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Bacteria

ABSTRACT: Bacterial diversity associated with the different shrimp farming systems in Bangladesh

PROVIDER: PRJNA976638 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24754600_1.fastq.gz	Fastqsanger.gz
	SRR24754600_2.fastq.gz	Fastqsanger.gz
	SRR24754601.fastq.gz	Fastqsanger.gz
	SRR24754601_1.fastq.gz	Fastqsanger.gz
	SRR24754601_2.fastq.gz	Fastqsanger.gz

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Project description:Vibrio parahaemolyticus is a Gram-negative bacterium commonly found in marine and estuarine environments. Acute hepatopancreatic necrosis disease (AHPND) caused by this bacterium is an ongoing problem among shrimp farming industries. V. parahaemolyticus proteins PirA and PirB have been determined to be major virulence factors that induce AHPND. In this study, Pacific white shrimp (Litopenaeus vannamei) were challenged with recombinant PirA and PirB by a reverse gavage method and then at 30 m, 1, 2, 4, and 6 h time points, the hepatopancreas of five individual shrimp were removed and placed into RNA later. We conducted RNA sequencing of the hepatopancreas samples from a no PirA/B control (n = 5) and PirA/B-treated shrimp at the different time intervals (n=5). We evaluated the different gene expression patterns between the time groups to the control with a focus on identifying differences in innate immune function.

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Bacteria

Project description:Bacterial diversity

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Project description:Fungal diversity under different farming practices

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Project description:Pseudomonas diversity under different farming practices

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Crohn’s Disease Differentially Affects Region Specific Composition and Aerotolerance Profiles of Mucosally-Adherent Bacteria

Project description:BACKGROUND: The intestinal microbiota play a key role in the onset, progression, and recurrence of Crohn’s disease (CD). Most microbiome studies assay fecal material, which does not provide region-specific information on mucosally adherent bacteria that directly interact with host systems. Changes in luminal oxygen has been proposed as a contributor to CD dybiosis. METHODS: 16S rRNA data was generated using colonic and ileal mucosal from patients with CD and without inflammatory bowel diseases (nonIBD). We developed profiles reflecting bacterial abundance within defined aerotolerance categories. Bacterial diversity, composition, and aerotolerance profiles were compared across intestinal regions and disease phenotypes. RESULTS: Bacterial diversity decreased in CD in both ileum and colon. Aerotolerance profiles significantly differed between intestinal segments in nonIBD, though both were dominated by obligate anaerobes, as expected. In CD, high relative levels of obligate anaerobes were maintained in the colon and increased in the ileum. Relative abundance of similar and distinct taxa were altered in colon and ileum. Notably, several obligate anaerobes, such as Bacteroides fragilis, dramatically increased in CD in one or both intestinal segments, though specific increasing taxa varied across patients. Increased abundance of taxa from the Proteobacteria phylum was found only in the ileum. Bacterial diversity was significantly reduced in resected pre-operative tissues of patients that developed disease recurrence across two independent cohorts, with common lower abundance of bacteria from the Bacteroides, Streptococcus, and Blautia genera. CONCLUSIONS: Mucosally adherent bacteria in colon and ileum show distinct alterations in CD that provide additional insights not revealed in fecal material.

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