Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...

Check out our new paper led by brilliant @jhuisman.bsky.social about how microbial communities cope with stress due to increasing salinity in their environment. We have all your favorites: isolate phenotyping, pairwise competitions, community propagations, and theory. #microsky #mevosky #ecosky

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements. Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal. journals.asm.org/doi/10.1128/... 🧵

Because of a lack of separation of the time scales for TF binding/unbinding and fluctuations in active TF levels, non-equilibrium gene regulation may be common in bacteria. Check out this nice piece by ‪@philipcball.bsky.social‬ on our new publication in PRX Life. physics.aps.org/articles/v18...

The Wadsworth Center, New York State Department of Health, is currently recruiting for a Research Scientist 5 (Assistant/Associate Professor equivalent) to lead an independent research program focused on zoonotic and/or vector-borne pathogens (viral and bacterial).

Flybase lost all of the NIH support overnight - it is a disaster for the community. Please consider donating. I just did! www.philanthropy.cam.ac.uk/give-to-camb...

One of the coolest papers I've ever read: www.nature.com/articles/s41... Within-colony bacterial dynamics. And the figures are absolutely striking and clear.

We organized this one: academic.oup.com/femsle/artic... in 2024. It is coming back in 2026 with 2 hubs in the US (Michigan and SoCal). It was a great experience

Bacteria have a simple yet potent mechanism that controls their sensitivity to environmental stimuli. A new study by researchers led by @erikvannimwegen.bsky.social @biozentrum.unibas.ch shows: the slower cells grow, the more sensitively they respond to their environment.

Nice review article on a fascinating problem—the coexistence of strains in microbial communities. @akshitg.bsky.social & @gchure.bsky.social enviromicro-journals.onlinelibrary.wiley.com/doi/full/10....

Whimsical Friday afternoon read—1976 study of the microbiomes of astronauts undergoing isolation training, which concluded B. theta abundance responds specifically to "anger stress"

Wow www.biorxiv.org/content/10.1... A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome

Kevin Hall, one of the only nutrition researchers in the world running controlled trials of ultraprocessed foods, just announced his early retirement from NIH, citing censorship of his research communications: www.cnn.com/2025/04/16/h...

... but how many genetic edits would one have to make to actually get a new species?

Taxa is hiring! We're looking for a Computational Biologist to spearhead the analysis of massive genomic datasets for our flagship probiotics. Exciting science, great team, and transparent compensation. Apply here 👇

Know any soon to graduate or recently graduated undergrads interested in a full year, paid postbac research position in microbiome sciences? Have them join our zoom Q&A session on Friday, April 11, 11:30am-12:30pm PST. More info here: sites.google.com/berkeley.edu...

Greatly enjoyed this thought provoking, deeply researched, and extremely well written review from @saradirienzi.bsky.social and Robert Britton www.sciencedirect.com/science/arti...

Super interesting study www.nature.com/articles/s41...

My lab at NYU is hiring a postdoc in microbial ecology and evolution! We are looking for someone interested in both wet and dry lab techniques, including experimental evolution, genome editing, bioinformatics, and some modeling. Apply here: apply.interfolio.com/164683

New online! Interactions and evolutionary relationships among bacterial mobile genetic elements

Finally, our paper, "A Conserved Bacterial Genetic Basis for Commensal-Host Specificity," has been officially published in Science. www.science.org/doi/10.1126/...

Interesting new study in @science.org: A conserved bacterial genetic basis for commensal-host specificity www.science.org/doi/10.1126/...

Please suggest a cool paper/preprint in your field in the last year or so! For a course I teach, I am collecting papers on: cell/dev bio, microbio, neuro, maths/stats/CS/chem/phys applied to biology. Students use one paper as the basis for a "research grant application" that they will write. 1/2

The bacteria in your gut depend on where you are in the social network around you. The microbes within us treat our social networks as the extended environment in which they thrive. They can spread from person to person. New #HNL work out today in @natureportfolio.bsky.social . 1/

I'm new here, so I'll share our recent work here too 😁🧫 Using Tn-seq + live imaging in engineered airway organoids, we explored the fitness tradeoffs P. aeruginosa faces while growing and surviving antibiotic treatment on the mucosal surface. Check it out: www.nature.com/articles/s41... #MicroSky

shout out to @jferrare.bsky.social !!!!!

From Ben Good: competition btwn linked mutations can..enhance selection for modifiers that increase benefits of future mutations, even when they impose a strong direct cost on fitness. However..modest direct benefits can..drive evolutionary dead ends to fixation. www.nature.com/articles/s41...

Experimental capture of genomic islands defines a widespread class of genetic element capable of non-autonomous transfer https://www.biorxiv.org/content/10.1101/2024.08.29.610337v1

I wrote a little perspective piece www.cell.com/cell/fulltex... on this mind-blowing paper www.sciencedirect.com/science/arti... by @asanchezlab.bsky.social and colleagues.

#MVIF #30 keynotes Kathryn Patras Marina Walther-Antonio Linda Brubaker Nichole Klatt & Ian Fields, as a moderator, will discuss vaginal microbiome and urobiome, endometrial and ovarian cancer, and bacterial vaginosis! Register here events.ringcentral.com/events/micro...

These ingestible pills are awesome—just a fantastic tool to see what's actually going on inside the gut elifesciences.org/articles/85567

Paradoxically, preventing infection with high ABX can make patients susceptible to subsequent infections like C diff as gut flora get wiped out. Developing ABX that act in concert with the commensal microbiome to resist pathogens is a triumph www.nature.com/articles/s41...

Scientists have managed to generate a full genetic sequence of #H5N1 #birdflu from store-bought milk, suggesting commercial milk products could be a way to monitor the outbreak in cows, given the lack of cooperation from dairy farmers. www.statnews.com/2024/05/21/b...

Firmicutes appear to harbor host-specificity genes that allow them to bind to particular physical niches in the host gut I got to play a very minor role in this amazing work, and I'm so excited to see it out www.biorxiv.org/content/10.1...

My first theory project! I've really enjoyed how we could decompose complex dynamics into those of individual lineages. This approach is quite flexible, and we're hoping to extend it to more complex scenarios, including N(t) and certain forms of positive selection!

Two new chapters from my open-access textbook in human population genetics are now online: - Population structure: I. Ancestry estimation - Population structure: II. More about admixture web.stanford.edu/group/pritch...

Now published: "Phage predation, disease severity, and pathogen genetic diversity in cholera patients" www.science.org/doi/10.1126/... Check out the podcast to hear co-senior author Eric Nelson talk about the twists and turns of our study (around 18:25): www.science.org/content/podc...

Join us–you get to work with Nandita, $100K in salary, and we have La Croix in the fridge

Really liked this—directing evolution with prophage www.sciencedirect.com/science/arti...

#MVIF #28 program is out! 🤩 ⭐️ Keynote: 🇺🇸Julia Oh ⭐️ Short talks: 🇨🇳 Lu Wu 🇨🇳 Yiqian Duan 🇺🇸 Zhenrun Jerry Zhang ⭐️ Highlights: 🇨🇳 Ye Peng 🇯🇵 Naoki Hayashi Registration: events.ringcentral.com/events/micro...

"Life finds a way" elifesciences.org/articles/90156

Was an honor to present at MVIF! The talks have all been fantastic—incredible opportunity to meet and talk with microbiome researchers from around the world.

Do you enjoy mysterious population stochasticity, chaotic dynamics, and/or popgen? Then this preprint might be for you! Super excited to share a project that has been an exciting journey, and a fun blend of theory and experiment! www.biorxiv.org/content/10.1...

ICYMI: I ❤️ this paper. It raises various possibilities to explain Lewontin's Paradox for super-abundant microbes like Pro & E. huxleyi. Provides essential pop-gen background and open questions. TLDR: every mutation happens in these species 10^11 times a day! 🤯🧪🧬 www.sciencedirect.com/science/arti...

So excited to be presenting my work on detecting adaptive horizontal gene transfer in the microbiome in this session!

#MVIF 26 program is out! 🤩 ⭐️ Keynote: 🇺🇸 Laura S. Weyrich ⭐️ Short talks: 🇨🇳 Ziye Wang 🇺🇸Kate Bowie 🇺🇸Richard Wolff 🇺🇸Ivan Zheludev More about talks here: www.microbiome-vif.org/en-US/-/futu...

Absolutely remarkable paper that everyone interested in microbial evolution should read

Ever wonder if V. cholerae loses genetic diversity due to bottlenecks as it passes through the gut? We have a little preprint about that! The answer, based on sequencing 200 genomes from 10 patients’ vomit and stool, is: maybe a little but not much!

New #LTEE paper out in #Science today. I wrote about it here, with an emphasis on "how civility, cooperation, and collaboration can succeed even in the highly competitive world of science." the-ltee.org/an-update-to... And here's a link to the paper itself: www.science.org/doi/10.1126/...