Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Md Zoqratt, Muhammad Zarul Hanifah, Eng, Wilhelm Wei Han, Thai, Binh Thanh, Austin, Christopher M., Gan, Han Ming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2018
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
_version_ 1783367944318746624
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
work_keys_str_mv AT mdzoqrattmuhammadzarulhanifah microbiomeanalysisofpacificwhiteshrimpgutandrearingwaterfrommalaysiaandvietnamimplicationsforaquacultureresearchandmanagement
AT engwilhelmweihan microbiomeanalysisofpacificwhiteshrimpgutandrearingwaterfrommalaysiaandvietnamimplicationsforaquacultureresearchandmanagement
AT thaibinhthanh microbiomeanalysisofpacificwhiteshrimpgutandrearingwaterfrommalaysiaandvietnamimplicationsforaquacultureresearchandmanagement
AT austinchristopherm microbiomeanalysisofpacificwhiteshrimpgutandrearingwaterfrommalaysiaandvietnamimplicationsforaquacultureresearchandmanagement
AT ganhanming microbiomeanalysisofpacificwhiteshrimpgutandrearingwaterfrommalaysiaandvietnamimplicationsforaquacultureresearchandmanagement