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Human salivary amylase gene copy number impacts oral and gut microbiomes

View ORCID ProfileAngela C. Poole, Julia K. Goodrich, Nicholas D. Youngblut, Guillermo G. Luque, Albane Ruaud, Jessica L. Sutter, Jillian L. Waters, Qiaojuan Shi, Mohamed El-Hadidi, Lynn M. Johnson, Haim Y. Bar, Daniel H. Huson, James G. Booth, Ruth E. Ley
doi: https://doi.org/10.1101/359737
Angela C. Poole
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
2Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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  • ORCID record for Angela C. Poole
Julia K. Goodrich
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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Nicholas D. Youngblut
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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Guillermo G. Luque
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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Albane Ruaud
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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Jessica L. Sutter
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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Jillian L. Waters
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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Qiaojuan Shi
2Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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Mohamed El-Hadidi
3Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany.
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Lynn M. Johnson
4Cornell Statistical Consulting Unit, Cornell University, Ithaca, NY 14853, USA.
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Haim Y. Bar
5Department of Statistics, University of Connecticut, Storrs, CT 06269, USA.
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Daniel H. Huson
3Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany.
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James G. Booth
6Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA.
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Ruth E. Ley
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
2Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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  • For correspondence: rley@tuebingen.mpg.de
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Summary

Host genetic variation influences the composition of the human microbiome. While studies have focused on associations between the microbiome and single nucleotide polymorphisms in genes, their copy number (CN) can also vary. Here, in a study of human subjects including a 2-week standard diet, we relate oral and gut microbiome to CN at the AMY1 locus, which encodes the gene for salivary amylase, active in starch degradation. We show that although diet standardization drove gut microbiome convergence, AMY1-CN influenced oral and gut microbiome composition and function. The gut microbiomes of low-AMY1-CN subjects had an enhanced capacity for breakdown of complex carbohydrates. Those of high-AMY1 subjects were enriched in microbiota linked to resistant starch fermentation, had higher fecal SCFAs, and drove higher adiposity when transferred to germfree mice. Gut microbiota results were validated in a larger separate population. This study establishes AMY1-CN as a genetic factor patterning microbiome composition and function.

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Posted June 30, 2018.
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Human salivary amylase gene copy number impacts oral and gut microbiomes
Angela C. Poole, Julia K. Goodrich, Nicholas D. Youngblut, Guillermo G. Luque, Albane Ruaud, Jessica L. Sutter, Jillian L. Waters, Qiaojuan Shi, Mohamed El-Hadidi, Lynn M. Johnson, Haim Y. Bar, Daniel H. Huson, James G. Booth, Ruth E. Ley
bioRxiv 359737; doi: https://doi.org/10.1101/359737
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Human salivary amylase gene copy number impacts oral and gut microbiomes
Angela C. Poole, Julia K. Goodrich, Nicholas D. Youngblut, Guillermo G. Luque, Albane Ruaud, Jessica L. Sutter, Jillian L. Waters, Qiaojuan Shi, Mohamed El-Hadidi, Lynn M. Johnson, Haim Y. Bar, Daniel H. Huson, James G. Booth, Ruth E. Ley
bioRxiv 359737; doi: https://doi.org/10.1101/359737

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