Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1019374 | ENA |
REPOSITORIES: ENA
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Project description:Pseudozyma hubeiensis is a basidiomycete yeast that has the highly desirable traits for lignocellulose valorisation of being equally efficient at utilization of glucose and xylose, and capable of their co-utilization. The species has previously mainly been studied for its capacity to produce secreted biosurfactants in the form of mannosylerythritol lipids, but it is also an oleaginous species capable of accumulating high levels of triacylglycerol storage lipids during nutrient starvation. In this study, we aimed to further characterize the oleaginous nature of P. hubeiensis by evaluating metabolism and gene expression responses during storage lipid formation conditions with glucose or xylose as a carbon source.
2023-03-09 | GSE193998 | GEO
Project description:Choline is a water-soluble nutrient essential for human life. Gut microbial metabolism of choline results in the production of trimethylamine (TMA), which upon absorption by the host is converted in the liver to trimethylamine N-oxide (TMAO). Recent studies revealed that TMAO exacerbates atherosclerosis in mice, and positively correlates with the severity of this disease in human. However, which microbes contribute to TMA production in the human gut; the extent to which host factors, e.g., genotype and diet, affect TMA production and colonization of these microbes; as well as the effects TMA-producing microbes have on bioavailability of dietary choline remain largely unknown. We screened a collection of 78 sequenced human intestinal isolates encompassing the major phyla found in the human gut and identified eight strains capable of producing TMA from choline in vitro. Gnotobiotic mouse studies showed that TMAO accumulates in the serum of animals colonized with TMA-producing species, but not in the serum of animals colonized with intestinal isolates that do not generate TMA from choline in vitro. Remarkably, low levels of colonization of TMA-producing bacteria significantly reduced choline levels available to the host. This effect was more pronounced as the abundance of TMA-producing bacteria increased. Our findings provide a framework for designing strategies aimed at changing the representation or activity of TMA-producing bacteria in the human gut and suggest the TMA producing status of the gut microbiota should be considered when making recommendations about choline intake requirements for humans.
2015-04-02 | GSE63461 | GEO
Project description:Infection caused by bacteria from environmental reservoirs such as E. coli and S. uberis have not decreased in prevalence. Lack of success in controlling bovine mastitis due to S. uberis is associated with the route of infection which is not well understood and there is inadequate information on pathogenesis of S. uberis. Therefore, this study was to investigate the virulence factors of S. uberis using comparative genome analyses using isolates from cows with clinical mastitis and isolates from cows with a low cell count in their milk using a Subtracted Diversity Array (SDA). This study also reports the construction and validation of a microarray capable of fingerprinting the virulent and non-virulent isolates using the SDA technique.
2016-12-31 | GSE63835 | GEO
Project description:Shotgun Proteomic Analysis of ESBL and non ESBL Producing Klebsiella Pneumoniae Clinical Isolates
2021-04-16 | PXD011693 | Pride
Project description:Shotgun Proteomic Analysis of ESBL and non ESBL Producing Klebsiella Pneumoniae Clinical Isolates
2022-02-24 | PXD011558 | Pride
Project description:Screening of protease producing bacterial isolates from Cholistan desert, Pakistan. Targeted loci cultured
| PRJNA573492 | ENA
Project description:Rhamnolipids (RL) are well-studied biosurfactants naturally produced by pathogenic strains of P. aeruginosa. Current methods to produce RLs in native and heterologous hosts have focused on carbohydrates as production substrate; however CH4 provides an intriguing alternative as a substrate for RL production because it is low-cost and may mitigate greenhouse gas emissions. Here we demonstrate RL production from CH4 by Methylotuvimicrobium alcaliphilum 20Z. RLs were inhibitory to M. alcaliphilum growth at low concentrations (<0.05 g/L), so adaptive evolution was performed by growing M. alcaliphilum in increasing concentrations of RLs, producing a strain that grew in the presence of 5 g/L of RLs. Metabolomics and proteomics of the adapted strain grown on CH4 in the absence of RLs revealed metabolic changes increase in fatty acid production and secretion, alterations in gluconeogenesis, and increased secretion of lactate and osmolyte products compared to the parent strain. Expression of plasmid-borne RL production genes in the parent M. alcaliphilum strain resulted in cessation of growth and cell death. In contrast, the adapted strain transformed with the RL production genes showed no growth inhibition and produced up to 1 M of RLs, a 600-fold increase compared to the parent strain. This work has promise for developing technologies to produce fatty acid-derived bioporducts, including biosurfactants, from CH4.
2022-09-19 | PXD029605 | Pride
Project description:Genomic comparisons among PDIM positive and negative isolates. Standard in vitro exponential phase cultures of M. tuberculosis H37Rv ATCC27294 were plated on 7H11 plates. Individual colonies were sub-cultured in 7H9 broth and metabolically labeled with [14C] propionic acid. The apolar lipid fraction was then extracted from those cultures and assayed for PDIM (phthiocerol dimycocerosate) content via TLC. Individual isolates producing and deficient in PDIM were selected for performing genomic comparisons.
2009-07-22 | GSE17232 | GEO
Project description:We describe sciMET-ATAC, a combinatorial indexing-based technique that is capable of producing single-cell DNA methylation plus chromatin accessibility datasets.
2024-08-30 | GSE272699 | GEO