Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers
Abstract 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...
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ftdatacite:10.6084/m9.figshare.c.5049377 2023-05-15T15:58:02+02:00 Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers Clerissi, Camille Guillou, Laure Jean-Michel Escoubas Toulza, Eve 2020 https://dx.doi.org/10.6084/m9.figshare.c.5049377 https://springernature.figshare.com/collections/Unveiling_protist_diversity_associated_with_the_Pacific_oyster_Crassostrea_gigas_using_blocking_and_excluding_primers/5049377 unknown figshare https://dx.doi.org/10.1186/s12866-020-01860-1 Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode CC-BY-4.0 CC-BY Microbiology FOS Biological sciences Cell Biology Molecular Biology Ecology Sociology FOS Sociology 69999 Biological Sciences not elsewhere classified Inorganic Chemistry FOS Chemical sciences Collection article 2020 ftdatacite https://doi.org/10.6084/m9.figshare.c.5049377 https://doi.org/10.1186/s12866-020-01860-1 2021-11-05T12:55:41Z Abstract 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. Article in Journal/Newspaper Crassostrea gigas Pacific oyster DataCite Metadata Store (German National Library of Science and Technology) Pacific |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Microbiology FOS Biological sciences Cell Biology Molecular Biology Ecology Sociology FOS Sociology 69999 Biological Sciences not elsewhere classified Inorganic Chemistry FOS Chemical sciences |
spellingShingle |
Microbiology FOS Biological sciences Cell Biology Molecular Biology Ecology Sociology FOS Sociology 69999 Biological Sciences not elsewhere classified Inorganic Chemistry FOS Chemical sciences Clerissi, Camille Guillou, Laure Jean-Michel Escoubas Toulza, Eve Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers |
topic_facet |
Microbiology FOS Biological sciences Cell Biology Molecular Biology Ecology Sociology FOS Sociology 69999 Biological Sciences not elsewhere classified Inorganic Chemistry FOS Chemical sciences |
description |
Abstract 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 |
Article in Journal/Newspaper |
author |
Clerissi, Camille Guillou, Laure Jean-Michel Escoubas Toulza, Eve |
author_facet |
Clerissi, Camille Guillou, Laure Jean-Michel Escoubas 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 |
figshare |
publishDate |
2020 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.5049377 https://springernature.figshare.com/collections/Unveiling_protist_diversity_associated_with_the_Pacific_oyster_Crassostrea_gigas_using_blocking_and_excluding_primers/5049377 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
https://dx.doi.org/10.1186/s12866-020-01860-1 |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode CC-BY-4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.5049377 https://doi.org/10.1186/s12866-020-01860-1 |
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1766393748107821056 |