Michael Wasney - Uniform bacterial genetic diversity of mice inoculated with human stool |MVIF40 S04 YouTube video by Microbiome Virtual International Forum

Finally, if interested, please check out @michaelwasney.bsky.social 's talk on this work, broadcasted by MVIF (and won best talk prize in his session!) www.youtube.com/watch?v=vAzH... (6/6)

This work was led by @michaelwasney.bsky.social and @leahbriscoe.bsky.social and was a fun collaboration with @ctropini.bsky.social's lab! Many thanks to @rwolff.bsky.social and Hans Gezzi for their hard work and insights as well in making this work possible. (5/n)

More work is needed in the future to understand if there is spatial segregation at finer scales as well as in the mucosa. But, for now, we start to obtain a picture of uniform diversity along the gut at the strain and evolutionary level. (4/n)

We found that these results replicate in both mice as well as humans. These results indicate that spatial segregation is not a requisite for strain coexistence in the gut microbiome (at least in the lumen) and that evolutionary changes do not face barriers in their spread. (3/n)

In this work we sought to understand how strains and their evolutionary adaptations are distributed along the lumen of the mouse gut. We found a surprising amount of uniformity despite there being extensive species-level heterogeneity along the gut. (2/n)

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.

thank you!!!

If you are interested in this work and are looking for a postdoc position, please get in touch -- we are actively looking for someone to join our group at UCLA!

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 ...

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...

thank you!

New research in #GENETICS from @azurita.bsky.social, Christopher Kyriazis, and @klohmueller.bsky.social demonstrates how unmodeled selection on synonymous mutations may affect downstream inferences of the distribution of fitness effects. buff.ly/IDY87W1

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

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.

I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!

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

The 2025 Freeman Hrabowski Scholars | HHMI Freeman Hrabowski Scholars are outstanding early career faculty who have the potential to become leaders in their research fields.

So excited to see @alisonfeder.bsky.social among the winners of the freeman hrabowski award!! www.hhmi.org/programs/fre...

Neanderthal introgressed ancestry reveals human genomic regions enriched with recessive deleterious mutations Negative natural selection on deleterious mutations plays a key role in shaping human genetic variation. Understanding the dominance of deleterious mutations is critical as it can fundamentally impact...

Super excited to share my latest preprint with @klohmueller.bsky.social! Here we leverage the unique signature that recessive deleterious variants can lead to an increase in archaic ancestry to tackle a classic question - the dominance distribution on the human genome www.biorxiv.org/content/10.1...

This work provides an unprecedented inference of the demographic histories and DFEs of ~25 common gut commensals. Inferring so many models was not an easy task, but was gamely taken on by the talented @jonmah.bsky.social. Many thanks also to @klohmueller.bsky.social for such a fun collaboration!

Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history Abstract. Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their

We are thrilled to share that our paper entitled "Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history" is officially out in MBE! academic.oup.com/mbe/advance-...

Assembly Graph as the Rosetta Stone of Ecological Assembly This paper introduces the assembly graph as an integrative lens to unify ecological assembly theories across dynamical, informational, and probabilistic approaches. In addition to theory, it also pre...

Thrilled to share my Perspective piece "Assembly Graph as the Rosetta Stone of Ecological Assembly" in Environmental Microbiology! Huge thanks to @asanchezlab.bsky.social for the invite & reviewers for insightful feedback.

Director, Institute for Quantitative and Computational Biosciences University of California, Los Angeles is hiring. Apply now!

UCLA QCBIO is looking for its next director! Please consider applying! recruit.apo.ucla.edu/JPF10007

A conserved bacterial genetic basis for commensal-host specificity Animals selectively acquire specific symbiotic gut bacteria from their environments that aid host fitness. To colonize, a symbiont must locate its niche and sustain growth within the gut. Adhesins are...

Finally, our paper, "A Conserved Bacterial Genetic Basis for Commensal-Host Specificity," has been officially published in Science.

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

Apply to work with Katherine! A fantastic opportunity!

Xue lab at UC Irvine Ecology and evolution in the human gut microbiome

Hi friends new and old! I study how microbes interact and evolve in complex communities like the human gut microbiome.🦠🧬💩 I'm thrilled to share that I'm starting a lab at UC Irvine in April 2025 and am recruiting at all levels - please spread the word! kxuelab.com More about my work below...🧵1/n

Leveraging ancient DNA to uncover signals of natural selection in Europe lost due to admixture or drift - Nature Communications Large-scale ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. Here the authors use aDNA from 708 European samples to ide...

Delighted to share that our paper on discovering selective sweeps with haplotype statistics in aDNA is now out in Nat. Comm! www.nature.com/articles/s41...

Wonderful collaboration with Vagheesh Narasimhan, Devansh Pandey, and @mharris.bsky.social

Conservation Genomics Faculty Position University of California, Los Angeles is hiring. Apply now!

Hi all! I'm excited to announce a tenure track faculty position in conservation genomics in EEB at UCLA! We're looking for candidates who use genomic tools to study evolutionary processes related to conservation. Note, the actual application deadline is Nov 29. recruit.apo.ucla.edu/JPF09875

Conservation Genomics Faculty Position University of California, Los Angeles is hiring. Apply now!

Job alert! We are searching for a faculty member to join us @UCLAEEB in the area of Conservation Genomics. I have had very positive experiences here at UCLA and would be happy to chat with you if you are interested! Please apply and be my colleague! recruit.apo.ucla.edu/JPF09875

The UCLA Goodman-Luskin Endowed Postdoctoral Fellowship in Microbiome Research ($100K in salary + supplies) deadline is June 1. Get in touch if you would like to write a proposal together!

And, get in touch even if your timeline is different - I am looking for a postdoc!

Congrats Zhiru and Ben!