Ontology highlight
ABSTRACT:
PROVIDER: PRJNA477750 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7422170.fastq.gz | Fastqsanger.gz | |||
| SRR7422171.fastq.gz | Fastqsanger.gz | |||
| SRR7422172.fastq.gz | Fastqsanger.gz | |||
| SRR7422173.fastq.gz | Fastqsanger.gz | |||
| SRR7422174.fastq.gz | Fastqsanger.gz |
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Project description:we report the identification and sequences of the tRNAome of industrially relevant microorganism Lactococcus lactis
2014-07-29 | GSE55392 | GEO
Project description:The indigenous human gut microbiota is a major contributor to the human superorganism with established roles in modulating nutritional status, immunity, and systemic health including diabetes and obesity. The complexity of the gut microbiota consisting of over 1012 residents and approximately 1000 species has thus far eluded systematic analyses of the precise effects of individual microbial residents on human health. In contrast, health benefits have been shown upon ingestion of certain so-called probiotic Lactobacillus strains in food products and nutritional supplements, thereby providing a unique opportunity to study the global responses of a gut-adapted microorganism in the human gut and to identify the molecular mechanisms underlying microbial modulation of intestinal physiology, which might involve alterations in the intestinal physico-chemical environment, modifications in the gut microbiota, and/or direct interaction with mucosal epithelia and immune cells. Here we show by transcriptome analysis using DNA microarrays that the established probiotic bacterium, L. plantarum 299v, adapts its metabolic capacity in the human digestive tract for carbohydrate acquisition and expression of exo-polysaccharide and proteinaceous cell surface compounds. This report constitutes the first application of global gene expression profiling of a gut-adapted commensal microorganism in the human gut. Comparisons of the transcript profiles to those obtained for L. plantarum WCFS1 in germ-free mice revealed conserved L. plantarum responses indicative of a core transcriptome expressed in the mammalian gut and provide new molecular targets for determining microbial-host interactions affecting human health. Hybridization of the samples against a common reference of gDNA isolated from L. plantarum 299v
2010-05-16 | E-GEOD-17634 | biostudies-arrayexpress
Project description:Biomineralization is a naturally occurred process, by which microorganism reduced mental ions to minerals. Bacteria-driven biomineralization is most applied in metal recycling or environmental governance, the biomineralized products are rarely used. This probably due to the attachments of microorganism derived components on minerals, such as proteins, which are treated as impurities and hard to remove. However, these microorganism generated molecules are potent in activation of immune systems, suggesting promising potentials of biomineralized products in developing immunotherapeutic strategies. In this research, we analyzed the protein components on DH5a Escherichia coli produced gold nanoparticles, to explored the generation process of gold nanoparticles in bacterial cells, as well as its immune adjuvant potentials.
2023-08-25 | PXD044359 | Pride
Project description:Interventions: Case series:N/A
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| 2706719 | ecrin-mdr-crc
Project description:The indigenous human gut microbiota is a major contributor to the human superorganism with established roles in modulating nutritional status, immunity, and systemic health including diabetes and obesity. The complexity of the gut microbiota consisting of over 1012 residents and approximately 1000 species has thus far eluded systematic analyses of the precise effects of individual microbial residents on human health. In contrast, health benefits have been shown upon ingestion of certain so-called probiotic Lactobacillus strains in food products and nutritional supplements, thereby providing a unique opportunity to study the global responses of a gut-adapted microorganism in the human gut and to identify the molecular mechanisms underlying microbial modulation of intestinal physiology, which might involve alterations in the intestinal physico-chemical environment, modifications in the gut microbiota, and/or direct interaction with mucosal epithelia and immune cells. Here we show by transcriptome analysis using DNA microarrays that the established probiotic bacterium, L. plantarum 299v, adapts its metabolic capacity in the human digestive tract for carbohydrate acquisition and expression of exo-polysaccharide and proteinaceous cell surface compounds. This report constitutes the first application of global gene expression profiling of a gut-adapted commensal microorganism in the human gut. Comparisons of the transcript profiles to those obtained for L. plantarum WCFS1 in germ-free mice revealed conserved L. plantarum responses indicative of a core transcriptome expressed in the mammalian gut and provide new molecular targets for determining microbial-host interactions affecting human health.
2010-01-01 | GSE17634 | GEO
Project description:Background: Lactococcus garvieae is a bacterial pathogen that affects different animal species and human. Despite the widespread distribution and emerging clinical significance of L. garvieae in both veterinary and human medicine, there is almost a complete lack of knowledge about the genetic content of this microorganism. In the present study the genomic content of L. garvieae CECT 4531 was analyzed by bioinformatic tools and microarray-based comparative genomic hybridizations (CGH) experiments, using Lactococcus lactis subsp. lactis IL1403 and Streptococcus pneumoniae TIGR4 as reference microorganisms. Results: The combination and integration of in silico analyses and in vitro (CGH) experiments performed between the reference microorganisms allowed establishing an inter-species hybridization framework with a detection threshold based on the sequence similarity ?70%. With this threshold value, 267 genes were identified as having an analogue in L. garvieae, most of which (n = 258) have been documented for the first time in this pathogen. Most of these genes are related to ribosomal, sugar metabolism or energy conversion systems. Some identified genes could be involved in the pathogenesis of L. garvieae infections. Conclusions: In this study a comparative analysis based on microarray interspecies hybridization and the use of bioinformatic tools were used for the first time to study the genetic content of L. garvieae CECT 4531. Towards this approach, we identified 267 potentially present genes in L. garvieae CECT 4531, some of which could be involved in the pathogenesis of L. garvieae infections, such as als or mycA. These results provide the first insight into the genome content of L. garvieae. Array-based comparative genome hybridization (CGH): The L. lactis subsp. lactis IL1403 and S. pneumoniae TIGR4 microarrays used for the CGH analysis were purchased from Eurogentec (Serain, Belgium). The L. lactis microarray contains 4608 spots: 2126 duplicated ORFs, 32 negative controls and 324 empty spots. The S. pneumoniae microarray contains 4608 spots: 2087 duplicated ORFs, 224 negative controls and 210 empty spots. The CGH experiments were performed by means of competitive hybridizations using DNA of L. lactis subsp. lactis IL1403 or S. pneumoniae TIGR4, depending on the array as positive controls. DNAs to be hybridized on the same array were labelled with Cy3-dUTP and Cy5-dUTP, respectively. For each microarray hybridization reaction, aliquots (1–2 µg) of labelled genomic DNAs of reference (labelled with Cy3) and test (labelled with Cy5) strains, were mixed in 45 µl EGT hybridization solution (Eurogentec, Serain, Belgium) and denatured at 65ºC for 2 min. The hybridization mixture was then loaded onto a microarray slide, covered with a coverslip and incubated at 38ºC overnight. Following hybridization, the slides were washed in 2 X SSC, 0.5% SDS for 5 min followed by 5 min in 1 X SSC, 0.25% SDS. Finally, slides were rinsed in 0.2 X SSC and dried by centrifugation. The results presented herein represent a compilation of sixteen separate CGH experiments: L. lactis subsp. lactis IL1403 arrays (reference microorganism) were hybridized with S. pneumoniae TIGR4 (test microorganism) (n=2); S. pneumoniae TIGR4 arrays (reference microorganism) were hybridized with L. lactis subsp. lactis IL1403 (test microorganism) (n=2); L. lactis subsp. lactis IL1403 arrays (reference microorganism) were hybridized with L.garvieae CECT 4531 (test microorganism) (n=8); S. pneumoniae TIGR4 arrays (reference microorganism) were hybridized with L.garvieae CECT 4531 (test microorganism) (n=4). Data acquisition and analysis: The microarray was scanned after hybridization using a Scanarray HT microarray scanner (Perkin-Elmer). The signal intensity of the two fluors was determined using ImaGene software (BioDiscovery, El Segundo, CA, USA). Microarray data were analysed using ImaGene software, Microsoft Excel and an in-house designed and built Microsoft Access database [30]. Gene calling was based on a signal-to-noise ratio (SNR) > 3 for each spot. After CGH experiments, a gene was considered to show a positive result when it was present in at least three of the four CGH assays. In the case of the L. garvieae CECT 4531 hybridizations with L. lactis subsp. lactis IL1403 arrays, it was necessary to perform a greater number of assays (n=8) due to the poor quality of one of the array batches used. Thus, the criteria chosen to determine a positive result in this case was when the gene was present in at least five of the eight CGH assays.
2010-03-23 | E-GEOD-19005 | biostudies-arrayexpress