An Anaerobic In Vitro Flow Model for Studying Interactions at the Gastrointestinal Host-Microbe Interface
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1200019 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This study characterizes the development of an anaerobic intestinal cell culture model based on a dual flow chamber system using Caco-2 cells. One goal of the study was to characterize the transcriptomic profile of Caco-2 cells grown in the anaerobic dual flow chamber system and characterizing the effect of oxygen- and flow conditions on the maturation of the cells.
2025-08-04 | GSE284670 | GEO
Project description:Changes in the human gastrointestinal microbiome are associated with several diseases. To infer causality, experiments in representative models are essential, but widely used animal models exhibit limitations. Here we present a modular, microfluidics-based model (HuMiX, human–microbial crosstalk), which allows co-culture of human and microbial cells under conditions representative of the gastrointestinal human–microbe interface. We demonstrate the ability of HuMiX to recapitulate in vivo transcriptional, metabolic and immunological responses in human intestinal epithelial cells following their co-culture with the commensal Lactobacillus rhamnosus GG (LGG) grown under anaerobic conditions. In addition, we show that the co-culture of human epithelial cells with the obligate anaerobe Bacteroides caccae and LGG results in a transcriptional response, which is distinct from that of a co-culture solely comprising LGG. HuMiX facilitates investigations of host–microbe molecular interactions and provides insights into a range of fundamental research questions linking the gastrointestinal microbiome to human health and disease.
2017-07-28 | MTBLS328 | MetaboLights
Project description:Per- and polyfluoroalkyl substances (PFAS), particularly the perfluorinated ones, are recalcitrant to biodegradation. By integrating an enrichment culture of reductive defluorination with biocompatible electrodes for the electrochemical process, a deeper defluorination of a C6-perfluorinated unsaturated PFAS was achieved compared to the biological or electrochemical system alone. Two synergies in the bioelectrochemical system were identified: i) The in-series microbial-electrochemical defluorination and ii) the electrochemically enabled microbial defluorination of intermediates. These synergies at the material-microbe interfaces surpassed the limitation of microbial defluorination and further turned the biotransformation end products into less fluorinated products, which could be less toxic and more biodegradable in the environment. This material-microbe hybrid system brings opportunities in the bioremediation of PFAS driven by renewable electricity and warrants future research on mechanistic understanding of defluorinating and electroactive microorganisms at the material-microbe interface for system optimizations.
| S-EPMC11295042 | biostudies-literature
Project description:Drosophila model for studying cystic fibrosis pathophysiology of the gastrointestinal system
| PRJNA1032632 | ENA
Project description:We have developed a microfluidics-based in vitro model of the human gut allowing co-culture of human and microbial cells and subsequent multi-omic assessment of the effect of the co-culture on the host transcriptome. We compare the transcriptional changes induced in the human epithelial cell line, Caco-2 after co-culture with Lactobacillus rhamnosus GG or a consortium of Lactobacillus rhamnosus GG and Bacteroides caccae.
2016-05-05 | GSE79383 | GEO
Project description:relied on two-dimensional (2D) static cultures which neglect the dynamic,three-dimensional (3D) nature of the biophysical tumour microenvironment (TME), especially the role and impact of interstitial fluid flow (IFF). To address this, we undertook a transcriptome-wide analysis of the impact of IFF-like perfusion flow using a spheroid-on-chip microfluidic platform using cell line MCF7 (pleural effusion of metastatic breast adenocarcinoma). IFF-like perfusion flow allows 3D cancer spheroids to be integrated into extracellular matrices (ECM)-like hydrogels and exposed to continuous perfusion, to mimic IFF in the TME. Importantly, we have performed these studies both in experimental (normoxia) and pathophysiological (hypoxia) oxygen conditions. Our data indicated that gene expression was altered by flow when compared to static conditions, and for the first time showed that these gene expression patterns differed in different oxygen tensions, reflecting a differential role of spheroid perfusion inIFF-like flow in tumour-relevant hypoxic conditions in the biophysical TME. We were also able to identify factors primarily linked with IFF-like conditions which are linked with prognostic value in cancer patients and therefore could correspond to a potential novel biomarker of IFF in cancer. This study therefore highlights the need to consider relevant oxygen conditions when studying the impact of flow in cancer biology, as well as demonstrating the potential of microfluidic models of flow to identify IFF-relevant tumour biomarkers.
2024-09-12 | E-MTAB-14446 | biostudies-arrayexpress
Project description:Changes in the human gastrointestinal microbiome are associated with several diseases. To infer causality, experiments in representative models are essential, but widely used animal models exhibit limitations. Here we present a modular, microfluidics-based model (HuMiX, human-microbial crosstalk), which allows co-culture of human and microbial cells under conditions representative of the gastrointestinal human-microbe interface. We demonstrate the ability of HuMiX to recapitulate in vivo transcriptional, metabolic and immunological responses in human intestinal epithelial cells following their co-culture with the commensal Lactobacillus rhamnosus GG (LGG) grown under anaerobic conditions. In addition, we show that the co-culture of human epithelial cells with the obligate anaerobe Bacteroides caccae and LGG results in a transcriptional response, which is distinct from that of a co-culture solely comprising LGG. HuMiX facilitates investigations of host-microbe molecular interactions and provides insights into a range of fundamental research questions linking the gastrointestinal microbiome to human health and disease.
| S-EPMC4865890 | biostudies-literature
Project description:Studying the physiology and pathology of gastrointestinal (GI) tissues requires tools that can accurately mimic their complex architecture and functionality in vitro. Organoids have emerged as one such promising tool, though their closed structures with poorly accessible lumen and limited observability makes readouts challenging. In this study, we introduce a bioengineered organoid platform that generates bilaterally accessible 3D tissue models, allowing independent manipulation of both the apical and basal sides of patterned epithelial monolayers. We successfully constructed gastric, small intestinal, caecal, and colonic epithelial models that faithfully reproduced tissue-respective geometries and exhibited high physiological relevance, evidenced by the regionalization of stem cells and transcriptional resemblance to real epithelia. The gained observability allowed single-cell tracking over time and studies into the motility of cells in immersion and air-liquid interface cultures. Additionally, this model recapitulated Trichuris muris infection of the caecum epithelium, allowing the first live imaging of syncytial tunnel formation. Overall, this platform offers accessible organoids with improved observability, making it a valuable tool for investigating the dynamics of GI epithelial cells and their interactions with pathogens.
2023-08-21 | GSE241012 | GEO
Project description:Hypoxia is the most common adverse event during gastrointestinal endoscopes sedated with propofol and sufentanil, especially in obese people. In the present study, high-flow nasal cannula oxygenation will be utilized in order to reduce the incidence of hypoxia among obesity.
| 2347835 | ecrin-mdr-crc
Project description:Cystic fibrosis (CF) is a recessive disease caused by mutations in theCF transmembrane conductance regulator(CFTR) gene. The most common symptoms include progressive lung disease and chronic digestive conditions. CF is the first human genetic disease to benefit from having five different species of animal models. Despite the phenotypic differences among the animal models and human CF, these models have provided invaluable insight into understanding disease mechanisms at the organ-system level. Here, we identify a member of the ABCC4 family, CG5789, that has the structural and functional properties expected for encoding theDrosophilaequivalent of human CFTR, and thus refer to it asDrosophila CFTR(Dmel\CFTR). We show that knockdown ofDmel\CFTRin the adult intestine disrupts osmotic homeostasis and displays CF-like phenotypes that lead to intestinal stem cell hyperplasia. We also show that expression of wild-type humanCFTR, but not mutant variants of CFTR that prevent plasma membrane expression, rescues the mutant phenotypes ofDmel\CFTR.Furthermore, we performed RNA sequencing (RNA-Seq)-based transcriptomic analysis usingDmel\CFTRfly intestine and identified a mucin gene,Muc68D, which is required for proper intestinal barrier protection. Altogether, our findings suggest thatDrosophilacan be a powerful model organism for studying CF pathophysiology.
2023-10-26 | GSE246379 | GEO