🚨 Last chance! Submit your abstracts or apply for scholarships by Sept 23 (11:59pm MDT) for the joint Keystone Symposia: Microbiome Metabolism & Metabolites / Human Microbiome. #KSMicroMetab26 #KSMicrobiome26

Phylogenetic tree inference from single-cell RNA sequencing data www.biorxiv.org/content/10.1... #singlecell

How much of selection in human microbiomes is driven by phage? Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important: Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin www.biorxiv.org/content/10.1... 🧵

/ps If somehow twin studies never happened and we started here: among siblings, genes account for 10% of the variance at the most abstract level, and 2% on the ground, people would have shrugged and said, that sounds about right. The whole modern nature-nurture debate wouldn't have happened.

Two conferences, one reg! Sign up for Microbiome Metabolism & Metabolites + get Human Microbiome FREE. Joint keynotes: Emily P. Balskus & Mohamed S. Abou Donia. keysym.us/KSMicroMetab26 @pieterdorrestein.bsky.social @mfgrp.bsky.social @inesthiele.bsky.social #KSMicroMetab26 #KSMicrobiome26

Join us in Banff for the January 2026 Keystone Microbiome Meeting! We have a great lineup, which will occur in parallel with a special meeting on metabolism in the microbiome. The deadline for both short talks and scholarships is TOMORROW September 23rd!! www.keystonesymposia.org/conferences/...

You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range. @rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social www.nature.com/articles/s41...

Have you ever wondered how the exact location of a gene affects it's activity? The main story of my PhD deals with exactly that question, and is now published in Science! ✨ www.science.org/doi/10.1126/... My amazing co-author and friend @mathiaseder.bsky.social summarized the highlights for you

First they came for the Immigrants. And I wrote a memo. Then they came for trans people. And I wrote a memo. Then they came for the comedians. And I wrote a memo. Then they came for me. And there was no one to write a memo for me.

Ecological diversification in rapidly evolving populations https://www.biorxiv.org/content/10.1101/2025.09.15.676408v1

This is one of the main "immune systems for the genome" - sophisticated machinery that can detect and suppress genome parasites (transposons). It's cool molecular biology and hat's off to @juliusbrennecke.bsky.social and team for working out yet more detail of it.

Microgeography of staphyloccoci in human tissue explains antibiotic failure https://www.biorxiv.org/content/10.1101/2025.09.12.675782v1

Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin https://www.biorxiv.org/content/10.1101/2025.09.09.675206v1

We're hiring! 5 tenure track assistant professors. 2 #microbiology, 2 #Evolution, 1 #biologicalclocks jobs.sciencecareers.org/job/675062/f...

In many cases, crowding results in greater disease transmission. However, in monarch butterflies high host density can reduce per capita infection risk. This happens when caterpillars gobble up parasites on milkweed, removing them from the environment.🧪 royalsocietypublishing.org/doi/full/10....

Crazy thing is that those with meat allergies due to lone star tick bites can actually eat the meat from these pigs too

Amazing real world (well, real cheese makers) evolution of Penicillium over 8 years from @benwolfe.bsky.social. "The most common genetic disruption of the alb1 genomic region was caused by putative transposable element insertions upstream of the gene.". Causes the fungus to grow better in the dark!

@science.org ⤵️challenges prevailing notion—repressor and activator act by distinct mechanisms: repressors block via steric hindrance/activators enable Pol II binding to promoter🧬 E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism | Science bit.ly/adv2064

We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome. We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated. Funded by a new grant from MIT-HEALS.

Strongly recommend working with Felix in amazing Berlin!

www.cell.com/cell-host-mi... #microsky #microbiome

New online: Computational design of sequence-specific DNA-binding proteins

A framework to detect positive selection using variant effect predictions reveals widespread adaptive evolution of human neurons https://www.biorxiv.org/content/10.1101/2025.09.11.675696v1

Join EMBL AI! We have ambitious plans to transform life sciences research through AI. Interested in using ML/AI to solve complex interdisciplinary challenges? We’re looking for two senior leaders based at EMBL Heidelberg👇

Sam Hart describes and applies a method to distinguish differences in mutational processes between groups of cancers without signature decomposition (joint work with @kelleyharris.bsky.social and in collaboration with @nalcala.bsky.social )! #Genomics 🖥️ 🧬 www.biorxiv.org/content/10.1...

Comparing EcoFab 2.0 results from 5 labs on 3 continents‼️ Breaking the reproducibility barrier with standardized protocols for plant–microbiome research @plosbiology.org by Vlastimil Novak et al from Trent Northen @jgi.doe.gov journals.plos.org/plosbiology/...

The professor has been fired and senior administrators removed from their post. No mention of this in the New York Times, The Free Press, The Atlantic or other outlets who drove the campus speech moral panic.

NEXT WEEK we are at #EESMicrobiome in Heidelberg @events.embl.org Full program: www.embl.org/about/info/c... On Tuesday, 16 Sept. see you at Session 1 from 15:30 ✨Liviana Ricci will give a talk "Microbial strain transmission between infants in nurseries drives gut microbiome development" 1/3

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

Here is a word cloud of the words that were missing from the noncompetitive renewal awards but had been present in the parent award. 3/4

Really excited to share our latest paper led by @simonaube.bsky.social. Fascinating results examining whether regulatory mutations can lead to adaptation as fast as coding mutations do. #mevosky #evobio #evoSky www.biorxiv.org/content/10.1...

In new study led by @ckikawa.bsky.social, we provide near real-time data on human neutralizing antibody landscape to influenza by measuring ~26,000 titers to >100 recent viral strains Data can inform vaccine selection & evolutionary/epidemiological modeling www.biorxiv.org/content/10.1...

That also indicates that program staff are absolutely busting their tails to issue NGAs before the end of the FY.

Astounding new structure of a nucleotide immune signal degrading enzyme. The field has found enzymes with this function that look like nucleases, enzymes that look like nucleotide binding proteins, even enzymes that look like proteases... but never a fold like this! www.biorxiv.org/content/10.1...

Happy to see this paper finally out in @pnas.org! #phage #microbiology #MicroSky #VirEvol 🦠 🧫 🔬 Gift link: www.pnas.org/eprint/YYDZ9...

Why hasn't Preprint Peer Review caught on more? I discovered a small, but simple reason - authors are missing out on the JOY of getting feedback because they aren't notified when feedback occurs. more in thread below!

Great mini thread here on lessons for GxG and GxE from non-human organisms:

Join us for an exciting #BiozentrumDiscovery lecture! Prof. Tami Lieberman from @mit.edu will speak about the dynamic selective landscape of human microbiomes. Her lab studies microbial evolution in real time, with a focus on mutations occurring within individual human microbiomes.

Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...

Here, have some birds perched on appropriate/delightful signage. You're welcome. 🧵 ⤵️ 1. Black Vulture (Coragyps atratus) by tysmith on iNaturalist

Legend David Baltimore died yesterday. He understood the way things should work: "the real contribution of MIT is that it doesn't take itself too seriously. It takes ideas seriously, but the people are relatively informal. They are not self-aggrandizing the way academics can be."

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny www.biorxiv.org/content/10.1... github.com/iqbal-lab-or...

The new -outfmt 20 in BLAST 😍. No more frustrated googling to remember which column is which.....

1/5 🧵 Stumbled on some wild history I hadn't heard about before. In 1935 Rutgers University's German department's sole anti-Nazi faculty member Lienhard Bergel, was forced out by department head Friedrich Hauptmann. There were tons of hearings and witnesses. Rutgers ended up dismissing Bergel.

Liberty depends on an accurate understanding of reality.

In a new work with Joseph Rich and Conrad Oakes we tackle the problem of how to best organize alluvial plots. We formalize two optimization problems and develop a solution for them based on the neighbornet algorithm, implemented in the program wompwomp: github.com/pachterlab/w...

Fellow NC constituents: I’ll be calling Tillis’s office shortly to thank him for challenging RFK’s right to inflict chaos on US public health infrastructure, and urging him to follow through by calling for Kennedy’s resignation/impeachment. Let’s make the most of this momentum!

Assistant Prof post in bacterial genomics @unibirmingham.bsky.social Come and join us!! @imibirmingham.bsky.social www.jobs.ac.uk/job/DOO184/a...

Last respiratory virus season 278 children in the US died of influenza, more than any year since 2009. The majority were previously healthy, but 90% had *not* received a flu vaccine. Facts are stubborn things www.nytimes.com/2025/09/04/h...

Exciting FULL PROFESSORSHIP at the Vienna BioCenter - Molecular Mechanisms of Disease Mechanisms: www.maxperutzlabs.ac.at/news/open-po... Come be our colleague!