Gut microbiota profiles of sympatric snub-nosed monkeys and macaques in Qinghai-Tibetan Plateau show influence of phylogeny over diet

Abstract

The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatric animal species living between 3600 and 4500 m asl. Results showed that within the same geographical environment, Macaca mulatta and Rhinopithecus bieti exhibited a gut microbiome composition similar to that of Tibetan people, influenced by genetic evolution of host, while significantly differing from other distantly related animals. The gut microbiota of plateau species has developed similar strategies to facilitate their hosts' adaptation to specific environments, including broadening its dietary niche and enhancing energy absorption. These findings will enhance our comprehension of the significance of primate gut microbiota in adapting to specific habitats.

Fig. 1. Niche differentiation of 7 sympatric species.

①–④: the gastrointestinal morphology of animals. A–I is illustrations of their dietary composition. A Bush fruits; B lichens; C mushrooms; D invertebrate, E Bush flowers and young leaves; F grass; G Bush fruits and mature leaves; H bark; I highland barley.

Fig. 2. Phylogeny and Gut microbiome structure in 8 sympatric species based on 16S rRNA gene amplicon.

Depicted are measures of beta diversity by Non-MetricMulti-Dimensional Scaling (NMDS), including Binary Jaccard distances graphed (A) and Bray Curtis distances graphed (B). C Comparison between gut microbiota tree and host phylogeny relationships, based on Unweighted Pair-group Method with Arithmetic Mean and National Center for Biotechnology Information Taxonomy database. Vegetarian are shaded in the phylogenetic tree.

Fig. 3

Relative abundance of gut bacterial taxa in different animals on the family level based on 16S rRNA gene amplicon analysis.

Fig. 4. The Venn diagram of the OTUs in all samples among groups via 16S rRNA gene amplicon analysis.

A 11 OTUs were shared by 8 sympatric species. B 35 OTUs were shared among the Cetartiodactyla and three primates. C 56 OTUs were shared among the three primates.

Fig. 5. Linear discriminant analysis effect size (LEfSe) analysis of gut microbiota composition among the sympatric species based on 16S rRNA gene amplicon analysis (LDA > 4, P < 0.05).

A taxonomic representation of statistically and biologically consistent differences between different geographical populations. Differences are represented by the color of the most abundant class. Each circle’s diameter is proportional to the taxon’s abundance and represent phylum, class, order, and family. B Histogram of the LDA scores computed for features differentially abundant among the sympatric species. LEfSe scores can be interpreted as the degree of consistent difference in relative abundance between features in the two classes of analyzed microbial communities. The histogram thus identifies which clades among all those detected as statistically and biologically differential explain the greatest differences between communities.

Fig. 6. Relative abundance differences of Methanobacteria within archaea by species based on 16S rRNA gene amplicon analysis.

The boxes represent 25–75th percentiles, the lines in the box indicate the median and whiskers extend to the maximum and minimum values within 1.5× the interquartile range. Significant differences were marked as “**” (P < 0.01), “***” (P < 0.001) by t-test.

Fig. 7

Map of sampling sites for 8 sympatric species in Markam, Tibet, China.

Fig. 8. Gut microbiome function of primates by metagenome analysis.

A analysis of Bray Curtis distances indicated an effect of species on pathway composition; B a comparison of the microbiome gene functions among primates in the KEGG 3 classification was conducted; C the functional annotations of primates based on the CAZy database, at family level.

Fig. 9. The main metabolic modules of gut microbiota functional genes in primates by metagenome analysis.

A The gluconeogenesis module (M00003); B the acetyl-CoA pathway module (M00422); C the methionine biosynthesis module (M00017, M00338); D the phosphate acetyltransferase-acetate kinase pathway module (M00579). Different colors signify diverse species. The boxes represent 25–75th percentiles, the lines in the box indicate the median and whiskers extend to the maximum and minimum values within 1.5× the interquartile range.