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

doi:10.1038/nmeth.3253

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 journal › Article › peer-review

70 Scopus citations

Abstract

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 language	English (US)
Pages (from-to)	223-226
Number of pages	4
Journal	Nature methods
Volume	12
Issue number	3
DOIs	https://doi.org/10.1038/nmeth.3253
State	Published - Feb 26 2015

All Science Journal Classification (ASJC) codes

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/nmeth.3253

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abstract = "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.",

author = "S{\"o}ren Abel and {Abel Zur Wiesch}, Pia and Chang, {Hsiao Han} and Davis, {Brigid M.} and Marc Lipsitch and Waldor, {Matthew K.}",

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AU - Abel Zur Wiesch, Pia

AU - Chang, Hsiao Han

AU - Davis, Brigid M.

AU - Lipsitch, Marc

AU - Waldor, Matthew K.

PY - 2015/2/26

Y1 - 2015/2/26

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AB - 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.

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JO - Nature methods

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Sequence tag-based analysis of microbial population dynamics

Abstract

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