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Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada
The shell microbial community of lobsters—a key factor in the development of epizootic shell disease (ESD)—is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently hea...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10658194/ https://www.ncbi.nlm.nih.gov/pubmed/38029079 http://dx.doi.org/10.3389/fmicb.2023.1245818 |
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author | Koepper, Svenja Clark, K. Fraser McClure, J. Trenton Revie, Crawford W. Stryhn, Henrik Thakur, Krishna K. |
author_facet | Koepper, Svenja Clark, K. Fraser McClure, J. Trenton Revie, Crawford W. Stryhn, Henrik Thakur, Krishna K. |
author_sort | Koepper, Svenja |
collection | PubMed |
description | The shell microbial community of lobsters—a key factor in the development of epizootic shell disease (ESD)—is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state. |
format | Online Article Text |
id | pubmed-10658194 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-106581942023-11-06 Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada Koepper, Svenja Clark, K. Fraser McClure, J. Trenton Revie, Crawford W. Stryhn, Henrik Thakur, Krishna K. Front Microbiol Microbiology The shell microbial community of lobsters—a key factor in the development of epizootic shell disease (ESD)—is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state. Frontiers Media S.A. 2023-11-06 /pmc/articles/PMC10658194/ /pubmed/38029079 http://dx.doi.org/10.3389/fmicb.2023.1245818 Text en Copyright © 2023 Koepper, Clark, McClure, Revie, Stryhn and Thakur. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Koepper, Svenja Clark, K. Fraser McClure, J. Trenton Revie, Crawford W. Stryhn, Henrik Thakur, Krishna K. Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada |
title | Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada |
title_full | Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada |
title_fullStr | Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada |
title_full_unstemmed | Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada |
title_short | Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada |
title_sort | long-read sequencing reveals the shell microbiome of apparently healthy american lobsters homarus americanus from atlantic canada |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10658194/ https://www.ncbi.nlm.nih.gov/pubmed/38029079 http://dx.doi.org/10.3389/fmicb.2023.1245818 |
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