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ORIGINAL RESEARCH article

Front. Microbiol.
Sec. Food Microbiology
Volume 15 - 2024 | doi: 10.3389/fmicb.2024.1504487

Comparative Evaluation of Specimen Type and Processing Conditions for Studying Oyster Microbiomes

Provisionally accepted
Esam Almuhaideb Esam Almuhaideb 1Nur A Hasan Nur A Hasan 2Christopher John Grim Christopher John Grim 3Shah Manzur Rashed Shah Manzur Rashed 4Salina Parveen Salina Parveen 1*
  • 1 University of Maryland Eastern Shore, Princess Anne, United States
  • 2 Ezbiome Inc, Maryland, United States
  • 3 United States Food and Drug Administration, Silver Spring, Maryland, United States
  • 4 Cosmos Corporation (United States), Bethesda, Maryland, United States

The final, formatted version of the article will be published soon.

    Metagenomic sequencing is increasingly being employed to understand the assemblage and dynamics of the oyster microbiome. Specimen collection and processing steps can impact the resultant microbiome composition and introduce bias.To investigate this systematically, a total of 54 farmed oysters were collected from Chesapeake Bay between May to September 2019. Six different specimen types and processing methods were evaluated for microbial community composition using shotgun metagenomics, namely fresh oyster homogenate (FOH), oyster homogenate after simulated temperature abuse (AOH), Luria broth-enriched oyster homogenate (EOH), dissected stomach homogenate (DSH), hemolymph (HLM), and stomach-gut content (SGC). In general, DSH, EOH, and FOH yielded the highest DNA concentration, while EOH had the highest microbial reads, followed by DSH, HLM, and FOH. HLM produced the highest bacterial species alpha diversity, followed by AOH, EOH, and SGC.Although alpha diversities didn't differ significantly, beta-diversity measurements showed significant dissimilarity among methods (P<0.05) indicating that the specimen types and processing steps do play an important role in representing the composition of the bacterial community. Bacterial species that had the highest log mean abundance included Cyanobium sp. PCC 7001 in FOH, Vibrio vulnificus in AOH, EOH, and DSH, and lastly Synechococcus sp. CB0205 in the DSH, HML, and SGC samples. EOH 2 displayed higher bacterial hits, distinct microbial composition, and higher values of bacterial, phages, and antimicrobial resistance gene reads. Therefore, if studying the overall oyster microbial community, prioritizing optimum specimen collection and processing methods that align with the overall goal of the study is recommended.

    Keywords: Oyster microbiome, Shotgun metagenomics, Crassostrea virginica, mollusk, Vibrio spp

    Received: 30 Sep 2024; Accepted: 19 Dec 2024.

    Copyright: © 2024 Almuhaideb, Hasan, Grim, Rashed and Parveen. 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) or licensor 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.

    * Correspondence: Salina Parveen, University of Maryland Eastern Shore, Princess Anne, United States

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.