A comparative study of the fecal microbiota of gray seal pups and yearlings - a marine mammal sentinel species

Abstract

Gray seals (Halichoerus grypus) can act as sentinel species reflecting the condition of the environment they inhabit. Our previous research identified strains of pathogenic Campylobacter and Salmonella, originating from both human and agricultural animal hosts, on rectal swabs from live gray seal (H. grypus) pups and yearlings on the Isle of May, Scotland, UK. We examined rectal swabs from the same pup (n = 90) and yearling (n = 19) gray seals to gain further understanding into the effects of age-related changes (pup vs. yearling) and three different natal terrestrial habitats on seal pup fecal microbiota. DNA was extracted from a subset of rectal swabs (pups n = 23, yearlings n = 9) using an optimized procedure, and the V4 region of the 16S ribosomal RNA gene was sequenced to identify each individual's microbiota. Diversity in pup samples was lower (3.92 ± 0.19) than yearlings (4.66 ± 0.39) although not significant at the p = 0.05 level (p = 0.062) but differences in the composition of the microbiota were (p < 0.001). Similarly, differences between the composition of the microbiota from pups from three different terrestrial habitats (Pilgrim's Haven [PH], Rona Rocks [RR], and Tarbet Slope [TS]) were highly significant (p < 0.001). Pairwise tests showed significant differences between all three habitats: PH versus TS (p = 0.019), PH versus RR (p = 0.042) and TS versus RR (p = 0.020). This preliminary study suggests a general trend, that seal microbiomes are modified by both age and, in pups, different terrestrial habitats. Furthermore, knowledge of the microbiota species present has the potential to be used in determining the environmental quality index.

Keywords: fecal microbiota; gray seal; pups; yearlings.

Figure 1

Map of seal sampling locations on the Isle of May, Scotland, UK. Circles: sampling sites of gray seal pups. Triangles: sampling sites of yearlings. Figures in parentheses are numbers of seal pups, sampled by rectal swab, from each of the three different natal terrestrial habitats that DNA was extracted successfully from. Scale bar: 250 m

Figure 2

Comparison, at the genus level, of the relative composition of the fecal microbiota of pups at different geographic locations and yearlings. Taxonomic composition of microbial communities at the genus level from fecal swabs from gray seal yearling (n = 9) and pups (n = 23 in total), the latter from the three different sampling locations. Genera with <1% relative abundance across the data set were grouped as Others

Figure 3

Differences in the abundance of the fecal microbiota of pups and yearlings, at the level of amplicon sequence variants. Analysis of compositions of microbiome (ANCOM) analysis of the differential abundance of amplicon sequence variants (ASVs) between gray seal pups (n = 23) and yearlings (n = 9). The centered‐log ratio (CLR) is negative for ASVs elevated in the pup samples, and positive for those elevated in the yearling samples. W is the ANCOM significance score, and ASVs which violate the null hypothesis, and therefore are significantly overrepresented, are shown in black‐filled circles. The ASVs which do not violate the null hypothesis (i.e., overrepresented but not significant) are shown as open circles (b)

Figure 4

Comparisons of the similarity between the fecal microbiota of pups versus yearlings, and pups at three different natal terrestrial habitats, at the level of amplicon sequence variants. Nonmetric multidimensional scaling (NMDS) ordination plots of Bray–Curtis similarity between amplicon sequence variants (ASV) of microbial communities in seal rectal swab samples. (a) Comparison of pup and yearling samples. Note outlier, a pup sampled at Pilgrim's Haven (marked PH‐9). (b) Pup samples from the three different natal terrestrial habitats. The Kruskal stress is shown on each plot (stress < 0.2 denotes a reliable ordination)