James Kosmopoulos

📢 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...

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...

🚨 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.

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...

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...

I've been playing with sylph and pavian all day today. Very neat tools, and excellent incorporation of databases!

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. ‼️

Viromics approaches for the study of viral diversity and ecology in microbiomes Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00871-wIn this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing on uncultivated viruses of microorganisms.

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

skDER and CiDDER: two scalable approaches for microbial genome dereplication An abundance of microbial genomes have been sequenced in the past two decades. For fundamental comparative genomic investigations, where the goal is to determine the major gain and loss events shaping...

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

Bacteriophage infection drives loss of β-lactam resistance in methicillin-resistant Staphylococcus aureus In methicillin-resistant Staphylococcus aureus, evolution of bacteriophage resistance causes trade-offs that re-sensitize the bacteriato β-lactam antibiotics.

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...

Capsular specificity in temperate phages of Klebsiella pneumoniae is driven by diverse receptor-binding enzymes Understanding host-range determinants in temperate bacteriophages is critical for elucidating phage-host co-evolution and advancing phage therapies. We analysed 3,900 Klebsiella genomes from diverse e...

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...

Loved this episode!

#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

I would have never thought to use Bowtie1 for spacer-protospacer alignments before. Very interesting work… will definitely consider this paper the next time I try to predict virus-host interactions!

Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems - Nature Communications Viruses are pivotal players in deep-sea hydrothermal vents, shaping microbiomes by preying on key hosts. Through a global-scale analysis of vent viruses and their interactions, this study reveals that...

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...

Congrats, Dave!

Ok, now this is just ridiculous

Engineering bacteriophages through deep mining of metagenomic motifs We unlock the potential encoded in phage metagenomes to engineer phages to change host range and kill pathogenic bacteria.

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

CLS Calls on the Trump Administration to Restore Research Funding - The Coalition for the Life Sciences On April 14, 2025, CLS Chair Jo Handelsman and Exec Director Adrienne Hallett sent a letter outlining the tremendous consequences of terminating research and asking that it be reinstated.

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

I was so upset that this wasn’t in their dictionary! This also happened to me before with “oncogenic,” and “cytosol.”

Opinion | The Uncertain Fate of the Young American Scientist (Gift Article) Young researchers are choosing between staying in science and staying in the United States.

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

2 watercolor grids of virus images

watercolor grid of virus images in purple and blue

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.

And of course, thanks to my lab mates @maggielangwig.bsky.social and Cody Martin for the good memories!

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.

zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters Abstract. Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together ena

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...