Longitudinal Stability and Composition of the Adult Gut Microbiome
The longitudinal stability and composition of the gut microbiome is relatively unknown beyond a period of days or months. Existing studies exploring compositional changes have focused on infants, young children, or on very small sample sizes of adults. Longer term stability of the adult gut microbiome is poorly characterized. In this study, we compare sequencing data that was collected from a subset of healthy adults who participated in two studies that were separated by 16 months. In the first study, participants collected 17 daily consecutive microbiome samples. In the second study, participants collected nine total samples in sets of 3 consecutive samples over an average collection period of 45 days. Fecal samples from both studies were sequenced with shotgun metagenomic sequencing and raw reads were reprocessed using identical methods for this study. We show that despite the time between the two studies, individuals cluster tightly with themselves. Stability was more variable than composition over time across individuals. These findings help to inform the planning of future longitudinal studies by demonstrating that while compositional changes are relatively small over time, stability may be more variable.