Bacterial Flora in the Gill Tissues and Intestinal Tracts of Male and Female Chinese Mitten Crabs (Eriocheir sinensis) with Different Diets in a Mud Pond.

The Chinese mitten crab, Eriocheir sinensis, is an economically valuable aquaculture species. Prior to sale, farmed crabs are often fattened with pellet feed or wild fish. In this study, PacBio Sequel sequencing was used to determine the bacterial flora in the intestinal tracts and gill tissues of male and female E. sinensis fed with various diets. The flora was then compared with the microorganisms found in environmental samples. The results showed that Proteobacteria was the dominant phylum in both tissue and environmental samples. The relative abundances of Proteobacteria in the water grass surface flushing samples and water grass samples were the highest, at up to 95.68% and 67.85%, respectively. Beyond that, Bacteroidetes, Firmicutes, and Tenericutes were the dominant phyla (>1%) in the intestinal samples, whereas Bacteroidetes and Actinobacteria were the dominant phyla in the gills. In addition, different environment samples contained diverse bacterial phyla, indicating some differences in the community composition between the different sample groups. Heat map clustering and principal coordinate plot analyses indicated that intestinal samples, crab gill samples, and environmental samples clustered together, respectively. Furthermore, an unweighted pair-group method with arithmetic mean technique confirmed that the intestinal and gill samples of crabs with different diets separately clustered together, suggesting the microbial assemblages of the same tissues share a greater similarity than those from crabs of different sex and eating different diets. What’s more, biomarker bacteria (LDA ≥ 4) from the different groups were identified. Pathogenic agents from the genus Aeromonas were abundant in the intestinal samples of crabs fed with pellet feed, and Vibrio species were prevalent in the intestinal samples of crabs fed with wild fishes.