Select bacterial genomes from the MET-1 human-derived gut microbial strain consortium

Clostridioides difficile (CD) is the leading cause of antibiotic-associated infectious diarrhea. The development of CD infection (CDI) is tied to perturbations of the bacterial community in the gastrointestinal tract, called the gastrointestinal microbiota (GIM). Repairing the GIM by introducing lab-designed bacterial communities, or defined microbial communities (DMCs), has recently shown promise as novel therapeutics against CDI, such as the use of a 33-member community called MET-1, however, the mechanisms of action of DMCs remain unclear. The goal of this work was to evaluate the ability of smaller consortiums made up of select organisms from MET-1, and their products, to protect against CDI in vitro and in vivo. Detection of specific organisms using Illumina next-generation sequencing guided the isolation and development of refined communities from MET-1, and elucidated keystone strains involved in protecting against disease. This study, for the first time, demonstrates the ability of refined bacterial communities and their products to protect against CDI; offering promising new therapeutic strategies against CDI.