The Gene Catalog and Comparative Analysis of Gut Microbiome of Big Cats Provide New Insights on Panthera Species

Abstract

Majority of metagenomic studies in the last decade have focused on revealing the gut microbiomes of humans, rodents, and ruminants; however, the gut microbiome and genic information (gene catalog) of large felids such as Panthera species are largely unknown to date. In this study, the gut bacterial, fungal, and viral metagenomic composition was assessed from three Panthera species (lion, leopard, and tiger) of Indian origin, which were consuming the same diet and belonged to the same geographical location. A non-redundant bacterial gene catalog of the Panthera gut consisting of 1,507,035 putative genes was constructed from 27 Panthera individuals, which revealed a higher abundance of purine metabolism genes correlating with their purine-rich dietary intake. Analysis with Carbohydrate Active enZyme (CAZy) and MEROPS databases identified enrichment of glycoside hydrolases (GHs), glycoside-transferases, and collagenases in the gut, which are important for nutrient acquisition from animal biomass. The bacterial, fungal, and viral community analysis provided the first comprehensive insights into the Panthera-specific microbial community. The Panthera gene catalog and the largest comparative study of the gut bacterial composition of 68 individuals of Carnivora species from different geographical locations and diet underscore the role of diet and geography in shaping the Panthera gut microbiome, which is significant for the health and conservation management of these highly endangered species.

Keywords: Indian Panthera; big cats; gut microbiome; hypercarnivores; metagenomics.

FIGURE 1

The alpha diversity estimates from (A) V3 hypervariable region of 16S rRNA and (B) ITS-1 amplicon sequences. The left charts show the rarefaction curves of the number of observed operational taxonomic units (OTUs) with respect to the number of sequences. The box plots in the right show the Shannon index estimates using the maximum number of sequences.

FIGURE 2

Bar plots showing the topmost abundant bacterial genera present in the Panthera gut microbiome. The genera with more than 1% abundance are shown.

FIGURE 3

Bar plots showing the topmost abundant fungal genera present in the Panthera gut microbiome. The genera with more than 1% abundance are shown.

FIGURE 4

Bar plots showing the topmost abundant virus families present in the Panthera gut microbiome. The families with more than 1% abundance are shown.

FIGURE 5

Box plots showing the top 10 most abundant functional pathways identified using the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation in gut (bacterial) microbiome of lion (green), leopard (orange), Bengal tiger (red), and Amur tiger (blue).

FIGURE 6

Differences in the fecal microbial communities of Panthera species using dimensionality reduction methods. (A) Principal coordinates analysis (PCoA) plot of weighted UniFrac distances of gut bacteria of the 21 individuals. (B) Principal component analysis (PCA) plot of gut bacterial composition of Indian leopard (this study), Amur, and North Chinese leopards (data from previous studies). (C) PCoA plot of Hellinger distances calculated using functional profile [Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthologs] in the 21 Panthera individuals (this study) and six Amur tigers.

FIGURE 7

Principal component analysis (PCA) plot showing the differences in the fecal microbial communities of 62 Carnivora individuals explaining 17% of the total variance. Fox (violet color) formed a separate cluster from all other species.