🚨VIROMICS WORKSHOP 2026🚨 Application is now OPEN for the 8th International Viromics Workshop, Oct. 14-16, 2026, in-person at Ohio State University. Application closes Aug. 7. Apply: forms.gle/pJFLDCNEBvAe... Full details: u.osu.edu/viruslab/vir... #viromics #viruses #ecology #workshop

Last week I had the pleasure of presenting my thesis work on developing bioinformatics tools and databases for viral gene discovery and classification at the Midwest Microbiome Symposium, hosted at my alma mater, UIUC. It was great to see what microbiome scientists across the Midwest are working on!

Check out this microbial ecology themed card game! I’ve been a fan of Ecologies for several years, so I was very excited to hear about their latest expansion. I think it would benefit from including more viruses… but I’m biased and still very impressed!

🏰 Debate the frontiers of soil virology in a 13th-century French château. A few places just opened up! Join an international community of soil virus researchers for: 🎤 Keynotes from leading voices 💬 Roundtables on the field's biggest questions 🤝 Rare connections 👇 Register now

ISVC2026

We are excited to announce and provide RSVP details for the next International Soil Virus Conference that will be held in Saint Loup Lamairé, France on June 16 – 18, 2026. The aim of the conference…

soilmicrobes.fr

Lots of people have reached out asking how they can support us after the devastating fire in the MSL building, the heart of @cmarinescience.bsky.social Here’s one way, a GoFundMe organized by our graduate students - gofund.me/4373c6ff3. Please share widely, and thanks for helping our community!

Donate to USF Marine Science: Fire Recovery Support, organized by Bella Iannotta

On Saturday, May 2nd the University of South Florida Marine Science Lab (MSL)… Bella Iannotta needs your support for USF Marine Science: Fire Recovery Support

gofund.me

Can’t believe what I found at an antique store in Madison, WI. A sketch of the Swope Center and Eel Pond at @mblscience.bsky.social. So interesting that it ended up all the way over here! This one’s going up on the wall.

Protein–protein interactions (PPIs) are key to discovering and interpreting new biological functions. We’re excited to introduce 𝑭𝒍𝒂𝒔𝒉𝑷𝑷𝑰: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.

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...

🚨vConTACT3 now in Nature Biotechnology: - >95% agreement with ICTV for known viruses - Classifies both prokaryotic and eukaryotic viruses - Extends beyond genus → subfamily, family & order - Systematically assigns taxonomy to tens of thousands of previously unclassified viruses

We made it to the university webpage for our latest paper in Nature Microbiology. 🦠 www.ed.ac.uk/news/peatlan...

Peatland viruses play active role in ecosystem health | News | The University of Edinburgh

Viruses found in peatlands could play a more important role in carbon storage than previously thought and become indicators of ecosystem health, a study says.

ed.ac.uk

I'm proud to share the latest methods work from my group. Led by @revathykri.bsky.social we wrote a book chapter on how we process and analyse viromes. Thanks to co-authors @rikhaagmans.bsky.social @ryancook94.bsky.social & Alise Ponsero link.springer.com/protocol/10....

Virome Analysis

Viruses are omnipresent and the most abundant biological entities on the planet. They play a critical role in shaping the ecology and evolution of all life forms. This chapter provides methods to perf...

link.springer.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 and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes

Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st

academic.oup.com

#Virus discovery has accelerated but linking viruses to hosts is hard. @sullivan-lab.bsky.social use synthetic #microbiomes to optimize & benchmark #Hi-C for virus-host linkage inference, applying this to existing #soil data to reveal 100s of novel linkages @plosbiology.org 🧪 plos.io/3MlAENO

Surely SOMEBODY mourns the wicked

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

🚨vConTACT3 preprint live!🚨(Peer Review soon...!) vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification. 🔗 Read the preprint: doi.org/10.1101/2025... Improvements details below 👇

Scalable and systematic hierarchical virus taxonomy with vConTACT3

Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...

doi.org

📢 Funded PhD opportunities for UK candidates in beautiful Edinburgh. Get in touch if you're interested in a PhD on understanding the mechanisms of soil carbon cycling and the role of microbes. We work in different ecosystems: peatlands, forests and agricultural soils. Please repost/spread the word.

This past year, my dad was diagnosed with Parkinson's disease. On October 5th, our family will walk together as Team Kosmo at Moving Day Chicago to celebrate his strength and support everyone living with Parkinson's.

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

Am I proud that I made an impulse buy? No. Am I okay with it because it was only $20 for a special series set of Canadian stamps with fungi and lichen? Yes.

CTV News Kitchener@ctvnewskitchener.bsky.social · 11mo ago

Canada Post features fungi and lichen in new stamp series - Canada Post has unveiled its new stamp collection Wednesday featuring fungi and lichens found in the country.

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

Looks like RFK Jr needs a lesson in viral taxonomy @evelienadri.bsky.social!!

Colin Carlson@colincarlson.bsky.social · 12mo ago

RFK has announced that he is developing a vaccine against all viruses. Yes, every single one. The whole, uh, "phylum"

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

Protein Structure Informed Bacteriophage Genome Annotation with Phold

Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

biorxiv.org

📢 New preprint on work by my first PhD student William Pallier. Recovery of microbial ecophysiology and carbon accrual functions in peatlands under restoration. We demonstrate that microbial ecophysiology predictably changes with peatland ecosystem health. www.biorxiv.org/content/10.1...

🚨 New preprint 🚨 My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky www.biorxiv.org/content/10.1...

Synteny-aware functional annotation of bacteriophage genomes with Phynteny

Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

biorxiv.org

Used any new tools or databases (released in the past ~year) for #metagenomics or #viromics? Found something especially useful- or seen recent insights using old methods? Reply with your favorites! I'm trying to compile a list of new resources and approaches.

Looks like a very useful database for classifying fungal sequences in soil metagenomes. Makes me realize I’ve probably overlooked a lot of fungal DNA in my soil datasets! www.biorxiv.org/content/10.1...

Improved detection of fungi and uncultivated microorganisms in soil metagenomes using a comprehensive genome database

Soils harbor diverse microbial communities crucial for ecosystem functioning, but poor genomic representation of many uncultured soil microorganisms limits the utility of existing databases to address...

biorxiv.org

My postdoc position is open again! If you’re interested and did not get your application in last time, please send one by end of this week! Start date asap, latest by end of Fall. ‼️

Morgan Sobol@msobol.bsky.social · last yr.

🚨 I’m hiring a postdoc for Fall 2025 with experience in microbial ‘omics data analysis and phylogenetics/genomics. Projects will be centered around ancient microbial ecology & evolution. Click here for more information: bpb-us-e1.wpmucdn.com/wp.txstate.e... Please share, thank you 🙏🏻