Karthik Anantharaman

ECR Viromics Webinar Series flyer https://coms.osu.edu/webinars/ecr-viromics-webinar-series

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...

James Kosmopoulos Karthik Anantharaman Lab Decoding viral gene function across ecosystems

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

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

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 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...

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

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

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 ...

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...

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...

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.

This research represents a significant step towards understanding the crucial roles of viruses in ecosystems. Excited to see where this will lead us in virology and microbial ecology!

Scalability for Viromics Research: The approach paves the way for high-throughput analysis, making it feasible to explore vast and previously uncharacterized viral genomes, ultimately unlocking their ecological roles.

Deciphering Auxiliary Metabolic Genes: Our model allows for a deeper exploration of auxiliary viral genes (AVGs), shedding light on their roles in viral life cycles and host interactions.

Key findings include:

Improved Protein Functional Prediction: Leveraging the Protein Set Transformer, we can make more accurate predictions about viral protein functions, even in cases where homology is absent.

Our research introduces a novel language model designed specifically for proteins, tackling the complexity of viral proteins—the "viral dark matter." PST enhances protein understanding and power high-throughput viromics to reveal hidden ecological & functional insights in viral genomic datasets.

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 ...

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

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.

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

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

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 💧

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.

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...

I hope you ate some "fry"

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...

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

#phagesky #microsky

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 ...

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: 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...

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...

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/...

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

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!

Tis the season! 😂🤣

#Microsky #Microbiomesky

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 …

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...

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).

📢 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...