Loved @jeffgroh.bsky.social's Crow talk at PEQG—a very beautiful and complete story

Kat Kerlin@katkerlin.bsky.social · last wk.

Some avocados are female in the morning and male in the afternoon, while others are on the opposite schedule. This helps them avoid self-pollination. How do they do it? A @ucdavis.bsky.social study explains. www.ucdavis.edu/food/news/st...

Super excited to share new work with my advisor @nanditagarud.bsky.social! We re-examine the rapidity of adaptation in the human gut microbiome and begin to characterize the adaptive architecture of selective sweeps spreading across human guts. www.biorxiv.org/content/10... 1/n:

Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomes

Recent work has shown that commensal gut bacteria can evolve rapidly within hosts on short timescales of days to months, fueled by the enormous mutational input generated daily in the microbiome. Yet ...

biorxiv.org

We are very excited to share our latest. We thought that soft sweeps would be the only type of sweep spreading across human gut microbiomes. Turns out many are hard! Reach @peterlaurin.bsky.social 's thread on why! And tomorrow at #SMBE2026 I will share this work and more!

Peter Laurin@peterlaurin.bsky.social · last mo.

Super excited to share new work with my advisor @nanditagarud.bsky.social! We re-examine the rapidity of adaptation in the human gut microbiome and begin to characterize the adaptive architecture of selective sweeps spreading across human guts. www.biorxiv.org/content/10... 1/n:

Spent the last two years developing a new Intro to Physics course for undergrad biology majors. It features tons of examples from biology (especially Ecology & Evolution!) and requires only middle school-level math. Lecture note here shorturl.at/0PiVp Any comments or feedback are highly welcome!

Our paper entitled "The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians" is now out in PNAS! www.pnas.org/doi/abs/10.1.... A really fun and informative collaboration with @mharris.bsky.social, Ziyi Mo and Adam Siepel. (1/n)

The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians | PNAS

The extent to which human adaptations have persisted throughout history despite strong eroding demographic events such as admixture, genetic drift,...

pnas.org

It looks like there will be an open postdoc position in my lab soon. I'll be looking for someone with substantial wet-lab experience in microbiology / microbial ecology / evolution / physiology. If everything goes well, an ad will be coming. But if you know someone, ask them to reach out already.

Really excited that this major work from my PhD is finally published in @plosbiology.org ! In it, we were trying to tackle a fundamental question in evolution - how do genetic mutations map onto evolutionary fitness? (1/n) journals.plos.org/plosbiology/...

Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments

Predicting the effect of a genetic mutation on fitness is a major challenge in evolutionary biology. This study uses fitness effects of a large collection of adaptive yeast mutants in multiple lab env...

journals.plos.org

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)

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

Fantastic to see this out at last

Gabriel Birzu@gbirzu.bsky.social · 7mo ago

Happy that our work on the evolution of Yellowstone cyanobacteria is now published in @elife.bsky.social: doi.org/10.7554/eLif...! Did a lot of work in revision—many thanks to the anonymous reviewers for great suggestions! Also see the eLife digest for a summary: elifesciences.org/digests/9084...

Working on this paper fundamentally changed how I thought about bacterial evolution, and I couldn't ask for a better to Hannukah present than to see it out, at last!

Nandita Garud@nanditagarud.bsky.social · 8mo ago

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

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...

Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature

Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

nature.com

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

Jana Huisman@jhuisman.bsky.social · 12mo ago

Have you ever wondered what increasing environmental stress will do to microbial communities? In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5) www.biorxiv.org/content/10.1...

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/... 🧵

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems

In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

journals.asm.org

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...

Different Bacterial Genes Have Different Turn-Ons

Not all genes respond in the same way to regulation by the same molecule—a property that might enable cells to produce complex genetic responses.

physics.aps.org

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...

Drosophila Genetic Database

The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...

philanthropy.cam.ac.uk

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.

Spatiotemporal development of expanding bacterial colonies driven by emergent mechanical constraints and nutrient gradients - Nature Communications

Bacterial colonies growing on solid surfaces can exhibit robust expansion kinetics, with constant radial growth and saturating vertical expansion. Here, the authors use modeling and experiments to sho...

nature.com

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

MEEhubs2024: A hub-based conference on microbial ecology and evolution fostering sustainability

This paper presents a multi-hub conference on microbial ecology and evolution, analyzing participant and organizer feedback to provide a template and recom

academic.oup.com

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.

Slow-growing bacteria respond more sensitively to their environment

Bacteria have a simple yet potent mechanism that controls their sensitivity to environmental stimuli. A new study by researchers at the Univer...

unibas.ch

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....

Paradox of the Sub‐Plankton: Plausible Mechanisms and Open Problems Underlying Strain‐Level Diversity in Microbial Communities

“Paradox of the sub-plankton: Plausible mechanisms and open problems underlying strain-level diversity in microbial communities” by Akshit Goyal* and Griffin Chure*. This work highlights the limitati...

enviromicro-journals.onlinelibrary.wiley.com

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...

Top NIH nutrition researcher studying ultraprocessed foods departs, citing censorship under Kennedy | CNN

When President Donald Trump named Robert F. Kennedy Jr. as his choice to lead the US Department of Health and Human Services, one group of health researchers was cautiously optimistic that their cause...

cnn.com

... 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 👇

Taxa hiring Computational Biologist in San Francisco, CA | LinkedIn

Posted 4:13:15 PM. The OpportunityWe are looking for a talented Computational Biologist to spearhead the analysis of…See this and similar jobs on LinkedIn.

linkedin.com

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...

Adaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners

The consumption of sugar has become central to the Western diet. Cost and health concerns associated with sucrose spurred the development and consumpt…

sciencedirect.com

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

Transient silencing of hypermutation preserves B cell affinity during clonal bursting - Nature

B cell germinal centres achieve a balance between clonal expansion and sequence diversification by suppressing somatic hypermutation during proliferative clonal bursts.

nature.com

The Rockefeller University @rockefeller.edu · last yr.

New imaging from @victora.bsky.social's lab reveals a built-in safeguard that allows B cell populations to rapidly expand in germinal centers without introducing deleterious mutations. #RockefellerScience