A microbe associated with sleep revealed by a novel systems genetic analysis of the microbiome in collaborative cross mice

Jason A. Bubier; Vivek M. Philip; Christopher Quince; James Campbell; Yanjiao Zhou; Tatiana Vishnivetskaya; Suman Duvvuru; Rachel Hageman Blair; Juliet Ndukum; Kevin D. Donohue; Carmen M. Foster; David J. Mellert; George Weinstock; Cymbeline T. Culiat; Bruce F. O'Hara; Anthony V. Palumbo; Mircea Podar; Elissa J. Chesler

doi:10.1534/genetics.119.303013

A microbe associated with sleep revealed by a novel systems genetic analysis of the microbiome in collaborative cross mice

Jason A. Bubier, Vivek M. Philip, Christopher Quince, James Campbell, Yanjiao Zhou, Tatiana Vishnivetskaya, Suman Duvvuru, Rachel Hageman Blair, Juliet Ndukum, Kevin D. Donohue, Carmen M. Foster, David J. Mellert, George Weinstock, Cymbeline T. Culiat, Bruce F. O'Hara, Anthony V. Palumbo, Mircea Podar, Elissa J. Chesler

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Abstract

The microbiome influences health and disease through complex networks of host genetics, genomics, microbes, and environment. Identifying the mechanisms of these interactions has remained challenging. Systems genetics in laboratory mice (Mus musculus) enables data-driven discovery of biological network components and mechanisms of host-microbial interactions underlying disease phenotypes. To examine the interplay among the whole host genome, transcriptome, and microbiome, we mapped QTL and correlated the abundance of cecal messenger RNA, luminal microflora, physiology, and behavior in a highly diverse Collaborative Cross breeding population. One such relationship, regulated by a variant on chromosome 7, was the association of Odoribacter (Bacteroidales) abundance and sleep phenotypes. In a test of this association in the BKS.Cg-Dock7m +/+ Lepr^db/J mouse model of obesity and diabetes, known to have abnormal sleep and colonization by Odoribacter, treatment with antibiotics altered sleep in a genotype-dependent fashion. The many other relationships extracted from this study can be used to interrogate other diseases, microbes, and mechanisms.

Original language	English
Pages (from-to)	719-733
Number of pages	15
Journal	Genetics
Volume	214
Issue number	3
DOIs	https://doi.org/10.1534/genetics.119.303013
State	Published - 2020

Bibliographical note

Funding Information:
David Durtschi, Gene Barker, and Ann Wymore performed genotyping and gene expression analysis for all samples. Darla Miller worked with the Collaborative Cross at Oak Ridge National Laboratory (ORNL). Matthew Vincent produced the “deSNPed” version of the Illumina probes for the Collaborative Cross founder strains. Jennifer Ryan, Neil Cole, Christine Rosales, Laura Anderson, and Samantha Burrill conducted db sleep studies and dissections. This research was sponsored by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the U. S. Department of Energy, under contract DE-AC05-00OR22725. J.A.B. was funded by National Institute on Drug Abuse grant U01 DA-043809.

Publisher Copyright:
Copyright © 2020 Bubier et al.

Keywords

Behavior
Bioinformatics
Genetics
Genomics
Sleep

ASJC Scopus subject areas

Genetics

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1534/genetics.119.303013

Cite this

Bubier, J. A., Philip, V. M., Quince, C., Campbell, J., Zhou, Y., Vishnivetskaya, T., Duvvuru, S., Blair, R. H., Ndukum, J., Donohue, K. D., Foster, C. M., Mellert, D. J., Weinstock, G., Culiat, C. T., O'Hara, B. F., Palumbo, A. V., Podar, M., & Chesler, E. J. (2020). A microbe associated with sleep revealed by a novel systems genetic analysis of the microbiome in collaborative cross mice. Genetics, 214(3), 719-733. https://doi.org/10.1534/genetics.119.303013

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abstract = "The microbiome influences health and disease through complex networks of host genetics, genomics, microbes, and environment. Identifying the mechanisms of these interactions has remained challenging. Systems genetics in laboratory mice (Mus musculus) enables data-driven discovery of biological network components and mechanisms of host-microbial interactions underlying disease phenotypes. To examine the interplay among the whole host genome, transcriptome, and microbiome, we mapped QTL and correlated the abundance of cecal messenger RNA, luminal microflora, physiology, and behavior in a highly diverse Collaborative Cross breeding population. One such relationship, regulated by a variant on chromosome 7, was the association of Odoribacter (Bacteroidales) abundance and sleep phenotypes. In a test of this association in the BKS.Cg-Dock7m +/+ Leprdb/J mouse model of obesity and diabetes, known to have abnormal sleep and colonization by Odoribacter, treatment with antibiotics altered sleep in a genotype-dependent fashion. The many other relationships extracted from this study can be used to interrogate other diseases, microbes, and mechanisms.",

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author = "Bubier, {Jason A.} and Philip, {Vivek M.} and Christopher Quince and James Campbell and Yanjiao Zhou and Tatiana Vishnivetskaya and Suman Duvvuru and Blair, {Rachel Hageman} and Juliet Ndukum and Donohue, {Kevin D.} and Foster, {Carmen M.} and Mellert, {David J.} and George Weinstock and Culiat, {Cymbeline T.} and O'Hara, {Bruce F.} and Palumbo, {Anthony V.} and Mircea Podar and Chesler, {Elissa J.}",

note = "Funding Information: David Durtschi, Gene Barker, and Ann Wymore performed genotyping and gene expression analysis for all samples. Darla Miller worked with the Collaborative Cross at Oak Ridge National Laboratory (ORNL). Matthew Vincent produced the “deSNPed” version of the Illumina probes for the Collaborative Cross founder strains. Jennifer Ryan, Neil Cole, Christine Rosales, Laura Anderson, and Samantha Burrill conducted db sleep studies and dissections. This research was sponsored by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the U. S. Department of Energy, under contract DE-AC05-00OR22725. J.A.B. was funded by National Institute on Drug Abuse grant U01 DA-043809. Publisher Copyright: Copyright {\textcopyright} 2020 Bubier et al.",

year = "2020",

doi = "10.1534/genetics.119.303013",

language = "English",

volume = "214",

pages = "719--733",

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Bubier, JA, Philip, VM, Quince, C, Campbell, J, Zhou, Y, Vishnivetskaya, T, Duvvuru, S, Blair, RH, Ndukum, J, Donohue, KD, Foster, CM, Mellert, DJ, Weinstock, G, Culiat, CT, O'Hara, BF, Palumbo, AV, Podar, M & Chesler, EJ 2020, 'A microbe associated with sleep revealed by a novel systems genetic analysis of the microbiome in collaborative cross mice', Genetics, vol. 214, no. 3, pp. 719-733. https://doi.org/10.1534/genetics.119.303013

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AU - Philip, Vivek M.

AU - Quince, Christopher

AU - Campbell, James

AU - Zhou, Yanjiao

AU - Vishnivetskaya, Tatiana

AU - Duvvuru, Suman

AU - Blair, Rachel Hageman

AU - Ndukum, Juliet

AU - Donohue, Kevin D.

AU - Foster, Carmen M.

AU - Mellert, David J.

AU - Weinstock, George

AU - Culiat, Cymbeline T.

AU - O'Hara, Bruce F.

AU - Palumbo, Anthony V.

AU - Podar, Mircea

AU - Chesler, Elissa J.

N1 - Funding Information: David Durtschi, Gene Barker, and Ann Wymore performed genotyping and gene expression analysis for all samples. Darla Miller worked with the Collaborative Cross at Oak Ridge National Laboratory (ORNL). Matthew Vincent produced the “deSNPed” version of the Illumina probes for the Collaborative Cross founder strains. Jennifer Ryan, Neil Cole, Christine Rosales, Laura Anderson, and Samantha Burrill conducted db sleep studies and dissections. This research was sponsored by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the U. S. Department of Energy, under contract DE-AC05-00OR22725. J.A.B. was funded by National Institute on Drug Abuse grant U01 DA-043809. Publisher Copyright: Copyright © 2020 Bubier et al.

PY - 2020

Y1 - 2020

N2 - The microbiome influences health and disease through complex networks of host genetics, genomics, microbes, and environment. Identifying the mechanisms of these interactions has remained challenging. Systems genetics in laboratory mice (Mus musculus) enables data-driven discovery of biological network components and mechanisms of host-microbial interactions underlying disease phenotypes. To examine the interplay among the whole host genome, transcriptome, and microbiome, we mapped QTL and correlated the abundance of cecal messenger RNA, luminal microflora, physiology, and behavior in a highly diverse Collaborative Cross breeding population. One such relationship, regulated by a variant on chromosome 7, was the association of Odoribacter (Bacteroidales) abundance and sleep phenotypes. In a test of this association in the BKS.Cg-Dock7m +/+ Leprdb/J mouse model of obesity and diabetes, known to have abnormal sleep and colonization by Odoribacter, treatment with antibiotics altered sleep in a genotype-dependent fashion. The many other relationships extracted from this study can be used to interrogate other diseases, microbes, and mechanisms.

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KW - Bioinformatics

KW - Genetics

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A microbe associated with sleep revealed by a novel systems genetic analysis of the microbiome in collaborative cross mice

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

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