Bacteroidales-specific antimicrobial gene analysis identifies gastrointestinal tract reservoirs of microbial sub strains selected for fecal dominance

To gain insight into the dynamics of selection for the dominant fecal microbe strain from the gut ecosystem, we analyzed individual fecal samples from 3 longitudinal metagenomic DNA sequencing data sets for genes encoding Bacteroidales -specific antimicrobial proteins (BSAP) that have functions to restrict species specific replication of Bacteroides uniformis (BSAP-2) or Bacteroides vulgatus (BSAP-3). Individuals had B. vulgatus or B. uniformis sub strains with either complete or deleted BSAP gene patterns that did not change over time, indicating an origin from a stable sub strain reservoir. In most individuals, the BSAP phenotype and gene pattern recovered after single or multiple antibiotics was the same as the pre antibiotic strain. In some individuals, strain change following antibiotics correlated with the presence of the BSAP positive phenotype. Our studies demonstrate the dominant fecal Bacteroides strain contains a defined BSAP phenotype that can influence the selection from the gut ecosystem sub strain reservoir.