Uncovering the taxonomic composition and functional capacity within the intestine microbial consortia of fishes under different conditions is of great importance to fish physiology and health. Nonetheless, no detailed information on the functional diversity of the fish intestine metagenomes in response to stress is available. The Asian seabass Lates calcarifer is an important farmed foodfish species, inhabiting coastal waters, estuaries, lagoons and rivers, widely distributed in the Indo-West Pacific region (FishBase: www.fishbase.org). This species feeds on crustaceans, molluscsmollusks, and smaller fish. In our study, we challenged Asian seabass with pathogens, salinity and fast conditions, and sequenced metagenomic DNA isolated from the fish post stressor challenge with the illumina high throughput sequencing technique platform.By using comparative metagenomic studies and analyses of selected gene sets by quantitative PCR, we determined the microbial gene catalogue and investigated the changes of the microbial composition and the host-microbe interactions in response to different stressors in the Asian seabass intestines.