Best practices for analysing microbiomes

Nature Reviews Microbiology, Journal Year: 2018, Volume and Issue: 16(7), P. 410 - 422

Published: May 23, 2018

Language: Английский

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The Human Urine Metabolome

PLoS ONE, Journal Year: 2013, Volume and Issue: 8(9), P. e73076 - e73076

Published: Sept. 4, 2013

Urine has long been a "favored" biofluid among metabolomics researchers. It is sterile, easy-to-obtain in large volumes, largely free from interfering proteins or lipids and chemically complex. However, this chemical complexity also made urine particularly difficult substrate to fully understand. As biological waste material, typically contains metabolic breakdown products wide range of foods, drinks, drugs, environmental contaminants, endogenous metabolites bacterial by-products. Many these compounds are poorly characterized understood. In an effort improve our understanding we have undertaken comprehensive, quantitative, metabolome-wide characterization human urine. This involved both computer-aided literature mining quantitative experimental assessment/validation. The portion employed NMR spectroscopy, gas chromatography mass spectrometry (GC-MS), direct flow injection (DFI/LC-MS/MS), inductively coupled plasma (ICP-MS) high performance liquid (HPLC) experiments performed on multiple samples. multi-platform metabolomic analysis allowed us identify 445 quantify 378 unique metabolite species. different analytical platforms were able (quantify) total of: 209 (209) by NMR, 179 (85) GC-MS, 127 (127) DFI/LC-MS/MS, 40 (40) ICP-MS 10 (10) HPLC. Our use technologies several previously unknown substantially enhance the level metabolome coverage. critically assess relative strengths weaknesses technologies. review led identification annotation another 2206 urinary was used help guide subsequent studies. An online database containing complete set 2651 confirmed species, their structures (3079 total), concentrations, related references links known disease associations freely available at http://www.urinemetabolome.ca.

Language: Английский

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Global metabolic profiling of animal and human tissues via UPLC-MS

Nature Protocols, Journal Year: 2012, Volume and Issue: 8(1), P. 17 - 32

Published: Dec. 6, 2012

Language: Английский

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Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery

International Journal of Molecular Sciences, Journal Year: 2018, Volume and Issue: 19(6), P. 1578 - 1578

Published: May 25, 2018

The therapeutic properties of plants have been recognised since time immemorial. Many pathological conditions treated using plant-derived medicines. These medicines are used as concoctions or concentrated plant extracts without isolation active compounds. Modern medicine however, requires the and purification one two There however a lot global health challenges with diseases such cancer, degenerative diseases, HIV/AIDS diabetes, which modern is struggling to provide cures. times "active compound" has made compound ineffective. Drug discovery multidimensional problem requiring several parameters both natural synthetic compounds safety, pharmacokinetics efficacy be evaluated during drug candidate selection. advent latest technologies that enhance design hypotheses Artificial Intelligence, use 'organ-on chip' microfluidics technologies, means automation become part discovery. This resulted in increased speed evaluation whilst allowing novel ways synthesis based on Recent advances analytical computational techniques opened new avenues process complex products their structures derive innovative drugs. Indeed, we era molecular design, applied products. Predictive softwares contributed targets derivatives. In future quantum computing, databases modelling interactions predicting features needed for development, pharmacokinetic pharmacodynamics, will result few false positive leads development. review discusses plant-based product how play role next-generation

Language: Английский

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Global metabolic profiling procedures for urine using UPLC–MS

Nature Protocols, Journal Year: 2010, Volume and Issue: 5(6), P. 1005 - 1018

Published: May 6, 2010

Language: Английский

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Fat, fibre and cancer risk in African Americans and rural Africans

Nature Communications, Journal Year: 2015, Volume and Issue: 6(1)

Published: April 28, 2015

Rates of colon cancer are much higher in African Americans (65:100,000) than rural South Africans (<5:100,000). The rates associated with animal protein and fat, lower fibre consumption, colonic secondary bile acids, short-chain fatty acid quantities mucosal proliferative biomarkers risk otherwise healthy middle-aged volunteers. Here we investigate further the role fat this association. We performed 2-week food exchanges subjects from same populations, where were fed a high-fibre, low-fat African-style diet high-fat, low-fibre western-style diet, under close supervision. In comparison their usual diets, changes resulted remarkable reciprocal aspects microbiota metabolome known to affect risk, best illustrated by increased saccharolytic fermentation butyrogenesis, suppressed synthesis Americans. have Africans, which is dietary metabolic differences. Here, O'Keefe et al.show that switching leads gut microbiota, metabolites biomarkers.

Language: Английский

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TFOS DEWS II Tear Film Report

The Ocular Surface, Journal Year: 2017, Volume and Issue: 15(3), P. 366 - 403

Published: July 1, 2017

Language: Английский

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Modern analytical techniques in metabolomics analysis

The Analyst, Journal Year: 2011, Volume and Issue: 137(2), P. 293 - 300

Published: Nov. 21, 2011

Metabolomics is the comprehensive assessment of endogenous metabolites and attempts to systematically identify quantify from a biological sample. Small-molecule have an important role in systems represent attractive candidates understand disease phenotypes. Metabolites diverse group low-molecular-weight structures including lipids, amino acids, peptides, nucleic organic vitamins, thiols carbohydrates, which makes global analysis difficult challenge. The recent rapid development range analytical platforms, GC, HPLC, UPLC, CE coupled MS NMR spectroscopy, could enable separation, detection, characterization quantification such related metabolic pathways. Owing complexity metabolome properties metabolites, no single platform can be applied detect all combined use modern instrumental approaches has unravelled ideal outcomes metabolomics, beneficial increase coverage detected that not achieved by single-analysis techniques. Integrated platforms been frequently used provide sensitive reliable detection thousands biofluid Continued these will accelerate widespread integration metabolomics into biology. Here, application each hyphenated technique discussed its strengths limitations are with selected illustrative examples; furthermore, this review comprehensively highlights integrated tools metabolomic research.

Language: Английский

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Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy

Chemical Society Reviews, Journal Year: 2010, Volume and Issue: 40(1), P. 387 - 426

Published: Aug. 17, 2010

The study of biological systems in a holistic manner (systems biology) is increasingly being viewed as necessity to provide qualitative and quantitative descriptions the emergent properties complete system. Systems biology performs studies focussed on complex interactions system components; emphasising whole rather than individual parts. Many perturbations mammalian (diet, disease, drugs) are multi-factorial small parts insufficient understand phenotypic changes induced. Metabolomics one functional level tool employed investigate metabolites with other (metabolism) but also regulatory role through interaction genes, transcripts proteins (e.g. allosteric regulation). Technological developments driving force behind advances scientific knowledge. Recent two analytical platforms mass spectrometry (MS) nuclear magnetic resonance (NMR) spectroscopy have driven forward discipline metabolomics. In this critical review, an introduction metabolites, metabolomes, metabolomics MS NMR will be provided. applications for health-disease continuum, drug efficacy toxicity dietary effects health reviewed. current limitations future goals discussed (374 references).

Language: Английский

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Metabolomics in Prediabetes and Diabetes: A Systematic Review and Meta-analysis

Diabetes Care, Journal Year: 2016, Volume and Issue: 39(5), P. 833 - 846

Published: April 14, 2016

To conduct a systematic review of cross-sectional and prospective human studies evaluating metabolite markers identified using high-throughput metabolomics techniques on prediabetes type 2 diabetes.We searched MEDLINE EMBASE databases through August 2015. We conducted qualitative studies. Additionally, meta-analyses markers, with data estimates from at least three studies, diabetes risk were conducted, multivariable-adjusted relative risks calculated per study-specific SD difference in given metabolite.We 27 19 publications reporting associations metabolites and/or diabetes. Carbohydrate (glucose fructose), lipid (phospholipids, sphingomyelins, triglycerides), amino acid (branched-chain acids, aromatic glycine, glutamine) higher individuals compared control subjects. Prospective provided evidence that blood concentrations several metabolites, including hexoses, branched-chain phospholipids, triglycerides, associated the incidence meta-analyzed results eight reported for diabetes, 8,000 whom 1,940 had found 36% isoleucine (pooled 1.36 [1.24-1.48]; I(2) = 9.5%), leucine (1.36 [1.17-1.58]; 37.4%), 35% valine (1.35 [1.19-1.53]; 45.8%), tyrosine [1.19-1.55]; 51.6%), 26% phenylalanine (1.26 [1.10-1.44]; 56%). Glycine glutamine inversely (0.89 [0.81-0.96] 0.85 [0.82-0.89], respectively; both 0.0%).In metabolomics, acids appear to be consistently developing

Language: Английский

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