Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes
Poole AC, Goodrich JK, Youngblut ND, Luque GG, Ruaud A, Sutter JL, Waters JL, Shi Q, El-Hadidi M, Johnson LM, Bar HY, Huson DH, Booth JG, Ley RE (2019) Cell Host Microbe. 2019 Apr;25(4): 553-564.e7. doi: 10.1016/j.chom.2019.03.001
Host genetic variation influences microbiome composition. While studies have focused on associations between the gut microbiome and specific alleles, genecopynumber (CN) also varies. We relate microbiome diversity to CN variation of the AMY1 locus, which encodes salivaryamylase, facilitating starch digestion.
After imputing AMY1-CN for ∼1,000 subjects, we identified taxa differentiating fecal microbiomes of high and low AMY1-CN hosts. In a month-long diet intervention study, we show that diet standardization drove gutmicrobiome convergence, and AMY1-CN correlated with oral and gut microbiome composition and function. The microbiomes of low-AMY1-CN subjects had enhanced capacity to break down complex carbohydrates. High-AMY1-CN subjects had higher levels of salivaryPorphyromonas; their gut microbiota had increased abundance of resistant starch-degrading microbes, produced higher levels of short-chain fatty acids, and drove higher adiposity when transferred to germ-free mice.
This study establishes AMY1-CN as a genetic factor associated with microbiome composition and function.
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