The Banfield Lab

🌀 We solved the structure for T. denticola periplasmic flagella!

I'm very happy to finally showcase this work. A huge collaborative effort between myself, @bindusmitapaul.bsky.social, @debnathghosal.bsky.social, Jack Kim, @banfieldlab.bsky.social, Eric Reynolds and the Chris Fenno lab.

🦠 Enjoy!

Today in Nature Communications, a team of IGI researchers from The Banfield Lab and Pam Ronald's labs uncover a new way to reduce methane emissions from rice by influencing the activity of rice paddy soil #microbes. Read more: https://ow.ly/45j150Y3WsI

🚨 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...

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

A new preprint from The Banfield Lab looks at mobile genetic elements with single-cell precision. Read here: https://ow.ly/hFBX50Y0nQA

#microbiology

A new preprint on expanding the genetic code, from IGI's Jill Banfield, Peter Penev, and collaborators across the country: https://ow.ly/HiYO50XVNXR

Revealing the pervasive landscape of MGE-host interactions in situ with single-cell genomics Mobile genetic elements (MGEs), including plasmids and viruses, drive microbial evolution and ecosystem dynamics, yet their distribution, host range, and functions remain poorly understood, especially...

New preprint out: Revealing the pervasive landscape of MGE-host interactions in situ with single-cell genomics
www.biorxiv.org/content/10.6...

@mingyan-igi.bsky.social

Postdoc - Microbiome - Innovative Genomics Institute University of California, Berkeley is hiring. Apply now!

🚨 Our Lab is HIRING! If you are interested in characterizing model microbiomes using genome-resolved methods, statistical/metabolic modeling, and/or machine learning please submit an application here: aprecruit.berkeley.edu/JPF05234

#postdoc #sciencejobs #biology #microbiome

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

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

✨New preprint!

🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al!
Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬

🔗👇

illustration of petri dishes growing microbes

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

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/...

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

Fresh from the press! Congrats @diamondlab.bsky.social

We tried to contact researchers at Sichuan Agricultural University who may have deposited this data (PRJNA601687) with no reply. Please let us know if you have any information.

Newest preprint from the group on megaplasmids in E. coli led by @assemblerag.bsky.social. In addition to our findings in metagenomic datasets, we identified an RNA-seq project from a giant panda gut sample with evidence of megaplasmids. We would like to include the data creators in our study.

The 2025 Banfield Retreat was fantastic 🦠 so many talented scientists in one place is a sure way to come up with some great ideas!
@banfieldlab.bsky.social

🚨 Fresh from the press! We created and analyzed over 100 in vitro cyanobacterial consortia using well-characterized model cyanobacterial hosts to better understand how cyanobacteria recruit and interact with their microbiomes.

Check it out: doi.org/10.1093/isme...

Overturning circulation structures the microbial functional seascape of the South Pacific Global overturning circulation partitions the deep ocean into regions, each with different physicochemical characteristics, but the extent to which these water masses represent distinct ecosystems rem...

manuscript here! www.science.org/doi/10.1126/...

Many of you gave me so much encouragement when I posted here earlier about my 10 year long passion project to make a microbial map of the ocean. Pinch me because I can't believe I get to update you that today that research was published in the journal SCIENCE! @science.org

Structure of an archaeal ribosome reveals a divergent active site and hibernation factor - Nature Microbiology Sequence and structural analyses reveal a divergent peptidyl transferase centre and a hibernation factor in archaea.

Out now:

Structure of an archaeal ribosome reveals a divergent active site and hibernation factor

@jhdcate.bsky.social @banfieldlab.bsky.social @diptinayak.bsky.social & co

#microsky

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

Tiny CRISPR Tool Opens the Door to Faster, Simpler Plant Genome Editing Tiny CRISPR Tool Opens the Door to Faster, Simpler Plant Genome Editing - Innovative Genomics Institute (IGI)

In a recent paper, IGI's @jenniferdoudna.bsky.social @doudna-lab.bsky.social and Jill Banfield @banfieldlab.bsky.social collaborate with UCLA's @jacobsenucla.bsky.social to create a new, tiny #CRISPR tool for quicker, easier plant genome editing! Read more in this Q&A with Steve: ow.ly/6Szs50VGElf

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

Excited to share new research led by our very own @lingdong-shi.bsky.social showing that many archaeal 23S rRNAs are circularized in active ribosomes. Check out the preprint below.

Genomes from long-read metagenomic assemblies contain rampant errors, highlighting the pressing need for stricter evaluation methods in long-read assembly algorithms. Read more in our paper with the Eren group. @floriantrigodet.bsky.social @merenbey.bsky.social