Microbiome analysis and detection of pathogenic bacteria of Penaeus monodon from Jakarta Bay and Bali

•Metagenomics of Indonesian shrimp feces under different environmental conditions.•Metagenomics were performed by qPCR and MiSeq.•Analysis comprised both bacterial communities and viruses.•Free-living shrimp from Bali and Jakarta Bay revealed different microbial communities.•Analysis revealed information on shrimp and human pathogens.

Penaeus monodon, the Asian black tiger shrimp is one of the most widely consumed marine crustaceans worldwide. In this study, we examine and compare the fecal microbiota of P. monodon from highly polluted waters around Jakarta Bay, with those of less polluted waters of Bali. Using next generation sequencing techniques, we identified potential bacterial pathogens and common viral diseases of shrimp. Proteobacteria (96.08%) was found to be the most predominant phylum, followed by Bacteriodetes (2.32%), Fusobacteria (0.96%), and Firmicutes (0.53%). On the order level, Vibrionales (66.20%) and Pseudoaltermonadales (24.81%) were detected as predominant taxa. qPCR profiling was used as a confirmatory step and further revealed Vibrio alginolyticus and Photobacterium damselae as two potential pathogenic species present in most of the samples. In addition, viral diseases for shrimp were discovered among the samples, WSSV in Jakarta free-living samples, YHV in Bali free-living samples and IHHNV in both.