PD mouse gut microbe
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ABSTRACT:
PROVIDER: PRJEB45414 | ENA |
REPOSITORIES: ENA
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Project description:The increasing prevalence of obesity and related metabolic disorders represents a growing public health concern. Despite advances in other areas of medicine, a safe and effective drug treatment for obesity has been elusive. Obesity has repeatedly been linked to reorganization of the gut microbiome 1-4 , yet to this point obesity therapeutics have been targeted exclusively toward the human host. Here we show that gut microbe-targeted inhibition of the metaorganismal trimethylamine N-oxide (TMAO) pathway protects mice against the metabolic disturbances associated with diet-induced obesity (DIO) or leptin deficiency (ob/ob). Selective small molecule inhibition of the gut microbial enzyme choline TMA-lyase (CutC) does not significantly reduce food intake, but instead is associated with beneficial remodeling of the gut microbiome, improvement in glucose tolerance, and enhanced energy expenditure. Leveraging untargeted metabolomics we discovered that CutC inhibition is associated with reorganization of host circadian control of both phosphatidylcholine and energy metabolism. Collectively, this study underscores the close relationship between microbe and host metabolism, and provides evidence that gut microbe-derived trimethylamine (TMA) is a key regulator of the host circadian clock. This work also demonstrates that gut microbe-targeted enzyme inhibitors can have profound effects on host energy metabolism, and have untapped potential as anti-obesity therapeutics.
2021-03-31 | GSE157925 | GEO
Project description:High-fat diet mouse gut Microbe Raw sequence reads
| PRJNA1194348 | ENA
Project description:BACKGROUND & AIMS: There is mounting evidence that microbes resident in the human intestine contribute to diverse alcohol-associated liver diseases (ALD) including the most deadly form known as alcoholic hepatitis (AH). However, mechanisms by which gut microbiota synergize with excessive alcohol intake to promote liver injury are poorly understood. Furthermore, whether drugs that selectively target gut microbial metabolism can improve ALD has never been tested. METHODS: We used liquid chromatography tandem mass spectrometry to quantify the levels of microbe and host choline co-metabolites in healthy controls and AH patients, and identified the metabolite trimethylamine (TMA) as a gut microbe-derived biomarker of AH. In subsequent studies, we treated mice with non-lethal mechanism-based bacterial choline TMA lyase inhibitors to blunt gut microbe-dependent production of TMA in the context of chronic ethanol administration. Indices of liver injury were quantified by complementary RNA sequencing, biochemical, and histological approaches. In addition, we examined the impact of ethanol consumption and TMA lyase inhibition on gut microbiome structure via 16S rRNA sequencing. RESULTS: We show the gut microbial choline metabolite trimethylamine (TMA) is elevated in AH patients, which is correlated with reduced hepatic expression of the TMA oxygenase flavin-containing monooxygenase 3 (FMO3). Provocatively, we find that small molecule inhibition of gut microbial choline TMA lyase activity protects mice from ethanol-induced liver injury. TMA lyase inhibitor-driven improvement in ethanol-induced liver injury is associated with distinct reorganization of the gut microbiome community and host liver transcriptome. CONCLUSIONS: The microbial metabolite TMA is a biomarker of AH, and blocking TMA production from gut microbes can blunt ALD in mice.
2021-03-31 | GSE157681 | GEO
Project description:collembolan gut microbe Raw sequence reads
| PRJNA1265909 | ENA
Project description:Genome scale metabolic model of Drosophila gut microbe Acetobacter fabarum
Abstract -
An important goal for many nutrition-based microbiome studies is to identify the metabolic function of microbes in complex microbial communities and their impact on host physiology. This research can be confounded by poorly understood effects of community composition and host diet on the metabolic traits of individual taxa. Here, we investigated these multiway interactions by constructing and analyzing metabolic models comprising every combination of five bacterial members of the Drosophila gut microbiome (from single taxa to the five-member community of Acetobacter and Lactobacillus species) under three nutrient regimes. We show that the metabolic function of Drosophila gut bacteria is dynamic, influenced by community composition, and responsive to dietary modulation. Furthermore, we show that ecological interactions such as competition and mutualism identified from the growth patterns of gut bacteria are underlain by a diversity of metabolic interactions, and show that the bacteria tend to compete for amino acids and B vitamins more frequently than for carbon sources. Our results reveal that, in addition to fermentation products such as acetate, intermediates of the tricarboxylic acid (TCA) cycle, including 2-oxoglutarate and succinate, are produced at high flux and cross-fed between bacterial taxa, suggesting important roles for TCA cycle intermediates in modulating Drosophila gut microbe interactions and the potential to influence host traits. These metabolic models provide specific predictions of the patterns of ecological and metabolic interactions among gut bacteria under different nutrient regimes, with potentially important consequences for overall community metabolic function and nutritional interactions with the host.IMPORTANCE Drosophila is an important model for microbiome research partly because of the low complexity of its mostly culturable gut microbiota. Our current understanding of how Drosophila interacts with its gut microbes and how these interactions influence host traits derives almost entirely from empirical studies that focus on individual microbial taxa or classes of metabolites. These studies have failed to capture fully the complexity of metabolic interactions that occur between host and microbe. To overcome this limitation, we reconstructed and analyzed 31 metabolic models for every combination of the five principal bacterial taxa in the gut microbiome of Drosophila This revealed that metabolic interactions between Drosophila gut bacterial taxa are highly dynamic and influenced by cooccurring bacteria and nutrient availability. Our results generate testable hypotheses about among-microbe ecological interactions in the Drosophila gut and the diversity of metabolites available to influence host traits.
2021-07-01 | MODEL2002040002 | BioModels
Project description:In this study we compare the CD4, CD8, and CD11c cell changes in the brain, ileum, and spleen of Parkinson's (PD) animals. A mouse model of PD was created as previously described by stereotactically injecting an AAV-expressing the human A53T-mutated form of a-Synuclein into the Substantia Nigra of adult mice, while controle mice were injected with an empty vector (EV). These mice exhibit neurodegneration and PD-like motor dysfunction. Five weeks after injection immune cells were isolated from the brain, spleen, and ileum of five mice per group. Similar organs from the same group were pooled and sorted for CD45+CD4+, CD45+CD8+, and CD45+CD11c+ cells. Twenty-thousand cells from the same group and organ were pooled and subjected to single cell sequencing. By comparing the cells from the different organs we were able to identify both T cell and CD11c+ cell populations that are shared between the brain and the gut and differentially regulated in PD.
2023-10-19 | GSE232840 | GEO
Project description:The gut microbiota is related to the antitumour efficacy of immune checkpoint blockade, but the mechanism(s) of action have not been fully elucidated. Here, we show that a novel Ruminococcaceae strain (designated YB328) isolated from the faeces of patients who responded to programmed cell death 1 (PD-1) blockade primes/activates tumour-specific CD8+ T cells through stimulation/maturation of CD103+CD11b- conventional dendritic cells (cDCs) which migrate from the gut to the tumour microenvironment (TME). YB328 administration improved the antitumour efficacy of PD-1 blockade even when it was added to faecal transplantation from non-responder patients in animal models. YB328 promoted the IRF8-driven differentiation of CD103+CD11b- cDCs expressing multiple Toll-like receptors, which received additional stimulation/maturation signals from other bacteria, and the accumulation of these DCs in tumour lesions. These CD103+CD11b- cDCs prolonged engagement with cognate antigen-specific CD8+ T cells, which induced the activation of CD8+ T cells specific for diverse tumour antigens and fostered PD-1 expression through NFATc1 nuclear translocation, thereby leading to an increase in PD-1+CD8+ T cells harbouring a broader T-cell receptor repertoire in the TME. We propose that the gut microbiota augments antitumour immunity by accelerating the differentiation/maturation and migration of DCs to increase CD8+ T cells responding to diverse tumour antigens.
2025-05-06 | GSE285376 | GEO
Project description:Mus musculus gut microbe bacteria metagenome Raw sequence reads
| PRJNA1046276 | ENA