Happy to share that @averynoonan.bsky.social paper “Phylogeny-agnostic strain-level prediction of phage–host interactions from genomes using machine learning” is now published in @natmicrobiol.nature.com 🎉🎊 👉🏽 rdcu.be/nR2NizD7H5va

Avery Noonan@averynoonan.bsky.social · 11mo ago

We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing. www.biorxiv.org/content/10.1...

Each Friday night, I write a briefing on what happened in US science & higher ed. 🧪  Sept 25 (Year 2, Week 39) - Justice Dept drops 50+ longstanding school desegregation cases - no new NIH EO (but threat isn’t past) - $1B in new pocket rescission & more buttondown.com/liminalcreat...

Year 2, Week 39

Sept 19-25 – digging in

buttondown.com

#RNASky #MicroSky

Jörg Stülke@joergstuelke.bsky.social · 3d ago

Identification of a novel RNA-modifying enzyme! RlmS! #SubtiWiki www.pnas.org/doi/10.1073/...

Mapping structural constraints and adaptive potential in a capsule-degrading phage tailspike protein | Science Advances www.science.org/doi/10.1126/... #phagesky

Mapping structural constraints and adaptive potential in a capsule-degrading phage tailspike protein

Bacteriophage tailspike proteins (TSPs) degrade bacterial capsules to enable infection, yet the molecular determinants of their function and host range remain unclear. We applied deep mutational scann...

science.org

A new review in Trends in Microbiology examines how, when, and through which routes microbes are shared between mothers and infants. 🔗Read more: https://www.cell.com/trends/microbiology/fulltext/S0966-842X(26)00216-7

Fake. USDA. Seals. Used by an NC meat processing plant on 83.5 TONS of meat. Produced entirely outside the federal inspection system, according to news reports. We are pretty close to The Jungle (second ed.) now, no? www.scrippsnews.com/life/recalls...

Interactive: Meat recall linked to fake USDA labels

Pork, beef and goat products are being recalled after a company allegedly used fake USDA inspection labels. Explore our interactive guide to see which products are affected and what to look for.

scrippsnews.com

😮😮 Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking: Current Biology www.cell.com/current-biol...

Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking

How did modernizing cheesemaking change the microbes inside the cheese? By sequencing preserved traditional Alpine cheese wheels spanning 142 years from a single Alpine dairy, Somerville et al. trace ...

cell.com

Stories of science funding being cut, labs shutting down and scientists losing jobs have flooded the media under Trump's administration. These six graphics show how those changes have affected U.S. biomedical research. n.pr/4ycseLJ

Under Trump, NIH funding disruptions have evolved. Here's what the numbers show

Stories of science funding being cut, labs shutting down and scientists losing jobs have flooded the media under Trump's administration. These six graphics show how those changes have affected U.S. biomedical research.

n.pr

Two preprints both out today identifying *different* reverse transcriptase systems associated with arrays reminiscent of CRISPR/Cas, encoded by different phage. One from Anthropic and one from Stanford. Worth pointing out that the Stanford work clearly began earlier, and has more wetlab follow-up:

Arc Institute@arcinstitute.org · 6d ago

Many important bacterial non-coding RNAs and structural elements remain undiscovered. To help, David Li, Garyk Brixi, Michael Fischbach, @brianhie.bsky.social & team introduce Minerva, which uses a genome language model to predict RNA base pairing, repeats, & other interactions from sequence alone.

A nice summary on the state of the art and context of the field.

Evelien Adriaenssens@evelienadri.bsky.social · 4d ago

Here are my first thoughts as a phage person about the @anthropic.com announcement about a novel enzyme on a phage: www.linkedin.com/pulse/my-tho...

The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4

The persistence of P. aeruginosa during chronic infection relies on the serine protease MucD to regulate alginate production. Yong-Gui Gao &co show that MucD can represse alginate biosynthesis post-translationally, in addition to its role in transcriptional regulation 🧪 #MicroSky buff.ly/IYXug6I

Using AI-agent I found a new phage full of new enzymes, I don’t know what they do. 😅

😨

CIDRAP@cidrap.bsky.social · 6d ago

Study: More than 1️⃣ in 10 US healthcare workers report ongoing long-COVID symptoms Older age, female sex, multiple underlying health conditions, and multiple COVID infections were also associated with persistent symptoms. Read more: https://bit.ly/4xGJkjW

State of us.

Mark Histed@markhisted.org · 7d ago

Can confirm (see 🧵 ). But let me share some optimism. A NIH colleague said today that against all odds, NIH has been…winning. “We made this EO a necessity. We fought hard. We threw sand in all the gears. All the lowdown ways of blocking grants failed to produce the results Vought et al wanted.”

I went into this summer as a photographer and came out of it as someone who has finally understood that the garden is not just a location, it's also a philosophy. The most powerful thing you can bring into the field isn't a better lens or a more dramatic location. It's a state of mind.

Check out @sulheim.bsky.social's paper! The latest from our lab showing that some species do actually coexist robustly, no matter what or how much you feed them, whether the environment around them is constant, and whether or not they depend on each other metabolically for amino acids and vitamins.

Snorre Sulheim@sulheim.bsky.social · 2w ago

Finally online! Cross-feeding enables robust coexistence between four bacterial species | PNAS www.pnas.org/doi/10.1073/... #microsky

We seek to recruit a visionary scientific leader in fundamental biology in one of four priority areas: Immunotherapy, Precision Oncology, Data Science, or Viruses and Vaccines (we interpret these areas broadly). We anticipate hiring at the senior Associate Professor level or higher.

If you ever wonder about all that is going on & how crazy this moment in US Science is: @lizneeley.bsky.social ‘s meeting the moment keeps track of all of it. 🙏🏽

Liz Neeley@lizneeley.bsky.social · last wk.

Each Friday night, I write a briefing on what happened in US science & higher ed. 🧪  Sept 18 (Yr 2, Wk 38) - CDC slow-walking Childhood Vaccine Program - NIH sued for censorship - the latest on NSF repurposing - EPA ending emissions controls & so much more buttondown.com/liminalcreat...

New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. https://doi.org/10.1038/s41564-026-02471-8

#PhageSky

Vivek Mutalik@vivekmutalik.bsky.social · last wk.

Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them, or even how the few we have infect a cell. Our new preprint takes this on 🧵👇

A man with an uncommon type of motor neuron disease experienced improved symptoms after becoming the first person to receive a drug designed to target the genetic mutation that causes his disease go.nature.com/4ArQ08j

First for RNA therapy: man with rare motor-neuron disease improves after treatment

Nature - Gene-targeting treatments could be used to treat other people with rare forms of amyotrophic lateral sclerosis (ALS).

go.nature.com

Fascinating stuff!!

Vivek Mutalik@vivekmutalik.bsky.social · last wk.

Preprint here: Please let us know if we have missed any references to cite. This is like looking at past 60 years of work with a small window. www.biorxiv.org/content/10.6...

It was an honour to play a very small part in this tour de force study from @vivekmutalik.bsky.social and @simrouxvirus.bsky.social! Exploring genes (chromosal & plasmid) required for infection by some my favourite phages (F plasmid-dependent phages) 🤩

Vivek Mutalik@vivekmutalik.bsky.social · last wk.

Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them, or even how the few we have infect a cell. Our new preprint takes this on 🧵👇

Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them, or even how the few we have infect a cell. Our new preprint takes this on 🧵👇

How can an unknown #bacteriophage be classified? A new guide presents 10 practical tips, covering genome quality, taxonomic tools, similarity searches, phylogenetics, protein structure, host range and ecology. 🦠🔬 #Virology  📄 https://doi.org/10.1371/journal.pcbi.1014403 👤 EVBC member: Colin Hill

Ten quick tips for classifying unknown bacteriophage

doi.org

Most #bacterial #immune systems raise an alarm when they sense a #phage. This Primer explores a @plosbiology.org study showing how type II Panoptes reverses this logic by maintaining a quiet signal & sensing infection through its sudden disappearance 🧪 Paper: buff.ly/1ixwg9v Primer: buff.ly/WmnHZBp

Michal Breker and I started our labs around the same time. Michal studies Chlamydomonas, and I plant microbiota. We joined forces to see how our bugs interact. This led us down a long and winding road, with 3 amazing PhDs and help from many friends. This is the first product of this collaboration.

Conserved inhibitory mechanisms of root-associated bacteria towards Arabidopsis thaliana and Chlamydomonas reinhardtii

Soil bacteria colonize plants without causing visible disease, yet many suppress host growth. The prevalence and evolutionary reach of this cryptic inhibition are unknown, because phenotyping hundreds...

biorxiv.org

Structural diversity and functional versatility in Gram-positive S-layers #microbiology #bacteria #MicroSky www.sciencedirect.com/science/arti...

New paper from the lab- Bacterial motility in rhizosphere colonization: mechanisms, constraints, and implications for microbial inoculants- in @isme-microbes.bsky.social Journal Led by Led by Tong Wang and @hangweihu.bsky.social . academic.oup.com/ismej/advanc...