Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing

Yu Guan,Siyu Han,Haitao Yang,Limin Feng,Jianping Ge,Tianming Wang

doi:10.1186/s13568-017-0517-8

Abstract

The gut microbiota is characterized as a complex ecosystem that has effects on health and diseases of host with the interactions of many other factors together. Sika deer is the national level for the protection of wild animals in China. The available sequencing data of gut microbiota from feces of wild sika deer, especially for Cervus nippon hortulorum in Northeast China, are limited. Here, we characterized the gastrointestinal bacterial communities of wild (7 samples) and captive (12 samples) sika deer from feces, and compared their gut microbiota by analyzing the V3–V4 region of 16S rRNA gene using high-throughput sequencing technology on the Illumina Hiseq platform. Firmicutes (77.624%), Bacteroidetes (18.288%) and Tenericutes (1.342%) were the most predominant phyla in wild sika deer. While in captive sika deer, Firmicutes (50.710%) was the dominant phylum, followed by Bacteroidetes (31.996%) and Proteobacteria (4.806%). A total of 9 major phyla, 22 families and 30 genera among gastrointestinal bacterial communities showed significant differences between wild and captive sika deer. The specific function and mechanism of Tenericutes in wild sika deer need further study. Our results indicated that captive sika deer in farm had higher fecal bacterial diversity than the wild. Abundance and quantity of diet source for sika deer played crucial role in shaping the composition and structure of gut microbiota.

Highlights

The sika deer (Cervus nippon) is a cervidae species, which distributed extensively in East Asia, including China, Korea, Vietnam and Taiwan, especially the Japanese archipelago (Goodman et al 2001)
Albeit part of researches have done for species diversity of sika deer on the basis of molecular biology in China (Lü et al 2006; Liu et al 2002; Wang et al 2008; Wu et al 2004, 2005), most of the previous studies aimed to its distribution, amount, activity patterns and trophic analysis (Fu et al 2006; Huang et al 2015; Liu et al 1999; Lui et al 2003; Xiao et al 2014)
Given that the plight of protection for wild sika deer in Northeast China, our prime aim of this work is to characterize the basic fecal bacterial community composition and structure of wild sika deer, and make a comparison of gut microbiota between wild and captive sika deer living in distinct environment, which may make a contribution to the study of gut microbiota for wild animals and provide ideas for protection toward these endangered and precious cervidae species

Summary

Introduction

The sika deer (Cervus nippon) is a cervidae species, which distributed extensively in East Asia, including China, Korea, Vietnam and Taiwan, especially the Japanese archipelago (Goodman et al 2001). Albeit part of researches have done for species diversity of sika deer on the basis of molecular biology in China (Lü et al 2006; Liu et al 2002; Wang et al 2008; Wu et al 2004, 2005), most of the previous studies aimed to its distribution, amount, activity patterns and trophic analysis (Fu et al 2006; Huang et al 2015; Liu et al 1999; Lui et al 2003; Xiao et al 2014). The detailed data, especially the gut microbiota data of wild sika deer in Northeast China, are comparatively insufficient. Given that the plight of protection for wild sika deer in Northeast China, our prime aim of this work is to characterize the basic fecal bacterial community composition and structure of wild sika deer, and make a comparison of gut microbiota between wild and captive sika deer living in distinct environment, which may make a contribution to the study of gut microbiota for wild animals and provide ideas for protection toward these endangered and precious cervidae species

Methods

Results

Conclusion