Fecal Bacterial Composition of the Endangered Yangtze Finless Porpoises Living Under Captive and Semi-natural Conditions

Abstract

Intestinal microbiota is essential to the health and physiology of host animals. We undertook the first microbiological study of the fecal bacterial composition from critically endangered (CR) Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis; YFPs) living under captive and semi-natural conditions using both high-throughput sequencing method and 16S rRNA gene clone library method. As determined by high-throughput sequencing of V3-V4 regions of the 16S rRNA gene, seminatural samples harbored 30 and 36 operational taxonomic units (OTUs), which was more than the 22 and 27 OTUs detected from YFPs living in captivity. In captive YFPs Firmicutes was the predominant phylum, whereas this was Proteobacteria for YFPs living in semi-nature conditions. This suggests habitat-specific fecal bacterial composition of YFPs. Plesiomonas spp. and Aeromonas spp., which are potentially pathogenic, were identified in all the feces. Bacterial diversity from one porpoise living in captivity was also determined by constructing a 16S rRNA gene clone library and only 1 phylum was identified. Highthroughput sequencing was more effective at determining the bacterial diversity compared to the 16S rRNA gene clone library. This study provides important information for the management and conservation of the CR YFPs.

Conservation Implications of Shifting Gut Microbiomes in Captive-Reared Endangered Voles Intended for Reintroduction into the Wild

“…Bray-Curtis distances showed that wild-captured samples clustered on their own while colony and colony-transitional samples clustered together ( Figure 4 a). This is in line with previous studies that show different microbial diversity and community structure in captive vs wild conspecifics [ 28 , 48 , 68 , 69 ]. PLS-DA analysis also indicated separation of wild-captured samples ( Figure 2 a).…”

Microbial communities in different regions of the gastrointestinal tract in East Asian finless porpoises (Neophocaena asiaeorientalis sunameri)

“…In previous studies, fecal samples were used to determine the microbiota present in the GI tract of cetaceans 13–17 . This was mainly due to the ease of sample collection compared to the invasive procedures required to collect samples from other GI regions.…”

Characterization, optimization, and validation of environmental DNA (eDNA) markers to detect an endangered aquatic mammal

“…Sampling locales for the Wuhan Baiji Dolphinarium (WBD; 30°31′28 N, 114°22′58E), Tian e-Zhou Baiji National Nature Reserve (TEZ; 29°51′11 N, 112°35′15E), and Gonghuwan lake for the negative control (31°27′21 N, 120°20′E) are illustrated using a grey circular marker. Map has been modified with permission from Wan et al (2016) time of sampling, the reserve contained a floating net cage (approximately15 × 15 m) with two YFPs being temporarily housed for breeding research. This area was connected to the rest of the oxbow reserve, where approximately 58 other YFPs live.…”