ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/005/SRR2075955/SRR2075955_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/008/SRR2075958/SRR2075958_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/006/SRR2075886/SRR2075886_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/006/SRR2075956/SRR2075956_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/003/SRR2075953/SRR2075953_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/009/SRR2075959/SRR2075959_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/005/SRR2075955/SRR2075955_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/009/SRR2075959/SRR2075959_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/008/SRR2075958/SRR2075958_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/006/SRR2075886/SRR2075886_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/006/SRR2075956/SRR2075956_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/003/SRR2075953/SRR2075953_1.fastq.gzprimaryOK200GenomicsLeibniz Institue for Natural Product Research and Infection Biology - Hans Knoell Institutehttps://www.ebi.ac.uk/ena/browser/view/PRJNA287496fish gut metagenomeIn this metagenomic study, we analysed parasites and bacterial communities of three important Indonesian food fish species, Epinephelus fuscoguttatus, E. sexfasciatus andAtule mate. We compared the biodiversity of parasites and bacterial communities among fishes collected in the highly polluted Jakarta Bay, less polluted Indonesian areas and from inside and outside a net cage in an open water mariculture facility. We focussed on parasites, core and shared microbiomes. The data revealed that the core microbiomes of phylogenetically closely and distantly related fish species were similar, the microbial biodiversity of distantly related fish species from the same area was closer related than of closer related species from a different region. Load of microbial pathogens correlated with a decreased number of endoparasites. Of overall three recorded pathogenic bacteria genera, Vibrio sp. was found preferentially in E. fuscoguttatus from mariculture, less in the vicinity of the net cage and much less in the fishes from the heavily polluted waters from Jakarta Bay. Flavobacterium sp. had highest counts inside the mariculture fish and Photobacteria sp. was most prominent inside and close to the net cage. Future studies are needed to test these findings, with high relevance for future finfish mariculture activities and management practices.ENAfalsefish gut metagenomegut metagenome Atule mate, E. sexfasciatus and E. fuscoguttatus2023-05-192015-07-03PRJNA2874961602388