The Banfield Lab
@banfieldlab.bsky.social
Located at the University of California-Berkeley at the Innovative Genomics Institute.
Purveyors of Microbial Ecology, Bioinformatics, & Nanogeoscience.
Reposts or likes≠endorsements.
https://www.banfieldlab.com/
Purveyors of Microbial Ecology, Bioinformatics, & Nanogeoscience.
Reposts or likes≠endorsements.
https://www.banfieldlab.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...
Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires
www.biorxiv.org/content/10.6...
January 23, 2026 at 1:21 AM
🚨 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...
Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires
www.biorxiv.org/content/10.6...
Reposted by The Banfield Lab
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
Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires https://www.biorxiv.org/content/10.64898/2026.01.21.700959v1
January 23, 2026 at 12:58 AM
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
Reposted by The Banfield Lab
A new preprint from The Banfield Lab looks at mobile genetic elements with single-cell precision. Read here: https://ow.ly/hFBX50Y0nQA
#microbiology
#microbiology
January 21, 2026 at 4:05 PM
A new preprint from The Banfield Lab looks at mobile genetic elements with single-cell precision. Read here: https://ow.ly/hFBX50Y0nQA
#microbiology
#microbiology
Reposted by The Banfield Lab
A new preprint on expanding the genetic code, from IGI's Jill Banfield, Peter Penev, and collaborators across the country: https://ow.ly/HiYO50XVNXR
January 15, 2026 at 5:05 PM
A new preprint on expanding the genetic code, from IGI's Jill Banfield, Peter Penev, and collaborators across the country: https://ow.ly/HiYO50XVNXR
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
www.biorxiv.org/content/10.6...
@mingyan-igi.bsky.social
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...
www.biorxiv.org
January 7, 2026 at 10:20 PM
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
www.biorxiv.org/content/10.6...
@mingyan-igi.bsky.social
Reposted by The Banfield Lab
🚨 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
#postdoc #sciencejobs #biology #microbiome
Postdoc - Microbiome - Innovative Genomics Institute
University of California, Berkeley is hiring. Apply now!
aprecruit.berkeley.edu
January 5, 2026 at 6:19 PM
🚨 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
#postdoc #sciencejobs #biology #microbiome
Reposted by The Banfield Lab
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
January 2, 2026 at 4:39 PM
Troubleshooting common errors in assemblies of long-read metagenomes - @merenbey.bsky.social @banfieldlab.bsky.social go.nature.com/44P7nSm
Reposted by The Banfield Lab
✨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🧬
🔗👇
🧵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🧬
🔗👇
December 9, 2025 at 7:52 AM
✨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🧬
🔗👇
🧵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🧬
🔗👇
Reposted by The Banfield Lab
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
December 8, 2025 at 3:50 PM
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
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
www.nature.com/articles/s41...
@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social
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...
www.nature.com
November 28, 2025 at 9:01 PM
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
www.nature.com/articles/s41...
@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social
Reposted by The Banfield Lab
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
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...
www.science.org
November 23, 2025 at 7:22 PM
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 🎉
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
November 20, 2025 at 7:53 PM
Incredible science coming out from our lab. Congrats @kivenson.bsky.social 🎉
Fresh from the press! Congrats @diamondlab.bsky.social
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....
@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
November 19, 2025 at 11:03 PM
Fresh from the press! Congrats @diamondlab.bsky.social
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.
October 6, 2025 at 11:42 PM
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.
Reposted by The Banfield Lab
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
@banfieldlab.bsky.social
May 1, 2025 at 6:06 PM
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
@banfieldlab.bsky.social
Reposted by The Banfield Lab
🚨 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...
Check it out: doi.org/10.1093/isme...
July 11, 2025 at 1:08 PM
🚨 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...
Check it out: doi.org/10.1093/isme...
Reposted by The Banfield Lab
manuscript here! www.science.org/doi/10.1126/...
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...
www.science.org
July 10, 2025 at 7:44 PM
manuscript here! www.science.org/doi/10.1126/...
Reposted by The Banfield Lab
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
July 10, 2025 at 7:29 PM
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
Reposted by The Banfield Lab
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...
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...
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.
www.nature.com
July 18, 2025 at 11:02 AM
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...
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...
Reposted by The Banfield Lab
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
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)
ow.ly
July 31, 2025 at 11:17 PM
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
Reposted by The Banfield Lab
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
Megaplasmids associate with Escherichia coli and other Enterobacteriaceae https://www.biorxiv.org/content/10.1101/2025.09.30.679422v1
October 1, 2025 at 5:10 AM
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.
Happy to share our recent work on rRNA processing and conformation: www.biorxiv.org/content/10.1...
Huge thanks to @ppenev.bsky.social @Amos Nissley @Dipti Nayak @Rohan Sachdeva @jhdcate.bsky.social @Jill Banfield @banfieldlab.bsky.social !!
Huge thanks to @ppenev.bsky.social @Amos Nissley @Dipti Nayak @Rohan Sachdeva @jhdcate.bsky.social @Jill Banfield @banfieldlab.bsky.social !!
Circular 23S rRNA within archaeal ribosomes
The ribosomal RNAs (rRNAs) that form the core of ribosomes are believed to occur as linear molecules. Here, we investigated rRNAs from diverse and mostly uncultivated archaea and found evidence that, ...
www.biorxiv.org
April 29, 2025 at 9:34 PM
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
April 28, 2025 at 9:29 PM
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