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

PeerJ

article

Muhammad Zarul Hanifah Zoqratt¹  Wilhelm Wei Han Eng¹  Binh Thanh Thai³  Christopher M. Austin¹  Han Ming Gan¹ 

[1]School of Science, Monash University Malaysia

[2]Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia

[3]Fisheries and Technical, Economical College

[4]Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University

关键词: Metagenomics;    Aquaculture;    Litopenaeus vannamei;    16S ribosomal RNA amplicons sequencing;    Vibrio parahaemolyticus;   

DOI  :  10.7717/peerj.5826

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY