.social @karthik-a.bsky.social on phage interactions with chemosynthetic symbionts was published today. #NSF and @schmidtocean.bsky.social supported. academic.oup.com/ismecommun/a...

Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection www.cell.com/cell-host-mi...

News article from @uwmadison.bsky.social describing our recent study on viruses in peatland soils! news.wisc.edu/viruses-foun...

New preprint led by @annaschreck.bsky.social that capitalized on the wealth of publicly available 18S rRNA datasets to explore the oceanic distribution and diversity of understudied anaerobic ciliates. www.biorxiv.org/content/10.6...

Cody also put in a ton of extra work to make the code organized and usable in the GitHub repo: github.com/Anantharaman... It links to a Colab notebook for model inference, training data, and pretrained models.

Excited for our new paper on a genome language model for viruses in @natcomms.nature.com: "Protein Set Transformer: a protein-based genome language model to power high-diversity viromics"! Led by PhD student Cody Martin in collaboration with @anthonygitter.bsky.social doi.org/10.1038/s414...

Excited to have our new study on viruses in peatlands out in @natmicrobiol.nature.com! #phagesky #MicroSky

Very excited to share this latest research in Nature Microbiology led by PhD student @kosmopoulos.bsky.social in collaboration with @ashish-malik.bsky.social. #phagesky #Microsky

Our paper "Ecosystem health shapes viral ecology in peatland soils" is out in Nature Microbiology! We show that peatland health strongly structures viral communities, shaping virus–host networks, and carbon and nutrient cycling. Please share. www.nature.com/articles/s41... #phagesky #Microsky

So happy this is finally out! We reconstructed the 1st large-scale spatiotemporal dataset of 600+ MAGs from San Francisco Bay and show they have functional redundancy in key N and S pathways. These functions may better recover from disturbance in this highly urban estuary 💧

Soil viruses are important regulators of ecosystem function, but what are their roles in environments that face long-term degradation and restoration? In our paper published today in Nature Micro, we asked how soil viruses influence peatland recovery, and vice versa. www.nature.com/articles/s41...

New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...

#phagesky #microsky

Thrilled to be recognized as a Highly Cited Researcher for 2025! This honor truly reflects the creativity, drive, and dedication of our lab team (past and present), and our incredible collaborators and scientific community. Here’s to pushing boundaries together! clarivate.com/highly-cited...

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.

Excited to share our new review article on Viral Dark Matter led by PhD student @kosmopoulos.bsky.social. We talk about what is known and unknown in the world of viruses (specifically phage), and highlight future opportunities for research and biotechnology. pubs.acs.org/doi/10.1021/...

A wonderful collaboration between my lab and Andy Ellington and Edward Marcotte here at UT. We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)

Delighted and honored to meet with the one and only Bruce Levin today who was the MDTP student invited speaker at UW-Madison!

#Microsky #Microbiomesky

New review paper on metabolic handoffs in microbiomes led by PhD student Katie Klier. We define major types of metabolic handoffs, examine their drivers and benefits, & describe their importance in different complex microbial systems and environments. www.sciencedirect.com/science/arti...

📢 New paper in @nature.com Microbes rock 🎸🤘 with sulfide and iron minerals I am very excited to share our recent study, which describes a previously unknown microbial energy metabolism ⚡⚡⚡🦠🧫⚡⚡⚡ 🆕 Microbial iron oxide respiration coupled to sulfide oxidation - MISO www.nature.com/articles/s41...

New paper alert! We suggest caution in the analyses of viral auxiliary metabolic genes and propose a new overarching term - 'auxiliary viral genes' (AVGs) to describe different types of such genes. @simrouxvirus.bsky.social #phagesky #Microsky www.nature.com/articles/s41...

Advice from NSF: grant proposals can still include outreach, community engagement, and so on. But avoid specifying particular groups

Tomorrow at 12:45-1:30 in the EEB Track Hub in the poster hall #ASMmicrobe I am talking about microbial diversity including Asgard archaea, and an expanded tree of life from marine sediments.

Excited to be a part of this effort from Mandy Joye's group showing the role of heterotrophs in deep sea carbon cycling!

Ultrafast and accurate sequence alignment and clustering of viral genomes | Nature Methods https://www.nature.com/articles/s41592-025-02701-7

Very excited this part of my PhD is out 🎉 We describe vent viral and microbial traits that govern viral biogeography and contribute to mounting evidence that these communities are highly endemic, and thus likely vulnerable to disruptive activities like deep sea mining #Microbiome #DeepSeaMining

A few weeks ago we met in the Scottish Highlands to launch our HFSP @hfspo.bsky.social funded project on virus-prokaryotic interactions in wetlands and impact on the methane cycle. What a fantastic team to be part of. @karthik-a.bsky.social @soilmicrobes.bsky.social & Joanne Emerson

#phagesky #microsky

Excited to share our lab's latest work led by PhD student @maggielangwig.bsky.social describing the ecology and evolution of viruses in globally distributed hydrothermal vents. www.nature.com/articles/s41...

Come and work with me! The Nature Micro team is expanding and we're looking for someone to champion microbial ecology, plant micro & related areas for the journal Knowledge of microbial ecology/plant micro is desirable but we're open to applications from all microbiologists Link below 👇

Our perspective on soil virus ecology research is out! Fantastic collab with @christinahazard.bsky.social @karthik-a.bsky.social @lukehillary.bsky.social @urineri.bsky.social @simrouxvirus.bsky.social @gtrubl.bsky.social @KurtWilliams @jeffinerca.bsky.social @graemenicol.bsky.social @JoanneEmerson

Amidst all the bad news, I still want to share two new preprints from our lab group. The first is led by newly minted Dr. Michelle Hauer, in collaboration with @karthik-a.bsky.social @katiekliermicrobe.bsky.social and @maggielangwig.bsky.social www.biorxiv.org/content/10.1...

This was published in the top newspaper in India. So much for "news". timesofindia.indiatimes.com/city/delhi/w...

Our lab had a great time at the IBSE Microbiome Symposium. Looking forward to this in the future again.

It was great to host @jeffinerca.bsky.social and learn about her inspirational work in the persistence of soil carbon. Hosted by the IBSE Microbiome Symposium at IIT Madras.

Great talk by Tanja Woyke on very exciting upcoming technological advancements in single cell genomics at @jgi.doe.gov Hosted by the IBSE Microbiome Symposium at IIT Madras.

Excited and grateful to have Brett Baker and Paul Wilmes at the IBSE Microbiome Symposium at IIT Madras. Forever amazed by their brilliant science. @archaeal.bsky.social @paulwilmes.bsky.social

Cody Martin from lab our presenting his work on deep learning and the development of 'PST' for viral ecology at the IBSE Microbiome Symposium at IIT Madras in Chennai, India.

Phage taxonomy doesn’t have to be taxing, my latest cartoon for the Phage journal. To illustrate 𝘁𝗮𝘅𝗠𝘆𝗣𝗵𝗮𝗴𝗲 lnkd.in/dAXK4sSt @milja001.bsky.social

Excited to have Jill Banfield present the opening keynote at the IBSE Microbiome Symposium at IIT Madras yesterday.

Studies only making reads available may satisfy journal requirements but do not serve the larger community. If you work with any form of metagenomics/genomics data, and are for open access and FAIR data policies...Please consider making ALL your data public (genomes, proteins, reads, metadata).

Putting on my editor's hat for my yearly rant about scientists who do not review manuscripts enough for journals. As a quantitative approach, consider reviewing 3X the papers submitted by you or your lab in a calendar year (the number 3X comes from if you expect 3 reviews for your own papers).

New lab paper alert: Presenting "Prophage-DB", a database of prophages mined from public databases along with metadata. environmentalmicrobiome.biomedcentral.com/articles/10....

🚨Postdoc position(s) alert🚨 If you like to develop new bioinformatic tools for *human* microbiome analysis, are interested by virus/phages, we (JGI Viral Genomics and Microbiome Data groups) may have a great position for you ! No official job posting yet, but email or DM if you are interested !

Check out our new preprint on viruses associated with Karenia brevis blooms! 🦠 🌊 🧪 🧬 @cmarinescience.bsky.social