Metavirome sequencing to evaluate norovirus diversity in sewage and related bioaccumulated oysters
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ABSTRACT:
PROVIDER: PRJEB34617 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3562240_1.fastq.gz | Fastqsanger.gz | |||
| ERR3562240_2.fastq.gz | Fastqsanger.gz | |||
| ERR3562250_1.fastq.gz | Fastqsanger.gz | |||
| ERR3562250_2.fastq.gz | Fastqsanger.gz | |||
| ERR3562241_1.fastq.gz | Fastqsanger.gz |
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Project description:Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were used to study norovirus diversity. A double approach, agnostic deep sequencing and a capture-based approach (VirCapSeq-VERT) was used to identify norovirus in environmental samples. Family-specific viral contigs were classified and sorted by SLIM and final norovirus contigs were genotyped using the online Norovirus genotyping tool v2.0. From sewage samples, 14 norovirus genogroup I sequences were identified of which six were complete genomes. For norovirus genogroup II, nine sequences were identified and three of them comprised more than half of the genome. In oyster samples bioaccumulated with these sewage samples, only the use of an enrichment step during library preparation allowed successful identification of nine different sequences of norovirus genogroup I and four for genogroup II (>500 bp). This study demonstrates the importance of method development to increase virus recovery, and the interest of a capture-based approach to be able to identify viruses present at low concentrations.
| S-EPMC6811496 | biostudies-literature
Project description:Hepatic transcriptional profiling of fish exposed to sewage to evaluate temporal and concentration trends.
2012-12-01 | GSE38925 | GEO
Project description:Bacteria and archaea associated with wild oysters in the North Sea
| PRJNA965952 | ENA
Project description:Background Triploidy can occur in all species but is often lethal in birds and mammals. In amphibian, invertebrates and numerous species of fishes, triploid animals are viable and undistinguishable from diploid individuals. Gametogenesis is often affected and most animals are sterile for at least one sex, and gametes for the other sex are often unfertile. Although the majority of triploid oysters are sterile (beta individuals, 3nb), a low but persistent proportion of male and female animals produce gametes (alpha individuals, 3na). Thus, oysters constitute a unique model to study the effect of triploidy on germ cells development of both male and females. In this study, we used microarray to study the consequences of polyploidy on triploid oyster germ cells mitosis and meiosis. Results We compared the transcriptome of gonads of 3na and 3nb oyster gonads over the course of gametogenesis to the transcriptome of diploid (2n) oyster gonads. This study allowed us to reveal an increase in DNA repair and apoptosis through the NF-kappaB pathway, and a decrease in actin remodeling and chromatin remodeling in all 3n oysters. The comparison of 3na and 3nb individuals with 2n revealed that a pachytene checkpoints may be responsible for the success in gametogenesis of 3na individuals and for the observed delay in gametogenesis. However, the sterility of 3nb individuals can be explained by a disruption of sex determinism mechanisms. Indeed 3nb females express male-specific genes including enkurin and an Elav-like gene, and 3nb males express female-specific genes including Forkhead box L2 and beta-catenin. Conclusions Our results bring back to the front of the research field the questions of genetic sex determinism, mitosis/meiosis control, pachytene checkpoint, and cell type specific DNA damage pathways. Furthermore, this study identifies numerous new candidate genes which function should now be studied in details in oysters and in other triploid animals in order to elucidate the complex mechanisms involved in the regulation of triploid cells division.
2015-03-26 | GSE40855 | GEO
Project description:Hepatic transcriptional profiling of fish exposed to sewage to evaluate temporal and concentration trends. Two experiments (Year 1 and 2), each with 6 concentrations (0%, 0.05%, 0.1%, 0.7%, 2% and 5/10%) of sewage diluted in seawater at 4 timepoints (1, 4, 8 and 16 days).
2012-12-01 | E-GEOD-38925 | biostudies-arrayexpress
Project description:Effluents from sewage treatment plants contain a mixture of micropollutants with the potential of harming aquatic organisms. Thus, addition of advanced treatment techniques to complement existing conventional methods has been proposed. Some of the advanced techniques could, however, potentially produce additional compounds affecting exposed organisms by unknown modes of action. In the present study the aim was to improve our understanding of how exposure to different sewage effluents affects fish. This was achieved by explorative microarray and quantitative PCR analyses of hepatic gene expression, as well as relative organ sizes of rainbow trout exposed to different sewage effluents (conventionally treated, granular activated carbon, ozonation (5 or 15 mg/L), 5 mg/L ozone plus a moving bed biofilm reactor, or UV-light treatment in combination with hydrogen peroxide). Exposure to the conventionally treated effluent caused a significant increase in liver and heart somatic indexes, an effect removed by all other treatments. Genes connected to xenobiotic metabolism, including cytochrome p450 1A, were differentially expressed in the fish exposed to the conventionally treated effluents, though only effluent treatment with granular activated carbon or ozone at 15 mg/L completely removed this response. The mRNA expression of heat shock protein 70 kDa was induced in all three groups exposed to ozone-treated effluents, suggesting some form of added stress in these fish. The induction of estrogen-responsive genes in the fish exposed to the conventionally treated effluent was effectively reduced by all investigated advanced treatment technologies, although the moving bed biofilm reactor was least efficient. Taken together, granular activated carbon showed the highest potential of reducing responses in fish induced by exposure to sewage effluents.
2012-05-10 | GSE37574 | GEO
Project description:Sewage samples were collected and concentrated for Human and animal viruses. Viruses were cultured on Buffalo Green Monkey Cells (BGMK) and their genomic DNA/RNA were extracted and labeled with Cy3 and Cy5 respectively. Labeled DNA/RNA were hybridized unto the array and signals generated were analyzed to indicate the presence of target viruses. Keywords: Detection of pathogens within environmental sample (Viruses)
2008-04-18 | GSE11195 | GEO
Project description:The shellfish aquaculture industry provides a sustainable food source and jobs for a growing population. Oysters are the primary aquaculture species produced in the United States and account for a significant portion of seafood exports. Shellfish hatcheries have been experiencing frequent mass mortality events over the last couple of decades that occur approximately 10-14 days after oyster settlement. Settlement is a process that shellfish such as oysters undergo in which they transform from a free-swimming pelagic larvae to a sessile juvenile oyster. In order for this energy-intensive process to be successful, the oyster has to undergo behavioral and morphological changes. This is a vulnerable period in the oyster life cycle and conditions need to be such that they aren’t creating added stress. However, due to the oysters’ vulnerability, this is often a time when bacterial infections can occur, which when occurring with environmental conditions that are unfavorable, can prove to be fatal. In order to help oysters survive this process, scientists at the Taylor Shellfish Hatchery in Quilcene, WA has experimented with altering abiotic and biotic factors such as algal diet densities, pH, water flow rate, among others. At this hatchery, Pacific oysters are typically reared at 23˚C, however preliminary research results have suggested that oysters may have a higher survival rate when held at 29˚C during the settlement period. This pilot experiment attempts to identify differences in protein expression between oyster seed held at 23˚C and 29˚C during the settlement period using novel proteomic technology. Our proteomic results, paired with survival data, suggest that holding oyster seed at 29˚C during the settlement period results in higher survival rates.
2022-03-03 | PXD015434 | Pride
Project description:Summer mortality of Crassostrea gigas is the result of a complex interaction between oysters, their environment and pathogens. A large genetic basis and a high heritability were demonstrated for the observed variation in resistance to summer mortality, which offered the possibility to develop lines of oysters that were resistant (R) or susceptible (S) to summer mortality. Previously, genome-wide expression profiling of R and S oyster gonads highlighted reproduction and antioxidant defense as constitutive pathways that operate differentially between these two lines. Here, we show that signaling in innate immunity also operates differentially between these lines and we postulated that it is at the main origin of their difference of survival in the field. From the already published microarray data, we employed an ANOVA analysis that reveals a specific “immune” profile at the date preceding the mortality. In addition, we conducted a microarray profiling of two other tissues, gills and muscle, that also showed an over-representation of the immune genes (46%) among the selected genes. Eleven genes were pinpointed to be simultaneously differentially expressed between R and S lines in the three tissues. Among them, ten are related to “Immune Response”. The kinetics of their mRNA levels appeared clearly different between lines and suggests that in environment, R oysters had the capacity to modulate signaling in innate immunity whereas S oysters did not. This study enhances our understanding of the complex summer mortality syndrome and provides candidates of interest for further functional and genetics studies.
2011-04-22 | GSE25614 | GEO