基于序列标签的微生物种群动态分析。

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

1] Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA. [2] Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.

1] Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA. [2] Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA.

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.

我们描述了基于序列标签的微生物群体分析（STAMP），用于表征感染过程中病原体群体动态。STAMP分析基因“条形码”化生物体的频率变化，以量化群体瓶颈并推断初始群体大小。对肠道内霍乱弧菌的分析揭示了感染阶段和区域特异性的宿主感染屏障，并显示出霍乱弧菌有与肠液流动方向相反的意外迁移。STAMP为体内微生物传播的高可信度表征提供了一个强大的、广泛适用的分析框架。