Category Archives: Uncategorized

Welcome Will and Ricky!

We are delighted to welcome William Shoemaker and Ricky Wolff to our growing group!

Will is an NSF-funded postdoctoral scholar and joining us from his PhD lab in Indiana University.

Ricky is an MS student in the EEB department, recently graduated from Columbia University.

Thrilled to have you both join us!

Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

We are happy to share our latest collaboration examining the evolutionary dynamics in a single indivudual with high-res longitudinal data generated with long-read sequencing technology. Here, we show that genetic compositons within species can change in response to antibiotic perturbations even when the species relative abundance does not change significantly with time (see figure from the paper below). This indicates that the genetic changes observed within microbiomes play an important role in responding to selective pressures.

Population Genetics in the Microbiome — Review for Trends in Genetics

We are very happy that our review on Population Genetics in the Microbiome has been recently accepted to Trends in Genetics! The review will be officially published in January, but in the meanwhile, a copy is available here. Below is one of our figures illustrating modes of horizontal gene transfer, incorporation of DNA into the receipient’s genome, and statistical signatures of recombination.

Welcome Leah, Spencer, and Sara!

We are excited to have Leah, Spencer, and Sara join us in the  lab. Leah is a 3rd year PhD student working on developing new statistical methods to quanitfy ecological and evolutionary dynamics in microbial communities and is co-advised by Dr. Eran Halperin at UCLA. Sara is an MS student in EEB and Spencer is a 3rd year undergraduate student majoring in CS.

Welcome BIG Summer Students

This summer, Daisy Chen and Sara Thornburgh join the lab! Sara and Daisy are  undergaduates from UCLA majoring in Ecology and Evolutionary Biology and CS, respectively. Both are a part of the Bruins in Genomics (BIG) summer research program on campus. We are excited to be working together!

Sara and Daisy with their colleagues from BIG, Jon and Miguel!

Paper published!

I’m thrilled to share that our paper on the Evolutionary dynamics of bacteria in the gut microbiome within and across hosts is now published in PLoS Biology!

What is the paper about?

The human gut microbiome is comprised of a complex ecosystem of microbes that reside inside of us and play an important role in our health. With as many as a billion new mutations entering our microbiomes per day, bacterial genomes inside us have a great opportunity to evolve rapidly, unlike our own genomes, which change very little throughout our lifetimes. For us humans, this genetic dynamism is both an opportunity (e.g., enabling digestion of new foods) and a challenge (e.g. the evolution of drug resistance). Despite the potential importance of these effects, we currently know very little about if and how bacteria living in us evolve. In our recent work, we quantify the evolutionary dynamics of ~40 prevalent species of gut bacteria. We find that gut bacteria can evolve within humans on short timescales (~6 months), but over our lifetimes resident bacteria are typically replaced by distantly related strains. These results suggest that gut bacteria can evolve on human-relevant timescales, but that there are limits to the extent of local adaptation.

Isabel Gordo wrote a very nice perspective featuring our work.