Estelle Pujos-Guillot

Mass-spectrometry-based metabolomics: limitations and recommendations for future progress with particular focus on nutrition research

Mass spectrometry (MS) techniques, because of their sensitivity and selectivity, have become methods of choice to characterize the human metabolome and MS-based metabolomics is increasingly used to characterize the complex metabolic effects of nutrients or foods. However progress is still hampered by many unsolved problems and most notably the lack of well established and standardized methods or procedures, and the difficulties still met in the identification of the metabolites influenced by a given nutritional intervention. The purpose of this paper is to review the main obstacles limiting progress and to make recommendations to overcome them. Propositions are made to improve the mode of collection and preparation of biological samples, the coverage and quality of mass spectrometry analyses, the extraction and exploitation of the raw data, the identification of the metabolites and the biological interpretation of the results.

Quantifying diet-induced metabolic changes of the human gut microbiome

The human gut microbiome is known to be associated with various human disorders, but a major challenge is to go beyond association studies and elucidate causalities. Mathematical modeling of the human gut microbiome at a genome scale is a useful tool to decipher microbe-microbe, diet-microbe and microbe-host interactions. Here, we describe the CASINO (Community And Systems-level INteractive Optimization) toolbox, a comprehensive computational platform for analysis of microbial communities through metabolic modeling. We first validated the toolbox by simulating and testing the performance of single bacteria and whole communities in vitro. Focusing on metabolic interactions between the diet, gut microbiota, and host metabolism, we demonstrated the predictive power of the toolbox in a diet-intervention study of 45 obese and overweight individuals and validated our predictions by fecal and blood metabolomics data. Thus, modeling could quantitatively describe altered fecal and serum amino acid levels in response to diet intervention.

Resveratrol prevents the wasting disorders of mechanical unloading by acting as a physical exercise mimetic in the rat

Long‐term spaceflight induces hypokinesia and hypodynamia, which, along microgravity per se, result in a number of significant physiological alterations, such as muscle atrophy, force reduction, insulin resistance, substrate use shift from fats to carbohydrates, and bone loss. Each of these adaptations could turn to serious health deterioration during the long‐term spaceflight needed for planetary exploration. We hypothesized that resveratrol (RES), a natural polyphenol, could be used as a nutritional countermeasure to prevent muscle metabolic and bone adaptations to 15 d of rat hindlimb unloading. RES treatment maintained a net protein balance, soleus muscle mass, and soleus muscle maximal force contraction. RES also fully maintained soleus mitochondrial capacity to oxidize palmitoyl‐carnitine and reversed the decrease of the glutathione vs. glutathione disulfide ratio, a biomarker of oxidative stress. At the molecular level, the protein content of Sirt‐1 and COXIV in soleus muscle was also preserved. RES further protected whole‐body insulin sensitivity and lipid trafficking and oxidation, and this was likely associated with the maintained expression of FAT/CD36, CPT‐1, and peroxisome proliferator‐activated receptor‐γ coactivator‐1α (PGC‐1α) in muscle. Finally, chronic RES supplementation maintained the bone mineral density and strength of the femur. For the first time, we report a simple countermeasure that prevents the deleterious adaptations of the major physiological functions affected by mechanical unloading. RES could thus be envisaged as a nutritional counter‐measure for spaceflight but remains to be tested in humans.—Momken, I., Stevens, L., Bergouignan, A., Desplanches, D., Rudwill, F., Chery, I., Zahariev, A., Zahn, S., Stein, T. P., Sebedio, J. L., Pujos‐Guillot, E., Falempin, M., Simon, C., Coxam, V., Andrianjafiniony, T., Gauquelin‐Koch, G., Picquet, F., Blanc, S. Resveratrol prevents the wasting disorders of mechanical unloading by acting as a physical exercise mimetic in the rat. FASEB J. 25, 3646–3660 (2011). www.fasebj.org

Mass Spectrometry-based Metabolomics for the Discovery of Biomarkers of Fruit and Vegetable Intake: Citrus Fruit as a Case Study

Elucidation of the relationships between genotype, diet, and health requires accurate dietary assessment. In intervention and epidemiological studies, dietary assessment usually relies on questionnaires, which are susceptible to recall bias. An alternative approach is to quantify biomarkers of intake in biofluids, but few such markers have been validated so far. Here we describe the use of metabolomics for the discovery of nutritional biomarkers, using citrus fruits as a case study. Three study designs were compared. Urinary metabolomes were profiled for volunteers that had (a) consumed an acute dose of orange or grapefruit juice, (b) consumed orange juice regularly for one month, and (c) reported high or low consumption of citrus products for a large cohort study. Some signals were found to reflect citrus consumption in all three studies. Proline betaine and flavanone glucuronides were identified as known biomarkers, but various other biomarkers were revealed. Further, many signals that increased after citrus intake in the acute study were not sensitive enough to discriminate high and low citrus consumers in the cohort study. We propose that urine profiling of cohort subjects stratified by consumption is an effective strategy for discovery of sensitive biomarkers of consumption for a wide range of foods.

Enterohaemorrhagic Escherichia coli gains a competitive advantage by using ethanolamine as a nitrogen source in the bovine intestinal content

The bovine gastrointestinal tract is the main reservoir for enterohaemorrhagic Escherichia coli (EHEC) responsible for food-borne infections. Characterization of nutrients that promote the carriage of these pathogens by the ruminant would help to develop ecological strategies to reduce their survival in the bovine gastrointestinal tract. In this study, we show for the first time that free ethanolamine (EA) constitutes a nitrogen source for the O157:H7 EHEC strain EDL933 in the bovine intestinal content because of induction of the eut (ethanolamine utilization) gene cluster. In contrast, the eut gene cluster is absent in the genome of most species constituting the mammalian gut microbiota. Furthermore, the eutB gene (encoding a subunit of the enzyme that catalyses the release of ammonia from EA) is poorly expressed in non-pathogenic E. coli. Accordingly, EA is consumed by EHEC but is poorly metabolized by endogenous microbiota of the bovine small intestine, including commensal E. coli. Interestingly, the capacity to utilize EA as a nitrogen source confers a growth advantage to E. coli O157:H7 when the bacteria enter the stationary growth phase. These data demonstrate that EHEC strains take advantage of a nitrogen source that is not consumed by the resident microbiota, and suggest that EA represents an ecological niche favouring EHEC persistence in the bovine intestine.

Metabolite Analysis of Human Fecal Water by Gas Chromatography/Mass Spectrometry with Ethyl Chloroformate Derivatization

Fecal water is a complex mixture of various metabolites with a wide range of physicochemical properties and boiling points. The analytical method developed here provides a qualitative and quantitative gas chromatography/mass spectrometry (GC/MS) analysis, with high sensitivity and efficiency, coupled with derivatization of ethyl chloroformate in aqueous medium. The water/ethanol/pyridine ratio was optimized to 12:6:1, and a two-step derivatization with an initial pH regulation of 0.1M sodium bicarbonate was developed. The deionized water exhibited better extraction efficiency for fecal water compounds than did acidified and alkalized water. Furthermore, more amino acids were extracted from frozen fecal samples than from fresh samples based on multivariate statistical analysis and univariate statistical validation on GC/MS data. Method validation by 34 reference standards and fecal water samples showed a correlation coefficient higher than 0.99 for each of the standards, and the limit of detection (LOD) was from 10 to 500pg on-column for most of the standards. The analytical equipment exhibited excellent repeatability, with the relative standard deviation (RSD) lower than 4% for standards and lower than 7% for fecal water. The derivatization method also demonstrated good repeatability, with the RSD lower than 6.4% for standards (except 3,4-dihydroxyphenylacetic acid) and lower than 10% for fecal water (except dicarboxylic acids). The qualitative means by searching the electron impact (EI) mass spectral database, chemical ionization (CI) mass spectra validation, and reference standards comparison totally identified and structurally confirmed 73 compounds, and the fecal water compounds of healthy humans were also quantified. This protocol shows a promising application in metabolome analysis based on human fecal water samples.

Development of a quantitative metabolomic approach to study clinical human fecal water metabolome based on trimethylsilylation derivatization and GC/MS analysis.

Metabolomic analysis of human fecal water recently aroused increasing attention with the importance of fecal metabolome in exploring the relationships between symbiotic gut microflora and human health. In this study, we developed a quantitative metabolomic method for human fecal water based on trimethylsilylation derivatization and GC/MS analysis. Methanol was found to be the best solvent for protein precipitation and extraction of fecal water metabolome. Within the optimized linear range of sampling volume (less than 50 microL), compounds showed a good linearity with a correlation coefficient higher than 0.99. The developed method showed good repeatability for both sample preparation and GC/MS analysis with the relative standard deviations lower than 10% for most compounds and less than 20% for a few other ones. The method was further validated by studying analytical variability using a set of clinical samples as well as a pooled sample. The pH value and matrix effects were the main factors affecting the accuracy of quantitative calibration curves. The increased pH value decreased the loss of short chain fatty acids during lyophilization. Spiking fecal water to a standard mixture significantly enhanced the accuracy of quantitative calibration curves, probably due to the inhibition of volatile loss during lyophilization and the increase of compound solubility in the derivatization medium. A strategy for calibration curve preparation was proposed in order to avoid the effects of pH and matrix. Totally, 133 compounds were structurally confirmed from a set of clinical samples, and 33 of them were quantified, which demonstrates the suitability of this method for a quantitative metabolomic study of human fecal water samples.

Untargeted metabolomics as a screening tool for estimating compliance to a dietary pattern.

There is a growing interest in studying the nutritional effects of complex diets. For such studies, measurement of dietary compliance is a challenge because the currently available compliance markers cover only limited aspects of a diet. In the present study, an untargeted metabolomics approach was used to develop a compliance measure in urine to distinguish between two dietary patterns. A parallel intervention study was carried out in which 181 participants were randomized to follow either a New Nordic Diet (NND) or an Average Danish Diet (ADD) for 6 months. Dietary intakes were closely monitored over the whole study period, and 24 h urine samples as well as weighed dietary records were collected several times during the study. The urine samples were analyzed by UPLC-qTOF-MS, and a partial least-squares discriminant analysis with feature selection was applied to develop a compliance model based on data from 214 urine samples. The optimized model included 52 metabolites and had a misclassification rate of 19% in a validation set containing 139 samples. The metabolites identified in the model were markers of individual foods such as citrus, cocoa-containing products, and fish as well as more general dietary traits such as high fruit and vegetable intake or high intake of heat-treated foods. It was easier to classify the ADD diet than the NND diet probably due to seasonal variation in the food composition of NND and indications of lower compliance among the NND subjects. In conclusion, untargeted metabolomics is a promising approach to develop compliance measures that cover the most important discriminant metabolites of complex diets.

A Liquid Chromatography−Quadrupole Time-of-Flight (LC−QTOF)-based Metabolomic Approach Reveals New Metabolic Effects of Catechin in Rats Fed High-Fat Diets

Unbalanced diets generate oxidative stress commonly associated with the development of diabetes, atherosclerosis, obesity and cancer. Dietary flavonoids have antioxidant properties and may limit this stress and reduce the risk of these diseases. We used a metabolomic approach to study the influence of catechin, a common flavonoid naturally occurring in various fruits, wine or chocolate, on the metabolic changes induced by hyperlipidemic diets. Male Wistar rats ( n = 8/group) were fed during 6 weeks normolipidemic (5% w/w) or hyperlipidemic (15 and 25%) diets with or without catechin supplementation (0.2% w/w). Urines were collected at days 17 and 38 and analyzed by reverse-phase liquid chromatography-mass spectrometry (LC-QTOF). Hyperlipidic diets led to a significant increase of oxidative stress in liver and aorta, upon which catechin had no effect. Multivariate analyses (PCA and PLS-DA) of the urine fingerprints allowed discrimination of the different diets. Variables were then classified according to their dependence on lipid and catechin intake (ANOVA). Nine variables were identified as catechin metabolites of tissular or microbial origin. Around 1000 variables were significantly affected by the lipid content of the diet, and 76 were fully reversed by catechin supplementation. Four variables showing an increase in urinary excretion in rats fed the high-fat diets were identified as deoxycytidine, nicotinic acid, dihydroxyquinoline and pipecolinic acid. After catechin supplementation, the excretion of nicotinic acid was fully restored to the level found in the rats fed the low-fat diet. The physiological significance of these metabolic changes is discussed.

Presence of low-grade inflammation impaired postprandial stimulation of muscle protein synthesis in old rats.

Aging is characterized by a decline in muscle mass that could be explained by a defect in the regulation of postprandial muscle protein metabolism. This study was undertaken to examine a possible link between the development of low-grade inflammation (LGI) in elderly and the resistance of muscle protein synthesis and degradation pathways to food intake. Fifty-five 20-month-old-rats were studied for 5 months; blood was withdrawn once a month to assess plasma fibrinogen and alpha2-macroglobulin. Animals were then separated into two groups at 25 months old according to their inflammation status: a control non-inflamed (NI, n=24) and a low-grade inflamed group (LGI, n=23). The day of the experiment, rats received no food or a meal. Muscle protein synthesis was assessed in vivo using the flooding dose method ([1-(13)C]phenylalanine) and muscle phosphorylation of protein S6 kinase, and protein S6 was measured in gastrocnemius muscle. Muscle proteolysis was assessed in vitro using the epitrochlearis muscle. Postabsorptive muscle protein synthesis and proteolysis were similar in NI and LGI. After food intake, muscle protein synthesis was significantly stimulated in NI but remained unresponsive in LGI. Muscle proteolysis was similar in both groups whatever the inflammation and/or the nutritional status. In conclusion, we showed that development of LGI during aging may be responsible, at least in part, for the defect in muscle protein synthesis stimulation induced by food intake in rats. Our results suggested that the control of LGI development in elderly improve meal effect on muscle protein synthesis and consequently slow down sarcopenia.