Changes in the fecal microbiome of the Yangtze finless porpoise during a short-term therapeutic treatment

Abstract

The fecal microbiome is an integral part of aquatic mammals, like an inner organ. But we know very little about this inner organ of the threatened aquatic species, Yangtze finless porpoise (YFP). Four YFPs were placed into a purse seine for skin ulceration treatment, and this opportunity was taken to nurse the animals closer. In particular, we collected the feces of the YFPs before and after the paired healing and therapeutic treatment, along with samples of their fish diet and water habitat, to explore the changes in their fecal microbiome. Firmicutes (20.9-96.1%), Proteobacteria (3.8-78.7%), Actinobacteria (0.1-35.0%) and Tenericutes (0.8-17.1%) were the most dominant phyla present in the feces. The proportion of Proteobacteria and Actinobacteria increased after the treatment. Firmicutes showed a significant decrease, and most potential pathogens were absent, which reflected the administration of ciprofloxacin hydrochloride. Moreover, environmental shifts can also contribute to changes in the fecal microbiome. These results indicate that certain microbial interactions can be affected by environmental shifts, dietary changes and health-care treatments, which can also help maintain the internal environment of YFPs. These findings will inform the future enhanced protection and management of endangered YFPs and other vulnerable aquatic animals.

Keywords: Yangtze finless porpoise; fecal microbiome; potential pathogens; therapeutic treatment.

Figure 1

The typical appearance of YFP before and after treatment. (a) YFP before treatment and (b) YFP after treatment.

Figure 2

Relative abundance of bacterial phyla in fish, water and intestines. FH group represents feces of animals in the FH group, and FT represents feces of animals under human intervention. F represents fish samples, and W represents water samples.

Figure 3

Weighted PCoA based on UniFrac distance in different groups. (a) Grouped by individual YFPs; (b) grouped by whether the animal obtained the therapeutic treatment. F represents fish samples and W for water samples.

Figure 4

Changes in microbiome phyla of fecal samples throughout the therapeutic treatment: (a) Firmicutes, (b) Proteobacteria, (c) Actinobacteria and (d) Tenericutes.

Figure 5

The Circos diagram of YFP sample groups: (a) phylum level and (b) genus level. UC represents unclassified. FH group represents feces of animals in the FH group, and FT represents feces of animals under human intervention.

Figure 6

Heatmap analysis of potential pathogen genera of all samples. The color of the bar represents the abundance of each bacteria species in all samples. The longitudinal clustering indicates the similarity of all species among different samples.

Figure A1

Rarefaction curves of intestinal contents, fish and water samples based on high throughput sequencing.

Figure A2

Neighbor-Joining tree showing sequences difference between OTUs of YFPs and pathogen species of Mycobacterium. Part A means that OTUs of YFPs in Mycobacterium; part B means OTUs with high significance level before and after the short-term feeding treatment; the remaining 43 branches are pathogens of Mycobacterium according to the data reported before.