MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses
View/ Open
Author
Bucci, Vanni
Tzen, Belinda
Simmons, Matt
Tanoue, Takeshi
Deng, Luxue
Yeliseyev, Vladimir
Liu, Qing
Olle, Bernat
Stein, Richard R.
Honda, Kenya
Note: Order does not necessarily reflect citation order of authors.
Published Version
https://doi.org/10.1186/s13059-016-0980-6Metadata
Show full item recordCitation
Bucci, V., B. Tzen, N. Li, M. Simmons, T. Tanoue, E. Bogart, L. Deng, et al. 2016. “MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses.” Genome Biology 17 (1): 121. doi:10.1186/s13059-016-0980-6. http://dx.doi.org/10.1186/s13059-016-0980-6.Abstract
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. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0980-6) contains supplementary material, which is available to authorized users.Other Sources
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893271/pdf/Terms of Use
This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAACitable link to this page
http://nrs.harvard.edu/urn-3:HUL.InstRepos:27662168
Collections
- HMS Scholarly Articles [17928]
Contact administrator regarding this item (to report mistakes or request changes)