Comparison of the gut microbiome in red deer (Cervus elaphus) and fallow deer (Dama dama) by high-throughput sequencing of the V3–V4 region of the 16S rRNA gene

Abstract

The gut microbiome is a complex ecosystem that plays an essential role in maintaining the host’s gut homeostasis and health. The available sequencing data for the Cervidae gut microbiome, especially for red deer and fallow deer in China, are limited. To improve the health of the two species in captivity, we characterized the gut microbiome of red deer and fallow deer via high-throughput Illumina sequencing of the 16S rRNA genes V3–V4 hypervariable regions. We found that the gut microbiome community of red deer included 20 phyla, 89 families and 193 genera, while the gut microbiome community of fallow deer included 18 phyla, 102 families and 227 genera. Firmicutes (red deer: 37.46–44.98%; fallow deer: 32.67–49.54%) was the most abundant phylum, followed by Bacteroidetes (red deer: 28.09–39.02%; fallow deer: 27.45–38.71%). The observed species and Shannon indices in red deer were higher than in fallow deer (p = 0.002, 0.016, respectively). Hence compared with fallow deer, red deer had higher diversity and species richness in their gut microbiome. The MRPP results showed that significant differences did occur in their microbiome compositions (A = 0.037, significance level α = 0.001). This study provides an initial understanding of the gut microbiome composition of red deer and fallow deer. The results may benefit captive management and future reintroduction programs.