Metagenomic analysis of captive Amur tiger faecal microbiome

Abstract

BackgroundThe gastrointestinal tracts of animals are home to large, complex communities of microbes. The compositions of these communities ultimately reflect the coevolution of microorganisms with their animal host and are influenced by the living environment, diet and immune status of the host. Gut microbes have been shown to be important for human disease and health, but little research exists in the gut microbiome of the Amur tiger, which is one of the most endangered species in the world.ResultsIn this study, we present the use of whole-metagenome shotgun sequencing to analyze the composition and functional structures of the gut microbiota in captive Amur tigers. Our results showed a high abundance of four major phyla in captive Amur tigers, including Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. Moreover, at the genus level, Escherichia, Collinsella and Fusobacterium were most abundant in the captive Amur tiger fecal metagenome. At the species level, Escherichia coli, Fusobacterium ulcerans and Fusobacterium varium were the species with highest abundances in the captive Amur tiger gut microbiota. The primary functional categories of the Amur tiger faecal metagenome were associated mainly with Carbohydrate metabolism, Membrane transport and Amino acid metabolism based on the KEGG pathway database. The comparative metagenomic analyses showed that the captive Amur tiger fecal metagenome had a lower abundance of Spirochaetes, Cyanobacteria and Ascomycota than other animals, and the primary functional categories were primarily associated with carbohydrate metabolism subsystems, clustering-based subsystems and protein metabolism.ConclusionsWe presented here for the first time the use of the shotgun metagenomic sequencing approach to study the composition and functional structures of the gut microbiota in captive Amur tiger.Electronic supplementary materialThe online version of this article (10.1186/s12917-018-1696-5) contains supplementary material, which is available to authorized users.

Gut microbiota and fecal metabolites in captive and wild North China leopard (Panthera pardus japonensis) by comparsion using 16 s rRNA gene sequencing and LC/MS-based metabolomics

“…In addition, Fusobacteria was the major phylum in captive leopard. Firmicutes, Bacteroides, Actinobacteria and Proteobacteria were the main microbes of the captive and wild leopards, consistent with the results of studies on other carnivores, such as snow leopard [19,20], wolves [21], Amur tiger [22], Amur leopard and cheetahs [19][20][21][22][23][24][25][26]. Fecal samples of healthy domestic cats (Felis catus) [27]and snow leopard (Panthera uncia) [19,20,28] featured similar phylum compositions with slightly different proportions.…”

Gut microbiota and fecal metabolites in captive and wild North China leopard (Panthera pardus japonensis) by comparsion using 16s rRNA gene sequencing and LC/MS-based metabolomics

“…In addition, Fusobacteria was the major phylum in captive leopard. Firmicutes, Bacteroides, Actinobacteria and Proteobacteria were the main microbes of the captive and wild leopards, consistent with the results of studies on other carnivores, such as snow leopard [19,20], wolves [21], Amur tiger [22], Amur leopard and cheetahs [25,26] [19][20][21][22][23][24][25][26]. Fecal samples of healthy domestic cats (Felis catus) [27]and snow leopard (Panthera uncia) [19,20,28] featured similar phylum compositions with slightly different proportions.…”

Gut microbiota and fecal metabolites in captive and wild North China leopard (Panthera pardus japonensis) by comparsion using 16s rRNA gene sequencing and LC/MS-based metabolomics

“…In addition, Fusobacteria was the major phylum in captive leopard. Firmicutes, Bacteroides, Actinobacteria and Proteobacteria were the main microbes of the captive and wild leopards, consistent with the results of studies on other carnivores [19][20][21][22][23][24][25][26]. Fecal samples of healthy domestic cats (Felis catus) [27]and snow leopard(Panthera uncia) [19,20,28] featured similar phylum compositions with slightly different proportions.…”