Metagenomic analysis of gut microbiome and resistome of Whooper and Black Swans: a one health perspective

Abstract

Background: With the promotion of "One Health," the health of animals and their impact on the environment have become major concerns recently. Widely distributed in China, the whooper swans (Cygnus cygnus) and black swans (Cygnus atratus) are not only important to the ecological environment, but they may also potentially influence public health security. The metagenomic approach was adopted to uncover the impacts of the gut microbiota of swans on host and public health.

Results: In this study, the intestinal microbiome and resistome of migratory whooper swans and captive-bred black swans were identified. The results revealed similar gut microbes and functional compositions in whooper and black swans. Interestingly, different bacteria and probiotics were enriched by overwintering whooper swans. We also found that Acinetobacter and Escherichia were significantly enriched in early wintering period swans and that clinically important pathogens were more abundant in black swans. Whooper swans and black swans are potential reservoirs of antibiotic resistance genes (ARGs) and novel ARGs, and the abundance of novel ARGs in whooper swans was significantly higher than that in black swans. Metagenomic assembly-based host tracking revealed that most ARG-carrying contigs originated from Proteobacteria (mainly Gammaproteobacteria).

Conclusions: The results revealed spatiotemporal changes in microbiome and resistome in swans, providing a reference for safeguarding public health security and preventing animal epidemics.

Keywords: Black swan; Microbiome; Resistome; Whooper swan.

Fig. 1

Comparison of gut microbiota and functional genes between whooper swans and black swans. (a) PCoA of gut microbiota. (b) Alpha diversity (Chao1 and Shannon indices) of gut microbiota. (c) PCoA of the functional genes. (d) alpha diversity (Chao1 and Shannon index) of functional genes. The PCoA was based on the Bray–Curtis distance. Boxes of alpha diversity denote the interquartile range (IQR) between the first and third quartiles (25th and 75th percentiles, respectively), and the line inside denotes the median. Whiskers denote the lowest and highest values within 1.5 times and the IQR from the first and third quartiles, respectively

Fig. 2

Biomarkers of intestinal microbes in whooper swans during overwintering. (a) Cladogram diagram showing the gut microbiota with significant differences among the three groups. Red, green, and blue indicate different groups, with the species classification at the phylum, class, order, family, and genus levels shown from inside to outside. (b) Plot of LEfSe data: The length of the bar column represents the LDA score

Fig. 3

Distribution of pathogens in whooper and black swans. (a) Relative abundance of the top 10 germs in whooper swans and black swans. (b) Overall abundance of viral families identified in whooper and black swans. Families of viruses that can cause disease in animals are marked in red. The results were analyzed and visualized using the taxonomy database of the National Center for Biotechnology Information (NCBI). The length of the bar corresponds to the total number of reads in 28 samples

Fig. 4

Distribution of antimicrobial resistance protein-coding genes in bacteria at different taxonomic levels. The rectangles represent different taxonomic levels. The height of the rectangles indicates the number of ARGs

Fig. 5

Different ARGs and novel ARGs between whooper swans and black swans and between whooper swans from different years. (a) Alpha diversity (Chao1 and Shannon index) of ARGs between whooper swans and black swans. (b) Relative abundance difference of novel ARGs between whooper swans and black swans. (c) Alpha diversity (Chao1 and Shannon index) of ARGs between whooper swans from different years. (d) Relative abundance of novel ARGs genes in whooper swans from different years. Boxes of alpha diversity denote the interquartile range (IQR) between the first and third quartiles (25th and 75th percentiles, respectively), and the line inside denotes the median. Whiskers denote the lowest and highest values within 1.5 times and the IQR from the first and third quartiles, respectively. The whiskers in the histogram denote the standard error, and the P-value was analyzed using a homogeneity test of variance