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
| Description | Quantity | Units | HDDC | Internal | Academic | Commercial |
|---|---|---|---|---|---|---|
| Project Set Up | 1 | each | 175.63 | 295.95 | 426.17 | 564.68 |
| Germ Free C57BL/6 Mice 8-10 weeks Old | 10 | each | 76.69 | 129.23 | 186.10 | 246.58 |
| BL2 Isolator Setup | 1 | each | 671.48 | 1,131.53 | 1,629.41 | 2,158.96 |
| BL2 Monthly Isolator Rent | 1 | each | 163.68 | 275.83 | 397.19 | 526.28 |
| Cage entry | 10 | per cage | 12.92 | 21.77 | 31.34 | 41.53 |
| Stool collection | 520 | each | 3.45 | 5.82 | 8.38 | 11.10 |
| 16s rRNA Sequencing | 260 | per genome | 15.35 | 25.87 | 37.25 | 49.36 |
| Microbiology - Anerobic Culture | 10 | each | 71.22 | 120.02 | 172.83 | 229.00 |
| Microbiology - Aerobic Culture | 10 | each | 32.60 | 54.94 | 79.11 | 104.82 |
| Monthly Sample Storage | 520 | each | 0.06 | 0.10 | 0.14 | 0.19 |
| Total Project Cost** | 8,761.29 | 14,767.51 | 21,261.97 | 28,173.62 |
**Approximate cumulative costs reflected over a two year study period