So proud to see this study out — a real honor to be involved in work from my PhD lab!

Nature Biotechnology@natbiotech.nature.com · last mo.

High-quality phage assembly from metagenomes with PALACE www.nature.com/articles/s41...

Big congrats to @ameliarnelson.bsky.social and coauthors on this new preprint. 🎉 We're excited to share this work on microbial CO2 fixation across diverse soil ecosystems, highlighting widespread carbon fixation potential and expanded RuBisCO diversity. Check it out: www.biorxiv.org/content/10.6...

🌲🔥🧬 New pre-print from Elliot Weiss in the Banfield Lab! We tested whether inoculating burned forest soils with native microbes could aid recovery. A single inoculation accelerated the return of symbiotic fungi and nitrogen cycling! www.biorxiv.org/content/10.6...

Microbial inoculation accelerates post-fire soil recovery in a mixed conifer forest

High-severity wildfires of increasing size and frequency result in release of carbon dioxide and loss of timber resources, reduction in biodiversity, loss of soil, diminished water quality, and reduce...

biorxiv.org

Big congrats to Susan Mullen and coauthors on this new preprint. 🎉 We're excited to share this work exploring microbial dispersal and establishment across river water, groundwater, soil, and hyporheic zone environments in the East River watershed. Read the preprint: www.biorxiv.org/content/10.6...

🧬 New preprint out from @lingdong-shi.bsky.social et al. on the origin and evolution of archaeal Borg extrachromosomal elements across different environments. Congratulations Ling-Dong and co-authors! 📄 doi.org/10.64898/202...

Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/t...

Congratulations @wshuai.bsky.social and co-authors! 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...

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...

Thrilled to share that my precious work on SpecImmune in Hong Kong is now published in Advanced Science! This algorithm represents a major step forward in using long-read sequencing to decode the highly polymorphic immune genes. Read the paper: advanced.onlinelibrary.wiley.com/doi/10.1002/...

A Scalable Framework for Comprehensive Typing of Polymorphic Immune Genes from Long‐Read Data

SpecImmune introduces a unified computational framework optimized for long-read sequencing to resolve over 400 highly polymorphic immune genes. This scalable approach achieves high-resolution typing,...

advanced.onlinelibrary.wiley.com

🚨 New pre-print alert! Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires www.biorxiv.org/content/10.6...

Ling-Dong Shi@lingdong-shi.bsky.social · 7mo ago

Excited to share our discovery of archaeal circular, jumbo extrachromosomal elements (up to ~535 kb genomes). One related, 409-kb genome is integrated in CH4-eating Methanoperedens, representing the largest integrative element in Archaea so far! Curious about what they are doing? See the paper

Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology

Long-read sequence assemblies from metagenomes contain frequent errors.

go.nature.com

My 2025 in GitHub

Out now in Nature Communications, from IGI's Jill Banfield (The Banfield Lab) and collaborators: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses Read here: https://www.nature.com/articles/s41467-025-65646-7

Incredible science coming out from our lab. Congrats @kivenson.bsky.social 🎉

Innovative Genomics Institute@innovativegenomics.bsky.social · 9mo ago

Out today in Science Magazine — First author Veronika Kivenson and PIs Jill Banfield (The Banfield Lab) and Alanna Schepartz team up to reveal a new genetic code in #archaea, with implications for #methane and #climate, and #bioengineering! Learn more: https://ow.ly/Kuem50Xurh0

We are thrilled to announce our latest publication in the Microbiome journal in collaboration with @thehesslab.bsky.social Supplementation with red seaweed in cows reduces methane and induces previously uncharacterized hydrogenotropic bacteria. microbiomejournal.biomedcentral.com/articles/10....

Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria - Microbiome

Background Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. Ho...

microbiomejournal.biomedcentral.com

We're excited to help launch the inaugural Gordon Research Conference on #microbiome #GenomeEditing, coming up in January in Pomona, CA! Learn more and register here: https://ow.ly/63z150X9XkG

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

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 11mo ago

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae https://www.biorxiv.org/content/10.1101/2025.09.30.679422v1