Host genetic and environmental effects on mouse intestinal microbiota View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-06-14

AUTHORS

James H Campbell, Carmen M Foster, Tatiana Vishnivetskaya, Alisha G Campbell, Zamin K Yang, Ann Wymore, Anthony V Palumbo, Elissa J Chesler, Mircea Podar

ABSTRACT

The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strain-specific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel. More... »

PAGES

2033-2044

References to SciGraph publications

  • 2009-08-27. Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2010-12-23. Genotype Is a Stronger Determinant than Sex of the Mouse Gut Microbiota in MICROBIAL ECOLOGY
  • 2004-11. The Collaborative Cross, a community resource for the genetic analysis of complex traits in NATURE GENETICS
  • 2011-03-16. Unravelling the effects of the environment and host genotype on the gut microbiome in NATURE REVIEWS MICROBIOLOGY
  • 2008-10. Symbiotic diversity in marine animals: the art of harnessing chemosynthesis in NATURE REVIEWS MICROBIOLOGY
  • 2007-07. The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics in MAMMALIAN GENOME
  • 2008-10. Worlds within worlds: evolution of the vertebrate gut microbiota in NATURE REVIEWS MICROBIOLOGY
  • 2011-12-15. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2009-08-20. Polymerase chain reaction primers miss half of rRNA microbial diversity in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2008-11-30. A core gut microbiome in obese and lean twins in NATURE
  • 2007-10-17. An ecological and evolutionary perspective on human–microbe mutualism and disease in NATURE
  • 2010-08-05. Dominant and diet-responsive groups of bacteria within the human colonic microbiota in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2010-08-18. Characterization of Housing-Related Spontaneous Variations of Gut Microbiota and Expression of Toll-Like Receptors 2 and 4 in Rats in MICROBIAL ECOLOGY
  • 2008-06. The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics in MAMMALIAN GENOME
  • 2010-11-29. Microbiota restoration: natural and supplemented recovery of human microbial communities in NATURE REVIEWS MICROBIOLOGY
  • 2010-01-21. Experimental factors affecting PCR-based estimates of microbial species richness and evenness in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2006-11-07. Quantitative PCR assays for mouse enteric flora reveal strain-dependent differences in composition that are influenced by the microenvironment in MAMMALIAN GENOME
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ismej.2012.54

    DOI

    http://dx.doi.org/10.1038/ismej.2012.54

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/22695862


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    35 schema:description The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived from a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strain-specific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.
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