Experimental Evolution on a Wild Mammal Species Results in Modifications of Gut Microbial Communities

Abstract

Comparative studies have shown that diet, life history, and phylogeny interact to determine microbial community structure across mammalian hosts. However, these studies are often confounded by numerous factors. Selection experiments offer unique opportunities to validate conclusions and test hypotheses generated by comparative studies. We used a replicated, 15-generation selection experiment on bank voles (Myodes glareolus) that have been selected for high swim-induced aerobic metabolism, predatory behavior toward crickets, and the ability to maintain body mass on a high-fiber, herbivorous diet. We predicted that selection on host performance, mimicking adaptive radiation, would result in distinct microbial signatures. We collected foregut and cecum samples from animals that were all fed the same nutrient-rich diet and had not been subjected to any performance tests. We conducted microbial inventories of gut contents by sequencing the V4 region of the 16S rRNA gene. We found no differences in cecal microbial community structure or diversity between control lines and the aerobic or predatory lines. However, the cecal chambers of voles selected for herbivorous capability harbored distinct microbial communities that exhibited higher diversity than control lines. The foregut communities of herbivorous-selected voles were also distinct from control lines. Overall, this experiment suggests that differences in microbial communities across herbivorous mammals may be evolved, and not solely driven by current diet or other transient factors.

Keywords: artificial selection; gut microbiome; herbivory; host-microbe interactions; voles.

Figure 1

Direct effects of 15 generations of selection on bank voles toward: high swim-induced aerobic metabolism, herbivorous capability measured as ability to maintain body mass on a low-quality diet, and predatory propensity measured as ranked time to attack a cricket. Comparison of the cumulative effects of selection in the three directions is expressed as a difference between the means of four selected (in each direction) and four control lines, expressed in units of phenotypic standard deviation. In generation 8 and 13 the food composition used in selection trial in the “Herbivorous” lines was different than in other generations, which resulted in the irregular pattern (marked with broken lines). In generation 12 selection in “Aerobic” lines was relaxed (broken line).

Figure 2

Shannon index of microbial communities in the ceca of voles selected for different traits. Points represent mean ± SEM. C, Control; A, Aerobic; H, Herbivorous; P, Predatory. Herbivorous-selected lines exhibited significantly higher biodiversity.

Figure 3

Principal coordinate analyses of cecal communities of voles selected for various traits. Community membership uses unweighted UniFrac distances, and thus investigates the presence or absence of bacterial lineages. Community structure uses weighted UniFrac distances, which take relative abundances of taxa into account.

Figure 4

Shannon index of microbial communities of voles selected for different traits. Points represent mean ± SEM. C, Control; H, Herbivorous. The foregut chamber harbored lower microbial diversity than the cecal chamber. No difference in diversity was observed between the foregut communities of Control and Herbivorous-selected voles. Cecal communities of Herbivorous-selected lines were significantly more diverse than Control lines. The points for cecal samples represent the same samples as presented in Figure 2, except here we used a lower number of sequences per sample for analysis, due to a slightly lower return of sequences from some foregut samples.

Figure 5

Principal coordinate analyses of foregut and cecal communities of control and herbivorous-selected voles. Community membership uses unweighted UniFrac distances, and thus investigates the presence or absence of bacterial lineages. Community structure uses weighted UniFrac distances, which takes relative abundances of taxa into account. The points for cecal samples represent the same samples as presented in Figure 3, except here we used a lower number of sequences per sample for analysis, due to a slightly lower return of sequences from some foregut samples.

Figure 6

Relative abundances of Treponema and Lactobacillus in the foregut chambers of control and herbivorous-selected voles. Points represent mean ± SEM.