Variation in the gut microbiota of laboratory mice is related to both genetic and environmental factors

Abstract

During recent years, the composition of the gut microbiota (GM) has received increasing attention as a factor in the development of experimental inflammatory disease in animal models. Because increased variation in the GM might lead to increased variation in disease parameters, determining and reducing GM variation between laboratory animals may provide more consistent models. Both genetic and environmental aspects influence the composition of the GM and may vary between laboratory animal breeding centers and within an individual breeding center. This study investigated the variation in cecal microbiota in 8-wk-old NMRI and C57BL/6 mice by using denaturing gradient gel electrophoresis to profile PCR-derived amplicons from bacterial 16S rRNA genes. Comparison of the cecal microbiotas revealed that the similarity index of the inbred C57BL/6Sca strain was 10% higher than that of the outbred Sca:NMRI stock. Comparing C57BL/6 mice from 2 vendors revealed significant differences in the microbial profile, whereas the profiles of C57BL/6Sca mice raised in separate rooms within the same breeding center were not significantly different. Furthermore, housing in individually ventilated cages did not lead to intercage variation. These results show that denaturing gradient gel electrophoresis is a simple tool that can be used to characterize the gut microbiota of mice. Including such characterizations in future quality-control programs may increase the reproducibility of mouse studies.

Figure 1.

Similarity indices from cluster analysis based on DGGE profiles representing the similarity in the composition of the cecum microbiota from Sca:NMRI and C57BL/6Sca mice. The similarity index for Sca:NMRI mice is 66.5% ± 6.8%; that for C57BL/6Sca mice is 77.8% ± 4.4%.

Figure 2.

Principal component analysis based on DGGE profiles of 16S rRNA gene-derived amplicons of cecal samples collected from C57BL/6Sca mice housed in IVC. Each cage is marked with a different color; mice from the same cage have the same colored dots. Yellow and red dots represent female mice, and green and blue dots represent male mice.

Figure 3.

Dendrogram based on DGGE profiles representing 16S rRNA gene-derived amplicons of cecal samples collected from C57BL/6Sca mice originating from 2 breeding rooms (R1 and R2) at the same laboratory animal vendor. Each figure within the groups indicates a sample from a single mouse (numbered from 1 to 15). The scale bar represents the similarity index as a percentage (100 indicates complete similarity and 0 complete dissimilarity). The overall similarity index is 83.7% ± 3.8%. The similarity index for room 1 is 86.0% ± 3.2%; that for room 2 is 84.4% ± 3.4%.

Figure 4.

Principal component analysis based on DGGE profiles of 16S rRNA gene-derived amplicons of cecal samples collected from C57BL/6 mice. (A) C57BL/6Sca mice originating from 2 breeding rooms within the same laboratory animal vendor. The 2 rooms are marked with circles and squares. (B) C57BL/6 mice originating from 2 different laboratory animal vendors. The 2 breeders are marked with circles and squares.

Figure 5.

Dendrogram based on DGGE profiles representing 16S rRNA gene-derived amplicons of cecal samples collected from C57BL6 mice originating from 2 breeding centers (B1 and B2). Each figure within the groups indicates a sample from a single mouse (numbered from 1 to 16). The scale bar represents the similarity index as a percentage (an index of 100% indicates complete similarity). The overall similarity is 75.6% ± 4.6%; that for animals from B1 is 82.8% ± 3.1%, that for B2 is 82.5.0% ± 4.2%.