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Cell Host Microbe. 2019 Apr 10;25(4):553-564.e7. doi: 10.1016/j.chom.2019.03.001.

Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes.

Author information

1
Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
2
Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
3
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
4
Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany.
5
Cornell Statistical Consulting Unit, Cornell University, Ithaca, NY 14853, USA.
6
Department of Statistics, University of Connecticut, Storrs, CT 06269, USA.
7
Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
8
Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA. Electronic address: rley@tuebingen.mpg.de.

Abstract

Host genetic variation influences microbiome composition. While studies have focused on associations between the gut microbiome and specific alleles, gene copy number (CN) also varies. We relate microbiome diversity to CN variation of the AMY1 locus, which encodes salivary amylase, 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 gut microbiome 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 salivary Porphyromonas; 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.

KEYWORDS:

AMY1; CNV; copy number variant; gene copy number; gut; intervention; longitudinal; microbiome; microbiota; saliva; salivary amylase

PMID:
30974084
DOI:
10.1016/j.chom.2019.03.001

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