Abel, Sörenzur Wiesch, Pia AbelChang, Hsiao-HanDavis, Brigid M.Lipsitch, MarcWaldor, Matthew2015-10-012014Abel, Sören, Pia Abel zur Wiesch, Hsiao-Han Chang, Brigid M. Davis, Marc Lipsitch, and Matthew K. Waldor. 2014. “STAMP: Sequence tag-based analysis of microbial population dynamics.” Nature methods 12 (3): 223-226. doi:10.1038/nmeth.3253. http://dx.doi.org/10.1038/nmeth.3253.1548-7091http://nrs.harvard.edu/urn-3:HUL.InstRepos:22856878We describe a new method (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 intra-intestinal Vibrio cholerae revealed infection-stage and region-specific host barriers to infection, and unexpectedly showed 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 Article2015-10-0110.1038/nmeth.3253