Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers
BACKGROUND: Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far. RESULTS: To tackle...
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ftpubmed:oai:pubmedcentral.nih.gov:7333408 2023-05-15T15:57:58+02:00 Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers Clerissi, Camille Guillou, Laure Escoubas, Jean-Michel Toulza, Eve 2020-07-03 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333408/ http://www.ncbi.nlm.nih.gov/pubmed/32620152 https://doi.org/10.1186/s12866-020-01860-1 en eng BioMed Central http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333408/ http://www.ncbi.nlm.nih.gov/pubmed/32620152 http://dx.doi.org/10.1186/s12866-020-01860-1 © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. CC0 PDM CC-BY BMC Microbiol Methodology Article Text 2020 ftpubmed https://doi.org/10.1186/s12866-020-01860-1 2020-07-12T00:32:15Z BACKGROUND: Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far. RESULTS: To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities were sequenced using metabarcoding. Alveolata, Stramenopiles and Archaeplastida were the main protist phyla associated with oysters. In particular, Codonellopsis, Cyclotella, Gymnodinium, Polarella, Trichodina, and Woloszynskia were the dominant genera. The potential pathogen Alexandrium was also found in high abundances within some samples. CONCLUSIONS: Our study revealed the main protist taxa within oysters as well as the occurrence of potential oyster pathogens. These new primer sets are promising tools to better understand oyster homeostasis and disease development, such as the Pacific Oyster Mortality Syndrome (POMS) targeting juveniles. Text Crassostrea gigas Pacific oyster PubMed Central (PMC) Pacific BMC Microbiology 20 1 |
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Methodology Article |
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Methodology Article Clerissi, Camille Guillou, Laure Escoubas, Jean-Michel Toulza, Eve Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers |
topic_facet |
Methodology Article |
description |
BACKGROUND: Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far. RESULTS: To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities were sequenced using metabarcoding. Alveolata, Stramenopiles and Archaeplastida were the main protist phyla associated with oysters. In particular, Codonellopsis, Cyclotella, Gymnodinium, Polarella, Trichodina, and Woloszynskia were the dominant genera. The potential pathogen Alexandrium was also found in high abundances within some samples. CONCLUSIONS: Our study revealed the main protist taxa within oysters as well as the occurrence of potential oyster pathogens. These new primer sets are promising tools to better understand oyster homeostasis and disease development, such as the Pacific Oyster Mortality Syndrome (POMS) targeting juveniles. |
format |
Text |
author |
Clerissi, Camille Guillou, Laure Escoubas, Jean-Michel Toulza, Eve |
author_facet |
Clerissi, Camille Guillou, Laure Escoubas, Jean-Michel Toulza, Eve |
author_sort |
Clerissi, Camille |
title |
Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers |
title_short |
Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers |
title_full |
Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers |
title_fullStr |
Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers |
title_full_unstemmed |
Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers |
title_sort |
unveiling protist diversity associated with the pacific oyster crassostrea gigas using blocking and excluding primers |
publisher |
BioMed Central |
publishDate |
2020 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333408/ http://www.ncbi.nlm.nih.gov/pubmed/32620152 https://doi.org/10.1186/s12866-020-01860-1 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
BMC Microbiol |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333408/ http://www.ncbi.nlm.nih.gov/pubmed/32620152 http://dx.doi.org/10.1186/s12866-020-01860-1 |
op_rights |
© The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
op_rightsnorm |
CC0 PDM CC-BY |
op_doi |
https://doi.org/10.1186/s12866-020-01860-1 |
container_title |
BMC Microbiology |
container_volume |
20 |
container_issue |
1 |
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1766393685843378176 |