Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Jan 8:15:1504487.
doi: 10.3389/fmicb.2024.1504487. eCollection 2024.

Comparative evaluation of specimen type and processing conditions for studying oyster microbiomes

Esam Almuhaideb  1 , Nur A Hasan  2   3 , Christopher Grim  4 , Shah Manzur Rashed  5 , Salina Parveen  1
Affiliations

Comparative evaluation of specimen type and processing conditions for studying oyster microbiomes

Esam Almuhaideb et al. Front Microbiol. .

Abstract

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 and 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 did not 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 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: Crassostrea virginica; Vibrio spp.; mollusk; oyster microbiome; shotgun metagenomics.

PubMed Disclaimer

Conflict of interest statement

NH was employed by EzBiome Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

Figure 1
Figure 1
Concentration of DNA isolated from each sample type. FOH, Fresh-oyster homogenate; AOH, Temperature abused-oyster homogenate; EOH, Enriched-oyster homogenate; DSH, Dissected stomach homogenate; SGC, Stomach gut contents; HLM, Oyster-hemolymph.
Figure 2
Figure 2
Log mean abundance of bacterial taxa within all sample types. FOH, Fresh-oyster homogenate; AOH, Temperature abused-oyster homogenate; EOH, Enriched-oyster homogenate; DSH, Dissected stomach homogenate; SGC, Stomach gut contents; HLM, Oyster-hemolymph.
Figure 3
Figure 3
Relative log abundance score of bacterial taxa in relation to sample type. FOH, Fresh-oyster homogenate; AOH, Temperature abused-oyster homogenate; EOH, Enriched-oyster homogenate; DSH, Dissected stomach homogenate; SGC, Stomach gut contents; HLM, Oyster-hemolymph.
Figure 4
Figure 4
Log abundance distribution of bacterial taxa in the FOH samples. LAS, log abundance score; FOH, Fresh-oyster homogenate.
Figure 5
Figure 5
Log abundance distribution of bacterial taxa in the AOH samples. LAS, log abundance score; AOH, Temperature abused-oyster homogenate.
Figure 6
Figure 6
Log abundance distribution of bacterial taxa in the EOH samples. LAS, log abundance score; EOH, Enriched-oyster homogenate.
Figure 7
Figure 7
Log abundance distribution of bacterial taxa in the DSH samples. LAS, log abundance score; DSH, Dissected stomach homogenate.
Figure 8
Figure 8
Log abundance distribution of bacterial taxa in the SGC samples. LAS, log abundance score; SGC, Stomach gut contents.
Figure 9
Figure 9
Log abundance distribution of bacterial taxa in the HLM samples. LAS, log abundance score; HLM, Oyster-hemolymph.
Figure 10
Figure 10
Shannon index representing the richness and evenness of bacterial species within all sample types. Each dot represents the Shannon diversity value for an individual sample. Statistical comparisons of medians across sample types were performed using a Wilcoxon rank-sum test. FOH, Fresh-oyster homogenate; AOH, Temperature abused-oyster homogenate; EOH, Enriched-oyster homogenate; DSH, Dissected stomach homogenate; SGC, Stomach gut contents; HLM, Oyster-hemolymph.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Abreu I. N., Cortinhas J. M., Dos Santos M. B., Queiroz M. A. F., da Silva A. N. M. R., Cayres-Vallinoto I. M. V., et al. . (2020). Detection of human polyomavirus 2 (HPyV2) in oyster samples in northern Brazil. Virol. J. 17, 1–6. doi: 10.1186/s12985-020-01360-8, PMID: - DOI - PMC - PubMed
    1. Bloomfield S. J., Zomer A. L., O'grady J., Kay G. L., Wain J., Janecko N., et al. . (2023). Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics. Food Microbiol. 110:104162. doi: 10.1016/j.fm.2022.104162, PMID: - DOI - PubMed
    1. Brown E., Dessai U., McGarry S., Gerner-Smidt P. (2019). Use of whole-genome sequencing for food safety and public health in the United States. Foodborne Pathog. Dis. 16, 441–450. doi: 10.1089/fpd.2019.2662, PMID: - DOI - PMC - PubMed
    1. Cai H., Wang K., Huang S., Jiao N., Chen F. (2010). Distinct patterns of picocyanobacterial communities in winter and summer in the Chesapeake Bay. Appl. Environ. Microbiol. 76, 2955–2960. doi: 10.1128/AEM.02868-09, PMID: - DOI - PMC - PubMed
    1. Chauhan A., Wafula D., Lewis D. E., Pathak A. (2014). Metagenomic assessment of the eastern oyster-associated microbiota. Genome Announc. 2, e01083–e01014. doi: 10.1128/genomeA.01083-14, PMID: - DOI - PMC - PubMed

LinkOut - more resources