A new statistical workflow (R-packages based) to investigate associations between one variable of interest and the metabolome.

INTRODUCTION: In metabolomics, the investigation of associations between the metabolome and one trait of interest is a key research question. However, statistical analyses of such associations are often challenging. Statistical tools enabling resilient verification and clear presentation are therefore highly desired. OBJECTIVES: Our aim is to provide a contribution for statistical analysis of metabolomics data, offering a widely applicable open-source statistical workflow, which considers the intrinsic complexity of metabolomics data. METHODS: We combined selected R packages tailored for all properties of heterogeneous metabolomics datasets, where metabolite parameters typically (i) are analyzed in different matrices, (ii) are measured on different analytical platforms with different precision, (iii) are analyzed by targeted as well as non-targeted methods, (iv) are scaled variously, (v) reveal heterogeneous variances, (vi) may be correlated, (vii) may have only few values or values below a detection limit, or (viii) may be incomplete. RESULTS: The code is shared entirely and freely available. The workflow output is a table of metabolites associated with a trait of interest and a compact plot for high-quality results visualization. The workflow output and its utility are presented by applying it to two previously published datasets: one dataset from our own lab and another dataset taken from the repository MetaboLights. CONCLUSION: Robustness and benefits of the statistical workflow were clearly demonstrated, and everyone can directly re-use it for analysis of own data.

Dynamics and determinants of human plasma bile acid profiles during dietary challenges.

In recent years, bile acids (BA) have received great interest due to their pleiotropic biological activity and the presence of plasma membrane-bound and nuclear receptors. Moreover, BA in blood have been identified by metabolite screening approaches as biomarkers that are associated with various diseases and even with a human longevity phenotype. With the growing interest in the microbiota contribution to the health-disease trajectory, BA that undergo deconjugation and other modifications by bacteria in the large intestine have become a prime target as a microbiome diversity modifier. We here profiled BA by a quantitative and a semiquantitative approach in 15 healthy and phenotypically very similar young individuals for over a 36-h fasting period, an oral glucose tolerance test (OGTT), and an oral lipid tolerance test (OLTT). We demonstrate a remarkable heterogeneity of the responses and describe the different dynamics of the plasma changes that likely originate from different routes by which BA enters the peripheral blood, and that may represent a direct secretion from the liver into the blood and a route that reaches the blood as a spill-over after passing from the gallbladder through the intestine and the portal system. We discuss the finding that an individual transport process involved in the passage of BA could be a critical determinant in the kinetics of plasma appearance and the overall phenotypic variability found.

Dietary Pattern and Plasma BCAA-Variations in Healthy Men and Women-Results from the KarMeN Study.

Branched-chain amino acids (BCAA) in plasma are discussed as risk factors for the onset of several diseases. Information about the contribution of the overall diet to plasma BCAA concentrations is controversial. Our objective was to investigate which dietary pattern is associated with plasma BCAA concentrations and whether other additional nutrients besides BCAA further characterize this dietary pattern. Based on the cross-sectional KarMeN study, fasting plasma amino acid (AA) concentrations, as well as current and habitual dietary intake were assessed in 298 healthy individuals. Using reduced rank regression, we derived a habitual dietary pattern that explained 32.5% of plasma BCAA variation. This pattern was high in meat, sausages, sauces, eggs, and ice cream but low in nuts, cereals, mushrooms, and pulses. The age, sex, and energy intake adjusted dietary pattern score was associated with an increase in animal-based protein together with a decrease in plant-based protein, dietary fiber, and an unfavorable fatty acid composition. Besides BCAA, alanine, lysine and the aromatic AA were positively associated with the dietary pattern score as well. All of these factors were reported to be associated with risk of type 2 diabetes and cardiovascular diseases before. Our data suggest that rather than the dietary intake of BCAA, the overall dietary pattern that contributes to high BCAA plasma concentrations may modulate chronic diseases risk.

Metabolite patterns predicting sex and age in participants of the Karlsruhe Metabolomics and Nutrition (KarMeN) study.

Physiological and functional parameters, such as body composition, or physical fitness are known to differ between men and women and to change with age. The goal of this study was to investigate how sex and age-related physiological conditions are reflected in the metabolome of healthy humans and whether sex and age can be predicted based on the plasma and urine metabolite profiles. In the cross-sectional KarMeN (Karlsruhe Metabolomics and Nutrition) study 301 healthy men and women aged 18-80 years were recruited. Participants were characterized in detail applying standard operating procedures for all measurements including anthropometric, clinical, and functional parameters. Fasting blood and 24 h urine samples were analyzed by targeted and untargeted metabolomics approaches, namely by mass spectrometry coupled to one- or comprehensive two-dimensional gas chromatography or liquid chromatography, and by nuclear magnetic resonance spectroscopy. This yielded in total more than 400 analytes in plasma and over 500 analytes in urine. Predictive modelling was applied on the metabolomics data set using different machine learning algorithms. Based on metabolite profiles from urine and plasma, it was possible to identify metabolite patterns which classify participants according to sex with > 90% accuracy. Plasma metabolites important for the correct classification included creatinine, branched-chain amino acids, and sarcosine. Prediction of age was also possible based on metabolite profiles for men and women, separately. Several metabolites important for this prediction could be identified including choline in plasma and sedoheptulose in urine. For women, classification according to their menopausal status was possible from metabolome data with > 80% accuracy. The metabolite profile of human urine and plasma allows the prediction of sex and age with high accuracy, which means that sex and age are associated with a discriminatory metabolite signature in healthy humans and therefore should always be considered in metabolomics studies.

The role of plant processing for the cancer preventive potential of Ethiopian kale (Brassica carinata).

Background: Ethiopian kale (Brassica carinata) is a horticulturally important crop used as leafy vegetable in large parts of East and Southern Africa. The leaves are reported to contain high concentrations of health-promoting secondary plant metabolites. However, scientific knowledge on their health benefits is scarce. Objective: This study aimed to determine the cancer preventive potential of B. carinata using a human liver in vitro model focusing on processing effects on the pattern of secondary plant metabolites and bioactivity. Design: B. carinata was cultivated under controlled conditions and differentially processed (raw, fermented, or cooked) after harvesting. Human liver cancer cells (HepG2) were treated with ethanolic extracts of raw or processed B. carinata leaves and analyzed for their anti-genotoxic, anti-oxidant, and cytostatic potential. Chemical analyses were carried out on glucosinolates including breakdown products, phenolic compounds, carotenoids, and chlorophyll content. Results: Pre-treatment with B. carinata extracts concentration dependently reduced aflatoxin-induced DNA damage in the Comet assay, reduced the production of reactive oxygen species as determined by electron paramagnetic resonance spectroscopy, and induced Nrf2-mediated gene expression. Increasing extract concentrations also promoted cytostasis. Processing had a significant effect on the content of secondary plant metabolites. However, different processing methodologies did not dramatically decrease bioactivity, but enhanced the protective effect in some of the endpoints studied. Conclusion: Our findings highlight the cancer preventive potential of B. carinata as indicated by the protection of human liver cells against aflatoxin in vitro. In general, consumption of B. carinata should be encouraged as part of chemopreventive measures to combat prevalence of aflatoxin-induced diseases.

The influence of a chronic L-carnitine administration on the plasma metabolome of male Fischer 344 rats.

SCOPE: L-carnitine has been advertised as a fat-lowering and performance-enhancing supplement, although scientific evidence for its effectiveness is lacking. The uptake of about 1-2 g of L-carnitine per day may result in the formation of metabolites like trimethylamine-N-oxide (TMAO), which in turn may be converted to potential carcinogens or promote the development of cardiovascular diseases. METHODS AND RESULTS: To assess whether an L-carnitine supplementation changes overall metabolism or causes the formation of previously unknown metabolites, we analyzed plasma samples from Fischer 344 rats originating from a previous study using a multi-platform metabolomics approach comprising LC-MS/MS and GC×GC-MS methods. Despite an intake of up to 352 mg L-carnitine/kg body weight/day for 1 year, plasma concentrations of only 29 out of 359 metabolites were significantly influenced, the induced concentration changes being often comparatively small. Nevertheless, a clear dose-response relationship and a substantial concentration increase were observed for TMAO, i.e. a tenfold higher TMAO level was measured in the high-dose group when compared to the control (2.5 versus 25.0 µM). CONCLUSION: Although L-carnitine supplementation did not cause large changes in the plasma metabolome, a higher risk for cardiovascular disease due to chronically elevated TMAO plasma concentrations cannot be excluded.

Fermentation of African kale (Brassica carinata) using L. plantarum BFE 5092 and L. fermentum BFE 6620 starter strains.

Vegetables produced in Africa are sources of much needed micronutrients and fermentation is one way to enhance the shelf life of these perishable products. To prevent post-harvest losses and preserve African leafy vegetables, Lactobacillus plantarum BFE 5092 and Lactobacillus fermentum BFE 6620 starter strains were investigated for their application in fermentation of African kale (Brassica carinata) leaves. They were inoculated at 1×107cfu/ml and grew to a maximum level of 108cfu/ml during 24h submerged fermentation. The strains utilized simple sugars (i.e., glucose, fructose, and sucrose) in the kale to quickly reduce the pH from pH6.0 to pH3.6 within 24h. The strains continued to produce both d and l lactic acid up to 144h, reaching a maximum concentration of 4.0g/l. Fermentations with pathogens inoculated at 104cfu/ml showed that the quick growth of the starters inhibited the growth of Listeria monocytogenes and Salmonella Enteritidis, as well as other enterobacteria. Denaturing gradient gel electrophoresis and 16S rRNA gene (V3-V4-region) amplicon sequencing showed that in the spontaneous fermentations a microbial succession took place, though with marked differences in biodiversity from fermentation to fermentation. The fermentations inoculated with starters however were clearly dominated by both the inoculated strains throughout the fermentations. RAPD-PCR fingerprinting showed that the strains established themselves at approx. equal proportions. Although vitamins C, B1 and B2 decreased during the fermentation, the final level of vitamin C in the product was an appreciable concentration of 35mg/100g. In conclusion, controlled fermentation of kale offers a promising avenue to prevent spoilage and improve the shelf life and safety.

Produce from Africa's Gardens: Potential for Leafy Vegetable and Fruit Fermentations.

A rich variety of indigenous fruits and vegetables grow in Africa, which contribute to the nutrition and health of Africa's populations. Fruits and vegetables have high moisture and are thus inherently prone to accelerated spoilage. Food fermentation still plays a major role in combating food spoilage and foodborne diseases that are prevalent in many of Africa's resource disadvantaged regions. Lactic acid fermentation is probably the oldest and best-accepted food processing method among the African people, and is largely a home-based process. Fermentation of leafy vegetables and fruits is, however, underutilized in Africa, although such fermented products could contribute toward improving nutrition and food security in this continent, where many are still malnourished and suffer from hidden hunger. Fermentation of leafy vegetables and fruits may not only improve safety and prolong shelf life, but may also enhance the availability of some trace minerals, vitamins and anti-oxidants. Cassava, cow-peas, amaranth, African nightshade, and spider plant leaves have a potential for fermentation, as do various fruits for the production of vinegars or fruit beers and wines. What is needed to accelerate efforts for production of fermented leaves and vegetables is the development of fermentation protocols, training of personnel and scale-up of production methods. Furthermore, suitable starter cultures need to be developed and produced to guarantee the success of the fermentations.

Age-Related Changes of Plasma Bile Acid Concentrations in Healthy Adults--Results from the Cross-Sectional KarMeN Study.

Bile acids (BA) play an important role in lipid metabolism. They facilitate intestinal lipid absorption, and BA synthesis is the main catabolic pathway for cholesterol. The objective of this study was to investigate associations of age, sex, diet (fat intake) and parameters of lipid metabolism (triglycerides, LDL, HDL, body fat content) with fasting plasma BA concentration of healthy individuals. Fasting plasma samples from a cross-sectional study were used to determine the concentrations of 14 BA using an LC-MS stable isotope dilution assay. Triglycerides, LDL and HDL were analyzed by standard clinical chemistry methods and body fat content was measured with a DXA instrument. The dietary fat intake of the 24 h period prior to the sampling was assessed on the basis of a 24 h recall. Subsequent statistical data processing was done by means of a median regression model. Results revealed large inter-individual variations. Overall, higher median plasma concentrations of BA were observed in men than in women. Quantile regression showed significant interactions of selected BA with age and sex, affecting primarily chenodeoxycholic acid and its conjugates. No associations were found for LDL and the amount of fat intake (based on the percentage of energy intake from dietary fat as well as total fat intake). Additional associations regarding body fat content, HDL and triglycerides were found for some secondary BA plasma concentrations. We conclude that age and sex are associated with the fasting plasma concentrations. Those associations are significant and need to be considered in studies investigating the role of BA in the human metabolism.

Degradation of folic acid in fortified vitamin juices during long term storage.

Folic acid (FA) concentrations of nine fortified vitamin juices were determined with the aim to study the FA degradation and to investigate the deviation from the declared label value. The juices were received shortly after bottling and were analyzed monthly during controlled storage conditions (light and dark) over one year. The analyses were performed by HPLC-MS/MS, which included a fast "dilute and shoot" sample preparation. Average decreases in FA concentration of 46% were observed after one year. Fresh juices (shortly after bottling) showed the highest deviations from the declared label value (up to+89%). Label values did not reflect the actual concentration of FA in these products, making it difficult to determine the intake of this vitamin.