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Interspecies variation in hominid gut microbiota controls host gene regulation

Amanda L. Muehlbauer, Allison L. Richards, Adnan Alazizi, Michael Burns, Andres Gomez, Jonathan B. Clayton, Klara Petrzelkova, Camilla Cascardo, Justyna Resztak, Xiaoquan Wen, View ORCID ProfileRoger Pique-Regi, View ORCID ProfileFrancesca Luca, View ORCID ProfileRan Blekhman
doi: https://doi.org/10.1101/2020.08.17.255059
Amanda L. Muehlbauer
1Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
2Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, Minnesota, USA
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Allison L. Richards
3Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
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Adnan Alazizi
3Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
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Michael Burns
4Department of Biology, Loyola University, Chicago, Illinois, 60660, USA
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Andres Gomez
5Department of Animal Science, University of Minnesota, Saint Paul, Minnesota, USA
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Jonathan B. Clayton
6Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
7Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Klara Petrzelkova
8The Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic
9Liberec Zoo, Liberec, Czech Republic
10The Czech Academy of Sciences, Institute of Parasitology, Ceske Budejovice, Czech Republic
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Camilla Cascardo
3Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
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Justyna Resztak
3Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
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Xiaoquan Wen
11Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
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Roger Pique-Regi
3Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
12Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
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  • ORCID record for Roger Pique-Regi
Francesca Luca
3Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
12Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
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  • For correspondence: blekhman@umn.edu fluca@wayne.edu
Ran Blekhman
1Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
2Department of Ecology, Evolution and Behavior, University of Minnesota, Minneapolis, Minnesota, USA
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  • ORCID record for Ran Blekhman
  • For correspondence: blekhman@umn.edu fluca@wayne.edu
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Abstract

The gut microbiome exhibits extreme compositional variation between hominid hosts. However, it is unclear how this variation impacts host physiology, and whether this effect can be mediated through microbial regulation of host gene expression in interacting epithelial cells. Here, we characterized the transcriptional response of colonic epithelial cells in vitro to live microbial communities extracted from humans, chimpanzees, gorillas, and orangutans. We found most host genes exhibit a conserved response, whereby they respond similarly to the four hominid microbiomes, while some genes respond only to microbiomes from specific host species. Genes that exhibit such a divergent response are associated with relevant intestinal diseases in humans, such as inflammatory bowel disease and Crohn’s disease. Lastly, we found that inflammation-associated microbial species regulate the expression of host genes previously associated with inflammatory bowel disease, suggesting health-related consequences for species-specific host-microbiome interactions across hominids.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 17, 2020.
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Interspecies variation in hominid gut microbiota controls host gene regulation
Amanda L. Muehlbauer, Allison L. Richards, Adnan Alazizi, Michael Burns, Andres Gomez, Jonathan B. Clayton, Klara Petrzelkova, Camilla Cascardo, Justyna Resztak, Xiaoquan Wen, Roger Pique-Regi, Francesca Luca, Ran Blekhman
bioRxiv 2020.08.17.255059; doi: https://doi.org/10.1101/2020.08.17.255059
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Interspecies variation in hominid gut microbiota controls host gene regulation
Amanda L. Muehlbauer, Allison L. Richards, Adnan Alazizi, Michael Burns, Andres Gomez, Jonathan B. Clayton, Klara Petrzelkova, Camilla Cascardo, Justyna Resztak, Xiaoquan Wen, Roger Pique-Regi, Francesca Luca, Ran Blekhman
bioRxiv 2020.08.17.255059; doi: https://doi.org/10.1101/2020.08.17.255059

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