MDSINE: Microbial Dynamical Systems INference Engine

Figure 1. Application of MDSINE to experimental dataset

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.

Publication:

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

Bucci V, Tzen B, Li N, Simmons M, Tanoue T, Bogart E, Deng L, Yeliseyev V, Delaney ML, Liu Q, Olle B, Stein RR, Honda K, Bry L, Gerber GK. MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses. Genome Biol. 2016; 17(1):121. PMID: 27259475.

Services Provided: 

The MHMC provided microbiologic preparation of consortia to inoculate germ free mice. MHMC technical staff inoculated the germ-free mice and fecal pellets were collected at numerous time points and stored. The MHMC performed molecular analysis for bacterial identification through 16S rRNA sequencing.

MDSINE Project Services and Costs

DescriptionQuantityUnitsHDDCInternalAcademicCommercial
Total Project Cost**8,761.2914,767.5121,261.9728,173.62
Project Set Up1each175.63295.95426.17564.68
Germ Free C57BL/6 Mice 8-10 weeks Old10each76.69129.23 186.10 246.58
BL2 Isolator Setup1each 671.481,131.531,629.412,158.96
BL2 Monthly Isolator Rent1each163.68 275.83397.19526.28
Cage entry10per cage12.9221.7731.3441.53
Stool collection 520each3.455.828.3811.10
16s rRNA Sequencing260per genome15.3525.8737.2549.36
Microbiology - Anerobic Culture10each71.22 120.02172.83 229.00
Microbiology - Aerobic Culture10each 32.6054.9479.11104.82
Monthly Sample Storage520each0.060.10 0.14 0.19
*FY 2018 Fee Schedule
**Approximate cumulative costs reflected over a two year study period