title: Microbiome analysis and detection of pathogenic bacteria of Penaeus monodon from Jakarta Bay and Bali.
abstract: 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.
authors.affiliation: Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany; Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany.
authors.forename: Vincensius S P
authors.initials: VS
authors.lastname: Oetama
authors.affiliation: Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany; Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Hennersdorf
authors.affiliation: Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany; Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia.
authors.forename: Muslihudeen A
authors.initials: MA
authors.lastname: Abdul-Aziz
authors.affiliation: Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany.
authors.forename: Grit
authors.initials: G
authors.lastname: Mrotzek
authors.affiliation: Gondol Research Institute for Mariculture GRIM, ds Penyabangan, Br. Gondol, PO. Box 140, Singaraja 81101, Bali, Indonesia.
authors.forename: Haryanti
authors.initials: H
authors.lastname: Haryanti
authors.affiliation: Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, D-07745 Jena, Germany; Friedrich Schiller University of Jena, Fürstengraben 1, D-07743 Jena, Germany.
authors.forename: Hans Peter
authors.initials: HP
authors.lastname: Saluz
mesh_terms: D000818:Animals; D061006:Bays / Q000382:microbiology* / Q000821:virology; D044822:Biodiversity; D005243:Feces / Q000382:microbiology / Q000821:virology; D020563:Gammaproteobacteria / Q000145:classification / Q000302:isolation & purification* / Q000472:pathogenicity*; D059014:High-Throughput Nucleotide Sequencing; D007214:Indonesia; D064307:Microbiota; D033561:Penaeidae / Q000382:microbiology* / Q000821:virology; D017422:Sequence Analysis, DNA
keywords: Aquaculture; Bali; Fecal microbiome; Free-living; Jakarta; Penaeus monodon