Statistical design of a synthetic microbiome that suppresses diverse gut pathogens.

ABSTRACT: Engineering functional microbiomes is challenging due to complex interactions between bacteria and their environments^1-6. Using a set of 848 gut commensal strains and clearance of multi-drug resistant Klebsiella pneumoniae (Kp-MH258) as a target function, we engineered a functional 15-member synthetic microbiome-SynCom15-through a statistical approach agnostic to strain phenotype, mechanism of action, bacterial interactions, or composition of natural microbiomes. Our approach involved designing, building, and testing 96 metagenomically diverse consortia, learning a generative model using community strain presence/absence as input, and distilling model constraints through statistical inference. SynCom15 cleared Kp-MH258 across in vitro, ex vivo,

SUBMITTER: Oliveira RA 

PROVIDER: S-EPMC12773023 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature