The intestinal microbiome of an Indo‐Pacific humpback dolphin (Sousa chinensis) stranded near the Pearl River Estuary, China

Abstract

The mammalian intestinal microbiome is critical for host health and disease resistance. However, the cetacean intestinal microbiota remains relatively unexplored. By using high-throughput 16S rRNA gene sequencing, we analyzed intestinal bacterial samples from an Indo-pacific humpback dolphin (Sousa chinensis) stranded near the Pearl River Estuary in China. The samples included 3 anatomical regions (foregut, midgut, and rectum) and 2 anatomical locations (content and mucus). Our analyses revealed that the dolphin intestinal bacteria contained 139 operational taxonomic units (OTUs), dominated at the phyla level by Firmicutes (47.05% in the content; 94.77% in the mucus), followed by Bacteroidetes (23.63% in the content; 1.58% in the mucus) and Gammaproteobacteria (14.82% in the content; 2.05% in the mucus). The intestinal bacteria had a small core community (15 OTUs, accounting for 99.74% of the reads), some of which could be potentially pathogenic to both human and dolphins. As an alternative to sampling the dolphin intestinal bacteria, fecal sampling could be used. Additionally, function potentials such as, xenobiotics biodegradation, beta-lactam resistance, and human disease-related pathways, were detected in the dolphin intestinal bacteria. These findings provide the first baseline knowledge of the intestinal microbiome of the Indo-Pacific humpback dolphin, which may offer new insights into cetacean conservation by using microbial surveillance.

Habitats Show More Impacts Than Host Species in Shaping Gut Microbiota of Sympatric Rodent Species in a Fragmented Forest

“…Gut microbiota are likely shaped by diverse host factors, such as behavioral (i.e., social contact patterns), heritable (e.g., evolutionary history and genetics), and environmental (e.g., diet and geography; Kasper, 2014;Perofsky et al, 2019;Li et al, 2021;Wan et al, 2021). In this study, our results showed that the diversity of gut microbiota in L. edwardsi was significantly different from those of A. draco and N. confucianus, while the interspecific differences of the other three rodent species were not significant, which support our first hypothesis.…”

Microbial diversity and structure in the gastrointestinal tracts of two stranded short‐finned pilot whales (Globicephala macrorhynchus) and a pygmy sperm whale (Kogia breviceps)

“…Studies on the microbial diversity and composition in the gastrointestinal tracts of cetaceans are very few. To our knowledge, only 3 papers investigated the microbial communities in different regions of the gastrointestinal tracts in cetaceans (Wan et al 2018(Wan et al , 2020Tian et al 2020).…”

Functional Diversity within Gut Microbiomes: Implications for Conserving Biodiversity

“…Samples can be taken post-mortem [117] or under sedation [118]; however, there are obvious animal welfare implications for these, something that is especially relevant in studies of protected species. Opportunistic sampling from deceased individuals can be useful if internal sampling is of particular importance [119]. Scat sampling is an invaluable tool for sampling the gut microbiome as it is non-invasive and can, in many cases, be done without trapping or handling the host animal.…”

“…For example, cetaceans are incredibly hard to sample due to their vast ranges and the inaccessibility of many feeding grounds to researchers. As a result, many samples are opportunistically collected from necropsies of beached individuals [119,129]. This opportunistic sampling can be an excellent tool to supplement traditional sampling of wild populations and help overcome the challenges of small samples sizes.…”