MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses

被引：186

作者：

Bucci, Vanni ^{[1
]}

Tzen, Belinda ^{[2
]}

Li, Ning ^{[2
]}

Simmons, Matt ^{[1
]}

Tanoue, Takeshi ^{[3
]}

Bogart, Elijah ^{[2
]}

Deng, Luxue ^{[2
]}

Yeliseyev, Vladimir ^{[2
]}

Delaney, Mary L. ^{[2
]}

Liu, Qing ^{[2
]}

Olle, Bernat ^{[4
]}

Stein, Richard R. ^{[5
]}

Honda, Kenya ^{[3
]}

Bry, Lynn ^{[2
]}

Gerber, Georg K. ^{[2
]}

机构：

[1] Univ Massachusetts Dartmouth, Dept Biol, Program Biotechnol & Biomed Engn, 285 Old Westport Rd, N Dartmouth, MA 02747 USA

[2] Harvard Univ, Brigham & Womens Hosp, Sch Med, Massachusetts Host Microbiome Ctr,Dept Pathol, 221 Longwood Ave, Boston, MA 02115 USA

[3] RIKEN Ctr Integrat Med Sci IMS, Yokohama, Kanagawa 2300045, Japan

[4] Vedanta Biosc, 501 Boylston St,Suite 6102, Boston, MA 02116 USA

[5] Dana Farber Canc Inst, Dept Biostat & Computat Biol, 450 Brookline Ave, Boston, MA 02215 USA

来源：

GENOME BIOLOGY | 2016年 / 17卷

基金：

美国国家科学基金会;

关键词：

GENE; BIOSYNTHESIS; MENAQUINONE; EXPRESSION; STRAIN; ACID; DIET;

D O I：

10.1186/s13059-016-0980-6

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 [微生物学]; 090105 [作物生产系统与生态工程];

摘要：

Predicting dynamics of host-microbial ecosystems is crucial for the rational design of bacteriotherapies. We present MDSINE, a suite of algorithms for inferring dynamical systems models from microbiome time-series data and predicting temporal behaviors. Using simulated data, we demonstrate that MDSINE significantly outperforms the existing inference method. We then show MDSINE's utility on two new gnotobiotic mice datasets, investigating infection with Clostridium difficile and an immune-modulatory probiotic. Using these datasets, we demonstrate new capabilities, including accurate forecasting of microbial dynamics, prediction of stable sub-communities that inhibit pathogen growth, and identification of bacteria most crucial to community integrity in response to perturbations.

引用

页数：17

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