The human intestinal tract is host to an extensive population of microorganisms working in concert to play a pivotal role in human health. Almost every aspect of modern lifestyles can impact the gut microbiota; recently diet and fitness have been established as important modulators. Previously, we observed that elite athletes have significantly increased gut microbial diversity compared to non-athlete controls. Functional metagenomic analysis revealed this elevated diversity translated into the athletes’ microbiome being primed for energy harvest as well as muscle and tissue repair. However, a subsequent 8-week exercise intervention study failed to reproduce the same high microbial diversity. This lead us to hypothesize that it’s physical fitness, not exercise, that is pivotal to increased microbial diversity. We propose to mine datasets to identify “fitness” associated microbes and metabolites and investigate their implications for human health.