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ABSTRACT:
PROVIDER: PRJNA393182 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In depth characterisation of the impact of wheat bran thermal treatment on the human gut microbiome
| PRJNA427167 | ENA
Project description:In depth characterisation of the microbial succesion during wheat bran fermentation by the human fecal microbiota
| PRJNA427170 | ENA
Project description:The goal was to study the dfactionation of different lignocelullose (glucose, wheat bran, wheat straw) by Streptomyces coelicolor A3(2) and the corresponding production of secondary metabolites. This was performed by multi-omic experiment such as transcriptomic/metabolomic and leads to the production of new metabolites. For that, the strain Streptomyces coelicolor A3(2) was subjected to two carbon sources in triplicate (wheat bran and glucose as control). Enzymatic activities were studied at different times and the expression of CAZYmes was studied by transcriptomic in order to detect which enzymes are needed for each carbon source
2020-10-01 | E-MTAB-8971 | biostudies-arrayexpress
Project description:The gut microbiome is significantly altered in inflammatory bowel diseases, but the basis of these changes is not well understood. We have combined metagenomic and metatranscriptomic profiling of the gut microbiome to assess changes to both bacterial community structure and transcriptional activity in a mouse model of colitis. Gene families involved in microbial resistance to oxidative stress, including Dps/ferritin, Fe-dependent peroxidase and glutathione S-transferase, were transcriptionally up-regulated in colitis, implicating a role for increased oxygen tension in gut microbiota modulation. Transcriptional profiling of the host gut tissue and host RNA in the gut lumen revealed a marked increase in the transcription of genes with an activated macrophage and granulocyte signature, suggesting the involvement of these cell types in influencing microbial gene expression. Down-regulation of host glycosylation genes further supports a role for inflammation-driven changes to the gut niche that may impact the microbiome. We propose that members of the bacterial community react to inflammation-associated increased oxygen tension by inducing genes involved in oxidative stress resistance. Furthermore, correlated transcriptional responses between host glycosylation and bacterial glycan utilisation support a role for altered usage of host-derived carbohydrates in colitis. Complementary transcription profiling data from the mouse hosts have also been deposited at ArrayExpress under accession number E-MTAB-3590 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3590/ ).
2015-05-22 | E-MTAB-3562 | biostudies-arrayexpress
Project description:Aging is associated with declining immunity and inflammation as well as alterations in the gut microbiome with a decrease of beneficial microbes and increase in pathogenic ones. The aim of this study was to investigate aging associated gut microbiome in relation to immunologic and metabolic profile in a non-human primate (NHP) model. 12 old (age>18 years) and 4 young (age 3-6 years) Rhesus macaques were included in this study. Immune cell subsets were characterized in PBMC by flow cytometry and plasma cytokines levels were determined by bead based multiplex cytokine analysis. Stool samples were collected by ileal loop and investigated for microbiome analysis by shotgun metagenomics. Serum, gut microbial lysate and microbe-free fecal extract were subjected to metabolomic analysis by mass-spectrometry. Our results showed that the old animals exhibited higher inflammatory biomarkers in plasma and lower CD4 T cells with altered distribution of naïve and memory T cell maturation subsets. The gut microbiome in old animals had higher abundance of Archaeal and Proteobacterial species and lower Firmicutes than the young. Significant enrichment of metabolites that contribute to inflammatory and cytotoxic pathways was observed in serum and feces of old animals compared to the young. We conclude that aging NHP undergo immunosenescence and age associated alterations in the gut microbiome that has a distinct metabolic profile.
2022-02-01 | E-MTAB-10160 | biostudies-arrayexpress
Project description:HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome. The results were used to demonstarte the usefulness of applying HuMiChip to human microbiome studies.
2014-02-04 | E-GEOD-54290 | biostudies-arrayexpress
Project description:Plant biomass is the most abundant and renewable carbon source for many fungal species. The composition of biomass consists of about 40-45% cellulose, 20-30% hemicellulose, and 15-25% lignin and varies among plant species. In the bio-based industry, Aspergillus species and other fungi are used for the production of lignocellulolytic enzymes to pretreat agricultural waste biomass (e.g. wheat bran). In this study, we aimed to evaluate if it would be possible to create an Aspergillus strain that releases but does not metabolize hexoses from plant biomass. For this purpose, metabolic mutants were generated that were (partially) impaired in glycolysis, by deleting the hexokinase (hxkA) and glucokinase (glkA) genes. To prevent repression of enzyme production due to the accumulation of hexoses, strains were generated in which these mutations were combined with a mutation in creA, encoding the repressor involved in carbon catabolism. Phenotypic analysis revealed that growth of the ΔhxkAΔglkA mutant was reduced on wheat bran. However, hexoses did not accumulate during growth of the mutants on wheat bran, suggesting that glucose metabolism is re-routed towards alternative carbon catabolic pathways. Deletion of creA combined with blocking glycolysis resulted in an increased expression of pentose catabolic and phosphate pathway genes. This indicates that the reduced ability to use hexoses as carbon sources has resulted in a shift towards the pentose fraction of wheat bran as a major carbon source to support growth.
2018-02-26 | GSE94775 | GEO