Ricky Wolff
@rwolff.bsky.social
Ecology and evolution of the human gut microbiome in Nandita Garud's lab at UCLA
Reposted by Ricky Wolff
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
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
Validate User
doi.org
September 29, 2026 at 12:05 PM
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
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
Loved @jeffgroh.bsky.social's Crow talk at PEQG—a very beautiful and complete story
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...
Study Reveals How Avocados Reverse Sexes Throughout the Day
Some avocados are female in the morning and male in the afternoon, while others are on the opposite schedule. How avocados do this has been unclear — until now, thanks to a UC Davis study.
www.ucdavis.edu
July 31, 2026 at 5:33 PM
Loved @jeffgroh.bsky.social's Crow talk at PEQG—a very beautiful and complete story
Reposted by Ricky Wolff
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:
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 ...
www.biorxiv.org
June 30, 2026 at 7:36 PM
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:
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:
Reposted by Ricky Wolff
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!
And tomorrow at #SMBE2026 I will share this work and more!
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:
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 ...
www.biorxiv.org
June 30, 2026 at 7:42 PM
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!
And tomorrow at #SMBE2026 I will share this work and more!
Reposted by Ricky Wolff
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!
Any comments or feedback are highly welcome!
physics_for_biologists.pdf
drive.google.com
June 16, 2026 at 2:37 PM
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!
Any comments or feedback are highly welcome!
Reposted by Ricky Wolff
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,...
www.pnas.org
May 6, 2026 at 9:37 PM
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)
Reposted by Ricky Wolff
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.
April 10, 2026 at 3:59 AM
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.
Reposted by Ricky Wolff
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/...
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
March 30, 2026 at 7:11 PM
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/...
journals.plos.org/plosbiology/...
Reposted by Ricky Wolff
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)
March 31, 2026 at 5:50 PM
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)
Reposted by Ricky Wolff
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.
February 12, 2026 at 7:18 PM
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
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...
Hybridization breaks species barriers in long-term coevolution of a cyanobacterial population
Analysis of hundreds of single-cell genomes from Yellowstone National Park shows bacterial species are less cohesive than previously thought.
doi.org
January 8, 2026 at 12:04 AM
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!
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...
www.nature.com/articles/s41...
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
www.nature.com
December 17, 2025 at 6:58 PM
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!
Reposted by Ricky Wolff
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...
#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–...
www.nature.com
November 26, 2025 at 9:55 PM
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...
#phagesky
www.nature.com/articles/s41...
Reposted by Ricky Wolff
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...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Ricky Wolff
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
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...
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...
Microbial communities demonstrate robustness in stressful environments due to predictable composition shifts
Environmental stress reduces species growth rates, but its impact on the function of microbial communities is less clear. Here, we experimentally demonstrate that increasing salinity stress shifts com...
www.biorxiv.org
August 25, 2025 at 2:47 PM
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
Reposted by Ricky Wolff
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/...
🧵
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
July 31, 2025 at 3:33 PM
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/...
🧵
Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.
journals.asm.org/doi/10.1128/...
🧵
Reposted by Ricky Wolff
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...
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
July 18, 2025 at 9:30 PM
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...
Check out this nice piece by @philipcball.bsky.social on our new publication in PRX Life.
physics.aps.org/articles/v18...
Reposted by Ricky Wolff
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).
June 3, 2025 at 9:21 PM
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).
Reposted by Ricky Wolff
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 ...
www.philanthropy.cam.ac.uk
June 3, 2025 at 6:23 PM
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...
Reposted by Ricky Wolff
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.
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...
www.nature.com
May 30, 2025 at 2:22 PM
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.
Within-colony bacterial dynamics.
And the figures are absolutely striking and clear.
Reposted by Ricky Wolff
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
May 26, 2025 at 4:55 PM
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
Reposted by Ricky Wolff
Bacteria have a simple yet potent mechanism that controls their sensitivity to environmental stimuli. A new study by researchers led by <a href="https://bsky.app/profile/did:plc:mpi2uwwkiofxvcgr5lzmjnra" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky-mention">@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...
www.unibas.ch
May 8, 2025 at 8:15 AM
Bacteria have a simple yet potent mechanism that controls their sensitivity to environmental stimuli. A new study by researchers led by <a href="https://bsky.app/profile/did:plc:mpi2uwwkiofxvcgr5lzmjnra" class="hover:underline text-blue-600 dark:text-sky-400 no-card-link" target="_blank" rel="noopener" data-link="bsky-mention">@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....
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
May 12, 2025 at 9:17 PM
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....
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"
May 9, 2025 at 9:18 PM
Whimsical Friday afternoon read—1976 study of the microbiomes of astronauts undergoing isolation training, which concluded B. theta abundance responds specifically to "anger stress"
Reposted by Ricky Wolff
Wow
www.biorxiv.org/content/10.1...
A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome
www.biorxiv.org/content/10.1...
A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome
May 6, 2025 at 2:09 PM
Wow
www.biorxiv.org/content/10.1...
A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome
www.biorxiv.org/content/10.1...
A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome