bioRxiv preprint doi: https://doi.org/10.1101/210955; this version posted September 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. preprint Evolutionary dynamics of bacteria in the gut microbiome within and across hosts Nandita R. Garud1Y*, Benjamin H. Good2,3,5,Y*, Oskar Hallatschek2,4,5, Katherine S. Pollard1,6,7 1 Gladstone Institutes, San Francisco, California, United States of America 2 Department of Physics, University of California, Berkeley, California, United States of America 3 Department of Bioengineering, University of California, Berkeley, California, United States of America 4 Department of Integrative Biology, University of California, Berkeley, California, United States of America 5 Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California, United States of America 6 Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, California, United States of America 7 Chan-Zuckerberg Biohub, San Francisco, California, United States of America YThese authors contributed equally and are ordered alphabetically *
[email protected] (B.H.G.),
[email protected] (N.R.G.) Abstract Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in ∼30 prevalent species in the human gut.