Computer-guided design of optimal microbial consortia for immune system modulation

• DOI: 10.7554/elife.30916
• Publication Date: 2018-04-17T00:00:16Z
• Authors: Richard R Stein; Takeshi Tanoue; Rose L Szabady; Shakti K Bhattarai; Bernat Olle; Jason M Norman; Wataru Suda; Kenshiro Oshima; Masahira Hattori; Georg K Gerber; Chris Sander; Kenya Honda; Vanni Bucci
• Keywords: Clostridia

Manipulation of the gut microbiota holds great promise for treatment diseases. However, a major challenge is identification therapeutically potent microbial consortia that colonize host effectively while maximizing immunologic outcome. Here, we propose novel workflow to select optimal immune-inducing from microbiome compositicon and immune effectors measurements. Using published newly generated regulatory T-cell (Treg) data germ-free mice, estimate contributions twelve Clostridia strains with known immune-modulating effect Treg induction. Combining this longitudinal data-constrained ecological model, predict ability every attainable ecologically stable subconsortium in promoting activation rank them by Induction Score (TrIS). Experimental validation selected indicates strong statistically significant correlation between predicted TrIS measured Treg. We argue computational indexes, such as TrIS, are valuable tools systematic selection bacteriotherapeutics.