Practical Aspects of NMR-Based Metabolomics

Wishart, David S.; Rout, Manoj Kumar; Lee, Brian L.; Berjanskii, Mark V.; LeVatte, Marcia; Lipfert, Matthias

doi:10.1007/164_2022_613

Cited by 2 publications

(1 citation statement)

References 213 publications

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“…One should note that quantitative metabolomic data are significantly more valuable than semi-quantitative ones since only quantitative data are available for future 'eternal' reuse, the addition of new samples or groups, the realization of new comparisons, data mining, new interpretations, and more [9]. Quantitative data can be obtained with the use of NMR spectroscopy, which suffers from relatively low sensitivity, but the peak areas of the metabolite signals in NMR spectra are directly proportional to the compound concentrations [10,11]. That makes the determination of the metabolite content in tissues rather easy and straightforward with the use of only one internal standard.…”

Section: Introductionmentioning

confidence: 99%

Animal Metabolite Database: Metabolite Concentrations in Animal Tissues and Convenient Comparison of Quantitative Metabolomic Data

Yanshole,

Melnikov,

Yanshole

et al. 2023

Metabolites

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The Animal Metabolite Database (AMDB, https://amdb.online) is a freely accessible database with built-in statistical analysis tools, allowing one to browse and compare quantitative metabolomics data and raw NMR and MS data, as well as sample metadata, with a focus on the metabolite concentrations rather than on the raw data itself. AMDB also functions as a platform for the metabolomics community, providing convenient deposition and exchange of quantitative metabolomic data. To date, the majority of the data in AMDB relate to the metabolite content of the eye lens and blood of vertebrates, primarily wild species from Siberia, Russia and laboratory rodents. However, data on other tissues (muscle, heart, liver, brain, and more) are also present, and the list of species and tissues is constantly growing. Typically, every sample in AMDB contains concentrations of 60–90 of the most abundant metabolites, provided in nanomoles per gram of wet tissue weight (nmol/g). We believe that AMDB will become a widely used tool in the community, as typical metabolite baseline concentrations in tissues of animal models will aid in a wide variety of fundamental and applied scientific fields, including, but not limited to, animal modeling of human diseases, assessment of medical formulations, and evolutionary and environmental studies.

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Section: Introductionmentioning

confidence: 99%

Animal Metabolite Database: Metabolite Concentrations in Animal Tissues and Convenient Comparison of Quantitative Metabolomic Data

Yanshole,

Melnikov,

Yanshole

et al. 2023

Metabolites

View full text Add to dashboard Cite

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Time‐Resolved Evaluation of L‐Dopa Metabolism in Bacteria‐Host Symbiotic System and the Effect on Parkinson's Molecular Pathology

Kim,

Nguyen,

Moon

et al. 2024

Small Methods

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The gut microbiome influences drug metabolism and therapeutic efficacy. Still, the lack of a general label‐free approach for monitoring bacterial or host metabolic contribution hampers deeper insights. Here, a 2D nuclear magnetic resonance (NMR) approach is introduced that enables real‐time monitoring of the metabolism of Levodopa (L‐dopa), an anti‐Parkinson drug, in both live bacteria and bacteria‐host (Caenorhabditis elegans) symbiotic systems. The quantitative method reveals that discrete Enterococcus faecalis substrains produce different amounts of dopamine in live hosts, even though they are a single species and all have the Tyrosine decarboxylase (TyrDC) gene involved in L‐dopa metabolism. The differential bacterial metabolic activity correlates with differing Parkinson's molecular pathology concerning alpha‐synuclein aggregation as well as behavioral phenotypes. The gene's existence or expression is not an indicator of metabolic activity is also shown, underscoring the significance of quantitative metabolic estimation in vivo. This simple approach is widely adaptable to any chemical drug to elucidate pharmacomicrobiomic relationships and may help rapidly screen bacterial metabolic effects in drug development.

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Practical Aspects of NMR-Based Metabolomics

Cited by 2 publications

References 213 publications

Animal Metabolite Database: Metabolite Concentrations in Animal Tissues and Convenient Comparison of Quantitative Metabolomic Data

Animal Metabolite Database: Metabolite Concentrations in Animal Tissues and Convenient Comparison of Quantitative Metabolomic Data

Time‐Resolved Evaluation of L‐Dopa Metabolism in Bacteria‐Host Symbiotic System and the Effect on Parkinson's Molecular Pathology

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