Metabolomics technology and bioinformatics

Metabolomics is the global analysis of all or a large number of cellular metabolites. Like other functional genomics research, metabolomics generates large amounts of data. Handling, processing and analysis of this data is a clear challenge and requires specialized mathematical, statistical and bioinformatics tools. Metabolomics needs for bioinformatics span through data and information management, raw analytical data processing, metabolomics standards and ontology, statistical analysis and data mining, data integration and mathematical modelling of metabolic networks within a framework of systems biology. The major approaches in metabolomics, along with the modern analytical tools used for data generation, are reviewed in the context of these specific bioinformatics needs.     

Lipids and life strategies of Calanus finmarchicus, Calanus glacialis and Calanus hyperboreus in late autumn, Kongsfjorden, Svalbard

Stage IV and V copepodites were the dominant forms of Calanus finmarchicus, C. glacialis and C. hyperboreus in Kongsfjorden in late September 1997. Stage IV and V copepodites of C. glacialis and C. hyperboreus were rich in lipid, largely wax esters, and were well fitted to overwinter. Stage IV copepodites of C. finmarchicus were also rich in wax esters, but stage V copepodites of C. finmarchicus were less wax ester-rich. Large size increments between stage IV and V copepodites and between stage V copepodites and females were noted in C. finmarchicus. A very large increment between stage IV and V copepodites was noted for C. glacialis but the size difference between stage V copepodites and females was very small in this species. Particularly large increments were noted between stage IV and V copepodites of C. hyperboreus and also between stage V copepodites and females of this species. The very large, wax ester-rich C. hyperboreus is well adapted to survive the most extreme variations in the Arctic, in Arctic basin waters, whereas the smaller, wax ester-rich C. glacialis is adapted to survive less extreme Arctic variations, as in Arctic shelf waters. The smallest of the three, C. finmarchicus, is best adapted to survive the more predictable waters of the North Atlantic and the Barents Sea. Accepted: 3 January 2000     

Dynamics of coexisting Calanus finmarchicus, Calanus glacialis and Calanus hyperboreus populations in a high-Arctic fjord

We studied the population dynamics of Calanus finmarchicus, Calanus glacialis and Calanus hyperboreus in Billefjorden, Svalbard (78°40N). All three species reproduced in the fjord with different timing. The maximum abundance of Calanus spp. copepodite stages peaked on the 11th of July (29,000 ind m^–2). C. glacialis was the dominant species accounting for 60–80% of the total Calanus abundance. C. finmarchicus appear to thrive in the fjord despite the low temperatures (–1.86°C to 5°C) and accounted for 20–30% of the total population. C. hyperboreus contributed less to the total abundance (5–20%). A 1-year life cycle is suggested for C. finmarchicus and C. hyperboreus in the fjord, C. glacialis has a 1- to 2-year life cycle. Highest mortality rates were observed for copepodite stage CV in C. finmarchicus and C. glacialis (0.09 and 0.075 d^–1, respectively) and for females in C. hyperboreus (0.149 d^–1). Mortality of copepodite stages was substantially lower in C. glacialis than in the other species. This is particularly obvious in the early and numerous copepodite stages (CI + CII) during the period of recruitment to these stages. This suggests that differences in secondary production in Arctic pelagic ecosystems are controlled partly by population loss rates.     

Investigation of species and environmental effects on rhubarb roots metabolome using <Superscript>1</Superscript>H NMR combined with high performance thin layer chromatography

Introduction

The pharmacological activities of medicinal plants are reported to be due to a wide range of metabolites, therein, the concentrations of which are greatly affected by many genetic and/or environmental factors. In this context, a metabolomics approach has been applied to reveal these relationships. The investigation of such complex networks that involve the correlation between multiple biotic and abiotic factors and the metabolome, requires the input of information acquired by more than one analytical platform. Thus, development of new metabolomics techniques or hyphenations is continuously needed.

Objectives

Feasibility of high performance thin-layer chromatography (HPTLC) were investigated as a supplementary tool for medicinal plants metabolomics supporting ¹H nuclear magnetic resonance (¹H NMR) spectroscopy.

Method

The overall metabolic difference of plant material collected from two species (Rheum palmatum and Rheum tanguticum) in different geographical locations and altitudes were analyzed by ¹H NMR- and HPTLC-based metabolic profiling. Both NMR and HPTLC data were submitted to multivariate data analysis including principal component analysis and orthogonal partial least square analysis.

Results

The NMR and HPTLC profiles showed that while chemical variations of rhubarb are in some degree affected by all the factors tested in this study, the most influential factor was altitude of growth. The metabolites responsible for altitude differentiation were chrysophanol, emodin and sennoside A, whereas aloe emodin, catechin, and rhein were the key species-specific markers.

Conclusion

These results demonstrated the potential of HTPLC as a supporting tool for metabolomics due to its high profiling capacity of targeted metabolic groups and preparative capability.

     

Metabolic classification of South American Ilex species by NMR-based metabolomics

The genus Ilex to which mate (Ilex paraguariensis) belongs, consists of more than 500 species. A wide range of metabolites including saponins and phenylpropanoids has been reported from Ilex species. However, despite the previous works on the Ilex metabolites, the metabolic similarities between species which can be used for chemotaxonomy of the species are not clear yet. In this study, nuclear magnetic resonance (NMR) spectroscopy-based metabolomics was applied to the classification of 11 South American Ilex species, namely, Ilex argentina, Ilex brasiliensis, Ilex brevicuspis, Ilex dumosa var. dumosa, I. dumosa var. guaranina, Ilex integerrima, Ilex microdonta, I. paraguariensis var. paraguariensis, Ilex pseudobuxus, Ilex taubertiana, and Ilex theezans. ¹H NMR combined with principal component analysis (PCA), partial least square-discriminant analysis (PLS-DA) and hierarchical cluster analysis (HCA) showed a clear separation between species and resulted in four groups based on metabolomic similarities. The signal congestion of ¹H NMR spectra was overcome by the implementation of two-dimensional (2D)-J-resolved and heteronuclear single quantum coherence (HSQC). From the results obtained by 1D- and 2D-NMR-based metabolomics it was concluded that species included in group A (I. paraguariensis) were metabolically characterized by a higher amount of xanthines, and phenolics including phenylpropanoids and flavonoids; group B (I. dumosa var. dumosa and I. dumosa var. guaranina) with oleanane type saponins; group C (I. brasiliensis, I. integerrima, I. pseudobuxus and I. theezans) with arbutin and dicaffeoylquinic acids, and group D (I. argentina, I. brevicuspis, I. microdonta and I. taubertiana) with the highest level of ursane-type saponins. Clear metabolomic discrimination of Ilex species and varieties in this study makes the chemotaxonomic classification of Ilex species possible.     

Evaluation of extraction methods for use with NMR-based metabolomics in the marine polychaete ragworm, Hediste diversicolor

The sediment-dwelling polychaete, Hediste diversicolor, is commonly found in Northern temperate estuaries. Its limited mobility and tolerance to polluted conditions makes it a good candidate for biological monitoring. Moreover, its importance in the functioning of the sediment ecosystem has caused it to be described as a keystone species. Here we present the development of analytical methodology that will enable the use of H. diversicolor in environmental metabolomics studies for the biomonitoring of estuarine ecosystems. Polar and non-polar extraction solvents have been used to solubilise a wide range of metabolites. Extraction solvents assessed include: aqueous phosphate buffer solution, methanol:chloroform:water (1:1:0.9), methanol:water (1:1 and 2:1) and chloroform. The metabolites were analysed using 1-dimensional (1D) ¹H nuclear magnetic resonance (NMR) spectroscopy. Using the methanol:water (1:1) method, previous freezing to aid cell rupture did not result in an enhanced extraction. Removal of methanol with a speed vacuum resulted in reduction in yield. Methanol:water (1:1) and chloroform extractions proved to be the most appropriate techniques based on the sample yield and repeatability. NMR-based metabolomics in the ragworm can now be used to understand the ecophysiology of this important estuarine organism and has applications in biomonitoring, biomarker development and ecotoxicological studies.     

Influence of ethanol concentration of extraction solvent on metabolite profiling for Salviae Miltiorrhizae Radix et Rhizoma extract by 1H NMR spectroscopy and multivariate data analysis

Salviae Miltiorrhizae Radix et Rhizoma (Danshen in China) and its related preparations are widely used in clinical practice due to its high medicinal value. In recent years, ¹H NMR technology has made great progress and demonstrated its unique advantages in the field of botanical metabolomics. In this study, ¹H NMR-based metabolomics was used to investigate the dissolution of various metabolites in Danshen as a function of ethanol concentration. ¹H NMR spectroscopy of Danshen extract identified 28 metabolites including 6 sugars, 11 amino acids, 3 organic acids, 4 salvianolic acids, and 4 tanshinones. Multivariate statistical analysis was used to classify and compare various Danshen extracts. PCA and HCA were used to obtain a global overview of the similarity in the samples and two-class OPLS-DA models were established for identifying characteristic metabolites. Then, ¹H-qNMR method was used to estimate the concentration of 22 metabolites, which is helpful to further describe the changes in metabolite ratios of various Danshen extracts. The result of this study laid the foundation for further biological activity research, and also provided an important reference for subsequent process research and quality control of Danshen related preparations.     

One-dimensional 13C NMR and HPLC-1H NMR techniques for observing carbon-13 and deuterium labelling in biosynthetic studies

For several decades isotope labelling techniques have been the indispensable tools used to unravel pathways of secondary product biosynthesis. NMR spectroscopy, together with mass spectrometry, is the most effective measuring technique used in the analysis of metabolites enriched with stable isotopes. ²H and ¹³C are the NMR-detectable nuclides which have been most frequently employed in plant secondary metabolite synthesis. Examples from the biosynthesis of phenylpropanoids, phenylphenalenones, and glucosinolates are used when discussing some aspects of one-dimensional NMR analysis of metabolites selectively labelled with ²H and ¹³C. Besides direct NMR detection of ¹³C-enriched metabolites, special emphasis is placed on indirect detection of ¹³C and ²H, especially by HPLC-¹H NMR coupling, to analyse the isotopomer pattern of compounds in low concentration. The examples discussed in this paper were obtained from studies with Anigozanthos preissii (root cultures) (Haemodoraceae) and Eruca sativa (Brassicaceae).     

Terrestrial and marine trophic pathways support young-of-year growth in a nearshore Arctic fish

River discharge supplies nearshore communities with a terrestrial carbon source that is often reflected in invertebrate and fish consumers. Recent studies in the Beaufort Sea have documented widespread terrestrial carbon use among invertebrates, but only limited use among nearshore fish consumers. Here, we examine the carbon source and diet of rapidly growing young-of-year Arctic cisco (Coregonus autumnalis) using stable isotope values (δ¹³C and δ¹⁵N) from muscle and diet analysis (stomach contents) during a critical and previously unsampled life stage. Stable isotope values (δ¹⁵N and δ¹³C) may differentiate between terrestrial and marine sources and integrate over longer time frames (weeks). Diet analysis provides species-specific information, but only from recent foraging (days). Average δ¹³C for all individuals was ?25.7 ‰, with the smallest individuals possessing significantly depleted δ¹³C values indicative of a stronger reliance of terrestrial carbon sources as compared to larger individuals. Average δ¹⁵N for all individuals was 10.4 ‰, with little variation among individuals. As fish length increased, the proportion of offshore Calanus prey and neritic Mysis prey increased. Rapid young-of-year growth in Arctic cisco appears to use terrestrial carbon sources obtained by consuming a mixture of neritic and offshore zooplankton. Shifts in the magnitude or phenology of river discharge and the delivery of terrestrial carbon may alter the ecology of nearshore fish consumers.     

生态代谢组学研究进展

代谢组学指某一生物系统中产生的或已存在的代谢物组的研究,以质谱和核磁共振技术为分析平台,以信息建模与系统整合为目标。随着代谢组学中的研究方法与技术成为生态学研究的有力工具,生态代谢组学概念应运而生,即研究某一个生物体对环境变化的代谢物组水平的响应。理清代谢组学与生态代谢组学学科发展的脉络,综述代谢组学研究中的常用技术及其优势与局限性,论述代谢组学技术在生态学研究中的应用现状,展望代谢组学技术与其他系统生物学组学技术的结合在生态学中的应用前景,提出生态代谢组学研究者未来要完成的任务和面对的挑战。     

Potential allelopatic effects of stilbenoids and flavonoids from leaves of Carex distachya Desf.

The potential allelopathic effects of 14 stilbenoids and five flavonoids, isolated from leaves of Carex distachya Desf., were evaluated on the seed germination and seedling growth of three coexisting Mediterranean species (Dactylis hispanica, Petrorhagia velutina, and Phleum subulatum). The structures of the metabolites have been elucidated on the basis of their spectroscopic features (1D and 2D NMR experiments and EI–MS and ESI–MS data). The bioassays showed species-specific effects of the metabolites from C. distachya, specially on the plant growth (root and shoot elongation) which resulted significantly stimulated or inhibited at 10⁻⁴ M concentration. The effects on root elongation is generally greater than the shoot growth at all the tested concentrations (10⁻⁴–10⁻⁸ M). Cluster of biological data showed interesting relationships between the chemical structures of the compounds and their biological effects.     

A fast NMR method for resonance assignments: application to metabolomics

We present a new method for rapid NMR data acquisition and assignments applicable to unlabeled (¹²C) or ¹³C-labeled biomolecules/organic molecules in general and metabolomics in particular. The method involves the acquisition of three two dimensional (2D) NMR spectra simultaneously using a dual receiver system. The three spectra, namely: (1) G-matrix Fourier transform (GFT) (3,2)D [¹³C, ¹H] HSQC–TOCSY, (2) 2D ¹H–¹H TOCSY and (3) 2D ¹³C–¹H HETCOR are acquired in a single experiment and provide mutually complementary information to completely assign individual metabolites in a mixture. The GFT (3,2)D [¹³C, ¹H] HSQC–TOCSY provides 3D correlations in a reduced dimensionality manner facilitating high resolution and unambiguous assignments. The experiments were applied for complete ¹H and ¹³C assignments of a mixture of 21 unlabeled metabolites corresponding to a medium used in assisted reproductive technology. Taken together, the experiments provide time gain of order of magnitudes compared to the conventional data acquisition methods and can be combined with other fast NMR techniques such as non-uniform sampling and covariance spectroscopy. This provides new avenues for using multiple receivers and projection NMR techniques for high-throughput approaches in metabolomics.     

Metabolic responses of Eucalyptus species to different temperature regimes

Species and hybrids of Eucalyptus are the world's most widely planted hardwood trees. They are cultivated across a wide range of latitudes and therefore environmental conditions. In this context, comprehensive metabolomics approaches have been used to assess how different temperature regimes may affect the metabolism of three species of Eucalyptus, E. dunnii, E. grandis and E. pellita.Young plants were grown for 53 d in the greenhouse and then transferred to growth chambers at 10°C, 20°C or30°C for another 7 d. In all three species the leaf chlorophyll content was positively correlated to temperature, and in E.pellita the highest temperature also resulted in a significant increase in stem biomass. Comprehensive metabolomics was performed using untargeted gas chromatography mass spectrometry(GC-MS) and liquid chromatography(LC)-MS.This approach enabled the comparison of the relativeabundance of 88 polar primary metabolites from GC-MS and625 semi-polar secondary metabolites from LC-MS. Using principal components analysis, a major effect of temperature was observed in each species which was larger than that resulting from the genetic background. Compounds mostly affected by temperature treatment were subsequently selected using partial least squares discriminant analysis and were further identified. These putative annotations indicated that soluble sugars and several polyphenols, including tannins, triterpenes and alkaloids were mostly influenced.     

Metabolite production by species of Stemphylium

Morphology and phylogeny have been used to distinguish members of the plant pathogenic fungal genus Stemphylium. A third method for distinguishing species of fungi is by chemotaxonomy. The main goal of the present study was to investigate the chemical potential of Stemphylium via HPLC-UV-MS analysis, while also exploring the potential of chemotaxonomy as a robust identification method for Stemphylium. Several species were found to have species-specific metabolites, while other species were distinguishable by a broader metabolic profile rather than specific metabolites. Many previously described metabolites were found to be important for distinguishing species, while some unknown metabolites were also determined to have important roles in distinguishing species of Stemphylium. This study is the first of its kind to investigate the chemical potential of Stemphylium across the whole genus.     

Feeding rates and selectivity among nauplii, copepodites and adult females of Calanus finmarchicus and Calanus helgolandicus

This study focuses on selective feeding by developmental stages of two oceanic copepods, Calanus finmarchicus and Calanus helgolandicus from nauplii to adults. A mixture of four algal species of different biochemical composition, Prorocentrum nanum (dinoflagellate), Thalassiosira minima (diatom), Rhodomonas baltica (cryptophyte) and Dunaliella tertiolecta (chlorophyte), added in an equal biovolume, was used in three different experimental set-ups. In set-up 1 the algal species were present as single cells of similar size (14 μm). In set-up 2 the diatom T. minima was present in chains of two or three cells and was therefore larger than the other algae, while the biovolume of all species remained the same. In set-up 3, the diatom T. minima was excluded from the mixture. Feeding selectivity of the copepods was assessed in relation to the quality of the algal species expressed in terms of carbon and nitrogen content, fatty acid composition, and chain length of the diatom. The results show that younger stages and adult females of C. finmarchicus and C. helgolandicus did not show a preference for an algal species when the algae were of similar size. In the feeding experiments where the diatoms were offered as chains, both copepod species showed a selective behaviour only on the basis of algal size. Individual ingestion rates increased from 0.4 to 0.7 μg C day^–1 for nauplii of both species to 5 μg C day^–1 for adult females of C. helgolandicus to 12 μg C day^–1 for C. finmarchicus. Individual filtration rates ranged from 5 ml day^–1 for C. finmarchicus nauplii to 70–98 ml day^–1 for adult females, and from 3 ml day^–1 for C. helgolandicus nauplii to 35–46 ml day^–1 for adult females. Ingestion and filtration rates per unit body carbon decreased gradually in both copepod species with increasing body carbon. The daily ingested amount of food decreased for C. finmarchicus from 124–134% of the body carbon for nauplii to 19% of the body carbon for adult females, and for C. helgolandicus from 117–137% of the body carbon for nauplii to 13–26% of the body carbon of adult females. Electronic Publication     

Identifying and quantifying metabolites by scoring peaks of GC-MS data

Background

Metabolomics is one of most recent omics technologies. It has been applied on fields such as food science, nutrition, drug discovery and systems biology. For this, gas chromatography-mass spectrometry (GC-MS) has been largely applied and many computational tools have been developed to support the analysis of metabolomics data. Among them, AMDIS is perhaps the most used tool for identifying and quantifying metabolites. However, AMDIS generates a high number of false-positives and does not have an interface amenable for high-throughput data analysis. Although additional computational tools have been developed for processing AMDIS results and to perform normalisations and statistical analysis of metabolomics data, there is not yet a single free software or package able to reliably identify and quantify metabolites analysed by GC-MS.

Results

Here we introduce a new algorithm, PScore, able to score peaks according to their likelihood of representing metabolites defined in a mass spectral library. We implemented PScore in a R package called MetaBox and evaluated the applicability and potential of MetaBox by comparing its performance against AMDIS results when analysing volatile organic compounds (VOC) from standard mixtures of metabolites and from female and male mice faecal samples. MetaBox reported lower percentages of false positives and false negatives, and was able to report a higher number of potential biomarkers associated to the metabolism of female and male mice.

Conclusions

Identification and quantification of metabolites is among the most critical and time-consuming steps in GC-MS metabolome analysis. Here we present an algorithm implemented in a R package, which allows users to construct flexible pipelines and analyse metabolomics data in a high-throughput manner.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0374-2) contains supplementary material, which is available to authorized users.     

Metabolic signatures of human Alzheimer’s disease (AD): 1H NMR analysis of the polar metabolome of post-mortem brain tissue

Brain tissue from so-called Alzheimer’s disease (AD) mouse models has previously been examined using ¹H NMR-metabolomics, but comparable information concerning human AD is negligible. Since no animal model recapitulates all the features of human AD we undertook the first ¹H NMR-metabolomics investigation of human AD brain tissue. Human post-mortem tissue from 15 AD subjects and 15 age-matched controls was prepared for analysis through a series of lyophilised, milling, extraction and randomisation steps and samples were analysed using ¹H NMR. Using partial least squares discriminant analysis, a model was built using data obtained from brain extracts. Analysis of brain extracts led to the elucidation of 24 metabolites. Significant elevations in brain alanine (15.4 %) and taurine (18.9 %) were observed in AD patients (p ≤ 0.05). Pathway topology analysis implicated either dysregulation of taurine and hypotaurine metabolism or alanine, aspartate and glutamate metabolism. Furthermore, screening of metabolites for AD biomarkers demonstrated that individual metabolites weakly discriminated cases of AD [receiver operating characteristic (ROC) AUC <0.67; p < 0.05]. However, paired metabolites ratios (e.g. alanine/carnitine) were more powerful discriminating tools (ROC AUC = 0.76; p < 0.01). This study further demonstrates the potential of metabolomics for elucidating the underlying biochemistry and to help identify AD in patients attending the memory clinic.     

Fin tissues as surrogates of white muscle when assessing carbon and nitrogen stable isotope levels for Arctic and brook char

Arctic char (Salvelinus alpinus) are a fish species ubiquitous to the fresh waters of Arctic region and brook char (Salvelinus fontinalis) are similarly common across the sub-Arctic region of eastern Canada. Populations can be small in numbers, especially farther north thus it is important to develop non-lethal methods of sampling these fish to minimize the invasiveness and impact of scientific research. We examined the stable isotopes of nitrogen and carbon in white muscle, caudal fin, and adipose fin tissues of Arctic char and brook char (S. fontinalis) from northern Quebec and Labrador, Canada. Our results revealed several broad conclusions. First, differences among muscle, caudal fin, and adipose fin tissues were ~1?‰ for freshwater Arctic and brook char. Second, the two species within the same drainage had similar stable isotope levels and tissue differences. Third, anadromous Arctic char show similar, non-significant differences among these tissues for δ¹⁵N, but muscle δ¹³C was highly enriched. Fourth, the stable isotope levels and tissue differences were the same for anadromous Arctic char from two watersheds where char use distinctly different ocean environments. Overall, it appears that caudal fin tissue in particular is a useful surrogate for white muscle δ¹³C and δ¹⁵N levels for Arctic and brook char in this region and thus, a non-lethal collection of a small sample of caudal fin tissue will provide an accurate measure of white muscle isotope levels.     

An introduction to biological nuclear magnetic resonance spectroscopy

Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful analytical techniques available to biology. This review is an introduction to the potential of this method and is aimed at readers who have little or no experience in acquiring or analyzing NMR spectra. We focus on spectroscopic applications of the magnetic resonance effect, rather than imaging ones, and explain how various aspects of the NMR phenomenon make it a versatile tool with which to address a number of biological problems. Using detailed examples, we discuss the use of ¹H NMR spectroscopy in mixture analysis and metabolomics, the use of ¹³C NMR spectroscopy in tracking isotopomers and determining the flux through metabolic pathways (‘fluxomics’) and the use of ³¹P NMR spectroscopy in monitoring ATP generation and intracellular pH homeotasis in vivo. Further examples demonstrate how NMR spectroscopy can be used to probe the physical environment of a cell by measuring diffusion and the tumbling rates of individual metabolites and how it can determine macromolecular structures by measuring the bonds and distances which separate individual atoms. We finish by outlining some of the key challenges which remain in NMR spectroscopy and we highlight how recent advances—such as increased magnet field strengths, cryogenic cooling, microprobes and hyperpolarisation—are opening new avenues for today's biological NMR spectroscopists.