Abstract
BackgroundThe animal gastrointestinal tract contains a complex community of microbes, whose composition ultimately reflects the co-evolution of microorganisms with their animal host and the diet adopted by the host. Although the importance of gut microbiota of humans has been well demonstrated, there is a paucity of research regarding non-human primates (NHPs), especially herbivorous NHPs.ResultsIn this study, an analysis of 97,942 pyrosequencing reads generated from Rhinopithecus bieti fecal DNA extracts was performed to help better understanding of the microbial diversity and functional capacity of the R. bieti gut microbiome. The taxonomic analysis of the metagenomic reads indicated that R. bieti fecal microbiomes were dominated by Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria phyla. The comparative analysis of taxonomic classification revealed that the metagenome of R. bieti was characterized by an overrepresentation of bacteria of phylum Fibrobacteres and Spirochaetes as compared with other animals. Primary functional categories were associated mainly with protein, carbohydrates, amino acids, DNA and RNA metabolism, cofactors, cell wall and capsule and membrane transport. Comparing glycoside hydrolase profiles of R. bieti with those of other animal revealed that the R. bieti microbiome was most closely related to cow rumen.ConclusionsMetagenomic and functional analysis demonstrated that R. bieti possesses a broad diversity of bacteria and numerous glycoside hydrolases responsible for lignocellulosic biomass degradation which might reflect the adaptations associated with a diet rich in fibrous matter. These results would contribute to the limited body of NHPs metagenome studies and provide a unique genetic resource of plant cell wall degrading microbial enzymes. However, future studies on the metagenome sequencing of R. bieti regarding the effects of age, genetics, diet and environment on the composition and activity of the metagenomes are required.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1378-7) contains supplementary material, which is available to authorized users.
Highlights
The animal gastrointestinal tract contains a complex community of microbes, whose composition reflects the co-evolution of microorganisms with their animal host and the diet adopted by the host
The raw read data were subjected to the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) v.3.0 online server quality control pipeline [26] to remove duplicate and low quality reads (Additional file 1)
We presented for the first-time the application of the shotgun metagenomic pyrosequencing approach to study the fecal microbiome of the R. bieti
Summary
The animal gastrointestinal tract contains a complex community of microbes, whose composition reflects the co-evolution of microorganisms with their animal host and the diet adopted by the host. The importance of gut microbiota of humans has been well demonstrated, there is a paucity of research regarding non-human primates (NHPs), especially herbivorous NHPs. The Yunnan snub-nosed monkey (Rhinopithecus bieti) is an endangered colobine endemic to high-altitude forests ranging from 3000 to 4400 meters in southwestern China and southeastern Tibet [1]. The Yunnan snub-nosed monkey (Rhinopithecus bieti) is an endangered colobine endemic to high-altitude forests ranging from 3000 to 4400 meters in southwestern China and southeastern Tibet [1] Overall, these colobines can be classified as herbivores, ingesting flowers, fruits, leaves, and seeds to varying degrees [2]. The R. bieti possesses specialized S-shaped and partitioned stomachs where microbial fermentation of cellulose takes place [3,4] This adaptation enables them to eat food containing high levels of structural polysaccharides, i.e., cellulose and related compounds. Researches on R. bieti have mostly focused on aspects of taxonomy, ecology, anatomy and conservation genetics
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