Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management

Md Zoqratt, Muhammad Zarul Hanifah, Eng, Wilhelm Wei Han, Thai, Binh Thanh, Austin, Christopher and Gan, Han Ming 2018, Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management, PeerJ, vol. 6, doi: 10.7717/peerj.5826.

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Title Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management
Author(s) Md Zoqratt, Muhammad Zarul Hanifah
Eng, Wilhelm Wei Han
Thai, Binh Thanh
Austin, ChristopherORCID iD for Austin, Christopher orcid.org/0000-0003-1848-6267
Gan, Han MingORCID iD for Gan, Han Ming orcid.org/0000-0001-7987-738X
Journal name PeerJ
Volume number 6
Article ID e5826
Total pages 22
Publisher PeerJ
Place of publication London, Eng.
Publication date 2018-10
ISSN 2167-8359
Keyword(s) 16S ribosomal RNA amplicons sequencing
Aquaculture
Litopenaeus vannamei
Metagenomics
Vibrio parahaemolyticus
Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
BACTERIAL COMMUNITY STRUCTURE
LITOPENAEUS-VANNAMEI
VIBRIO SPP.
GENE-SEQUENCES
DISEASE
IDENTIFICATION
PARAHAEMOLYTICUS
TEMPERATURE
DIVERSITY
SEVERITY
Summary Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3-V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.
Language eng
DOI 10.7717/peerj.5826
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2018, Md Zoqratt et al.
Persistent URL http://hdl.handle.net/10536/DRO/DU:30115199

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