دورية أكاديمية
Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics
| العنوان: | Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics |
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| المؤلفون: | Arianna Basile, Almut Heinken, Johannes Hertel, Larry Smarr, Weizhong Li, Laura Treu, Giorgio Valle, Stefano Campanaro, Ines Thiele |
| المصدر: | Gut Microbes, Vol 15, Iss 1 (2023) |
| بيانات النشر: | Taylor & Francis Group, 2023. |
| سنة النشر: | 2023 |
| المجموعة: | LCC:Diseases of the digestive system. Gastroenterology |
| مصطلحات موضوعية: | Flux balance analysis, longitudinal data, inflammatory bowel diseases, colonic inflammation, metagenomics, microbiota, Diseases of the digestive system. Gastroenterology, RC799-869 |
| الوصف: | ABSTRACTWe report the first use of constraint-based microbial community modeling on a single individual with episodic inflammation of the gastrointestinal tract, who has a well documented set of colonic inflammatory biomarkers, as well as metagenomically-sequenced fecal time series covering seven dates over 16 months. Between the first two time steps the individual was treated with both steroids and antibiotics. Our methodology enabled us to identify numerous time-correlated microbial species and metabolites. We found that the individual’s dynamical microbial ecology in the disease state led to time-varying in silico overproduction, compared to healthy controls, of more than 24 biologically important metabolites, including methane, thiamine, formaldehyde, trimethylamine N-oxide, folic acid, serotonin, histamine, and tryptamine. The microbe-metabolite contribution analysis revealed that some Dialister species changed metabolic pathways according to the inflammation phases. At the first time point, characterized by the highest levels of serum (complex reactive protein) and fecal (calprotectin) inflammation biomarkers, they produced L-serine or formate. The production of the compounds, through a cascade effect, was mediated by the interaction with pathogenic Escherichia coli strains and Desulfovibrio piger. We integrated the microbial community metabolic models of each time point with a male whole-body, organ-resolved model of human metabolism to track the metabolic consequences of dysbiosis at different body sites. The presence of D. piger in the gut microbiome influenced the sulfur metabolism with a domino effect affecting the liver. These results revealed large longitudinal variations in an individual’s gut microbiome ecology and metabolite production, potentially impacting other organs in the body. Future simulations with more time points from an individual could permit us to assess how external drivers, such as diet change or medical interventions, drive microbial community dynamics. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 19490976 1949-0984 1949-0976 |
| Relation: | https://doaj.org/toc/1949-0976; https://doaj.org/toc/1949-0984 |
| DOI: | 10.1080/19490976.2023.2226921 |
| URL الوصول: | https://doaj.org/article/f68113bb297d46ef9c834c7918c9fcc8 |
| رقم الأكسشن: | edsdoj.f68113bb297d46ef9c834c7918c9fcc8 |
| قاعدة البيانات: | Directory of Open Access Journals |
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Full Text Finder | تدمد: | 19490976 19490984 |
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| DOI: | 10.1080/19490976.2023.2226921 |