STAMP: Sequence tag-based analysis of microbial population dynamics

We 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 rev...

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Detalles Bibliográficos
Autores principales: Abel, Sören, zur Wiesch, Pia Abel, Chang, Hsiao-Han, Davis, Brigid M., Lipsitch, Marc, Waldor, Matthew K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2015
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344388/
https://www.ncbi.nlm.nih.gov/pubmed/25599549
http://dx.doi.org/10.1038/nmeth.3253
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author Abel, Sören
zur Wiesch, Pia Abel
Chang, Hsiao-Han
Davis, Brigid M.
Lipsitch, Marc
Waldor, Matthew K.
author_facet Abel, Sören
zur Wiesch, Pia Abel
Chang, Hsiao-Han
Davis, Brigid M.
Lipsitch, Marc
Waldor, Matthew K.
author_sort Abel, Sören
collection PubMed
description We 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.
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spelling pubmed-43443882015-09-01 STAMP: Sequence tag-based analysis of microbial population dynamics Abel, Sören zur Wiesch, Pia Abel Chang, Hsiao-Han Davis, Brigid M. Lipsitch, Marc Waldor, Matthew K. Nat Methods Article We 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. 2015-01-19 2015-03 /pmc/articles/PMC4344388/ /pubmed/25599549 http://dx.doi.org/10.1038/nmeth.3253 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Abel, Sören
zur Wiesch, Pia Abel
Chang, Hsiao-Han
Davis, Brigid M.
Lipsitch, Marc
Waldor, Matthew K.
STAMP: Sequence tag-based analysis of microbial population dynamics
title STAMP: Sequence tag-based analysis of microbial population dynamics
title_full STAMP: Sequence tag-based analysis of microbial population dynamics
title_fullStr STAMP: Sequence tag-based analysis of microbial population dynamics
title_full_unstemmed STAMP: Sequence tag-based analysis of microbial population dynamics
title_short STAMP: Sequence tag-based analysis of microbial population dynamics
title_sort stamp: sequence tag-based analysis of microbial population dynamics
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344388/
https://www.ncbi.nlm.nih.gov/pubmed/25599549
http://dx.doi.org/10.1038/nmeth.3253
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