Ontology highlight
ABSTRACT:
PROVIDER: PRJNA326269 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| PDZG01.dat.gz | Other | |||
| PDZG01.fasta.gz | Fasta.gz | |||
| PDZG01.master.dat | Other | |||
| PDZH01.dat.gz | Other |
Items per page: 5 1 - 5 of 81 |
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Project description:Two microbial organisms, one violacein producing strains (mixed) Genome sequencing
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Project description:Violacein, an indole-derived purple-colored natural pigment isolated from Chromobacterium violaceum has shown multiple biological activities. In this study, we report that violacein activates murine macrophages through the up-regulation of TNF-α expression at non-cytotoxic concentrations (2 µmol/L). This was evaluated by measurement of TNF-α expression using real-time qRT-PCR. In addition, we obtained evidence of the molecular mechanism of activation by determining the mRNA expression pattern upon treatment with violacein. Interestingly, the mRNA expression pattern also allowed us to observe that incubation with violacein caused activation of pathways related with an immune and inflammatory response. Together, our data indicate that violacein activates the TLR8 receptor signaling pathway, and in consequence induces production of inflammatory cytokines such as TNF-α, CCL3 and CCL4 and of negative regulators of TLR signaling such as AP20, IRG1, IκBα and IκBε. Finally, we studied the interaction of TLR8 with violacein in silico, and obtained evidence that violacein could bind to TLR8 in a similar fashion to imidazoquinoline compounds. Therefore, our results indicate that violacein could be a candidate to be applied in immune therapy.
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Project description:Unknown- violacein producing organism genome sequencing
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Project description:Strains: non-producing refernece strain pXMJ19 (CR099 pXMJ19; Goldbeck et al., 2021) and Pediocin-producer pxMJ19 ped (CR099 pXMJ19 Ptac pedACDCg, Goldbeck et al., 2021) Pediocin-producing and non-producing strains of Corynebacterium glutamicum were compared in a whole genome microarray analysis setup in order to identify potential strain optimization targets
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Project description:This clinical trial tests whether daily fiber supplementation will change the mucosal microbiome of the colon. The microbiome are microorganisms that live in the human gut. They serve a vital role in maintaining health. Certain microbial strains are associated with the growth of colon polyps, which eventually could go on to form colon cancer. Giving dietary fiber supplements may help prevent precancerous polyps from ever developing.
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Project description:To investigate gene expression differences of different tylosin high-producing strains, transcriptomes of three tylosin high-producing engineered strains (TLPH08-2, TLPH11 and TLPH17) and the vector control strain TLSET152 were analyzed by RNA-Seq. Different strains (TLSET152, TLPH08-2, TLPH11 and TLPH17) were harvested at 96 h of fermentationat and then RNA isolation, transcriptome sequencing and data analysis were conducted.
2023-08-08 | GSE228908 | GEO
Project description:Biogenic amine-producing bacteria are responsible for the production of basic nitrogenous compounds, such as histamine, cadaverine, tyramine and putrescine, after foods spoil due to microorganisms. In the present work, we applied a shotgun proteomics approach to quickly and easily characterize 15 different foodborne strains of biogenic amine-producing bacteria. A total of 10673 peptide spectrum matches (PSMs) belonging to 4081 nonredundant peptides and corresponding to 1811 annotated proteins were identified. With the results, relevant functional pathways were determined and the strains were differentiated into different Euclidean hierarchical clusters. Moreover, a predicted protein‒protein interaction network of biogenic amine foodborne strains was created. The whole confidence network contains 260 nodes and 1973 interactions. Most of the identified proteins were related to pathways and networks of energy, putrescine metabolism and host‒virus interaction. In addition, a total of 556 nonredundant peptides were identified as virulence factors, and most of these peptides corresponded to functions such as toxins, antimicrobial compound production, antimicrobial resistance, additional resistances and tolerances, host colonization and immune evasion, ABC transporters, phage proteins, and alternative virulence factors and proteins involved in horizontal transfer. Potential species-specific peptide biomarkers were screened. Thus, 77 species-specific peptide biomarkers belonging to 64 different proteins were proposed to identify 10 species (Enterobacter aerogenes, Enterobacter cloacae, Hafnia alvei, Klebsiella oxytoca, Morganella morganii, Proteus mirabilis, Proteus penneri, Proteus vulgaris, Raoutella planticola, Stenotrophomonas maltophilia). All of these results constitute the first major dataset of peptides and proteins of seafood biogenic amine-producing strains. This repository may be useful for further studies, for the development of new therapeutic treatments for food intoxication and for tracking microbial sources in foodstuffs.
2023-07-20 | PXD039320 | Pride
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