Sequence tag-based analysis of microbial population dynamics

Sören Abel, Pia Abel Zur Wiesch, Hsiao Han Chang, Brigid M. Davis, Marc Lipsitch, Matthew K. Waldor

Research output: Contribution to journalArticlepeer-review

70 Scopus citations


We 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.

Original languageEnglish (US)
Pages (from-to)223-226
Number of pages4
JournalNature methods
Issue number3
StatePublished - Feb 26 2015

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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