Studying DNA modification in microbes shouldn't be limited by methodology. 🧬
We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage. Check out the preprint: www.biorxiv.org/content/10.6...

Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains www.biorxiv.org/content/10.64898/2026.03...

From microscale to microbial insights: validating high-throughput microvolume extraction (HiMEx) methods for marine microbial ecology Abstract. Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitating th

Think you need large volumes for microbial experiments?
Our recent publication introduces HiMEx, a simple, scalable method for microbial ecology. academic.oup.com/ismecommun/a...
🦠 it provides an easy, efficient approach to capturing viral diversity, opening new opportunities for virome analysis.

Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses - Nature Communications Borgs are large extrachromosomal elements of anaerobic methane-oxidizing archaea. Here, via in silico protein structure prediction of ~10,000 Borg proteins, the authors reveal that Borgs share numerou...

Out now in Nature Communications: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses

www.nature.com/articles/s41...

@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social

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/...

Recurrent acquisition of nuclease-protease pairs in antiviral immunity Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...

Our nuclease-protease story is out! We explored a fascinating case of coevolution and modularity in prokaryotic immune systems: www.science.org/doi/10.1126/...

Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social

There is still much to uncover about these megaplasmids and their role in various environments! Thanks to everyone involved, especially @wshuai.bsky.social who investigated modification/methylation patterns to identify the hosts of these plasmids in the gut microbiome.

Almost 80% of the predicted proteins on the plasmids have hypothetical or unknown annotations by various tools. We used structural predictions to help elucidate some of the major functions including potential virulence, antibiotic resistance, and strategies to overcome bacterial host defences.

Next we used a few tools to search public datasets and found similar megaplasmids in adult guts, chicken guts, and panda guts. These elements are also in wastewater, soil, and hospital sinks. Most interesting to us was their discovery in E. coli and Salmonella enterica isolate genomes.

Here are a few highlights:
We first identified a 1.58 Mbp plasmid in an infant gut metagenome thanks to @pacbio.bsky.social sequencing. The average bacterial genome size in these communities is usually less than 5 Mbp so this was curious to us. We then found similar elements in other infants.

Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social

Amazing work by the team at McMaster & the IIDR! Finding new antibiotics is not easy. Congrats to Manoj et al on this significant discovery!