Ricky Wolff

Fantastic to see this out at last

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!

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–...

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

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, ...

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/...
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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.

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).

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 ...

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...

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...

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.

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

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

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...

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.

Durable coexistence of donor and recipient strains after fecal microbiota transplantation The mystery of the success of clinical microbial transplant therapy is beginning to be decoded.

To me, it's telling that even strains that have evolved separately for a long time coexist readily (see FMT study below). I feel this strongly implicates physiological/metabolic flexibility, rather than fixed niche differentiation, as a driver of coexistence

www.science.org/doi/10.1126/...

What does the fact that we see closely related bacterial strains stably coexisting in the human gut microbiome, in cheese cultures, in solar salterns, in the LTEE—really wherever we look—tell us about microbial physiology, ecology, and evolution?

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...

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....

so much creativity!

Human fecal flora: variation in bacterial composition within individuals and a possible effect of emotional stress | Applied and Environmental Microbiology Data are presented on the distribution of 101 bacterial species and subspecies among 1,442 isolates from 25 fecal specimens from three men on: (i) their normal diet and normal living conditions, (ii) normal living conditions but eating the controlled ...

Paper is both a little silly and very forward thinking—fun to read!

journals.asm.org/doi/abs/10.1...

following up in a different study system,

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

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...

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 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.

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...

I love that "adaptation" here is explored across scales—from physiology/gene regulation, to ecology, to evolution over short (within host) and long (across many host lifetimes) timescales

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…

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