Jesse Shapiro

Our latest, spearheaded by the truly indefatigable @emderrick.bsky.social in which we search for selective sweeps in nature and genetic targets of selection within a species in the context of a diverse background community @isme-microbes.bsky.social doi.org/10.1093/isme... 🧵 1/n

New pre-print and tool alert ! This one addressing a long-standing viromics issue: we were missing a tool that can reliably assign broad host categories (e.g. prokaryote vs eukaryote) to novel viruses. VHAMSTeR is now available for this thanks to very talented postdoc @susiegriggo.bsky.social !!

Your monthly reminder that if you're using ChatGPT to do your science, you're failing your colleagues, community, and all of us. Here, ChatGPT makes up data and presents it as the real thing — then apologizes when confronted.

Happy World Phage Day to all who celebrate... ... delighted to share new work led by Jacopo Marchi, Chadiga Khalek & joint w/Remy Chait on stable coexistence of phage with migrating bacteria driven by the forces of infection, lysis, and chemotaxis. A 🧵 at the interface between known & unknown.

The very last bit of data from my PhD is out! Read on to learn more about why the presence of A. baumannii results in more CRISPR-based #phage resistance in P. aeruginosa 🦠🧫 www.cell.com/current-biol...?

New preprint from our lab, with @sultannazir.bsky.social! 🚨 Defense systems in pro- and eukaryotes are often derived from the very parasites they now defend against. Here we show how this all starts with the emergence of cheaters in parasite populations! www.biorxiv.org/content/10.6...

Sharing the link to our updated Vibrio preprint, where we compare and contrast Ecospecies with other genetic structures, and using the opportunity to fix typos and update some bluesky handles! with @danielfalush.bsky.social @whqqq.bsky.social @yjchao.bsky.social @chaooo.bsky.social

New preprint from the Gurney Lab, on bioRxiv: The Phage Time Continuum: Genome Organization Constrains Anti-CRISPR Success. www.biorxiv.org/content/10.6... I think this is one of the cooler things I'll ever do. Work lead by @sczerwinski.bsky.social he coined the term Phage Time Continuum. 1/10

The tea room at my host lab in France is everything I’d imagined and more

Check out our recent observation piece 🦠 Artificial genetic augmentation of T6SS activity affects effector repertoire and host toxicity | Microbiology Spectrum journals.asm.org/doi/10.1128/...

I do not do much on social media right now. Making an exception. I talked to a lot of reporters during the pandemic. I don't think any of them would be surprised or offended if I say Helen was the best 1/n

We are looking for a Research Technician interested in advancing their career at St. Jude Children's Research Hospital. In our lab, we investigate the molecular and environmental drivers controlling the emergence and transmission of bacterial pathogens: stjude.wd1.myworkdayjobs.com/stjude/job/M...

This👇 is such a good example of how on top of her game Helen was. While she was keeping us all updated on Ebola, MERS, flu, and so many of all the other infectious diseases out there, she immediately grasped the gravity of the first warning sign of what we now remember as SARS-CoV-2 / COVID-19.

We lost a good one 😢

We are going to miss you very much, Helen. https://www.statnews.com/2026/10/13/helen-branswell-stat-reporter-obituary/

Introducing Microbiome Repo, a catalog of every public human gut metagenome (>500k samples) with metadata pulled straight from sequence archives, papers, and supplements! olmlab.github.io/microbiome_r... Published gut metagenomes? Search your name and see if it got your study! Feedback welcome

Great journal, even better colleagues and community! Highly recommend!

Pleased that the second paper from my PhD is now out at ISME Comms @isme-microbes.bsky.social 🦠🧫 We looked at how bacteria-phage interactions are obscured by the host environment by injecting 4,608 Galleria mellonella larvae with 64 diverse Staphylococcaceae isolates +/- the phage ISP... 🧵 1/4

Interested in urinary tract infections and the urobiome? Take a moment to read our latest perspective on the role of eco-evolutionary interactions in UTIs.

Tired of predatory journal mass emails, AI slop, paying thousands to for-profit publishers? Come join our editorial team at @microbiologysociety.org #MGen, become part of a very nice community, supporting research integrity & ethical publishing practices(1/3) microbiologysociety.org/who-we-are/j...

Very excited to share our latest paper, with my terrific student @prakharj.bsky.social, and wonderful collaborators Dan Coombs, Caroline Wagner, and @troyday.bsky.social We use simple models to explore how interventions could mitigate post-infection morbidity www.pnas.org/doi/10.1073/...

Glad to share this new Microbial Primer on Mirror Biology written w/ Jolien Sweere. It's free to all in the @microbiologysociety.org journal Microbiology, edited by Steve Diggle. Thanks for this opportunity to outline our scientific knowledge of this significant topic. doi.org/10.1099/mic....

THERE IS NOTHING WRONG WITH THE PROJECT GRANT PROGRAM EXCEPT IT IS UNDERFUNDED. Breaking it, redesigning it, etc, cannot fix this.

More CIHR musings, because I think we don't actually know what's going on in important ways that might influence how we think about prospective solutions. These are questions CIHR could answer if it wanted to.

PSA for those submitting genome assemblies to NCBI… Had a complete bacterial genome submitted and stuck at “processing” since April. It took one email and it’s being released soon. Know I’m not the only one in that boat

Not sure I’ve ever seen an essay that so precisely hits the mark as this. Read it. Share it.

I'm really excited to share my latest research paper with the world. It has been a long and bumpy road to finish this project and get it published, but finally, it is out!

this is such a cool paper - Microbial community dynamics in a traditional Swiss mountain cheese over 142 years of cheesemaking www.cell.com/current-biol...

As AI increases both productivity & ease of creating slop, there's a big challenge for those of us disseminating science. This from @pracheeac.bsky.social is an essential read. [disclaimer: she & I've spent 10+ years a̶r̶g̶u̶i̶n̶g̶ ̶a̶b̶o̶u̶t̶ discussing this stuff] 1/n pracheeac.substack.com/p/arxiv-is-k...

Cover image alert 🎨🚨👇🏼 - check out the amazing drawing of Sophia Zimmermann from our group in Nature Microbiology @natmicrobiol.nature.com ! Fun fact: Sophia initially drew it as a present to Dorentina @humollidorentina.bsky.social when we celebrated her recent paper on TnSeq with phages 🥂😊.

Minimoy, the cat we are cat-sitting for the year, is my sabbatical spirit animal

At Montrouge ( Rosa la Rouge)

📣 New preprint: We looked at population survival and recovery of the thermophilic archaeon Sulfolobus acidocaldarius at near-boiling temperatures—conditions that occur in its environmental niche. www.biorxiv.org/content/10.6...

Our village is celebrating the rainy season

Pleased to share my first preprint from my postdoc, where I ask what drives mobile DNA movement between bacterial cells in complex communities like the gut microbiome. To answer this, we built a way to capture mobile DNA in the act of moving between cells, using short-read metagenomics. 🧵

#plasmidbiology #plasmid Just out! 🚀 Thrilled by our discovery: the function of the C-terminal domain of MOBH1 relaxases! We uncovered this thanks to a fertility inhibitor encoded by a parasitic mobile genetic element. Congrats to Florence on a great piece of work! 👏 academic.oup.com/nar/article/...

Application review for the GRC in Microbial Population Biology will start October 15th! Please apply before then if you are keen on coming. www.grc.org/microbial-po...

Spread the word! I’m looking to recruit a PhD student to grow the Paulinella project. Some details can be found here: www.vanettenlab.org/join

Glyphosate-based herbicide exposure triggers genetic adaptation but not diversity collapse within bacterioplankton species (reposting with the article title and a gratuitous glam shot of the lake these bugs called home until we rudely plopped them into experimental ponds...)

bioRxiv has a dedicated section for negative results. Use it. Share negative results. Your colleagues will appreciate it.

Omigod, this is the most heartwarming story possible! Backpack (bear 89) is the son of the 2019 winner of Fat Bear Week, Holly (bear 435). In 2007, he injured his foot & a practice of riding on momma's Holly's back had a new meaning: he was mobility-restricted while it healed. So Holly moved him.

Postdoc position available in my group to work on ERC funded project on evolutionary biology of antibiotic resistance. Looking for someone with expertise in bacterial genetics, AMR, and evolutionary biology. www.jobs.ac.uk/job/DSZ416/p...

5 potatoes cubed is still 5 potatoes because potatoes are root vegetables

I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you? PhD required, start date hopefully Nov 1! (end date Sep 30 2028) Please share! abetterscientist.wordpress.com/2026/09/29/p...

🎃 Pumpkin Spice GLP-1 season 🍂

Single-cell biologists: I am trying to find examples in which people have encapsulated individual cells into droplets, let them grow and performed PCR at two loci with droplet-specific barcoded primers to link the genotypes at these loci using sequencing.

We have an open Assistant/Associate Professor position in Pathogen Biology at the Department of Genetics - come and join us! 🦠 🧫 🧬https://www.cam.ac.uk/jobs/assistantassociate-professor-in-pathogen-genetics-pc51175