At the phylum level, the dominant phyla in all groups were Proteobacteria, Chloroflexi, Actinobacteria, Firmicutes, Cyanobacteria, Bacteroidetes,Acidobacteria, Verrucomicrobia,Saccharibacteria.Proteobacteria were the most abundant and largest phylum except in the intestine of marine cultured shrimp and Actinobacteria may be enriched in the shrimp intestine from sediment.