Comparative Analysis of Microbial Community Structure and Function in the Gut of Wild and Captive Amur Tiger

Abstract

It has been well acknowledged that the gut microbiome is important for host health, composition changes in these microbial communities might increase susceptibility to infections and reduce adaptability to environment. Reintroduction, as an effective strategy for wild population recovery and genetic diversity maintenance for endangered populations, usually takes captive populations as rewilding resource. While, little is known about the compositional and functional differences of gut microbiota between captive and wild populations, especially for large carnivores, like Amur tiger. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function variations of gut microbiota communities between captive and wild Amur tiger populations based on total 35 fecal samples (13 from captive tigers and 22 from wild tigers). Our results showed that captive Amur tigers have higher alpha diversity in gut microbiota, but that the average unweighted UniFrac distance of bacterial taxa among wild Amur tigers was much larger. The function differences involve most aspects of the body functions, especially for metabolism, environmental information processing, cellular processes, and organismal systems. It was indicated that the diet habit and environment difference between captive and wild populations lead to composition differences of gut microbiota and then resulted in significant differences in functions. These contrasts of functional and compositional variations in gut microbiota between wild and captive Amur tigers are essential insights for guiding conservation management and policy decision-making, and call for more attention on the influence of gut microbiota on the ability of captive animals to survive in the wild.

Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

“…Functions related to metabolism, environmental information, and human diseases had higher abundance in the free-range deer. This was likely because the free-range deer had more opportunities to eat more diverse types of food (especially regarding greenfeed), faced more environmental challenges, and had a greater risk of infection, which is in line with previous studies ( 28 , 29 ). All the metabolism KEGG level 2 subcategories, including the metabolism of amino acids, carbohydrates, nucleotides, and xenobiotics, were more abundant in the free-range deer.…”

Possibilities and limits for using the gut microbiome to improve captive animal health

“…There are alternative interpretations of microbial differences between wild and captive animals that do not presume the captive microbiome is less favorable [e.g. 35 , 86 – 88 ] or potentially detrimental [ 1 ]; these are important to consider in the absence of species-specific experimental evidence. First, microbiomes may have changed to match the new captive environment in a beneficial manner [ 89 ].…”

Compound Probiotics Improve the Diarrhea Rate and Intestinal Microbiota of Newborn Calves

“…The bacterial 16S rRNA gene's hypervariable V3-V4 areas were amplified with the primer sequence 338F (5 -ACTCCTACGGGAGGCAGCAG-3 ) and 806R (5 -GGACTACHVGGGTWTCTAAT-3 ) using an ABI GeneAmp ® 9700 PCR thermocycler (Applied Biosystems, Foster City, CA, USA). The 16S rRNA gene's PCR amplification was carried out according to the design of the Ning et al [12]. The PCR mixtures contained 4 µL of 5× TransStart FastPfu buffer, 2 µL of 2.5 mM dNTPs, 0.8 µL each of the forward and inverse primers (5 µM each), 0.4 µL of TransStart FastPfu DNA polymerase, 10 ng of template DNA, and ddH2O up to 20 µL.…”