Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada

Svenja Koepper; K Fraser Clark; J Trenton McClure; Crawford W Revie; Henrik Stryhn; Krishna K Thakur

doi:10.3389/fmicb.2023.1245818

Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada

Front Microbiol. 2023 Nov 6:14:1245818. doi: 10.3389/fmicb.2023.1245818. eCollection 2023.

Authors

Svenja Koepper¹, K Fraser Clark², J Trenton McClure¹, Crawford W Revie³, Henrik Stryhn¹, Krishna K Thakur¹

Affiliations

¹ Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada.
² Department of Animal Sciences and Aquaculture, Faculty of Agriculture, Dalhousie University, Bible Hill, NS, Canada.
³ Department of Computer and Information Sciences, University of Strathclyde, Glasgow, United Kingdom.

Abstract

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.

Keywords: 16S rRNA gene; Aquimarina; PacBio; core microbiome; epizootic shell disease; microbial ecology.

Grants and funding

This project received funding via the OFI Phase-2 One Ocean Health Grant (Ocean Frontiers Institute, Dalhousie University, Nova Scotia, Canada) through the Canada First Research Excellence Fund. Additional funding was received from the Atlantic Veterinary College Research Fund (University of Prince Edward Island, Prince Edward Island, Canada).