Abstract
The human gut microbiome undergoes dynamic changes over time that can be linked to environmental exposures and host physiological status. We followed up 338 individuals after four years and quantified the temporal changes in the microbiome at both compositional and genetic level. We observe that gut microbial communities with higher baseline diversity are more stable over time, and genetic makeup is more stable than microbial composition. By combining the compositional and genetic makeup of microbes, we can uniquely distinguish metagenomic samples from the same individuals with 85% accuracy. We further report 100 associations between microbial and phenotypic changes over time, 73 of them involving temporal changes in microbial structural variations. Our results also raises concerns about a significant increase in antibiotic resistance genes, which is associated with meat consumption. These results enhance our view of the genetic stability and dynamics of the gut microbiome and its relevance in human health.
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