Abel, SörenAbel zur Wiesch, PiaChang, Hsiao-HanDavis, Brigid M.Lipsitch, MarcWaldor, Matthew2016-03-082015Abel, Sören, Pia Abel zur Wiesch, Hsiao-Han Chang, Brigid M Davis, Marc Lipsitch, and Matthew K Waldor. 2015. “Sequence Tag–based Analysis of Microbial Population Dynamics.” Nat Meth 12 (3) (January 19): 223–226. doi:10.1038/nmeth.3253.1548-7091http://nrs.harvard.edu/urn-3:HUL.InstRepos:25753229We describe sequence tag-based analysis of microbial populations (STAMP) for characterization of pathogen population dynamics during infection. STAMP analyzes the frequency changes of genetically 'barcoded' organisms to quantify population bottlenecks and infer the founding population size. Analyses of intraintestinal Vibrio cholerae revealed infection-stage and region-specific host barriers to infection and showed unexpected V. cholerae migration counter to intestinal flow. STAMP provides a robust, widely applicable analytical framework for high-confidence characterization of in vivo microbial dissemination.en-USJournal Article2015-12-30Marc Lipsitch2016-03-0810.1038/nmeth.3253