Mammalian Genome

, Volume 17, Issue 11, pp 1093–1104 | Cite as

Quantitative PCR assays for mouse enteric flora reveal strain-dependent differences in composition that are influenced by the microenvironment

  • A. Deloris Alexander
  • Roger P. Orcutt
  • JaNell C. Henry
  • Joseph BakerJr.
  • Anika C. Bissahoyo
  • David W. Threadgill


The mammalian gastrointestinal (GI) tract is inhabited by over a hundred species of symbiotic bacteria. Differences among individuals in the composition of the GI flora may contribute to variation in in vivo experimental analyses and disease susceptibility. To investigate potential interindividual differences in GI flora composition, we developed real-time quantitative PCR-based assays for the detection of the eight members of the Altered Schaedler Flora (ASF) as representative members of different bacterial niches within the mammalian GI tract. Quantitative and reproducible strain-specific variations in the numbers of the ASF members were observed across 23 different barrier-housed inbred mouse strains, suggesting that the ASF assays can be used as sentinels for changes in GI flora composition. A significant cage effect was also detected. Isogenic mice that cohabited at weaning, whether from the same or different litters, showed little variation in ASF profiles. Conversely, litters split among different cages at weaning showed divergence in ASF profiles after three weeks. Individual ASF profiles, once established, were highly stable over time in the absence of environmental perturbation. Furthermore, cohabitation of different inbred strains maintained most of the interstrain variation in the GI flora, supporting a role of host genetics in determining GI flora composition.



The authors thank Dr. H.S. Kim for assistance in preparing the qPCR primers and dual-labeled probes, and Maureen Bower, Jerri Shaw, Doug Behnke, and Gary Grimm of the UNC CGIBD Gnotobiotic Core for assistance in maintaining germfree mice. This work was supported by a Pilot and Feasibility grant from the UNC GCIBD, supported by NIH grant DK34987, by a Research Supplement for Underrepresented Minorities to NIH grant CA79869 and by NIH grant CA84239.


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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • A. Deloris Alexander
    • 1
  • Roger P. Orcutt
    • 2
    • 3
  • JaNell C. Henry
    • 1
  • Joseph BakerJr.
    • 1
  • Anika C. Bissahoyo
    • 1
  • David W. Threadgill
    • 1
  1. 1.Department of Genetics and Center for Gastrointestinal Biology and DiseaseUniversity of North CarolinaChapel HillUSA
  2. 2.Mutant Mouse Regional Resource Center (MMRRC)State University of New York, AlbanyAlbanyUSA
  3. 3.TaconicGermantownUSA

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