Gammaproteobacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB12072 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR314276_1.fastq.gz | Fastqsanger.gz | |||
| DRR314276_2.fastq.gz | Fastqsanger.gz | |||
| DRR314277_1.fastq.gz | Fastqsanger.gz | |||
| DRR314277_2.fastq.gz | Fastqsanger.gz | |||
| DRR314278_1.fastq.gz | Fastqsanger.gz |
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Project description:AMR bacterial strains in Japanese long-term-care facilities
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Project description:Urinary tract infection (UTI) is a common problem in long-term care facilities. Roselle (Hibiscus sabdariffa Linn.) has been used in fold medicine as an anti-inflammatory agent. In this study, we surveyed the effect of roselle drink on the prevention of UTI in long-term care facilities and analyzed the anti-inflammatory potential of roselle on lipopolysaccharide (LPS)-induced renal inflammation. By survey questionnaires, we found that roselle drink was the most commonly used treatment for the routine care of residents. In addition, taking roselle drink in residents with urinary catheters reduced the incidence of UTI by 36%. Roselle suppressed LPS-induced nuclear factor-κB (NF-κB) activation in cells in a dose-dependent manner, and the maximal inhibition (73.75±4.11%) was observed at 100 μg/ml roselle drink. Roselle also suppressed LPS-induced interleukin-1β (IL-1β) production in mice. Gene expression profile of roselle in kidney showed that roselle downregulated the expression of inflammatory genes, and NF-κB was the main transcription factor involved in the regulation of roselle-regulated gene expression. Immunohistochemical staining further showed that roselle inhibited LPS-induced NF-κB activation and inflammatory cell infiltration in kidney. In conclusion, our findings suggested that roselle drink might be a potent benefit herbal supplement for UTI. Moreover, roselle ameliorated LPS-induced renal inflammation via regulating inflammatory gene expression and NF-κB pathway.
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Project description:<p>The study of antimicrobial resistance (AMR) in infectious diarrhea has generally been limited to cultivation, antimicrobial susceptibility testing and targeted PCR assays. When individual strains of significance are identified, whole genome shotgun (WGS) sequencing of important clones and clades is performed. Genes that encode resistance to antibiotics have been detected in environmental, insect, human and animal metagenomes and are known as "resistomes". While metagenomic datasets have been mined to characterize the healthy human gut resistome in the Human Microbiome Project and MetaHIT and in a Yanomani Amerindian cohort, directed metagenomic sequencing has not been used to examine the epidemiology of AMR. Especially in developing countries where sanitation is poor, diarrhea and enteric pathogens likely serve to disseminate antibiotic resistance elements of clinical significance. Unregulated use of antibiotics further exacerbates the problem by selection for acquisition of resistance. This is exemplified by recent reports of multiple antibiotic resistance in Shigella strains in India, in Escherichia coli in India and Pakistan, and in nontyphoidal Salmonella (NTS) in South-East Asia. We propose to use deep metagenomic sequencing and genome level assembly to study the epidemiology of AMR in stools of children suffering from diarrhea. Here the epidemiology component will be surveillance and analysis of the microbial composition (to the bacterial species/strain level where possible) and its constituent antimicrobial resistance genetic elements (such as plasmids, integrons, transposons and other mobile genetic elements, or MGEs) in samples from a cohort where diarrhea is prevalent and antibiotic exposure is endemic. The goal will be to assess whether consortia of specific mobile antimicrobial resistance elements associate with species/strains and whether their presence is enhanced or amplified in diarrheal microbiomes and in the presence of antibiotic exposure. This work could potentially identify clonal complexes of organisms and MGEs with enhanced resistance and the potential to transfer this resistance to other enteric pathogens.</p> <p>We have performed WGS, metagenomic assembly and gene/protein mapping to examine and characterize the types of AMR genes and transfer elements (transposons, integrons, bacteriophage, plasmids) and their distribution in bacterial species and strains assembled from DNA isolated from diarrheal and non-diarrheal stools. The samples were acquired from a cohort of pediatric patients and controls from Colombia, South America where antibiotic use is prevalent. As a control, the distribution and abundance of AMR genes can be compared to published studies where resistome gene lists from healthy cohort sequences were compiled. Our approach is more epidemiologic in nature, as we plan to identify and catalogue antimicrobial elements on MGEs capable of spread through a local population and further we will, where possible, link mobile antimicrobial resistance elements with specific strains within the population.</p>
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Project description:Genome sequencing and assembly of Klebsiella pneumoniae subsp. pneumoniae from Long-term acute care rehabilitation facilities
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Project description:Isolation of S. aureus from oral cavity and rectal of the residents in long-term care facilities
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Project description:Shotgun metagenome sequencing of oral and stool samples from Japanese long-term care facility residents
| PRJDB16443 | ENA
Project description:Gene expression profiles by microarray have contributed for a elucidation of an immune-response and a determination of efficiency in vaccination. Recent day, edwardsielosis have caused a fatal damage in the aquaculture of Japanese flounder, Paralichthys olivaceus. However the formalin killed-cell vaccines made from Edwardsiella tarda isolated same fish species were not efficient. Recent our study revealed the mixed FKC vaccine made from the two different type of E. tarda protected Japanese flounder against Edwardsiella tarda infection for long-term. In this study, we analyzed the immune-response of a vaccinated fish kidney using the mixed FKC vaccine against Edwardsiella tarda with an Agilent custom-oligo DNA microarray on 9,573 probes of Japanese flounder. Our study revealed that the mixed FKC vaccine confered a strong immune-response and keeped a efficient for long-term on Japanese flounder.
2014-12-31 | GSE26808 | GEO