MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses.
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.
Department of Biology, Program in Biotechnology and Biomedical Engineering, University of Massachusetts Dartmouth, 285 Old Westport Road, N. Dartmouth, MA, 02747, USA. vanni.bucci@umassd.edu.
Vanni
V
Bucci
Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA.
Belinda
B
Tzen
Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA.
Ning
N
Li
Department of Biology, Program in Biotechnology and Biomedical Engineering, University of Massachusetts Dartmouth, 285 Old Westport Road, N. Dartmouth, MA, 02747, USA.
Matt
M
Simmons
RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan.
Takeshi
T
Tanoue
Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA.
Elijah
E
Bogart
Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA.
Luxue
L
Deng
Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA.
Vladimir
V
Yeliseyev
Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA.
Mary L
ML
Delaney
Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA.
Qing
Q
Liu
Vedanta Biosciences, 501 Boylston Street, Suite 6102, Boston, MA, 02116, USA.
Bernat
B
Olle
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
Richard R
RR
Stein
RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan.
Kenya
K
Honda
Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA.
Lynn
L
Bry
Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA. ggerber@bwh.harvard.edu.
Georg K
GK
Gerber
D000465:Algorithms; D000818:Animals; D016360:Clostridioides difficile / Q000235:genetics* / Q000254:growth & development / Q000472:pathogenicity; D054884:Host-Pathogen Interactions / Q000235:genetics*; D051379:Mice; D064307:Microbiota / Q000235:genetics*; D008962:Models, Theoretical