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

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 Prevotella , and reduced levels of the genus Bacteroides . We found that the relative abundances of Bacteroides and Prevotella were significantly correlated with certain serum metabolites, including omega -6 fatty acids. Primary dimensions in distance -based redun- dancy analysis of clinical chemistries explained 18.5% of the variance in bacterial community composition, and revealed a Bacteroides/ Prevotella dichotomy aligned with inflammation and dietary markers. Finally, longitudinal analysis of gut microbiome dynamics within individuals showed that direct transitions between Bacteroides - dominated and Prevotella -dominated communities were rare, sug- gesting the presence of a barrier between these states. One implication is that interventions seeking to transition between Bacteroides - and Prevotella -dominated communities will need to identify permissible paths through ecological state -space that circumvent this apparent barrier.