Stability and Variability of the Human Fecal Microbiome Over Two Years in the Multiethnic Cohort Study: A Metagenomic Analysis.

Abstract

Background: Understanding the longitudinal variability of the gut microbiome is essential for advancing microbiome-based measurements and designing robust sampling protocols in observational and intervention studies of cancer and other health outcomes. The aim of this study was to explore the temporal variability and stability of the fecal microbiome over a 2-year period, using intraclass correlation (ICC) analysis of metagenomic sequencing data.

Methods: We studied 25 older adults from the Multiethnic Cohort Adiposity Phenotype Study (MEC-APS, 2013-2016). Stool samples were collected every six months over a two-year period (5 samples) and analyzed using metagenomic sequencing. The temporal stability was evaluated using ICCs across taxonomic levels, diversity, and functional genes and pathways.

Results: The microbial community showed stability in alpha diversity and overall structure, with no significant changes across time points (Shannon diversity, p = 0.95). Taxonomic composition showed strong reliability over time, with median ICCs of 0.7 at the genus level and 0.75 at species level. Functional genes also demonstrated good stability (median ICC = 0.68). However, microbial pathways were more variable, with a fair median ICC of 0.49.

Conclusion: While the fecal microbiome was generally stable, some taxa and functions were more dynamic and responsive to external influences.

Impact: Findings highlight the need for reliable microbiome measurements and sampling strategies to reduce bias in studies of the microbiome and cancer.