Bacterial community composition and distribution in different segments of the gastrointestinal tract of wild‐caught adult Penaeus monodon

Bacterial community associated with the gastrointestinal (GI) tract of aquaculture animals can play important roles in health, nutrition and disease. Compared with the GI tract of aquatic vertebrates such as fish, crustacean GI tract has unique structures and surfaces in different segments that may contribute to differences in the bacterial communities. This study examined the bacterial composition and distribution in different segments along the GI tract and in digesta of wild‐caught adult Penaeus monodon using Automated Ribosomal Intergenic Spacer Analysis (ARISA), real‐time quantitative PCR and clone libraries of 16S rRNA genes. Thirty‐nine bacterial species in four phyla including Proteobacteria (α, β, ε, γ), Firmicutes, Bacteroidetes and Actinobacteria were represented in the GI tract of adult P. monodon. Proteobacteria comprised over 80% abundance of the bacterial community in most segments of the GI tract, except the middle intestine that was dominated by Firmicutes (~50% abundance). The results also showed that bacterial communities showed significant differences along the GI tract segments, particularly the hindgut (p < .001) with Vibrio and Ferrimonas as dominant genera. The knowledge about the distribution of bacteria could be useful in understanding interaction of commensal bacteria and pathogens in different segments, and its potential influence on the effectiveness of probiotic bacteria in the GI tract of shrimp.