High-Throughput Analysis Reveals Seasonal Variation of the Gut Microbiota Composition Within Forest Musk Deer (Moschus berezovskii)

Abstract

The gut microbiota plays a key role in the nutritional ecology of ruminants, and host diet has a significant effect on these microbial communities. Longitudinal studies assessing variation of seasonal microbiota in animals can provide a comparative context for interpreting the adaptive significance of such changes. However, few studies have investigated the effects of seasonally-related dietary shifts on the gut microbial communities of endangered forest musk deer (FMD), and the national breeding programs need this information to promote the growth of captive populations. The present study applied bacterial 16S rRNA genes based on high-throughput sequencing to profile the fecal microbial communities of FMD across four seasons. Microbial diversity was higher in seasons with dry leaf diets (winter and spring) compared to seasons with fresh leaf diets (summer and autumn). The dominant microbial phyla were Firmicutes and Bacteroidetes, and the core bacterial taxa also comprised mostly (94.40% of shared OTUs) Firmicutes (37 taxa) and Bacteroidetes (6 taxa), which were relatively stable across different seasons. The Firmicutes–Bacteroidetes ratio declined in seasons with fresh leaf diets relative to seasons with dry leaf diets, and the dominant genera among the four seasons showed no significant variation in abundance. This work explores the seasonal variation in the microbial communities of FMD for the first time, and reveals how gut microbial community dynamics vary seasonally in accordance with differences in dietary plants (fresh and dry leaf). These results indicate that the annual cyclic reconfiguration of FMD gut microbiota could be associated with shifts in dietary nutrients, which is important information to inform captive FMD management.

Seasonal Variation in Gut Microbiota Composition: Comparative Analysis of Siberian Musk Deer (Moschus moschiferus) and Forest Musk Deer (Moschus berezovskii)

“…The core bacterial phyla in both musk deer species were Firmicutes and Bacteroidetes, which is consistent with previous studies of the microbiota of musk deer [18,25,26] and other ruminants [27][28][29]. The phyla are found in the guts of many mammals, which suggest the importance of these bacteria in the gut ecosystem [30].…”

“…We characterized the seasonal variation in the gastrointestinal microbiota of Siberian musk deer and forest musk deer using high-throughput sequencing of the 16S rRNA gene in fecal samples. According to the research results of Hu et al [18] that the in uence of seasonal factors on the gut microbiota of forest musk deer, and daily food of the siberian musk deer have obvious seasonal changes, we selected representative winter and summer seasons for this research.The main objectives of present study are: (1) to compare the composition and diversity gut microbiota of two species; (2) to determine seasonally (i.e., summer and winter) variations in the microbial community composition and disease of Siberian musk deer; (3) to examine the changes in signaling pathways and functional genes, and; (4) to discuss their potential functions in the diagnosing diseases of the digestive system and for improving feeding methods.…”

Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration

“…The effect of seasonality on both diet and the microbiome has only recently been explored in the current literature. Free ranging animal models have suggested that seasonality may affect the function and composition of the gut microbiota [87,88] in response to a seasonal change in diet. In 2017, researchers collected 350 faecal samples from the Tanzanian Hadza tribe over the span of a year [76].…”

Geography, seasonality, and host‐associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal

“…It provides insight into evolutionary history, and the bacterial community demonstrates phenotypic plasticity that affects the host's capacity to adapt to changing environmental pressures (Antwis et al, ; Bahrndorff et al, ; Girard et al, ). In mammals, the gastrointestinal microbiome has been shown to be affected by captivity (Li et al, ), kinship (Yuan et al, ), disease (Wasimuddin et al, ), and season (Hu et al, ). More specifically, many comprehensive microbiome studies have been performed on ungulate species because their unique morphological traits impact the gut bacterial composition, and in return, the bacterial composition impacts fitness (Bergmann et al, ; Gruninger, Sensen, McAllister, & Forster, ; Koike, Yoshitani, Kobayashi, & Tanaka, ; Li et al, ; Pope et al, ; Qi et al, ; Salgado‐Flores, Bockwoldt, Hagen, Pope, & Sundset, ).…”

“…Despite this general similarity among herbivores, the relative abundance of the bacteria making up the microbiome differs between individuals and can be artificially altered by changing factors of diet (Escobar‐Zepeda, De León, & Sanchez‐Flores, ; Koike et al, ; Tian, Wu, Chen, Yu, & He, ). In some populations, diet is altered by shifting seasons and both diet and seasonality have been documented to influence the bacteria community structure in ruminants, including forest musk deer (Hu et al, ), and muskoxen (Ungerfeld, Leigh, Forster, & Barboza, ). While ungulate and ruminant microbiomes have been generally well‐studied, there is little information on population‐level microbiome variation in these species.…”