Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome.

Abstract

The Pioneer 100 Wellness Project involved quantitatively profiling 108 participants' molecular physiology over time, including genomes, gut microbiomes, blood metabolomes, blood proteomes, clinical chemistries, and data from wearable devices. Here, we present a longitudinal analysis focused specifically around the Pioneer 100 gut microbiomes. We distinguished a subpopulation of individuals with reduced gut diversity, elevated relative abundance of the genus <i>Prevotella</i>, and reduced levels of the genus <i>Bacteroides</i> We found that the relative abundances of <i>Bacteroides</i> and <i>Prevotella</i> were significantly correlated with certain serum metabolites, including omega-6 fatty acids. Primary dimensions in distance-based redundancy analysis of clinical chemistries explained 18.5% of the variance in bacterial community composition, and revealed a <i>Bacteroides/Prevotella</i> dichotomy aligned with inflammation and dietary markers. Finally, longitudinal analysis of gut microbiome dynamics within individuals showed that direct transitions between <i>Bacteroides</i>-dominated and <i>Prevotella</i>-dominated communities were rare, suggesting the presence of a barrier between these states. One implication is that interventions seeking to transition between <i>Bacteroides</i>- and <i>Prevotella</i>-dominated communities will need to identify permissible paths through ecological state-space that circumvent this apparent barrier.