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ABSTRACT: Amplification of full length 16S for water samples and shrimp intestine tissues

PROVIDER: PRJNA736625 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14780300_1.fastq.gz	Fastqsanger.gz
	SRR14780301_1.fastq.gz	Fastqsanger.gz
	SRR14780302_1.fastq.gz	Fastqsanger.gz
	SRR14780303_1.fastq.gz	Fastqsanger.gz
	SRR14780304_1.fastq.gz	Fastqsanger.gz

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Project description:Amplification of 16S V4 region for water samples and shrimp intestine tissues

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Effect of diurnal oxygen variation on gene expression in Pacific white shrimp reared in green water system tanks

Project description:World aquaculture production of the Pacific white shrimp (Litopenaeus vannamei) is estimated to account for 80% of the total shrimp produce worldwide. The global demand for shrimp has driven the industry to utilize and rely on semi-intensive and intensive shrimp systems. In the United States, Pacific white shrimp production can take place in semi-intensive earthen ponds, recirculating aquaculture systems (RAS), biofloc technology and green water. In this study, the effects of lowering dissolved oxygen conditions in outdoor green water tanks on global gene expression is examined. Tissue samples from the gill and intestine were collected for gene expression analysis via RNA sequencing. Among all comparisons, RNA sequencing revealed the up-regulation of a single gene: hydroxyacid oxidase 1 gene. The HOA1 gene was found to be 7-fold higher in the intestine sample at the medium aeration level compare to that of the high (control) level. The HAO1 gene, also known as glycolate oxidase 1 (GOX1) is a gene related to the 2-hydroxyacid oxidase enzyme that is part of the oxidoreductase family and plays a role in glyoxylate and dicarboxylate metabolism. The identification of a single differentially expressed gene across all analyzed samples suggests that Pacific white shrimp exposed to lowering dissolved oxygen set points does not induce global changes in gene expression at these levels.

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ecological metagenomes

Project description:Amplicon sequencing of full-length 16S rRNA gene in water samples

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Characterization of the Bacterial Diversity of Drinking Water From 3 Parisian Treatment Plants Using Genomic Approaches

Project description:We characterized the bacterial diversity of chlorinated drinking water from three surface water treatment plants supplying the city of Paris, France. For this purpose, we used serial analysis of V6 ribosomal sequence tag (SARST-V6) to produce concatemers of PCR-amplified ribosomal sequence tags (RSTs) from the V6 hypervariable region of the 16S rRNA gene for sequence analysis. Using SARST-V6, we obtained bacterial profiles for each drinking water sample, demonstrating a strikingly high degree of biodiversity dominated by a large collection of low-abundance phylotypes. In all water samples, between 57.2-77.4% of the sequences obtained indicated bacteria belonging to the Proteobacteria phylum. Full-length 16S rDNA sequences were also generated for each sample, and comparison of the RSTs with these sequences confirmed the accurate assignment for several abundant bacterial phyla identified by SARST-V6 analysis, including members of unclassified bacteria, which account for 6.3-36.5% of all V6 sequences. These results suggest that these bacteria may correspond to a common group adapted to drinking water systems. The V6 primers used were subsequently evaluated with a computer algorithm to assess their hybridization efficiency. Potential errors associated with primer-template mismatches and their impacts on taxonomic group detection were investigated. The biodiversity present in all three drinking water samples suggests that the bacterial load of the drinking water leaving treatment plants may play an important role in determining the downstream community dynamics of water distribution networks.

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Project description:full-length 16S sequencing

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Project description:Shrimp Intestine Microbiota 16S rRNA

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