great article in @quantamagazine.bsky.social by natalie wolchover on the bacterial flagellum and proton motive force. alas, I missed this great model on what happens to the stators during gear-shifting. see it in STC:
smallthingsconsidered.blog/schaechter/2...
#MicroSky

My super department @warwicklifesci.bsky.social is hiring 6 assistant profs in the wake of recent retirements. We're looking for people in microbiology/infection, cellular disease / immunity; environmental biology; and plant/crop science. #MicroSky warwick-careers.tal.net/vx/lang-en-G...

Getting LLMs to simulate “true” randomness or generate diverse outputs is surprisingly difficult. We found a simple prompting trick that solves this by having the model generate and manipulate a random string. To be presented at #ICLR2026 this week!

Blog: pub.sakana.ai/ssot

The role of space in explaining macroecological patterns of microbial abundance www.biorxiv.org/content/10.64898/2026.04...

Creating baby geniuses to thwart the AI threat? (Yes, really.) The new wave of Silicon Valley–backed gene-editing startups is straight out of “Brave New World.”

Creating baby geniuses to thwart the AI threat? (Yes, really.) www.motherjones.com/politics/202... - smart people being really stupid about intelligence

This is from 7 years ago (merenlab.org/2019/02/24/f...). We are talking about the same things today. We will be talking about the same things 7 years from now. There is no one to blame for this apart from ourselves. I find it very depressing.

Diversity-generating retroelements for programmable targeted hypermutagenesis - Nature Biotechnology Diversity-generating retroelements are engineered for directed evolution in E.coli.

🔈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...

Whereas additional studies are needed, our results support Burnet's/Goodnow's hypotheses. Somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. [20/]

Using this single-nucleus whole-genome data, we reconstructed a phylogeny showing that some clones had accrued 5-6 driver mutations (including quadruple loss of TNFRSF14 and CD274/PDL1) over many years (even decades) of silent evolution before diagnosis. [17/]

Excited to share our latest work in Nature. Applying single-molecule and single-cell DNA sequencing methods, we uncover an extraordinary landscape of somatic mutations in immune checkpoint genes in autoimmune B cells, suggesting that somatic mutations may be key to autoimmunity [1/n] rdcu.be/fdqbr

a man sitting at a table with the words " i have a question " on the bottom ALT: a man sitting at a table with the words " i have a question " on the bottom

Silly question, but I hope someone can direct me: has anyone done RNA-seq to learn what genes are expressed in bacterial colonies vs liquid culture?

I believe it. The lesson I recall from the crassphage discovery paper that multi-sample assembly reduces recall.

Whoa—machine learning strikes again (in a good way)

www.pnas.org/doi/10.1073/...

Totally agree. The best approach is hybrid - use vibe coding for speed on boilerplate, but keep 'thinking as a programmer' for architecture and debugging. That combo is hard to beat.

"the article sheds new and urgent light on a decades-long dispute regarding the relationship between Fisher’s eugenical commitments and his scientific contributions, at a moment in which his legacies are being actively debated once more"

The female urogenital microbiome: Ecological insights, therapeutic strategies, and molecular mechanisms In the urogenital tract, dominant lactobacilli shape vaginal immunity and community stability. In this review, Dillen and Dricot et al. integrate clinical and mechanistic evidence on their molecular s...

Female urogenital microbiome: Review by Sarah Lebeer & Co

In urogenital tract, dominant lactobacilli shape vaginal immunity & community stability. Review examines molecular strategies & rational design of next-generation microbiome-based therapies
www.cell.com/cell-host-mi...

My lab at Pitt is looking for a Research Scientist to help us make phage therapy for patients with antibiotic-resistant infections. Please share and apply! cfopitt.taleo.net/careersectio...

Sam Altman May Control Our Future—Can He Be Trusted? New interviews and closely guarded documents shed light on the persistent doubts about the head of OpenAI.

The reporting on OpenAI and Sam Altman I've been working on for the past year and a half, for @newyorker.com, with Andrew Marantz: www.newyorker.com/magazine/202...

I have been reading through papers on evolution and microbes from the 1940s to 1960s. I have found some amazing work, but I am sure that there is much more that I haven’t found. Can you send me links to classic evolution+microbiology papers from pre Levin era?

Few people are aware of how much progress has been made against cancers.

Leukemia is probably the most striking example.

Before the 1970s, most children affected by leukemia would soon die from it.

Now, most children in rich countries survive.
ourworldindata.org/childhood-le...

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣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.

We’ve been talking in our lab meetings about sexual conflict and sexual dimorphism, and have some thoughts. What if animal genomes are far more sex-specific and less cosntrained than we assume? @linley-sherin.bsky.social pulled it all together here www.zoology.ubc.ca/mank-lab/pdf... 1/n

Excited to see our work out in Science today! Using machine learning to identify prokaryotic immune systems www.science.org/doi/10.1126/...

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Baktfold: Sensitive protein functional annotation across the microbial tree of life using structural information [new]
Annotates microbial proteins via struct info, converts seqs to 3Di tokens for DB searches to ID hypothetical ones.

Here's a little widget to play with the data across journals (as well as download the raw CSVs).

sashagusev.github.io/Genetics_Pub...

This flu season I've learned...

1. Home tests are readily available, including combined flu/covid tests.

2. Antivirals need to be taken within 48 h.

3. Xofluza is better than Tamiflu (one dose; more effective against flu B) but few know about it.

4. Antivirals can be taken as prophylaxis.

1/4

Phages communicate across species to shape microbial ecosystems Gallego-del-Sol et al. show that arbitrium-coding phages can sense non-cognate peptide signals from other phages to regulate lysis-lysogeny decisions. This crosstalk affects lysis-lysogeny outcomes of...

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...

I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications! www.nature.com/articles/s41.... (1/n)

Heritability is a statistical description of sources of trait variation in a specific set of people under a specific set of environmental conditions. It doesn’t show how malleable the trait is, doesn't index an underlying feature of human biology, & can’t say anything about you as an individual.

Gut microbiota within-host evolution enforces colonization resistance against enteric infection www.biorxiv.org/content/10.64898/2026.03...