Ling-Dong Shi @lingdong-shi.bsky.social · 24/05/2026Super excited to share the final project of my postdoc career! We found that Borgs and mini-Borgs are widespread across diverse ecosystems. They don't just exist in Banfield Lab — they are everywhere! 🌎 11510
Reposted by Ling-Dong ShiMarie C. Schölmerich @mschoelmerich.bsky.social · 11/04/2026New preprint alert 🚨: Who actually drives methane production in anoxic sediments 🧬🔥? We point to a transcriptionally dominant 🦠 clade: VadinHA17. shorturl.at/Rijc0 @bledinadede.bsky.social @taylorpriest.bsky.socialbiorxiv.org 1137
Reposted by Ling-Dong ShiShuai Wang @wshuai.bsky.social · 30/03/2026Studying 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...biorxiv.org 41813
Reposted by Ling-Dong ShiMichael Murphy @mmurphyrna.bsky.social · 30/01/2026Very interesting observation on the ribosomes of our distant relatives! link.springer.com/article/10.1...link.springer.comCircularization of 23S rRNA but not 16S rRNA within archaeal ribosomes - Genome BiologyBackground Processing of archaeal 16S and 23S rRNAs is believed to involve excision of individual rRNAs from polycistronic precursors, circularization of excised rRNAs, and re-linearization before the... 153
Reposted by Ling-Dong ShiInnovative Genomics Institute @innovativegenomics.bsky.social · 26/01/2026Today 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: ow.ly/45j150Y3WsI 1157
Ling-Dong Shi @lingdong-shi.bsky.social · 23/01/2026Excited 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 11812
Reposted by Ling-Dong ShiThe Banfield Lab @banfieldlab.bsky.social · 28/11/2025Out 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.socialnature.comConvergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses - Nature CommunicationsBorgs 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... 07028
Reposted by Ling-Dong ShiFabai Wu @fabaiwu.bsky.social · 21/10/2025Glad to share our paper out today @NatureEcoEvo: “Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor”. www.nature.com/articles/s41... #microsky #archaeaskynature.comSerial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor - Nature Ecology & EvolutionPhylogenetic and biochemical analyses show a diversity of components of the DNA replication machinery in different Asgard archaea that contributed to the eukaryotic DNA replication machinery. 56728
Reposted by Ling-Dong ShiNature Microbiology @natmicrobiol.nature.com · 18/07/2025Out 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...nature.comStructure of an archaeal ribosome reveals a divergent active site and hibernation factor - Nature MicrobiologySequence and structural analyses reveal a divergent peptidyl transferase centre and a hibernation factor in archaea. 14918
Reposted by Ling-Dong ShiBethany Kolody, PhD @bethanykolody.bsky.social · 10/07/2025Many 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 41810
Reposted by Ling-Dong ShiAndreja Kust @andrejakust.bsky.social · 11/07/2025🚨 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... 34624
Ling-Dong Shi @lingdong-shi.bsky.social · 29/04/2025Happy 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 !!biorxiv.orgCircular 23S rRNA within archaeal ribosomesThe 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, ... 0127
