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Temporal variability and stability of the fecal microbiome: the Multiethnic Cohort Study.
Cancer Epidemiology, Biomarkers & Prevention 2018 September 12
BACKGROUND: Measurement reliability and biological stability need to be considered when developing sampling protocols for population-based fecal microbiome studies.
METHODS: Stool samples were collected biannually over a two-year period and sequenced for the V1-V3 region of the 16S rRNA gene in 50 participants from the Multiethnic Cohort Study. We evaluated the temporal stability of the fecal microbiome on a community level with permutational multivariate analysis of variance (PERMANOVA), as well as on taxa and diversity measures with intraclass correlation coefficients.
RESULTS: Inter-individual differences were the predominant source of fecal microbiome variation, and variation within individual was driven more by changing abundances than the complete loss or introduction of taxa. Phyla and diversity measures were reliable over the two years. Most genera were stable over time, although those with low abundances tended to be more dynamic. Reliability was lower among participants who used antibiotics, with the greatest difference seen in samples taken within one month of reported use.
CONCLUSIONS: The fecal microbiome as a whole is stable over a two-year period, although certain taxa may exhibit more temporal variability.
IMPACT: When designing large epidemiologic studies, a single sample is sufficient to capture the majority of the variation in the fecal microbiome from 16S rRNA gene sequencing, while multiple samples may be needed for rare or less abundant taxa.
METHODS: Stool samples were collected biannually over a two-year period and sequenced for the V1-V3 region of the 16S rRNA gene in 50 participants from the Multiethnic Cohort Study. We evaluated the temporal stability of the fecal microbiome on a community level with permutational multivariate analysis of variance (PERMANOVA), as well as on taxa and diversity measures with intraclass correlation coefficients.
RESULTS: Inter-individual differences were the predominant source of fecal microbiome variation, and variation within individual was driven more by changing abundances than the complete loss or introduction of taxa. Phyla and diversity measures were reliable over the two years. Most genera were stable over time, although those with low abundances tended to be more dynamic. Reliability was lower among participants who used antibiotics, with the greatest difference seen in samples taken within one month of reported use.
CONCLUSIONS: The fecal microbiome as a whole is stable over a two-year period, although certain taxa may exhibit more temporal variability.
IMPACT: When designing large epidemiologic studies, a single sample is sufficient to capture the majority of the variation in the fecal microbiome from 16S rRNA gene sequencing, while multiple samples may be needed for rare or less abundant taxa.
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