The Human Urine Metabolome

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

Bacilli as sources of agrobiotechnology: recent advances and future directions

The group bacilli represent the Gram-positive ubiquitous spore-forming bacteria. Their diversity, versatility and the ability of producing diverse secondary metabolites including enzymes created enormous potential for applications in agriculture, biotechnology, environment and medicine. The bacilli are considered as one of the most studied groups of bacteria providing plant growth-promotion and biocontrol of multiple diseases reflecting their vital role in enhancing plants’ tolerance to biotic and abiotic stresses. Some of the Bacillus species are available commercially as phytostimulants, biopesticides, and biofertilizers. Genetically engineered plants such as maize, cotton, brinjal with endotoxins producing genes from Bacillus thuringiensis (Bt) has revolutionized agriculture. Many of these applications have been widely adopted in various fields as viable and environmentally friendly alternatives of synthetic chemical fertilizers and pesticides. A better understanding of the biology, ecology, and mechanisms of action of the beneficial strains of bacilli are needed for the development of products to support green biotechnology in agriculture and industries. This report comprehensively reviewed the applications of bacilli in agriculture and industry and discussed their potentials for the development of new products of biotechnological implications

Bioactive compounds from the endophytic fungus <i>Fusarium proliferatum</i>

<p>The crude extract of an endophytic fungus isolated from <i>Syzygium cordatum</i> and identified as <i>Fusarium proliferatum</i> showed 100% cytotoxicity against the brine shrimp <i>Artemia salina</i> at 100 μg/mL. Seven coloured, biologically active metabolites – including ergosta-5,7,22-trien-3β-ol, nectriafurone-8-methyl ether, 9-<i>O</i>-methyl fusarubin, bostrycoidin, bostrycoidin-9-methyl ether and 8-hydroxy-5,6-dimethoxy-2-methyl-3-(2-oxo-propyl)-1,4-naphthoquinone– were isolated from the extract.</p

DrugBank 4.0: shedding new light on drug metabolism

DrugBank (http://www.drugbank.ca) is a comprehensive online database containing extensive biochemical and pharmacological information about drugs, their mechanisms and their targets. Since it was first described in 2006, DrugBank has rapidly evolved, both in response to user requests and in response to changing trends in drug research and development. Previous versions of DrugBank have been widely used to facilitate drug and in silico drug target discovery. The latest update, DrugBank 4.0, has been further expanded to contain data on drug metabolism, absorption, distribution, metabolism, excretion and toxicity (ADMET) and other kinds of quantitative structure activity relationships (QSAR) information. These enhancements are intended to facilitate research in xenobiotic metabolism (both prediction and characterization), pharmacokinetics, pharmacodynamics and drug design/discovery. For this release, >1200 drug metabolites (including their structures, names, activity, abundance and other detailed data) have been added along with >1300 drug metabolism reactions (including metabolizing enzymes and reaction types) and dozens of drug metabolism pathways. Another 30 predicted or measured ADMET parameters have been added to each DrugCard, bringing the average number of quantitative ADMET values for Food and Drug Administration-approved drugs close to 40. Referential nuclear magnetic resonance and MS spectra have been added for almost 400 drugs as well as spectral and mass matching tools to facilitate compound identification. This expanded collection of drug information is complemented by a number of new or improved search tools, including one that provides a simple analyses of drug-target, -enzyme and -transporter associations to provide insight on drug-drug interactions. \ua9 2013 The Author(s). Published by Oxford University Press.Peer reviewed: YesNRC publication: Ye

Concentrations of acylcarnitines, amino acids, biogenic amines, lysophosphatidylcholines, phosphatidylcholines and sphingomyelins in human urine by combined DFI/LC-MS/MS (BIOCRATES kit).

*<p>Concentration of metabolite (Mean±SD) is expressed by µM. aa: diacyl; ae: acyl-alkyl.</p

Concentrations [Mean (range)] and % occurrence of urine metabolites as determined by NMR.

*<p>Concentration of metabolite (Mean ± SD) is expressed by µM.</p>a<p>The mean daily vitamin B6 intake was well below the recommended dietary allowance for men and woman;</p>b<p>depends greatly on amount of alcohol consumed;</p>c<p>after administration of lactose;</p>d<p>after administration of 1 g of coumarin;</p>e<p>After styrene exposure; and</p>f<p>after consumption of chocolate.</p><p>NA: not available; NA**: not available for healthy adults; ADP: Adenosine-5-diphosphate; HPHPA: 3-(3-hydroxyphenyl)-3-hydroxypropanoic acid; Oc: occurrence.</p

Concentrations of metabolites in human urine as measured by GC-MS.

*<p>Concentration of metabolite (Mean ± SD) is expressed by µM. HPHPA: 3-(3-hydroxyphenyl)-3-hydroxypropanoic acid; NA: not available; NA**: not available for healthy adults.</p

Concentrations of isoflavones and thiols as determined by HPLC.

a<p>Isoflavone metabolites measured by HPLC/UV.</p>b<p>Thiol metabolites measured by HPLC/FD.</p><p>Oc: occurrence;</p><p>NA: not available.</p

Compound names, HMDB identification numbers, unique masses, mean mass spectral match quality, retention times, and NIST retention indices for volatile compounds in urine analyzed by HS-SPME-GC/MS.

<p>Compound names, HMDB identification numbers, unique masses, mean mass spectral match quality, retention times, and NIST retention indices for volatile compounds in urine analyzed by HS-SPME-GC/MS.</p