Ben Good

Faculty Professor Associate - Full-Time | Vaughn Cooper We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine. 1) Fundamental researc...

🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...

Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University.
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...

The constant barrage of terrible news on bluesky has made me feel weird about promoting papers, but people in the lab have been doing so much amazing work over the past few months that I want to share a few brief teasers/links:

Frequency-dependent fitness effects are ubiquitous In simple microbial populations, the fitness effects of most selected mutations are generally taken to be constant, independent of genotype frequency. This assumption underpins predictions about evolutionary dynamics, epistatic interactions, and the maintenance of genetic diversity in populations. Here, we systematically test this assumption using beneficial mutations from early generations of the Escherichia coli Long-Term Evolution Experiment (LTEE). Using flow cytometry-based competition assays, we find that frequency-dependent fitness effects are the norm rather than the exception, occurring in approximately 80\% of strain pairs tested. Most competitions exhibit negative frequency-dependence, where fitness advantages decline as mutant frequency increases. Furthermore, we demonstrate that the strength of frequency-dependence is predictable from invasion fitness measurements, with invasion fitness explaining approximately half of the biological variation in frequency-dependent slopes. Additionally, we observe violations of fitness transitivity in several strain combinations, indicating that competitive relationships cannot always be predicted from fitness relative to a single reference strain alone. Through high-resolution measurements of within-growth cycle dynamics, we show that simple resource competition explains a substantial portion of the frequency-dependence: when faster-growing genotypes dominate populations, they deplete shared resources more rapidly, reducing the time available for fitness differences to accumulate. Our results demonstrate that even in a simple model system designed to minimize ecological complexity, subtle ecological interactions between closely related genotypes create frequency-dependent selection that can fundamentally alter evolutionary dynamics. ### Competing Interest Statement The authors have declared no competing interest.

How common are frequency dependent fitness effects?

New preprint out today 👇
doi.org/10.1101/2025...

Limited codiversification of the gut microbiota with humans A recent study by Suzuki & Fitzstevens et al ([1][1]) argued that dozens of species of gut bacteria have codiversified with modern human populations. Reanalysis of their data reveals that the correlat...

Drifting into speculation: I think these data support the picture that gut microbes can spread much faster than human genes. Strong geographic barriers can be still be very important (as in the Tsimane & Hadza case) but the magnitude of this effect
stands out compared to other contemporary pop'ns.

A figure panel depicting the amount of recent strain sharing of Ruminococcus bromii strains between different human populations.

Interestingly, of the subset of species shared w/ industrialized pop'ns, some show evidence of recent transmission, while others suggest a more ancient association. Among these, the genetic isolation between Tsimane & Hadza strains was generally larger than between comparable industrialized pop'ns

Dynamics of bacterial recombination in the human gut microbiome Recombination is a ubiquitous force in bacterial evolution, but its dynamics are poorly characterized in many natural populations. This study presents a metagenomic approach for quantifying the landsc...

We developed several methods to detect & date the onset of genetic isolation between these microbial pop'ns, which leverage the fact that gut bacteria constantly exchange DNA w/ each other. In most species, we found patterns of divergence & gene flow consistent w/ prehistoric co-migration w/ humans.

A figure panel from the paper showing the relative fraction of microbial species observed in the Tsimane and Hadza cohorts.

We were surprised to see right off the bat that - despite their long history of geographic separation - most of the microbial species in the Tsimane microbiome were also found in the Hadza (and most of these are either rare or absent in industrialized populations).

Benefiting from decades of work by the Tsimane Life History Project (tsimane.anth.ucsb.edu) and a previous set of samples collected by Melanie Martin, @danielsprockett.bsky.social & co, we used deep metagenomic sequencing to reconstruct ~12k microbial genomes from ~80 Tsimane adults.

Here we tried to get around this challenge by analyzing two geographically distant populations – the Tsimane of Bolivia and the Hadza of Tanzania – whose ancestors have been separated for more than 10,000 years prior to recent human globalization.

Why am I so excited about this work? There’s been a lot of interest in understanding how gut bacteria might have evolved (or co-evolved) w/ humans. But the plasticity of the microbiome can make it difficult to distinguish long-term associations from more recent acquisitions from the environment.

Prehistoric Global Migration of Vanishing Gut Microbes With Humans The gut microbiome is crucial for health and greatly affected by lifestyle. Many microbes common in non-industrialized populations are disappearing or extinct in industrialized populations. Understand...

Excited to share a new preprint w/ the Sonnenberg lab, led by Matt Carter, @zzzhiru.bsky.social & @mattolm.bsky.social. We analyzed the microbiomes of two non-industrialized populations from opposite sides of the globe to try to reconstruct the recent evolutionary history of our gut microbiota.

Incredibly proud of this work where we developed a method for understanding the information contained in millions of genomes. Another example of NIH funded research.

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/...
🧵

I'm thrilled that my lab at NYU is now supported by an NIH MIRA grant! I'm looking to hire 1-2 senior lab members (outstanding postdoc candidates or experienced staff scientists) with expertise in computational or statistical methods in human genetics or genomics. Please share!

Junior, Assistant, or Associate Specialist – Xue Lab University of California, Irvine is hiring. Apply now!

The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601

Finding easy regions for short-read variant calling from pangenome data arxiv.org/abs/2507.03718 🧬🖥️🧪 github.com/lh3/panmask

Staff scientist position (computational):

I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs

Check out Laura's thread on our latest preprint demonstrating best methods for low biomass skin sampling.

Next up is Sophie Walton, who will be talking about some new in vitro experiments to quantify the dynamics of selection among conspecific strains in larger microbial communities (Monday 9:30am, Evolutionary Ecology I).

Two members of our group will be presenting at #evolution2025 this year. First up is Anastasia Lyulina, who will be presenting some new theory on the site frequency spectrum of selected mutations in non-equilibrium populations (Saturday at 4:15; Population Genetics Theory IV).

I think this emphasizes the need for more concrete models of pleiotropy to help us know when these verbal models should even apply in principle (let alone in expts like @oliviamghosh.bsky.social's). In that vein, was very excited about the new work that @djhelam1.bsky.social‬ talked about at NITMB

Thanks for these questions @skryazhi.bsky.social! I might add that we’ve been playing around a bit with FGM-like models to see when you might expect behavior like this, and it turns out to be a lot more complex than (at least I) expected.

I think it would be super cool to explore some of these assumptions and models theoretically, but (spoiler alert) we don't actually find evidence for the pleiotropic expansion model in our data! So perhaps these assumptions are not borne out in reality (in our system at least).

There are some implicit assumptions that must be true for this pleiotropic expansion model to work. First, just to clarify, the fact that a box is colorful does not mean it has a positive effect on fitness, it just means it is relevant. So a mutant's affect on a trait can be good in E1, bad in E2

Thanks for taking a look! We actually have an updated v2 manuscript that I think clarifies our two competing hypotheses in figure 1:

www.biorxiv.org/content/10.1...

@oliviamghosh.bsky.social @grantkinsler.bsky.social @benjaminhgood.bsky.social @petrovadmitri.bsky.social: I am reading your “Low-dimensional genotype-fitness mapping ... ” preprint. Very interesting!

Can you help me understand the "pleiotropic expansion model" (Fig 1a)?

shorturl.at/qRYfJ

I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required.

Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.

Super excited to release a huge evolution project on the works for many years:

Evolution experiments synchronized across climates to understand rapid adaptation

Preprint: doi.org/10.1101/2025...
All data available: www.grene-net.org/data

#MOILAB
@ucberkeleyofficial.bsky.social
@hhmi.org

🧵👇

1/n 🧵 Excited to share our new paper! We developed a framework to reveal hidden simplicity in how organisms adapt to different environments, particularly focusing on antibiotic resistance evolution. #EvolutionaryBiology #MachineLearning