Characterizing the ecological niche of insertion sequences within prokaryotic genomes academic.oup.com/ismej/advanc... #jcampubs

Are restriction/modification modules only used for host defense? @selmamhm.bsky.social shows an alternative use. "Restriction-modification systems are required for Neisseria gonorrhoeae pilin antigenic variation" www.pnas.org/doi/10.1073/pnas.2602688123 #Microd #Microsky. #Microbiology

I will arrive at your therapeutic area with a molecule so chiral, so offensive to your multi-parameter optimization algorithm, that your model will flag it as “not drug-like.” It will then proceed to work, in vivo. inpreparation.substack.com/p/go-ahead-a...

@ohadroth.bsky.social and @soreklab.bsky.social discover bacterial enzymes that cleave the immune signal 2'cADPR explaining the mystery of XopQ virulence proteins in plant pathogens. Beautiful results mirroring phage inhibition of 2'- and 3'cADPR in bacteria! 🌱✂️ www.biorxiv.org/content/10.6...

We should ban all social media for under-18s except for text based hobbyists forums (video games, cars, decorative topiary, etc.). It’s good to have the experience of being arbitrarily banned by a 35-year old basement dwelling moderator for posting a point by point refutation of their arguments

Multiplexing antibiotic screening assay in droplet microfluidics #microbiology #antibiotics #microfluidics #MicroSky doi.org/10.1038/s415...

#microsky #phagesky #phage www.science.org/doi/10.1126/...

@romihadary.bsky.social and @soreklab.bsky.social 's discovery that sponge proteins constitute enormous families of viral immune evasion factors is now out in @natmicrobiol.nature.com @reneechang.bsky.social and our lab were happy to help with this story! www.nature.com/articles/s41...

"determined to be of absolutely no value to the US taxpayer" and it's HMMER, a piece of software I use almost every single day

HMMER is an integral part of the software my whole career is built on. Software that researchers at the DOE have run millions of times. Complete, utter bollocks.

The paper on my Ph.D. work is fully online! We used a ribozyme that barcodes 16S rRNA to track the transduction range of phage P1 in a synthetic community and real wastewater communities, while diving deeper into the unique range conferred by P1s two tail fibers. www.nature.com/articles/s41...

Ancient wars between microbes gave us key immune defenses | @science.org | AAAS www.science.org/content/arti... #microsky #virosky #immunosky

This one means a lot. Our paper, “Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome,” is out! doi.org/10.1038/s414...

A new method for inference and tracking the transmission of strains in metagenomes #MicroSky #MicroEco www.nature.com/articles/s41...

Hurwitz, @shoppins.bsky.social and colleagues leverage a powerful FRET system to uncover novel insights into the energetic landscape and conformational dynamics of mitofusin, the mitochondrial outer membrane fusion machine. rupress.org/jcb/article/... #Mitochondria

📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

🚨New pre-print!🚨 Because influenza virions are highly variable in form no single method can show their molecular architecture in detail. Here, we integrate multiple structural and compositional approaches to identify new features of these beautiful virus particles www.biorxiv.org/content/10.6...

Out Now! A bacterial CARD–NLR-like immune system controls the release of gene transfer agents #MicroSky

🔈Paper out! We turned the most fascinating phage host-switch mechanism, diversity-generating retroelements, into a programmable mutagenesis tool, DGRec. You can perform targeted hypermutation of any 50-200bp sequence directly in vivo in E. coli www.nature.com/articles/s41...

Across scales from cells🦠 to atoms⚛️ – We reveal how anaerobic #bacteria break down very stable aromatic compounds found e.g. in oil spills 🛢️ #Bioremediation #TeamTomo 🧪 🧶🧬 🔬 Awesome collab with Lena, Matthias, @schullerjm.bsky.social @rnfr2d2.bsky.social @tomaspascoa.bsky.social @tamb-o.bsky.social

Makin a bunch more stability updates and bug fixes for my TUI plasmid editor. Currently workin on a pLannotate wrapper module so you can annotate plasmids imported where the author did not fully annotate all the features. I'll eventually try to pull plasmidsaurus seq results too

An Asgard archaeon from a modern analog of ancient microbial mats (Current Biology) Beautiful microscopy of an Asgard archaeon, in the same family as Lokiarchaea, in syntrophy with a sulfate-reducing bacteria Very very nice paper we saw in preprint form: www.cell.com/current-biol...

Out in @natcomms.nature.com! We show that while most MGEs are blocked by RM systems🛡️, the chromosome is still mobile! 🧬And that cells with defective systems act as "gateways" for HGT. Can you find the hidden Easter egg🐇🥚? Hint: There's a nod to my 🇲🇽 heritage in one of the figures! rdcu.be/fbUC8

Hot off the press! 📣 "A family of endonucleases blocks nanotube-mediated plasmid exchange". @natmicrobiol.nature.com #bacterialnanotube www.nature.com/articles/s41...

This paper started as an idea @albertomarina.bsky.social had many years ago… which of course means he was right all along 😄. Some of us just needed a few years (and a lot of experiments) to catch up. Grateful (and slightly humbled) to be part of this. Thanks Alberto! www.cell.com/cell/fulltex...

How common is multicellularity in bacteria? And archaea? And how does it evolve? We wrote a short review "On the architecture and evolution of prokaryotic multicellularity". Preprint link: bit.ly/4ta06Gq Sharing and comments are much appreciated. 1/4

Nice surprise this morning! A Dispatch on our paper on paralog interference now out in Current Biology! By Krishna Swamy and Jun-Yi Leu. www.cell.com/current-biol...

Caroline West finds viruses 🛑 inside a bacteria 🦠 inside a fungus 🍄‍🟫 that can be found in plants and people 🚶‍♂️ This is work from the @lablabella.bsky.social & @morgancarterphd.bsky.social & the RAW labs. #fungal26

I love writing Mathematica so much. Every line is simultaneously a heroic triumph over your mortal enemy—you ten minutes ago—and a challenge to your new arch-nemesis, you ten minutes from now.

New preprint! We show that conjugation accelerates the segregation of #plasmid alleles -> horizontal transfer is a route for allele segregation in MGE evolution. Led by Lisa Hartmann, with @mariosanter.bsky.social &Nils Hülter. Naturally, reviewed by @qedscience.bsky.social! doi.org/10.64898/202...

Living cells are nonequilibrium systems, constantly spending energy in seemingly one-way processes like transcribing DNA into RNA, to keep life going. In a new paper, SFI's James Holehouse develops tools to study that irreversibility across thousands of genes, revealing interesting patterns.

At the RNA level, ωRNA maturation and splicing compete for the same sequence — and only one can win!

How do fish localize sound without interaural cues? @johve.bsky.social et al. found a behavioral algorithm for directional hearing that predicts behavior from a pressure/motion phase comparison and accounts for how this relationship varies with distance. www.cell.com/current-biol...

Out Now! Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation #MicroSky

A jumbo cyanophage encodes the most complete ribosomal protein set in the known virosphere www.biorxiv.org/content/10.1...

Out now! In collaboration with Leifu Chang, we uncover the molecular and structural underpinnings of CRISPR-Cas12f-like RNA-guided transcription systems! Links to the published articles: tinyurl.com/55kpavet tinyurl.com/sk6djwx3 Previous thread for the preprint: bsky.app/profile/did:...

Green tea contains antioxidants called catechins. For humans, they are linked to health benefits, but they can also defend plants against pests. A new study uncovers how the spider mite overcomes these defences using a gene borrowed from fungi. 🔗 buff.ly/nAcO5xq

Scientists have seen Asgard archaea crawling for the first time. When it comes to the origin of eukaryotes, this is like seeing a feathered dinosaur in the wild. (Video courtesy of Philipp Ralder)

Active virus-host system in a Lokiarchaeon culture https://www.biorxiv.org/content/10.64898/2026.02.13.705702v1

Check out our latest preprint from @jnvmartinson.bsky.social and @leosong.bsky.social! 🌟🦠 We found that conjugative plasmids can actively eliminate recipient bacteria that resist plasmid acquisition. 🧵

Our new paper in @natcomms.nature.com is now online-early! We describe independent evolution of bacterial genomes of only ~50–52 kb — the smallest known outside cellular organelles — revealing striking convergence toward minimal gene sets. 🔗 doi.org/10.1038/s414...

Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction. www.biorxiv.org/content/10.6...

How do bacterial pangenomes evolve, what controls their dynamics, why do they exist? Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle

Rendering the Staphylococcus cell wall to the scale of the #phage makes us wonder if flexibility is what helps phage JS1 to snake through the canyons of the bacterial cell wall. doi.org/10.1128/mbio... #MicroSky @macsys.bsky.social @staph-papers.bsky.social @stcmicrobeblog.bsky.social

'to treat peer review as a throughput problem is to misunderstand what is at stake. Review is not simply a production stage in the research pipeline; it is one of the few remaining spaces where the scientific community talks to itself.' 1/3

Can plant pathogens boost vector fitness? Together with @hassansalem.bsky.social, we review how phytopathogens can spread further by moonlighting as insect symbionts 🪲 More on this nifty lifestyle in @annualreviews.bsky.social! www.annualreviews.org/content/jour...

#NatMicroPicks A bacterial symbiont wraps its flagllar filaments around its cell body to propel itself through narrow gut passages in its stinkbug host and hook flexibility is key for this 🪲🦠 by Yoshitomo Kikuchi & co @natcomms.nature.com www.nature.com/articles/s41...

Thrilled that the lab's first @hhmijanelia.bsky.social project is up on bioRxiv! Story behind the story to follow. www.biorxiv.org/content/10.6...

I first saw the heretical combination of the subheading of "ECOLOGY" and title, "The beauty of slag," and I swooned. Check out this terrific and fun story in UChicago Magazine about the novel ecosystem/slag research we're working on locally! #WildCalumet mag.uchicago.edu/science-medi...

Very interesting paper. www.science.org/doi/10.1126/...