Sequence tag-based analysis of microbial population dynamics

Nat Methods. 2015 Mar;12(3):223-6, 3 p following 226. doi: 10.1038/nmeth.3253. Epub 2015 Jan 19.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Bacterial Load / genetics
  • Cholera / microbiology*
  • Expressed Sequence Tags*
  • Female
  • High-Throughput Nucleotide Sequencing
  • Host-Pathogen Interactions / genetics*
  • Intestines / microbiology*
  • Male
  • Rabbits
  • Vibrio cholerae / genetics*
  • Vibrio cholerae / pathogenicity