Spatiotemporal variation in the fecal microbiota of mule deer is associated with proximate and future measures of host health

Abstract

Background Mule deer rely on fat and protein stored prior to the winter season as an energy source during the winter months when other food sources are sparse. Since associated microorganisms (‘microbiota’) play a significant role in nutrient metabolism of their hosts, we predicted that variation in the microbiota might be associated with nutrient storage and overwintering in mule deer populations. To test this hypothesis we performed a 16S rRNA marker gene survey of fecal samples from two deer populations in the western United States before and after onset of winter. Results PERMANOVA analysis revealed the deer microbiota varied interactively with geography and season. Further, using metadata collected at the time of sampling, we were able to identify different fecal bacterial taxa that could potentially act as bioindicators of mule deer health outcomes. First, we identified the abundance of Collinsella (family: Coriobacteriaceae) reads as a possible predictor of poor overwintering outcomes for deer herds in multiple locations. Second, we showed that reads assigned to the Bacteroides and Mollicutes Order RF39 were both positively correlated with deer protein levels, leading to the idea that these sequences might be useful in predicting mule deer protein storage. Conclusions These analyses confirm that variation in the microbiota is associated with season-dependent health outcomes in mule deer, which may have useful implications for herd management strategies.

Analysis of the Intestinal and Faecal Bacterial Microbiota of the Cervidae Family Using 16S Next-Generation Sequencing: A Review

“…Nutrient procurement is a fundamental challenge for wild animals as the availability and nutritional content of feed can vary temporally and spatially in response to changes in climate and geography. This variation leads to a change in the host gut microbiota [ 17 , 66 , 67 , 68 ]. However, there are core bacterial communities that coincide among individuals of the same species that have remained for a long time within a host and are identified at any season of the year [ 65 ].…”

“…In two mule deer ( O. hemionus ) populations from Cache County and Monroe Valley in Utah, USA, differences associated with microbial abundance, geography, and seasonal changes were reported. There was mainly an increase in the abundance of Coriobacteriales in the Cache population, which was related to the fat content in deer [ 17 ].…”

“…Studies on gut microbiota composition showed that the alpha diversity of bacterial communities was higher in the summer than in the winter, which was related to a decrease in the availability of feed for mule deer [ 17 ] and white-tailed deer [ 19 ]. In white-lipped deer ( Cervus albirostris ), the phyla Firmicutes, Bacteroidetes, and Patescibacteria were enriched during the herbaceous season, whereas the abundances of Actinobacteria and Proteobacteria were increased in the wilting season [ 33 ].…”

“…Since then, several studies have used sequencing technologies to describe intestinal microbiota in cervids, generating knowledge on bacterial abundance and diversity [10][11][12][13]. However, several factors influence bacterial community composition, such as sex [14], diet [15], spatial distribution [16,17], and even seasonal variation [18,19]. Parallel to studies on GIT…”

“…Since then, several studies have used sequencing technologies to describe intestinal microbiota in cervids, generating knowledge on bacterial abundance and diversity [ 10 , 11 , 12 , 13 ]. However, several factors influence bacterial community composition, such as sex [ 14 ], diet [ 15 ], spatial distribution [ 16 , 17 ], and even seasonal variation [ 18 , 19 ]. Parallel to studies on GIT bacteria, various other studies have been conducted on the composition and function of ruminal microorganisms, especially bacteria, archaea, and protozoa [ 20 , 21 , 22 , 23 , 24 , 25 , 26 ].…”