Ben Good

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

Growth rate controls the sensitivity of gene regulatory circuits Through the simple effect of dilution rate, regulatory circuits systematically change their sensitivity with growth rate.

The most profound insights are often also the most simple:
growth-rate, by setting the dilution rate of intra-cellular molecules, controls the sensitivity of gene regulatory circuits. In retrospect it seems crazy that this effect seems to have been overlooked so far.
www.science.org/doi/10.1126/...

I’m thrilled to share my first ever publication, now published in PNAS! www.pnas.org/doi/10.1073/...

With mentorship from the amazing @ksxue.bsky.social, I looked at how the outcomes of species introductions to microbial communities are influenced by the number of introduced microbes.

Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!

Transformation, Recombination and horizontal transfer

The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate : doi.org/10.1101/2025... (for the very busy: 1-6% of gene gains) #MicroSky

Thank you Rich and everyone! Delighted for this opportunity to serve our microbiology community!

This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g., A→C, A→G, etc.) and can vary between sites ...

Building on the UShER tree of millions of SARS-CoV-2 genomes maintained by Angie Hinrichs, Hugh Haddox and Georg Angehrn (and others in @matsen.bsky.social lab and @jbloomlab.bsky.social) have looked into how the neutral mutation rate varies along the genome:

[1/N]

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

Quantifying the evolutionary dynamics of structure and content in closely-related E. coli genomes Abstract. Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics

Thrilled to announce that our work (w. with fantastic @neher.io and Liam Shaw) has been published on Molecular Biology and Evolution! 🎉

academic.oup.com/mbe/advance-...

Are you curious about how fast the genome of E.coli evolves structurally (gains, rearrangements...) ? 🧬

A summary thread [1/N]🧵

Global niche partitioning of purine and pyrimidine cross-feeding among ocean microbes Global marine microbial marketplace for DNA building blocks drives biogeochemical cycling and ecological signaling in the ocean.

Very excited to share final version of our paper! What forces shape evolution of cross-feeding among planktonic ocean microbes, and how does it in turn drive self-organization of biogeochemical cycles? These are the questions we explore here:

www.science.org/doi/full/10....

Check out the team battling the bananapocalypse! 🍌 Fantastic collab on Ralstonia emergence in Indonesia.

Thanks for the video and support @mpi-bio-fml.bsky.social + @maxplanck.de

I really believe more folks should start off staring at a kinship matrix rather than STRUCTURE, PCA, etc. Such a rich visual of the data.

If you do GWAS or rare variant association studies, check out this short thread on the concept of SPECIFICITY, and why it is a major determinant of what we find:

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55