Gut microbiota
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA971893 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24652900_1.fastq.gz | Fastqsanger.gz | |||
| SRR24652900_2.fastq.gz | Fastqsanger.gz | |||
| SRR24652901_1.fastq.gz | Fastqsanger.gz | |||
| SRR24652901_2.fastq.gz | Fastqsanger.gz | |||
| SRR24652902_1.fastq.gz | Fastqsanger.gz |
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Project description:The human gut microbiota is crucial for degrading dietary fibres from the diet. However, some of these bacteria can also degrade host glycans, such as mucins, the main component of the protective gut mucus layer. Specific microbiota species and mucin degradation patterns are associated with inflammatory processes in the colon. Yet, it remains unclear how the utilization of mucin glycans affects the degradation of dietary fibres by the human microbiota. Here, we used three dietary fibres (apple pectin, β-glucan and xylan) to study in vitro the dynamics of colon mucin and dietary fibre degradation by the human faecal microbiota. The dietary fibres showed clearly distinguishing modulatory effects on faecal microbiota composition. The utilization of colon mucin in cultures led to alterations in microbiota composition and metabolites. Metaproteome analysis showed the central role of the Bacteroides in degradation of complex fibres while Akkermansia muciniphila was the main degrader of colonic mucin. This work demonstrates the intricacy of complex glycan metabolism by the gut microbiota and how the utilization of host glycans leads to alterations in the metabolism of dietary fibres. Metaproteomics analysis of this data reveals the functional activities of the bacteria in consortia, by this contributing to a better understanding of the complex metabolic pathways within the human microbiota that can be manipulated to maximise beneficial microbiota-host interactions. In this study two different mucin samples were used: commercial porcine gastric mucin and in house prepared porcine colonic mucin. This dataset analyses the proteome of: A) autoclaved porcine colonic mucin; B) not autoclaved porcine colonic mucin; C) porcine gastric mucin.
2024-06-13 | PXD036037 | Pride
Project description:The human gut microbiota is crucial for degrading dietary fibres from the diet. However, some of these bacteria can also degrade host glycans, such as mucins, the main component of the protective gut mucus layer. Specific microbiota species and mucin degradation patterns are associated with inflammatory processes in the colon. Yet, it remains unclear how the utilization of mucin glycans affects the degradation of dietary fibres by the human microbiota. Here, we used three dietary fibres (apple pectin, β-glucan and xylan) to study in vitro the dynamics of colon mucin and dietary fibre degradation by the human faecal microbiota. The dietary fibres showed clearly distinguishing modulatory effects on faecal microbiota composition. The utilization of colon mucin in cultures led to alterations in microbiota composition and metabolites. Metaproteome analysis showed the central role of the Bacteroides in degradation of complex fibres while Akkermansia muciniphila was the main degrader of colonic mucin. This work demonstrates the intricacy of complex glycan metabolism by the gut microbiota and how the utilization of host glycans leads to alterations in the metabolism of dietary fibres. Metaproteomics analysis of this data reveals the functional activities of the bacteria in consortia, by this contributing to a better understanding of the complex metabolic pathways within the human microbiota that can be manipulated to maximise beneficial microbiota-host interactions.
2024-06-13 | PXD035981 | Pride
Project description:Increasing the consumption of dietary fibre has been proposed to alleviate the progression of non-communicable diseases such as obesity, type 2 diabetes and cardiovascular disease, yet the effect of dietary fibre on host physiology remains unclear. In this study, we performed a multiple diet feeding study in C57BL/6J mice to compare high fat and high fat modified with dietary fibre diets on host physiology and gut homeostasis by combining proteomic, metagenomic, metabolomic and glycomic techniques with correlation network analysis. We observed significant changes in physiology, liver proteome, gut microbiota and SCFA production in response to high fat diet. Dietary fibre modification did not reverse these changes but was associated with specific changes in the gut microbiota, liver proteome, SCFA production and colonic mucin glycosylation. Furthermore, correlation network analysis identified gut bacterial-glycan associations.
2021-09-08 | PXD014132 | Pride
Project description:A whole-food, plant-based diet rich in fruits and vegetables in addition to whole grains and legumes is highly praised for its positive health benefits. A reason for that is the high content of dietary fibres that are essential for optimal health and well-being. However, most people in the UK do not meet the minimum daily intake of at least 30 g. Gum Arabic (GA), a safe and rich source of soluble fibre, could potentially be incorporated into a typical Western diet as more evidence-based research confers its positive impact on health. To elucidate the mechanisms of action of GA’s role in health improvement, we combined bioinformatics (RNA-seq and 16S rRNA microbiome analysis) with metabolomics in combination with the zebrafish (Danio rerio) model. The results of this study show that a two-week diet consisting of 60% GA can significantly (adjusted p-value < 0.05) alter the expression levels of three genes related to appetite control and neuroprotection in the zebrafish brain. Our analysis also shows that incorporating GA into the diet affects the structure of the microbiota. It induces a variation in richness and bacterial taxa abundance by reducing microbiome alpha diversity and increasing the similarity in the microbial structure of the treated samples which is suggestive of a possible strain-specific selectivity mechanism. Overall, the significance of this report lies in its ability to underscore the importance of dietary fibre on health but specifically the role of GA as a prebiotic and a promising dietary soluble fibre in the context of the gut-microbiota-brain axis.
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Project description:Adverse effects of pharmaceutical agents are commonly attributed to direct drug toxicity. However, many drugs also disrupt gut microbial composition, and the resulting dysbiosis can influence drug metabolism, therapeutic efficacy, and host tissue responses. Disentangling microbiota-mediated effects from direct drug action remains a major challenge in understanding treatment-associated pathology. Here, we dissected the direct and microbiota-mediated effects of cytarabine (Ara-C), a widely used chemotherapeutic agent that frequently induces life-threatening gastrointestinal toxicity, on colonic barrier function and transcriptional responses. Using epithelial cell lines, ex vivo gut organ cultures, and in vivo models, we show that both Ara-C and its associated dysbiotic microbiota independently increase gut permeability, but through distinct molecular pathways: direct Ara-C exposure elicits interferon-driven inflammatory programs, whereas post-Ara-C microbiota activate mucosal defense and barrier-reinforcement gene sets. These findings establish chemotherapy-induced microbiota dysbiosis as an independent contributor to intestinal pathology and support microbiome-targeted strategies to mitigate gut toxicity.
2025-11-12 | GSE303815 | GEO
Project description:Adverse effects of pharmaceutical agents are commonly attributed to direct drug toxicity. However, many drugs also disrupt gut microbial composition, and the resulting dysbiosis can influence drug metabolism, therapeutic efficacy, and host tissue responses. Disentangling microbiota-mediated effects from direct drug action remains a major challenge in understanding treatment-associated pathology. Here, we dissected the direct and microbiota-mediated effects of cytarabine (Ara-C), a widely used chemotherapeutic agent that frequently induces life-threatening gastrointestinal toxicity, on colonic barrier function and transcriptional responses. Using epithelial cell lines, ex vivo gut organ cultures, and in vivo models, we show that both Ara-C and its associated dysbiotic microbiota independently increase gut permeability, but through distinct molecular pathways: direct Ara-C exposure elicits interferon-driven inflammatory programs, whereas post-Ara-C microbiota activate mucosal defense and barrier-reinforcement gene sets. These findings establish chemotherapy-induced microbiota dysbiosis as an independent contributor to intestinal pathology and support microbiome-targeted strategies to mitigate gut toxicity.
2025-11-12 | GSE303818 | GEO
Project description:Background: Macrophages represent an important part of the immune system in the intestine and are crucial for maintaining homeostasis. As part of research investigating the effect of dietary fibres on the intestinal immune barrier THP-1 macrophages were used as model system. Methods: THP-1 monocytes were stimulated for 48 hours with 100 ng/ml PMA and 48 hours rested in medium. Subsequently, they were stimulated with 500 ug/ml dietary fibres and the maximal observed LPS contamination to serve as background control. After 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify dietary fibre induced gene expression profiles in dietary fibre gene responses were compared to medium samples. Furthermore, to analyse differentiatlly affected pathways Ingenuite Pathway Analysis was employed. Results: There was a clear difference in significantly differentially expressed genes (gene cut-off p<0.05) with beta-glucan oat medium viscosity and GOS changing transcription of a relative small amount of genes and Sugar beet pectin and Resistant starch a relative large amount of genes. These latter two were also the only dietary fibres to demonstrate an increase in Fc-receptor-related pathway activation. Alternatively, beta-glucan oat medium viscosity and GOS were the only dietary fibres to activate pathways related to cellular movement and the only two to not activate the Ahr-signaling pathway (p<0.05). Conclusion: our data indicate that the in vitro THP-1 macrophage model can be used to differentiate in immunomodulatory potential of dietary fibres and provide hypotheses for functional differentiation.
2022-05-30 | GSE99611 | GEO
Project description:Dietary methionine restriction represses growth and improves therapeutic responses in several pre-clinical settings. However, how this dietary intervention impacts cancer progression in the context of the immune system is unknown. Here we analyzed the CD45+ immune cells from the small intestine of control (CTRL) diet or methionine-restricted (MR) diet fed tumor-free C57BL/6J donor mice and tumor-bearing Apc <min+/-> recipient mice transplanated with feces from these diet-fed tumor-free C57BL/6J mice by scRNA-seq. Our analysis indicate that fecal microbes from methionine-restricted tumor-free C57BL/6J mice are sufficient to represss T cell activation in the small intestine of Apc <min+/-> mice.
2023-06-14 | GSE181220 | GEO
Project description:Gut microbiota-derived peptidoglycan fragments (PGNs) are key signaling molecules that regulate multiple aspects of the host’s health. Yet the exact structures of natural PGNs in hosts have not been fully elucidated. Herein, we developed an LC-HRMS/MS analytical platform for global quantification and profiling of natural PGN subtypes in host gut and sera, unexpectedly revealing the abundance of PGN-derived saccharide moieties that do not resemble canonical ligands of mammalian NOD1/2 receptors. Focusing on the disaccharide GlcNAc-MurNAc (GM), which does not activate NOD1/2 yet still exhibits immunostimulatory effects in host immune cells, we established GM as a mild TLR4 agonist, illustrating an alternate PGN sensing mechanism other than NOD signaling. Importantly, the administration of GM mitigates colonic inflammation in the DSS-induced colitis model in mice via a TLR4-dependent manner, highlighting the in vivo significance of gut microbiota-derived PGN saccharides in maintaining host intestinal homeostasis.
2025-05-28 | GSE298370 | GEO
Project description:Background: Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Dietary fibres have been descirbed to be beneficial for intestinal health. Therefore, in this study we explored the applicability of an in vitro model, namely human intestinal Caco-2 cells, to study the effect of dietary fibres on intestinal health. Transcriptomics was applied to obtain more insight into their mode of actions in the intestinal cells. Methods: Caco-2 cells were stimulated with 500 ug/ml dietary fibres and the maximal observed LPS contamination to serve as background control for 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify dietary fibre induced gene expression profiles in dietary fibre gene responses were compared to medium samples. Furthermore, to analyse differentiatlly affected pathways Ingenuite Pathway Analysis was employed. Results: Pathway analysis revealed a distinct separation between the dietary fibres. GOS and beta-glucan oat medium viscosity affected transcription of a lower amount of genes (gene cut-off p<0.05) and gen transcription changes suggest an increase in vesicle transport and altered cholesterol regulation. On the other hand, the other dietary fibres differentially regulated a larger numbers of genes (gene cut-off p<0.05) and all appeared related to immune responses. We observed an increase in intracellular and extracellular anti-bacterial pathways and production of cytokines specifically aimed at communication with the adaptive immune system. Conclusion: GOS and beta-glucan oat medium viscosity appeared to induce intestinal epithelial communication with the body, whereas the other dietary fibres appeared recognized as PAMP and induce epithelial cells to interact with the immune system.
2022-05-30 | GSE99610 | GEO