Significant Differences in Intestinal Microbial Communities in Aquatic Animals from an Aquaculture Area

Abstract

While much attention has been given to the role of animal intestinal microbes, few studies have focused on microbial communities and associated functions in cultured aquatic animals. In this study, high–throughput sequencing was used to analyze intestinal microbial communities and functions in fish, shrimp, crab and razor clams. Alpha diversity analyses showed significant differences in intestinal microbial diversity amongst these aquatic animals, and that shrimp intestines harbored the highest diversity and species numbers. T–test analyses (p < 0.05) showed significant differences in dominant microbial operational taxonomic units (OTUs) between all aquatic animals. Predominant intestinal bacteria included; Gammaproteobacteria, Fusobacteria, Mollicutes, Spirochaetia, Cyanobacteria, Bacteroidia and Bacilli. Similarly, anaerobic bacteria were highly diverse in animal intestines and included; Vibrio, Photobacterium, Cetobacterium, Propionigenium, Candidatus Hepatoplasma, Paraclostridium, and Lactobacillus. Principal co–ordinate analysis indicated that the distribution characteristics of intestinal microbes varied with animal species; in particular, we observed a high variability among shrimp intestinal samples. This variability indicated these genera had suitability for the different intestinal environment. Function prediction analysis indicated significant differences amongst different animals in the major functional groups, and that microbial functional profiles were strongly shaped by the intestinal environment. Thus, this study provides an important reference for future studies investigating crosstalk between aquatic animal hosts and their intestinal microbiota.