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Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management
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 po...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214229/ https://www.ncbi.nlm.nih.gov/pubmed/30397546 http://dx.doi.org/10.7717/peerj.5826 |
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author | Md Zoqratt, Muhammad Zarul Hanifah Eng, Wilhelm Wei Han Thai, Binh Thanh Austin, Christopher M. Gan, Han Ming |
author_facet | Md Zoqratt, Muhammad Zarul Hanifah Eng, Wilhelm Wei Han Thai, Binh Thanh Austin, Christopher M. Gan, Han Ming |
author_sort | Md Zoqratt, Muhammad Zarul Hanifah |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6214229 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-62142292018-11-05 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 M. Gan, Han Ming PeerJ Aquaculture, Fisheries and Fish Science 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. PeerJ Inc. 2018-10-30 /pmc/articles/PMC6214229/ /pubmed/30397546 http://dx.doi.org/10.7717/peerj.5826 Text en ©2018 Md Zoqratt et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Aquaculture, Fisheries and Fish Science Md Zoqratt, Muhammad Zarul Hanifah Eng, Wilhelm Wei Han Thai, Binh Thanh Austin, Christopher M. Gan, Han Ming Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management |
title | Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management |
title_full | Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management |
title_fullStr | Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management |
title_full_unstemmed | Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management |
title_short | Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management |
title_sort | microbiome analysis of pacific white shrimp gut and rearing water from malaysia and vietnam: implications for aquaculture research and management |
topic | Aquaculture, Fisheries and Fish Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6214229/ https://www.ncbi.nlm.nih.gov/pubmed/30397546 http://dx.doi.org/10.7717/peerj.5826 |
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