Our Department of Microbiology & Immunology at UCSF is running a faculty search this year for a new Assistant Professor! Please see the ad below for details. Searching for a great colleague, mentor, and scientist! aprecruit.ucsf.edu/JPF05807

Join us tomorrow if you can. Link below to register.

New blog post! metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper: rrwick.github.io/2025/09/23/a... Both tools improved considerably! Time to update your conda environments 😄

The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word! jobs.colostate.edu/postings/165...

❤️❤️❤️ CSU. Fort Collins is a lovely place to live, and students / faculty are awesome. I should know, I taught there for 15 years! Apply!

This is the dept where I got my PhD! Hiring for microbiology!

How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense www.biorxiv.org/content/10.1...

🦠Exciting PhD opportunity @ ETH Zürich! Our Environmental Microbiology group is looking for a motivated student to study microbial processes in peatland restoration — from fieldwork to metagenomics and lab experiments. 🗓 Start: Spring 2026 ⏳ Deadline: 3 Oct 2025 👉 Apply: lnkd.in/eSPiy6vQ Please 🔁

📢 🦠 A new methanotroph from Czech peat! Through an effort led by PhD student in my group Justus Nweze we isolated and describe a new CH4-muncher. Potential for a flexible (annaerobic) metabolisms and cool pH adaptations. www.biorxiv.org/content/10.1... #microbesky #microbiomesky

The beautiful, ever-expanding universe of viral proteins targeting nucleotide immune signals! Paper by @reneechang.bsky.social in @cp-molcell.bsky.social on a nucleotide sponge www.cell.com/molecular-ce... and preprint by @doudna-lab.bsky.social on viral nucleases www.biorxiv.org/content/10.1...

New pre-print from Doudna lab members @erinedoherty.bsky.social & @jnoms.bsky.social ✨ Here we explore how recurrent adaptation of a single anti-defense protein fold enables evasion of distinct immune systems.

At the request of @bradleyph.bsky.social, we have now added the Bacterial and Archaeal trees (credit to @aroneys.bsky.social) used to infer the GlobDB taxonomy to the website globdb.org Feel free to reach out if there's other resources you'd like to see added. No promises, but happy to chat 🖥️🧬🦠

Does sequence clustering confound AlphaFold2? www.sciencedirect.com/science/arti... From @hkws.bsky.social

New preprint up now! Interested in the evolution of halophily within DPANN archaea we decided to investigate the sister phylum to the Nanohaloarchaeota, GTDB phylum EX4484-52, for which we propose the name Caliditerrarchaeota www.biorxiv.org/content/10.1...

Excited to finally share this work! We noticed a pair of genes - a nuclease and a protease - shuffles between antiviral systems. We show how proteolysis activates the nuclease, triggering defense in known and unknown immune contexts. tinyurl.com/2uwwy4ty

‼️ New pre-print from co-leads @owentuck.bsky.social and Jason Hu! Check out this fascinating example of how coevolution enables defense system innovation.

Very proud to have our lab’s first work published in @cp-cellhostmicrobe.bsky.social! In this work, we use functional metagenomics to find phage defenses from human and soil microbiomes! Congrats to first author @luis840alberto.bsky.social ! www.cell.com/cell-host-mi... (1/3)

if i were a better person i would do a tweetorial on our recent paper - but, hey, read the paper. its right there, waiting for you. #Giantvirus #histones are cool! their #nucleosomes are cool. check it out.! thats the tweetorial. rdcu.be/exXBX

1. 🧵 New preprint out! WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs. Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA. #ArchaeaSky #MEvoSky #MicroSky 🔗 doi.org/10.1101/2025... 💻 github.com/stephkoest/w...

Our latest work, driven by the fabulous @stephkoe.bsky.social! WitChi takes care of compositional bias in large phylogenomic datasets! WitChi is fast, efficient and free, try it out! With @kassipan.bsky.social and @danieltamarit.bsky.social

#Archaea #GRC folks, be sure to catch work by @oceancait.bsky.social representing our group this week in Switzerland. She'll talk about new Asgard archaea enrichments form the Oregon coast. Talk on Sunday, Poster during the week.

In a couple of days, my grad student Stavros Trimmer will present his new Asgard archaea culture at the GRC Archaea. He named it Skadiarchaeum after Skadi, the Norse goddess of skiing and hunting. Cartoon of Skadi based on cryoET, which was performed together with with @florianwollweber.bsky.social

Designed protein pockets recognize intrinsically disordered protein regions @science.org www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... www.statnews.com/2025/07/17/n...

This #WorldZoonosesDay, learn five key facts about #zoonotic diseases and how we can prevent future outbreaks. Check out our infographic: onehealthtrust.org/publications...

🚨 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...

Structural motif search across the protein-universe with Folddisco www.biorxiv.org/content/10.1... Code: github.com/steineggerla... Web app: search.foldseek.com/folddisco

Franklin W. Stahl, 95, Dies; Helped Create a ‘Beautiful’ DNA Experiment. Gift article: www.nytimes.com/2025/07/07/s...

Lots of other fun Antarctic-themed things happening all week for the Family Fiesta too! www.monash.edu/performing-a...

📑 Programs? Printed. 🏛️ Venue? Looking amazing. 🧪 Energy? Building fast. We're almost ready to welcome the HFSP community to Melbourne for an unforgettable week of science and connection! Who's coming to the 24th HFSP Awardees Meeting? #HFSP #HFSPmtg2025

@science.org Zincore-coregulator dedicated to zinc🖐️ TFs essential in development www.science.org/doi/10.1126/... @rborza.bsky.social @sgregoricchio.bsky.social @amazouzi.bsky.social @zwartlab.bsky.social @lindersimon.bsky.social @tassosperrakis.bsky.social @thijnbrummel.bsky.social + al.

Beautiful work by Pam et al. !!

Congrats @sgribaldo.bsky.social !!

Bay Area friends! I’ll be around for the next few weeks. If you’re nearby and want to catch up - science chats, hikes, coffee, or just vibes — send me a message. Would love to reconnect

Our new consensus statement on reducing and reporting contamination in microbiome studies is the cover image of this month's Nature Microbiology: www.nature.com/articles/s41... In the cover photo, you can see our postdoc Sophie Holland in fully PPE sampling the atmosphere of terrestrial Antarctica.

Happy #WorldMicrobiomeDay! #PacBio is honoring the tiny microbial communities making a big impact on discovery. HiFi sequencing empowers researchers to explore the #microbiome with exceptional accuracy, strain-level ID, complete genomes, and deep functional insights. (1/2)

DAFNEE is a great resource for #Biology #Evolution #Ecology and genuinely most Life Science disciplines. Choose journals run by the community and that invest back into the community. The journals in DAFNEE also include multidisciplinary journals that would take #Genetics #MolBiol etc...

Preprint🚨 #microsky 🦠 “Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota”, authored by @kohtzarchaeota.bsky.social & Sylvia Nupp, expands the diversity of methanogens! 90% enriched, methylotrophic culture from a hot spring. A 🧵 tinyurl.com/yw8ku2bj

🧵🦠🖥️🧬🧪 Please RePost 🙏 We just released reference genomes for another 250 strains to the ATCC Genome Portal (genomes.ATCC.org)! We now have assemblies for _5,750 microbial genomes_ AND all assemblies w/ @nanoporetech.com data will include DNA methylation profiles too (details👇) #genomics 1/

Manuscript/resource alert #microsky 🦠 My lab offers the community a collection of 30 E. coli (CloneFISH) cultures, each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from one of 30 lineages of archaea, including 19 yet uncultured ones.

What a vibrant community! I had so much fun.

We’re happy to share our preprint where applied phages to Microbiomes to test microbial interaction hypotheses - without losing the relevance of the community. Bonus: using SNPs we studied how our targeted organism recovers from infection, and find how the community likely influences this process.

Dan Portik (@dportik.bsky.social) from #PacBio is live at #ASMicrobe sharing insights on oral microbiome assembly using HiFi long-read sequencing until 11:30 AM. Catch him at poster 974 in section HMB in the exhibit hall. He’ll be back again from 3 to 4 PM!

Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes. 🔗: doi.org/10.1016/j.ce... #Genomics #Evolution #CellBiology #LECA

A short preprint describing the GlobDB is now on arXiv: arxiv.org/abs/2506.11896 If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.

It may be an oldie, but it's also a goodie! Learn about RNA interference and how to express shRNAs in our newest blog post. While you're at it, check out our updated collection of shRNA plasmids! https://twp.ai/4iobKc

Just lovely work from @floravincent.bsky.social and team, one of @embl.org’s faculty that is really focused on bring molecular biology into understand our planet its biological environment

Excited to be visiting Brisbane, please if you are around send me a message would love to connect!

We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change. Please see the official job ad here, and spread the word: jobs.awi.de/Vacancies/20...

Proud to present the lab's latest work. The full structure of the sodium translocating methyltransferase (Mtr) bound to a small oxygen-responsive small protein MtrI. Work by Tristan and together with @schmitzstreitslab.bsky.social . www.biorxiv.org/content/10.1101/2025.06.02.657420v1

New manuscript out in @asm.org MRA! We develop a new R package called methylMapR to characterize the prokaryotic functional methylome from long read PacBio data. journals.asm.org/eprint/SNT8I... Check it out and do give the package a try! github.com/therealtotod...