Fig. 9: Personalized probiotic cocktails effectively decolonize C. difficile.
From: An ecological framework to understand the efficacy of fecal microbiota transplantation
a An ecological network involving the GnotoComplex microflora (a mixture of human commensal bacterial type strains) and C. difficile was inferred from mouse data65. Node C represents C. difficile. The edge width and node size indicate the interspecies interaction strength and the intrinsic growth rate, respectively. Red (or blue) edges indicate the direct promotion (or inhibition), respectively. b A disrupted microbiota due to a hypothetic antibiotic administration. c The restored microbiota due to the administration of a particular probiotic cocktail Rglobal. d The trajectory of C. difficile abundance over three different time windows: (1) the initial healthy microbiota, (2) the disrupted microbiota, and (3) the microbiota post probiotic administration. In the third time window, we compare the performance of various probiotic cocktails in terms of their ability to decolonize C. difficile. Those cocktails were designed by considering direct inhibitors only (Rd), the global ecological network (Rglobal), the n-step ego-networks of C. difficile with n = 1, 2, 3 (Rego-1, Rego-2, and Rego-3), and randomly chosen subsets of Rglobal (R1, R2, and R3). Rnear-optimal is obtained by excluding species-12 (i.e., K. oxytoca, which is an opportunistic pathogen) from Rglobal. Note that Rego-1 is not necessarily always the same as Rd because Rego-1 needs to consider the net impact among neighbors of the focal species. e–g We start from the same initial microbiota as shown in panel (a). But another hypothetic antibiotic administration can lead to a different disrupted microbiota (f), which can be restored through probiotic administration (g). h Performance of different probiotic cocktails in decolonizing C. difficile vary.
