I am really excited to see this article on basic experimental design principles published. Definitely will be mandatory reading for incoming graduate students in my lab. Maggie Wagner who led this article did an amazing job with the illustrations of basic principles www.nature.com/articles/s41...

Phosphite oxidizers 🤝 Methanogens In our new paper on “Lithosyntrophy” we show that phosphite oxidation drives methanogenesis through interspecies H2 transfer. Lithosyntrophy establishes a novel mechanistic link between the #phosphorus and carbon redox cycles

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve. Preprint 📝: biorxiv.org/content/10.1... 🧵 1/n

Our latest, lead by @ahoiching.bsky.social, uncovering physiological vulnerabilities and helping to explain growth rate limitation in SAR11. Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.biorxiv.org/content/10.1... #jcampubs

The latest publication from our lab! The famous "glomalin" from arbuscular mycorrhizal (AM) fungi is not a protein but a polysaccharide from AM fungi, so we renamed it "glomalose". Glomalin-related proteins are bacterial proteins stuck in this glomalose. nph.onlinelibrary.wiley.com/doi/10.1111/...

Success in academia often has more to do with luck, patronage and the job market than “hard work”. Good academics acknowledge this. I worked hard, but I was in the right place at the right time on occasion. Historians far more talented than I have fallen between the cracks.

Neat study: the classic enzyme DMSO reductase also acts on various other S-/N-oxides that are produced by reactions with HOCl. Two quick reasons a microbiologist should take note for their research: doi.org/10.1128/jb.0...

In our study, we showed that intestinal Methanosarcinales have reduced genomes and obligately dependent on H2 and CH3 compounds for #CH4 production. They lost the Wood–Ljungdahl pathway and membrane complexes (Rnf, Fpo, Ech). academic.oup.com/femsec/artic... @femsjournals.bsky.social @femsmicro.org

TIL you can add .txt to a biorxiv fulltext link and get plain text. Handy for pasting into LLMs, e.g., the new BindCraft revision www.biorxiv.org/content/10.1...

We're gearing up to tackle new kingdoms of life, thanks to generous support from @wellcometrust.bsky.social. Get in touch! Read more on our blog: cultivarium.substack.com/p/fungi-and-...

Almost every line of this story would have been simply unbelievable a few months ago: —Pioneering cancer researcher; —*Arrested* at airport in Boston; —Now indefinite ICE detention in Louisiana; —"Crime": not declaring some frog-embryo samples for research. Read it. www.nbcnews.com/news/us-news...

I told everyone! 😏 If you want to co-culture CPR/DPANN epibionts, try to filter-purify them and add them into pure cultures. For Minisyncoccus they used 0.45 um filters and a suspected host. I'd recommend 0.2 um filters and a panel of various isolates. tylerbarnum.com/2021/05/14/t...

Unlock new organisms quickly with a genetic methods “cheat-sheet”🔬 Our Portal’s new Reported Methods section streamlines access to established genetic tools and related literature. Read more here: tinyurl.com/yj33bnyr

Our technique for studying strain-level IgA binding in the microbiome is out now at @naturemicrobiol.bsky.social! Fascinated by IgA since Sean Spencer told me about it, here we make some fundamental discoveries about strain-level IgA dynamics in the healthy human gut (1/5) doi.org/10.1038/s415...

Super cool - amoebae and ciliates live in close association with lots of weird, host-associated bacteria. Including CPR/Patescibacteria.

OUT NOW: Metagenomic immunoglobulin sequencing (MIg-seq) reveals IgA coating of microbial strains in the healthy human gut by Justin Sonnenburg, Matt Olm, Sean Spencer & co #microsky www.nature.com/articles/s41...

I want to highlight a new resource for microbiology on the @cultivarium.bsky.social portal: we’ve created a database of published genetic methods for every microorganism. And if your microbe *doesn’t* have genetic tools, we point you to the closest relative that does.

Since I now have 1k followers: RUMEN PROTOZOA TIME! Rumen protozoa are all members of the class Litostomatea in phylum Ciliophora, and are the least well-studied group of organisms in the rumen. 1/?

Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil www.biorxiv.org/content/10.1... #jcampubs

After many years of work we present a preprint that doubles the numbers of Asgard genomes, revealing lots of new insights into their metabolism. Notably, lineages closely related to eukaryotes are capable of aerobic respiration! www.biorxiv.org/content/10.1...

@tylerbarnumphd.bsky.social has landed on bluesky, give him a follow! I wanted to further highlight some of the use cases of GenomeSPOT, described in his behemoth of a work here - there's lots to dive into, but you could go right to the github here: github.com/cultivarium/... 1/5

New resource from Cultivarium: models to predict oxygen tolerance, temperature, salinity, and pH optima from a genome - without using pesky gene annotations. They work for incomplete MAGs, so we could predict growth conditions across all bacteria and archaea, cultivated or not. Data available.