RNASeq of Drosophila intestinal progenitor cells upon Notch knockdown or microbiome alterations
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE138555 | GEO | 2019/10/09
REPOSITORIES: GEO
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Project description:RNASeq of Drosophila intestinal progenitor cells upon Notch knockdown or microbiome alterations
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Project description:The spatiotemporal structure of the human microbiome, proteome, and metabolome reflects and determines regional intestinal physiology and may have implications for disease. Yet, we know little about the distribution of microbes, their environment, and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals. To address these deficiencies, we developed and evaluated a safe, ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion and maintains the viability of microbes from these locations. The collection of 240 intestinal samples from 15 healthy individuals using the device and subsequent multi-omics analyses revealed significant differences between microbes, phages, host proteins, and metabolites present in the intestines versus stool. Certain microbial taxa and gene classes were differentially enriched, and prophage induction was more prevalent in the intestines than in stool. The host proteome and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundancepredicted species that altered the bile acid pool through deconjugation. Furthermore,microbially conjugated bile acids displayed amino acid-dependent trends in concentration that were not apparent in stool. Overall, non-invasive longitudinal profilingof microbes, proteins, and bile acids along the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in humanphysiology and disease.
2023-01-18 | PXD038906 | Pride
Project description:Objectives: Obstructive Sleep Apnea (OSA) is related to repeated upper airway collapse, intermittent hypoxia, and intestinal barrier dysfunction. The resulting damage to the intestinal barrier may affect or be affected by the intestinal microbiota. Methods: A prospective case-control was used, including 48 subjects from Sleep Medicine Center of Nanfang Hospital. Sleep apnea was diagnosed by overnight polysomnography. Fecal samples and blood samples were collected from subjects to detect intestinal microbiome composition (by 16S rDNA gene amplification and sequencing) and intestinal barrier biomarkers – intestinal fatty acid-binding protein (I-FABP) and D-lactic acid (D-LA) (by ELISA and colorimetry, respectively). Results: The severity of OSA was related to differences in the structure and composition of the intestinal microbiome. Enriched Fusobacterium, Megamonasa, Lachnospiraceae_UCG_006, and reduced Anaerostipes was found in patients with severe OSA. Enriched Ruminococcus_2, Lachnoclostridium, Lachnospiraceae_UCG_006, and Alloprevotella was found in patients with high intestinal barrier biomarkers. Lachnoclostridium and Lachnospiraceae_UCG_006 were the common dominant bacteria of OSA and intestinal barrier damage. Fusobacterium and Peptoclostridium was independently associated with apnea-hypopnea index (AHI). The dominant genera of severe OSA were also related to glucose, lipid, neutrophils, monocytes and BMI. Network analysis identified links between the intestinal microbiome, intestinal barrier biomarkers, and AHI. Conclusions: The study confirms that changes in the intestinal microbiota are related to intestinal barrier biomarkers among patients in OSA. These changes may play a pathophysiological role in the systemic inflammation and metabolic comorbidities associated with OSA, leading to multi-organ morbidity of OSA.
2023-08-30 | GSE181270 | GEO
Project description:The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tg(cldn15la:GFP) intestine-specific transgene was used to ease dissections. RNAseq was performed at 5, 7, 9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5, 7, 9 dpf on wild type dissected intestines to check the intestinal presence of active (H3K4me3) and repressive (H3K27me3) chromatin marks and to correlate their presence with intestinal gene expression.
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Project description:The aim of the study will be to analyze the microbiome in the blood and stomach in patients with intestinal metaplasia (IM) and / or gastric cancer (GC). As far as IM is concerned, it has been found that the incomplete type is related to GC mainly intestinal-type. Studies show differences in the microbiome in patients with IM and in patients with GC, but do not specify whether these differences are related to histological types.
Our intention is to further analyze the microbiome based on histological types. Most studies on stomach cancer have focused on the microbiota of gastric microbiota. Recent data have shown that the microbiome of the small intestine, especially the mucosa, can play a key role in the condition of the gastrointestinal tract. Disturbance of the microbiome of the small intestine has been found in celiac disease, chronic liver disease, diabetes and irritable bowel syndrome. However, information on the role of the microbiome in IM remains limited.
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Project description:The gut microbiome plays an important role in normal immune function and has been implicated in several autoimmune disorders. Here we use high-throughput 16S rRNA sequencing to investigate the gut microbiome in subjects with multiple sclerosis (MS, n=61) and healthy controls (n=43). Alterations in the gut microbiome in MS include increases in the genera Methanobrevibacter and Akkermansia and decreases in Butyricimonas, and correlate with variations in the expression of genes involved in dendritic cell maturation, interferon signaling and NF-kB signaling pathways in circulating T cells and monocytes. Patients on disease-modifying treatment show increased abundances of the genera Prevotella and Sutterella, and decreased Sarcina, compared to untreated patients. MS patients of a second cohort show elevated breath methane compared to controls, consistent with our observation of increased gut Methanobrevibacter in MS in the first cohort. Further study is required to assess whether the observed alterations in the gut microbiome play a role in, or are a consequence of, MS pathogenesis.
2016-05-11 | GSE81279 | GEO
Project description:Arid1a, a subunit of the SWI/SNF chromatin remodeling complex, have been reported in multiple human cancers, however, its functional role in intestinal homeostasis remains unclear. To investigate the role of Arid1a in murine intestine, we have employed whole genome microarray expression profiling of Arid1a conditional knock out mouse intestines. We found that Wnt signaling is downregulated in Arid1a conditional knock out mouse intestines compared to that of wild type mouse intestines.
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