Taxonomic composition and functional potentials of gastrointestinal microbiota in 12 wild-stranded cetaceans

Abstract

Cetaceans play a crucial role in marine ecosystems; however, research on their gastrointestinal microbiota remains limited due to sampling constraints. In this study, we collected hindgut samples from 12 stranded cetaceans and performed 16S rRNA gene amplicon sequencing to investigate microbial composition and functional potentials. Analysis of ZOTUs profiles revealed that the phyla Firmicutes, Proteobacteria, and Bacteroidetes dominated all hindgut samples. However, unique microbial profiles were observed among different cetacean species, with significant separation of gut microbiota communities according to biological evolutionary lineages. Different genera that contain pathogens were observed distinguishing delphinids from physeteroids/ziphiids. Delphinid samples exhibited higher abundances of Vibrio, Escherichia, and Paeniclostridium, whereas physeteroid and ziphiid samples showed higher abundances of Pseudomonas, Enterococcus, and Intestinimonas. Functional analysis indicated convergence in the gut microbiota among all cetaceans, with shared bacterial infection pathways across hindgut samples. In addition, a comparison of the gastrointestinal microbial composition between a stranded short-finned pilot whale (Globicephala macrorhynchus) and a stranded rough-toothed dolphin (Steno bredanensis) using 16S rRNA gene sequencing revealed distinct microbial community structures and functional capacities. To the best of our knowledge, this study represents the first report on the gastrointestinal microbiota of the pantropical spotted dolphin (Stenella attenuata), Blainville's beaked whale (Mesoplodon densirostris), and rough-toothed dolphin, with various comparisons conducted among different cetacean species. Our findings enhance the understanding of microbial composition and diversity in cetacean gastrointestinal microbiota, providing new insights into co-evolution and complex interactions between cetacean microbes and hosts.

Keywords: delphinids; food digestion; functional potentials; gastrointestinal microbiota; gut microbiota; physeteroids and ziphiid; stranded cetaceans.

Figure 1

Stranded cetaceans sampling area. The red dots indicate the sampling locations in the coastal areas of southern China, mainly distributed in the Hainan Provinces, Guangdong Provinces, Fujian Provinces, and Guangxi Zhuang Autonomous Region.

Figure 2

Phylogenetic tree of prokaryotic ZOTUs and distribution of relative abundances in the 12 hindgut samples. Relative abundance heatmap values are −log10 transformed. The outside circles represent the phylum and family taxonomic classification of the ZOTUs.

Figure 3

Gut microbiota composition differs among cetacean individuals. (A) PCoA of 12 hindgut samples at the ZOTU level based on Bray Curtis distances. (B) Boxplot showing the comparison of the α-diversity indices Chao1 index between the eight delphinid samples and four physeteroid and ziphiid samples. (C,D) The stacked bar chart shows the average prokaryotic relative abundance of hindgut samples at the phylum and genus level of the two cetacean lineages. (C) A comparison of the microbiota of delphinids, physeteroids, and ziphid and the phylum level. A total of 13 phyla were detected, while the unclassified taxa were named “Unassigned.” (D) A comparison of the microbiota of delphinids, physeteroids, and ziphid and the genus level. A total of 128 genera were detected, only the top 15 most abundant genera are shown here, and the remaining genera including unclassified taxa were grouped as “Other”.

Figure 4

Predicted functional potential of the cetacean hindgut microbiota. (A,B) PCoA based on the Bray Curtis distance of KEGG pathways and enzyme functional abundance profiles, respectively. (C) A total of 43 enzymes were over-represented for the two cetacean lineages.

Figure 5

Taxonomic composition of four Indo-Pacific humpback dolphins. (A,B) Comparisons of α-diversity indices, including Chao1 index (A) and Shannon index (B), of the four Indo-Pacific humpback dolphins stranded in Qinzhou City and Zhanjiang City. (C,D) Stacked bar chart showing the average relative abundance at the phylum (C) and genus (D) levels for the four Indo-Pacific humpback dolphin hindgut samples.

Figure 6

Comparisons of the prokaryotic diversity and composition in the gastrointestinal tract of rough-toothed dolphin and short-finned pilot whales. (A,B) Boxplots showing the α-diversity indices comparisons, including Chao1 index (A) and Shannon index (B), of the gastrointestinal tract samples from rough-toothed dolphin (SB) and four from the short-finned pilot whale (GM). (C) PCoA based on the Bray Curtis distance to visualize the structure of prokaryotic communities in the stomach (GMS1, GMS2, and GMS3), foregut (GMFG), and hindgut (GMHG) of GM samples and stomach (SBS1 and SBS2), foregut (SBFG), and hindgut (SBHG) of SB samples. (D) Stacked bar chart showing the prokaryotic relative abundance in the stomach, foregut, and hindgut samples of GM and SB at the genus level. (E) Prokaryotic biomarkers significantly enriched in the GM and SB gastrointestinal tract samples determined by the linear discriminant analysis effect size (LEfSe) analysis.

Figure 7

Comparative analyses of potential functions in the stomach, foregut, and hindgut of the short-finned pilot whale (GM) and rough-toothed dolphin (SB) gastrointestinal samples. (A) PCoA based on the Bray Curtis distance of the KEGG pathway functional profiles of the two delphinids. (B) PCoA based on the Bray Curtis distance of the enzyme profiles. (C) Relative abundance heatmap of 55 KEGG pathways significantly enriched in stomach samples from the two delphinids.