#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.

🚨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 👇

📢 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...

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.

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...

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

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...

📢 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...

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...

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. ‼️

New online! Viromics approaches for the study of viral diversity and ecology in microbiomes

Great to see our manuscript on skDER & CiDDER - programs for selection of representative microbial genomes - now published. Please give them a try and if you have any feature requests or issues, just let us know. www.microbiologyresearch.org/content/jour... github.com/raufs/skDER

I'm excited to announced that the version of record of this article is out in @elife.bsky.social. With the other first coauthor My Tran, we found that phage resistance cause reduced beta-lactam resistance and reduced virulence phenotypes in diverse MRSA strains. elifesciences.org/articles/102...

This work was equally driven by two PhD students, Aleksandra Otwinowska (experiments) and Janusz Koszucki (bioinformatics). Check out the preprint or DM if you want to learn more. www.biorxiv.org/content/10.1...

#MicroSky with this author, karen lloyd, this is sure to be an entertaining read. and an exciting one at that...

Tool Choice drastically Impacts CRISPR Spacer-Protospacer Detection https://www.biorxiv.org/content/10.1101/2025.05.06.652306v1

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...

Engineering bacteriophages through deep mining of metagenomic motifs www.science.org/doi/full/10.... #jcampubs

Abrupt termination of research doesn't stop waste, it CREATES waste! We call on @hhsgov.govmirrors.com to restore the funding without delay! #Cuts2Science

Great opinion article in the @nytimes.com today: www.nytimes.com/2025/04/03/o...

🚨New paper!🚨 A comprehensive take on the origins and evolution of translation factors & how these essential players evolved across the tree of life. 🌍🧬 Led by Evrim Fer @uwmadisonmdtp.bsky.social grad student! 👏 Free access: www.sciencedirect.com/science/arti... @cp-trendsgenetics.bsky.social

Hey Bluesky, I heard u like viruses artologica.etsy.com 🧪🐡🦠

we recently found some really neat RNA-guided DNA-cutting systems in phages. Despite remarkable similarities to CRISPR systems, including encoding guide RNAs in arrays, they appear entirely evolutionarily distinct (but definitely related to snoRNAs 🤓) We decided to call them TIGR-Tas systems 🐯

I’m thrilled to share my first ever publication, now published in PNAS! www.pnas.org/doi/10.1073/... With mentorship from the amazing @ksxue.bsky.social, I looked at how the outcomes of species introductions to microbial communities are influenced by the number of introduced microbes.

A little late, but I had a wonderful time at the 5th IBSE international symposium at IIT Madras. Thank you to @karthik-a.bsky.social and Karthik Raman for organizing a conference with an excellent collection of speakers and students.

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

Difficult to focus on science during these times, but if you have the bandwidth, our study on zol is now out in NAR: academic.oup.com/nar/article/... GitHub: github.com/Kalan-Lab/zol Please give the software a try and let us know if you have any feedback! And stay tuned for new features...

🧪🦠 this thread has the letter I wrote to ASM about their removal of IDEAA websites, highlights of Black and other underrepresented scientists, and lack of information about the 2025 ABRCMS meeting in what looks like anticipatory obedience to the new administration. Subquoted thread has related info.

News and Views by @naturemicrobiol.bsky.social on our recent papers describing the 20-year study of ecology and evolution of viruses and bacteria in freshwater systems. @archaeal.bsky.social @quendi.bsky.social @uwmadison.bsky.social www.nature.com/articles/s41...

Two decades of bacterial ecology and evolution in a freshwater lake www.nature.com/articles/s41... #jcampubs

Unravelling viral ecology and evolution over 20 years in a freshwater lake www.nature.com/articles/s41... #jcampubs

Check out our recent publication on our continued research on soil viruses of nitrifers! @MiaSungeunLEE @christinahazard.bsky.social @graemenicol.bsky.social academic.oup.com/ismej/articl...

It might be tiny, but it’s an RNA pellet! Finally worked after weeks of troubleshooting.

Out in NAR, AntiDefenseFinder & our "systematic" analysis of inhibitors of antiphage systems wt Bondy-Denomy lab led by @ftesson.bsky.social and E. Huiting. Not so "systematic" as very few known, fun stuff on MGE, antidefense islands and cool phages exaptations! academic.oup.com/nar/advance-...

If you like old school hip hop, check out this mix by my favorite DJ (who also happens to be my dad) www.mixcloud.com/djkosmo/my-h...

I’m proud to join more than 30 colleagues today in sharing our analysis of potential risks from “mirror life”. We summarize our findings in a @science.org article, and in greater detail in a 300pg technical report: Article: www.science.org/doi/10.1126/... Report: purl.stanford.edu/cv716pj4036

Shareable link to @carlzimmer.bsky.social article in NYTimes on serious concerns over mirror bacteria, published in Science today. www.nytimes.com/2024/12/12/s...

Putting together a Phage starter pack, please let me know if you'd like to be put on the list! go.bsky.app/UNaEwKi I'm also trying to workout how to resurrect my popular paper bot Phage papers here on Bsky. @phagepapers.bsky.social

Love this idea for helping the community make the transition to Bluesky, so I’ve compiled a woefully incomplete list of microbial ecologists and -omics peeps I know are here. Please make suggestions and share. Let me know if you’d like to be added. go.bsky.app/TQpaTqF

If you do #viromics or study #phage communities, you’ve likely dealt with viromes & mixed-metagenomes. But how do viral communities differ between them? What does this mean for interpreting viral ecology? Find out in my latest paper with @karthik-a.bsky.social

Excited to share our latest work on the impacts of using metagenomics vs viromics on viral community ecology and other applications. This work was led by PhD student @kosmopoulos.bsky.social. Please share and we are happy for any feedback. microbiomejournal.biomedcentral.com/articles/10....

What happens when non-rhizobial bacteria make their way into root nodules? R.T. Batstone-Doyle, K.D. Heath, and I found two nodule-isolated bacteria that interfered with a mutualist’s ability to form nodules on its legume host. Read more in our latest paper: cdnsciencepub.com/doi/full/10....

Reposting this message: I am looking to hire a lab manager/research technician for our laboratory. Please help us spread the word. If you know of any motivated candidates, please encourage them to contact me. Microbiology lab experience would be preferred. Looking for at least a 1.5 year commitment.