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...

Phage-microbe interactions may contribute to the population structure and dynamics of hydrothermal vent symbionts

Abstract. Deep-sea hydrothermal vent ecosystems are sustained by chemoautotrophic bacteria that symbiotically provide organic matter to their animal hosts

academic.oup.com

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

Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection

Auxiliary metabolic genes, acquired by cyanobacterial viruses (cyanophages) from their hosts, are thought to manipulate host metabolism during infection. A recent study by Nadel et al. performed in vi...

cell.com

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

Viruses found in carbon-storing wetlands play an active role in shaping ecosystem health

The viruses could also help determine if a wetland has been damaged or if restoration efforts are working.

news.wisc.edu

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...

A meta-analysis of environmental sequencing data reveals the global distribution and hidden diversity of marine anaerobic ciliates

Anaerobic protists are diverse, ecologically important members of anoxic microbial communities, acting as grazers, nutrient cyclers, and partners in multi-domain associations, yet remain understudied ...

biorxiv.org

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.

GitHub - AnantharamanLab/protein_set_transformer: Protein Set Transformer (PST) framework for training protein-language-model-based genome language models. Inference is possible for viral genomes usin...

Protein Set Transformer (PST) framework for training protein-language-model-based genome language models. Inference is possible for viral genomes using our pretrained viral foundation model. - Anan...

github.com

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...

Protein Set Transformer: a protein-based genome language model to power high-diversity viromics - Nature Communications

A genome language model, Protein Set Transformer, trained on viral datasets, uncovers evolutionary rules of protein content and organization driving precise virus identification, host prediction, and ...

doi.org

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

Nature Microbiology@natmicrobiol.nature.com · 8mo ago

#NewResearch Viral diversity and community structure are shaped by geography and ecosystem health status, positioning viruses as unexpected players in peatland restoration. @kosmopoulos.bsky.social @ashish-malik.bsky.social @karthik-a.bsky.social #MicroSky 🦠 www.nature.com/articles/s41...

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

Nature Microbiology@natmicrobiol.nature.com · 8mo ago

#NewResearch Viral diversity and community structure are shaped by geography and ecosystem health status, positioning viruses as unexpected players in peatland restoration. @kosmopoulos.bsky.social @ashish-malik.bsky.social @karthik-a.bsky.social #MicroSky 🦠 www.nature.com/articles/s41...

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

Ecosystem health shapes viral ecology in peatland soils - Nature Microbiology

Metagenomics shows that viral diversity and community structure are shaped by geography and ecosystem health status, positioning viruses as unexpected players in peatland restoration.

nature.com

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 💧

Metabolic capacity is maintained despite shifts in microbial diversity in estuary sediments

Abstract. Estuaries are highly productive ecosystems where microbial communities drive nutrient and carbon cycling, supporting complex food webs. With inte

academic.oup.com

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...

Ecosystem health shapes viral ecology in peatland soils - Nature Microbiology

Metagenomics shows that viral diversity and community structure are shaped by geography and ecosystem health status, positioning viruses as unexpected players in peatland restoration.

nature.com

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

An archaeal genetic code with all TAG codons as pyrrolysine

Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...

science.org

#phagesky #microsky

Karthik Anantharaman@karthik-a.bsky.social · 9mo ago

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/...

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...

Clarivate Highly Cited Researchers 2025

The Highly Cited Researchers 2025 list identifies and celebrates individuals who have demonstrated significant and broad influence in their fields of research. Through rigorous selection criteria and ...

clarivate.com

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.

Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises

Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...

pubs.acs.org

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/...

Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises

Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...

pubs.acs.org

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)

Plastic degradation by enzymes from uncultured deep sea microorganisms

Abstract. Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are

academic.oup.com

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

Karthik Anantharaman@karthik-a.bsky.social · 11mo ago

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 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...

An updated view of metabolic handoffs in microbiomes

From the human gut to the deep ocean, diverse microbial communities underpin essential ecosystem processes. Limited understanding of the dynamics and …

sciencedirect.com

📢 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...

Microbial iron oxide respiration coupled to sulfide oxidation - Nature

Genomic and biochemical analyses of prokaryotic sulfur metabolism identify diverse microorganisms with the capacity to oxidize sulfide using iron(iii).

nature.com

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...

A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology

This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

nature.com

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!

Nature Communications@natcomms.nature.com · last yr.

Deep-sea #hydrothermal plumes support an array of microbial metabolisms, but the fate of organic C is unknown. Here, the authors used metabolic rate assays and metagenomic data to show that heterotrophic bacteria contribute significantly to C cycling in the deep #sea. www.nature.com/articles/s41...

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

Ultrafast and accurate sequence alignment and clustering of viral genomes - Nature Methods

Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.

nature.com