ArticleFrontiers in microbiology2024
Comparative evaluation of specimen type and processing conditions for studying oyster microbiomes.
Article in Frontiers in microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- Detection of an ExPEC-likeBiotech (Basel (Switzerland)) · 2026Article
- Effects of aquaculture practices onApplied and environmental microbiology · 2026Article
- Microbiological spectrum and antimicrobial resistance patterns in pediatric acute appendicitis: implications for evidence-based empirical therapy.Frontiers in pediatrics · 2026Article
- Sampling method influences hemolymph bacterial communities in the eastern oyster,Frontiers in microbiology · 2026Article
- Comparative genomics reveals specialization and divergent virulence potential inApplied and environmental microbiology · 2025Article
- Hybridization capture sequencing formBio · 2025Article
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5 authors.
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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 (
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