The aquatic organisms in peat swamp forests are under threat due to habitat degradation resulting from human activities. This study determines the fish gut microbes’ diversity, composition, taxa biomarkers, and functional genes in peat swamp forests and its converted areas in North Selangor, Malaysia. Three undisturbed and disturbed areas nearby the peat swamp forests were selected. First, the 16S amplicon metagenomic analysis was conducted to assess the composition and diversity of bacterial communities in fish gut contents from both areas. Then, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and Linear discriminant analysis Effect Size (LEfSe) were used to predict disease/pathogen related functional genes. This study revealed Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Actinobacteria as the predominant phyla in both studied areas. In contrast, bacterial community profiles of disturbed and undisturbed areas were slightly dissimilar. Metagenome predictions revealed that genes are related to metabolism, environmental information processing, genetic information processing, cellular processes, human diseases, and organismal systems. Further investigation revealed six potential biomarker genes, including chronic myeloid leukaemia in an undisturbed area, Vibrio cholerae infection, bladder cancer, pathogenic Escherichia coli infection, Staphylococcus aureus infection, and pertussis in disturbed areas. This study revealed that the fish gut microbiome could be used as an indicator in comparing the undisturbed and disturbed ecosystems.

Grouper and Asian seabass are among the economically important cultured marine fish in Malaysia. However, fry productions in large scale tend to introduce stress that changes the fish microbiota and increases susceptibility to diseases. Currently, high-throughput sequencing is used to study fish microbiota and their respective gene functions. In this study, we investigate the diversity, abundance and functional genes of intestinal microbiota of tiger grouper and Asian seabass that were reared in a semi-closed hatchery during dry and wet seasons. Intestinal samples were collected from tiger grouper and Asian seabass of different sizes before proceeded to DNA extraction. The extracted DNA were then subjected to 16S rRNA gene amplicon sequencing using the Illumina Miseq platform targeting V3 and V4 regions for determination of the bacterial diversity, abundance and functional genes in both seasons. The results revealed that intestinal microbiota of Asian seabass were dominated by the phylum Proteobacteria and order Vibrionales in both seasons. Meanwhile, intestinal microbiome of tiger groupers were shifted from domination of phylum Firmicutes and order Clostridiales in dry season to Proteobacteria and order Lactobacillales in wet season. PICRUSt analysis revealed that the functional genes that were dominantly present were the genes encoded for metabolism, genetic information processing, environmental information processing, cellular process and human diseases. Remarkably, SIMPER analysis showed several potential metagenomics biomarker genes in dry and wet seasons. This study revealed the importance of utilizing amplicon metagenomics approaches in microbiome studies for better identification of the microbial profiling in aquaculture systems.