The Banfield Lab @BanfieldLab
Located at the University of California-Berkeley. Purveyors of Microbial Ecology, Bioinformatics, & Nanogeoscience. RT≠endorsements. nanogeoscience.berkeley.edu Berkeley, CA Joined March 2017-
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We're moving off of X! Find us at BlueSky at bsky.app/profile/banfie…. Hope to see you there!
🌊 Through metagenomics and hydrographic data, Bethany Kolody and team uncovered 6 microbial cohorts and 10 functional zones structured by ocean circulation in the South Pacific. Congrats on this breakthrough in ocean microbial ecology!🌎doi.org/10.1101/2025.0…
I’m very excited to finally share the results of a passion project that has been on my mind for nearly a decade. You can find the pre-print below, but what follows is the saga of how this project came to be:
Proteomics confirmed many new Pyl-containing proteins, raising questions about the role of this amino acid in protein structure and function. We also used Pyl machinery from Code 34 archaea to introduce new-to-nature pyrrolysine analogs into proteins in E. coli! @v_kivenson (2/2)
🚨 We discovered a new genetic code, "Genetic Code 34," sporadically distributed in archaea. Select archaea have genome-wide recoding of the TAG stop codon to pyrrolysine; the adoption of this code was likely driven by metabolic processes. (1/2) biorxiv.org/content/10.110…
Recent research from our lab, led by @LingDongShi1, unveils "mini-Borgs" – smaller linear extrachromosomal elements in Methanoperedens archaea. These mini-Borgs resemble previously described Borgs and could modulate their hosts' activity. Read more: rdcu.be/dLP3t
Excited to share this amazing work led by @TheHessLab and @Dr__Diamond at @igisci and sponsored by @TheAudaciousPrj. We use multi-omics to show how the rumen microbiome responds to methanogenesis suppression and identify a Duodenibacillus Sp. as an alternative hydrogen sink. biorxiv.org/content/10.110… I'd like to highlight major findings in this study. Thread is here:
COBRA, a method for joining viral contigs in metagenomic assembly, significantly improves accuracy and completeness, leading to more reliable analysis of gene content, diversity, and evolution @ChenLinxing @BanfieldJill nature.com/articles/s4156…
Check out Clare's newly published paper on bacteriophage dynamics in the infant gut microbiome!
🦠What are the early-life colonization & assembly dynamics of bacteriophages? Out today online in @cellhostmicrobe, our paper took a strain-resolved approach to investigate early phage colonizers. Article: doi.org/10.1016/j.chom…
New research from @AndrejaKust and the @Dr__Diamond lab on cyanobacterial communities! Which microbes like to live with Cyanobacteria in model communities? Take a look here and find out: biorxiv.org/content/10.110…
Excited to share our preprint on cyanobacterial communities and their core microbiome, with @Dr__Diamond as corresponding author and incredible help from @jkzorz, @K_BoumaGregson, @catacruanas, @BanfieldLab. #microbiome #Genomics #WomenInSTEM biorxiv.org/content/10.110…
Enormously excited to share the Nature article written about our recent work with the giant proteins! nature.com/articles/d4158…
Trust @Jwestrob and @BanfieldLab to come up with nature's weirdest. 1/2 The world’s largest proteins? These mega-molecules turn bacteria into predators nature.com/articles/d4158…
It's (double) prime time: now in @CurrentBiology, our latest rubisco work with @NogalesLab, @BanfieldLab, @SibylsSAXS, and more! Structural studies of metagenomic form Iα and I′′ enzymes illuminate the evolutionary trajectory of rubisco oligomerization: authors.elsevier.com/sd/article/S09…
And the second part of our two-part preprint bonanza- @Jwestrob (your esteemed banfield lab twitter admin) and the giant proteins! Click through for some beautiful alphafold-predicted protein structures from the biggest (predicted) proteins you've ever seen.
I'm thrilled to present the research I've been working on for the last few years in preprint format. We've found giant genes (>30,000 amino acids!!) across domain bacteria, but concentrated in the candidate phylum Omnitrophota. biorxiv.org/content/10.110…
I'm thrilled to present the research I've been working on for the last few years in preprint format. We've found giant genes (>30,000 amino acids!!) across domain bacteria, but concentrated in the candidate phylum Omnitrophota. biorxiv.org/content/10.110…
The first of our two-part preprint bonanza: @luisarchaeota and his fantastic preprint on the newly presented phylum of Asgard Archaea, the Atabeyarchaeota!
1/🧵 I’m really excited to share our new pre-print on #AsgardArchaeaa manuscript now on #bioRxiv with co-first @katy_appler! We described soil-associated Asgard archaea predicted to be non-methanogenic acetogens. Kuddos to @val_deanda @BanfieldLab @MSchoelmerich
Shouts out to the stellar @luisarchaeota for winning Best Graduate Student Oral Presentation at SACNAS!
Deeply honored and humbled to receive the Best Graduate Student Oral Presentation at @SACNAS . With so many incredible speakers, this recognition means a lot. Thanks to my advisor @BanfieldLab and collaborators. Luis Valentin-Alvarado de Santa Isabel, PR 🇵🇷 para el mundo 🌎
thanks @igisci ☺️💕
Deeply honored and humbled to receive the Best Graduate Student Oral Presentation at @SACNAS . With so many incredible speakers, this recognition means a lot. Thanks to my advisor @BanfieldLab and collaborators. Luis Valentin-Alvarado de Santa Isabel, PR 🇵🇷 para el mundo 🌎
Check out Clare's new preprint on phage ecology in infant gut microbiomes!
🚨 New preprint: #phage strain colonization dynamics in infant gut #microbiomes🧵 biorxiv.org/content/10.110…
1. Borgs with active nanowires ⛓️ and a constellation of mini-Borgs, viruses, plasmids and mysterious elements circling the mothership of methane-oxidizing archaea! 🚀
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