Site and strain-specific variation in gut microbiota profiles and metabolism in experimental mice

Abstract

Background: The gastrointestinal tract microbiota (GTM) of mammals is a complex microbial consortium, the composition and activities of which influences mucosal development, immunity, nutrition and drug metabolism. It remains unclear whether the composition of the dominant GTM is conserved within animals of the same strain and whether stable GTMs are selected for by host-specific factors or dictated by environmental variables.

Methodology/principal findings: The GTM composition of six highly inbred, genetically distinct strains of mouse (C3H, C57, GFEC, CD1, CBA nu/nu and SCID) was profiled using eubacterial -specific PCR-DGGE and quantitative PCR of feces. Animals exhibited strain-specific fecal eubacterial profiles that were highly stable (c. >95% concordance over 26 months for C57). Analyses of mice that had been relocated before and after maturity indicated marked, reproducible changes in fecal consortia and that occurred only in young animals. Implantation of a female BDF1 mouse with genetically distinct (C57 and Agoutie) embryos produced highly similar GTM profiles (c. 95% concordance) between mother and offspring, regardless of offspring strain, which was also reflected in urinary metabolite profiles. Marked institution-specific GTM profiles were apparent in C3H mice raised in two different research institutions.

Conclusion/significance: Strain-specific data were suggestive of genetic determination of the composition and activities of intestinal symbiotic consortia. However, relocation studies and uterine implantation demonstrated the dominance of environmental influences on the GTM. This was manifested in large variations between isogenic adult mice reared in different research institutions.

Figure 1. Strain-dependent clustering of mouse GTMs.

UPGMA cluster analysis of fecal DGGE profiles from six genetically distinct strains of mice. Acronyms refer to mouse strain. All samples originated from distinct mice.

Figure 2. Temporal GTM stability within a single C57 strain mouse sampled over a 30-month period.

(UPGMA cluster analysis of fecal DGGE profiles).

Figure 3. Effect of relocation on the GTM profiles of highly immunocompromised SCID mice (UPGMA cluster analysis of fecal DGGE profiles).

All animals were housed in environment A until 8 weeks of age. Samples obtained during this period are designated by blue symbols. Red symbols represent fecal samples obtained from animals that remained in the original environment (A) (sampled in the animals over 8 weeks of age); open symbols represent animals relocated to environment B. Numbers indentify individual animals; numbers in parenthesis give the age of animal in weeks.

Figure 4. Age-dependent effects of relocation on the GTM profiles and urinary metabolite profiles of C3H mice.

(a) UPGMA cluster analysis of fecal DGGE profiles. Blue symbols represent fecal samples obtained from animals housed in the original environment (A). Samples obtained from mice relocated at 4 weeks of age are represented by open symbols; red symbols represent animals relocated to environment B at over 8 weeks of age. Numbers identify individual animals; numbers in parenthesis give the age of animal in weeks and (b) UPLC-MS PCA results from the analysis of urine samples from these animals showing the effect of relocation on metabolite profiles.

Figure 5. GTM development in genetically distinct, uterine-implanted mice.

(a) UPGMA cluster analysis of fecal DGGE profiles; (b) PCA score plot of the two first PCs of analysis of UPLC-MS urine analysis data set (gender is indicated). The model describes 82% of the variation. Urinary metabolite profiles cluster on the basis of gender (blue cluster boundary, males; pink cluster boundary, females) but not genotype. C57 (blue triangles) and Agoutie; AG (red diamonds) gestated in a BDF1 strain mother (green cross).

Figure 6. Institution-specific GTMs in C3H mice.

A UPGMA dendrogram generated from fecal bacterial fingerprints of C3H mice housed at within UK (University of Manchester) and USA (Stanford University) institutes. All sample originated from distinct mice.