Metagenomic analysis of the bacterial microbiota associated with cultured oysters (Crassostrea sp.) in estuarine environments

Horodesky, Aline; Castilho-Westphal, Gisela Geraldine; Pont, Giorgi Dal; Faoro, Helisson; Balsanelli, Eduardo; Tadra-Sfeir, Michelle Z.; Cozer, Nathieli; Pie, Márcio R.; Ostrensky, Antônio

doi:10.1590/0001-3765202020180432

Cited by 10 publications

(6 citation statements)

References 30 publications

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“…The Oceanospirillum is one of the common inhabitants of marine environments (Leonard et al, 2000). It has been identi ed to be potentially pathogenic to paci c white shrimp, oysters and humans (Horodesky et al, 2020;Ostrensky et al, 2018;Zhang et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Microbial Communities Associated With Stunted Growth Syndrome In Penaeus Vannamei Farming

Jangam

Nathamuni

Katneni

et al. 2021

Preprint

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Purpose: Stunted/slow growth syndrome is one of the yield-limiting diseases in Penaeus vannamei farming. Limited information is available on the aetiology of this condition, which needs to be studied to devise prophylactic measures to minimise the production losses. Amongst the factors that influence this condition, microbial communities in the growing environment play an important role. This study aimed at understanding major microbial associations of affected and healthy pond waters through shotgun metagenomics.Method: The water samples were filtered through vacuum filtration to extract suspended microbes. Subsequently, DNA was isolated from the filtrate using PowerSoil® DNA Isolation Kit. Libraries prepared from isolated DNA were sequenced using the shotgun metagenomic method on the Illumina HiSeq platform. The microbial profiling and their functional prediction of the shotgun metagenome sequences were carried out using stand-alone versions of Kaiju, OmicsBox respectively. Results: The taxonomic classification results revealed that species of Oceanospirillum, and vibrio were high in the disease sample, while Rhodobacteraceae bacterium and Neptunomonas were high in the healthy sample. The alpha diversity analysis showed slightly higher diversity in the healthy sample compared to the disease infected. The taxonomic biomarkers for healthy and infected states reported in previous studies were also observed in this study. The major functional associations of both the healthy and infected groups include amino acid transport and metabolism, cell wall/membrane/envelope biogenesis, and energy production and conversion. Conclusion: The study identified major taxonomical and functional associations of ponds affected and unaffected with stunted growth syndrome. These associations significantly varied between the samples, indicating dysbiosis of the microbial profiles in the pond waters. This dysbiosis could be a potential cause for the manifestation of stunted growth syndrome. Microbial associations along with other pond environmental factors need to be further explored for an in-depth understanding of stunted growth syndrome.

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Section: Discussionmentioning

confidence: 99%

Microbial Communities Associated With Stunted Growth Syndrome In Penaeus Vannamei Farming

Jangam

Nathamuni

Katneni

et al. 2021

Preprint

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“…Mycoplasma spp. lack cell walls and have often been found to associate with a host organism, including oysters based on in situ analysis [44][45][46][47][48][49]. Some of them also represent a pathogenic threat to animals, including humans and fish, especially within the host mucosal layers [50][51][52].…”

Section: Plos Onementioning

confidence: 99%

Analysis of the core bacterial community associated with consumer-ready Eastern oysters (Crassostrea virginica)

et al. 2023

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Shellfish, such as the Eastern oyster (Crassostrea virginica), are an important agricultural commodity. Previous research has demonstrated the importance of the native microbiome of oysters against exogenous challenges by non-native pathogens. However, the taxonomic makeup of the oyster microbiome and the impact of environmental factors on it are understudied. Research was conducted quarterly over a calendar year (February 2020 through February 2021) to analyze the taxonomic diversity of bacteria present within the microbiome of consumer-ready-to-eat live Eastern oysters. It was hypothesized that a core group of bacterial species would be present in the microbiome regardless of external factors such as the water temperature at the time of harvest or post-harvesting processing. At each time point, 18 Chesapeake Bay (eastern United States) watershed aquacultured oysters were acquired from a local grocery store, genomic DNA was extracted from the homogenized whole oyster tissues, and the bacterial 16S rRNA gene hypervariable V4 region was PCR-amplified using barcoded primers prior to sequencing via Illumina MiSeq and bioinformatic analysis of the data. A core group of bacteria were identified to be consistently associated with the Eastern oyster, including members of the phyla Firmicutes and Spirochaetota, represented by the families Mycoplasmataceae and Spirochaetaceae, respectively. The phyla Cyanobacterota and Campliobacterota became more predominant in relation to warmer or colder water column temperature, respectively, at the time of oyster harvest.

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“…One reason for the interest in the denitrification potential of bacteria associated with the Eastern oyster is that oyster aquaculture is associated with low greenhouse gas emissions [38]. Metagenomics sequencing technologies have aided in the identification of archaea and bacteria associated with oyster anatomical parts including the gills, gut, hemolymph, mantle, pallial fluid, stomach, and shell [37,[39][40][41][42][43]. In studies with a focus on the denitrification potential of the oyster microbiome [37,42], the bacteria genera identified include Clostridium, Endozoicomonas, Erythrobacter, Mycoplasma, Neptunibacter, Pleurocapsa, Psychrobacter, Pseudomonas, Pseudoalteromonas, Shewanella, Synechococcus, and Vibrio.…”

Section: Introductionmentioning

confidence: 99%

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Isokpehi,

Kim,

Krejci

et al. 2024

Microorganisms

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Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

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Metagenomic analysis of the bacterial microbiota associated with cultured oysters (Crassostrea sp.) in estuarine environments

Cited by 10 publications

References 30 publications

Microbial Communities Associated With Stunted Growth Syndrome In Penaeus Vannamei Farming

Microbial Communities Associated With Stunted Growth Syndrome In Penaeus Vannamei Farming

Analysis of the core bacterial community associated with consumer-ready Eastern oysters (Crassostrea virginica)

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

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