Gut microbiome variations in Rhinopithecus roxellanae caused by changes in the environment

Abstract

Background: The snub-nosed monkey (Rhinopithecus roxellanae) is an endangered animal species mainly distributed in China and needs to be protected. Gut microbiome is an important determinant of animal health and population survival as it affects the adaptation of the animals to different foods and environments under kinetic changes of intrinsic and extrinsic factors. Therefore, this study aimed to elucidate gut fecal microbiome profiles of snub-nosed monkeys affected by several extrinsic and intrinsic factors, including raising patterns (captive vs. wild), age, sex, and diarrheal status to provide a reference for making protection strategies.

Results: The 16S rRNA gene sequencing was firstly used to pre-check clustering of 38 fecal samples from the monkeys including 30 wild and 8 captive (5 healthy and 3 diarrheal) from three Regions of Shennongjia Nature Reserve, Hubei Province, China. Then the 24 samples with high-quality DNA from 18 wild and 6 captive (4 healthy and 2 diarrheal) monkeys were subjected to shotgun metagenomic sequencing to characterize bacterial gut microbial communities. We discovered that the raising pattern (captive and wild) rather than age and sex was the predominant factor attributed to gut microbiome structure and proportionality. Wild monkeys had significantly higher bacterial diversity and lower Bacteroidetes/Firmicutes ratios than captive animals. Moreover, the gut microbiomes in wild healthy monkeys were enriched for the genes involved in fatty acid production, while in captive animals, genes were enriched for vitamin biosynthesis and metabolism and amino acid biosynthesis from carbohydrate intermediates. Additionally, a total of 37 antibiotic resistant genes (ARG) types were detected. Unlike the microbiome diversity, the captive monkeys have a higher diversity of ARG than the wild animals.

Conclusion: Taken together, we highlight the importance of self-reprogramed metabolism in the snub-nosed monkey gut microbiome to help captive and wild monkeys adapt to different intrinsic and extrinsic environmental change.

Keywords: Adaptation; Antibiotic resistant genes; Bacteroidetes/Firmicutes ratio; Gut microbiome; Metagenomics; Rhinopithecus roxellanae.

Fig. 1

Difference in the fecal microbial communities of R. roxellanae. a The similarity of fecal microbiomes measured by UniFrac distance considering sex, raising patterns, and age. Results are derived from bacterial 16 s V4 rRNA data sets. **, p < 0.01 (Kruskal–Wallis test). b PCoA based on the Unweighted UniFrac distance from the genera profiles of the captive healthy monkeys (Captive-H)and wild monkeys (Wild). c The dendrogram based on each sample was developed demonstrating all 6 captive healthy monkeys were clustered together, while the wild monkeys were better clustered into another group compared PCoA

Fig. 2

Community constituents of gut microbiomes among R. roxellanae based on shotgun sequencing of fecal DNA from a subset of 24 fecal samples. a The top 10 phylum of the R. roxellanae gut microbiome. Each column represents the gut microbial community from a single monkey. Phylum Firmicutes and Bacteroidetes made up the majority of phyla in each monkey. b The top 10 species of the R. roxellanae gut microbiome. Captive: captive monkeys; Wild: wild monkeys

Fig. 3

Microbial community profiles of captive healthy monkeys (Captive-H) and wild monkeys (Wild) based on shotgun sequencing. a The Venn diagram of the microbial composition of wild and captive healthy monkeys at the genus level. Wild monkeys have 74 unique genera, while captive healthy monkeys have 10 unique genera. b The pie chart of most dominant phylum in wild monkeys or captive healthy monkeys. c Comparison of the Shannon index among wild monkeys and captive healthy monkeys based on the genera profile. Wild monkeys represent higher bacterial diversity than captive healthy monkeys (p < 0.01). d The differential genera between captive healthy monkeys and wild monkeys measured by MetaStats (Version 2009.04.14, p value ≤ 0.05, q value ≤ 0.05)

Fig. 4

The differential functional genes between captive healthy monkeys (Captive-H) and wild monkeys (Wild). a Heatmap of the differential KEGG ECs between wild monkeys and captive healthy monkeys, which were involved in the carbohydrate, amino acid, and vitamins metabolism. The abundance profile was transformed into Z scores by subtracting the average abundance and dividing the standard deviation of all samples. b Spearman’s correlation between differential genera and differential ECs involved in the carbohydrate, amino acid, and vitamins metabolism. The color was scaled with the correlation coefficients. + , adjust p value < 0.01; *, adjust p value < 0.05

Fig. 5

Differences in metabolism of sugar and vitamin synthesis between captive healthy monkeys and wild monkeys. Diagram of KEGG pathway for glycolysis (a) and pyruvate metabolism (b). The ECs colored in red and the ECs colored in green indicated a higher abundance of Wild monkeys and Captive healthy monkeys respectively. c Diagram of KEGG pathway for riboflavin and folate biosynthesis, ECs colored in green represent a higher abundance of captive healthy monkeys when compared with wild monkeys. The p values and q values for the ECs can be found in additional file 10. d The differential CAZy families between captive healthy monkeys and wild monkeys. The abundance profile was transformed into Z scores by subtracting the average abundance and dividing the standard deviation of all samples. e Diagram for difference in metabolism of sugar. The red box represented the tendency for wild monkeys to utilize the sugar in comparison with captive healthy monkeys (green box). The p values and q values for the differential ECs and CBMs can be found in additional file 10 and additional file 12 respectively

Fig. 6

The difference in the fecal microbiomes between captive healthy monkeys (Captive-H) and diarrheal monkeys (Captive-D). a The similarity of fecal microbiota measured by UniFrac distance derived from bacterial 16 s V4 rRNA data sets. b The pie chart of most dominant phylum in healthy monkeys and diarrheal monkeys. c The heatmap of differential species (p < 0.001)

Fig. 7

The antibiotic resistant genes (ARG) and the distribution of corresponding resistant drug classes in the gut microbiomes of R. roxellanae. a Broad spectrum profiles of the 37 ARGs in 24 samples. b Accumulated abundance of different ARG in 24 samples. c abundance of ARG in the 9 antibiotic classes in 24 samples. The abundance of ARG was transformed into log scores and illustrated in the heatmap by red to grey with the abundance of high to low