The Microflora Structure in the Digestive Tract, Culture Water, and Feed of Hybrid Grouper (Epinephelus fuscoguttatus♀ × E. polyphekadion♂) Cultured in an Outdoor Pond Based on a High-Throughput Sequencing Technique

Abstract

Nutrition, disease, and general wellbeing can be affected by the microbial communities associated with the digestive tracts of aquaculture species. Different sections of aquaculture species’ digestive tracts have distinctive surfaces and structures, which can change microbial communities. The present study examined the composition and distribution of bacterial species in the intestine of hybrid grouper (Epinephelus fuscoguttatus E. polyphekadion) and its aquaculture environment. Using high-throughput pyrosequencing, a 16S rRNA sequence analysis was performed on hybrid grouper foregut, midgut, and hindgut, as well as cultured water and feed. There were 610,452 sequences obtained from five components (foregut, midgut, hindgut, water, and feed). Among operational taxa (OTUs), 506 of them were detected in the foregut, 605 in the midgut, 510 in the hindgut, and 573 in aquaculture water and feed samples. A total of 113 were detected in 5 samples. A species annotation revealed that hybrid grouper intestinal tracts were dominated by Proteobacteria (67.3%–73.7%), Firmicutes (8.4%–14.0%), and Actinobacteria (6.9%–10.5%). In aquaculture culture water, Proteobacteria were predominant (36.3%), Actinobacteria (30.0%), and Planctomycetes (14.0%). Acinetobacter (1.4%–17.9%) and Photobacterium (32.0%–57.5%) dominated the intestine. Photobacterium (3.6%) and Mycobacterium (7.1%) dominated the water bacteria. The water and intestine contained five potentially pathogenic bacteria: Pseudomonas, Flavobacterium, Escherichia coli, Aeromonas bacteria, and Vibrio. The highest proportion of Vibrio was found in the water (1.7%), while Pseudomonas dominated the midgut (2.6%). Six potential probiotics were detected in the aquaculture water and intestine (Lactococcus, Streptococcus, Bdellovibrio, Lactobacillus, Bacillus, and Bacteroides). Aquaculture water and intestines contained Bacillus, Bacteroides, and Lactobacillus. According to the findings, the intestinal flora of hybrid grouper is closely correlated with its pond culture environment. Results from the study provide an experimental basis for the controlled breeding of hybrid groupers and the regulation of their microecological processes in the breeding environment deepen our understanding of the intestinal bacterial population of healthy hybrid groupers.